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fix merge conflict

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This commit is contained in:
James McClure 2021-03-20 20:40:16 -04:00
commit 9fddfff384
50 changed files with 2424 additions and 2468 deletions
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2
CMakeLists.txt
View File

@ -150,7 +150,7 @@ IF ( NOT ONLY_BUILD_DOCS )
CONFIGURE_NETCDF()
CONFIGURE_SILO()
CONFIGURE_LBPM()
CONFIGURE_TIMER( 0 "${${PROJ}_INSTALL_DIR}/null_timer" )
CONFIGURE_TIMER( 0 "${${PROJ}_INSTALL_DIR}/null_timer" FALSE )
CONFIGURE_LINE_COVERAGE()
# Set the external library link list
SET( EXTERNAL_LIBS ${EXTERNAL_LIBS} ${TIMER_LIBS} )

32
IO/IOHelpers.h
View File

@ -10,9 +10,9 @@ namespace IO {
// Find a character in a line
inline size_t find( const char *line, char token )
{
size_t i=0;
size_t i = 0;
while ( 1 ) {
if ( line[i]==token || line[i]<32 || line[i]==0 )
if ( line[i] == token || line[i] < 32 || line[i] == 0 )
break;
++i;
}
@ -21,17 +21,17 @@ inline size_t find( const char *line, char token )
// Remove preceeding/trailing whitespace
inline std::string deblank( const std::string& str )
inline std::string deblank( const std::string &str )
{
size_t i1 = str.size();
size_t i2 = 0;
for (size_t i=0; i<str.size(); i++) {
if ( str[i]!=' ' && str[i]>=32 ) {
i1 = std::min(i1,i);
i2 = std::max(i2,i);
for ( size_t i = 0; i < str.size(); i++ ) {
if ( str[i] != ' ' && str[i] >= 32 ) {
i1 = std::min( i1, i );
i2 = std::max( i2, i );
}
}
return str.substr(i1,i2-i1+1);
return str.substr( i1, i2 - i1 + 1 );
}
@ -42,14 +42,14 @@ inline std::vector<std::string> splitList( const char *line, const char token )
size_t i1 = 0;
size_t i2 = 0;
while ( 1 ) {
if ( line[i2]==token || line[i2]<32 ) {
std::string tmp(&line[i1],i2-i1);
tmp = deblank(tmp);
if ( line[i2] == token || line[i2] < 32 ) {
std::string tmp( &line[i1], i2 - i1 );
tmp = deblank( tmp );
if ( !tmp.empty() )
list.push_back(tmp);
i1 = i2+1;
list.push_back( tmp );
i1 = i2 + 1;
}
if ( line[i2]==0 )
if ( line[i2] == 0 )
break;
i2++;
}
@ -57,8 +57,6 @@ inline std::vector<std::string> splitList( const char *line, const char token )
}
};
}; // namespace IO
#endif

715
IO/Mesh.cpp
View File

@ -1,4 +1,5 @@
#include "Mesh.h"
#include "IO/IOHelpers.h"
#include "common/Utilities.h"
#include <limits>
@ -19,104 +20,110 @@ inline Point nullPoint()
/****************************************************
* Mesh *
****************************************************/
Mesh::Mesh( )
{
}
Mesh::~Mesh( )
{
}
* Mesh *
****************************************************/
Mesh::Mesh() {}
Mesh::~Mesh() {}
/****************************************************
* MeshDataStruct *
****************************************************/
bool MeshDataStruct::check() const
* MeshDataStruct *
****************************************************/
#define checkResult( pass, msg ) \
do { \
if ( !( pass ) ) { \
if ( abort ) \
ERROR( msg ); \
return false; \
} \
} while ( 0 )
bool MeshDataStruct::check( bool abort ) const
{
enum VariableType { NodeVariable=1, EdgeVariable=2, SurfaceVariable=2, VolumeVariable=3, NullVariable=0 };
bool pass = mesh != nullptr;
for ( const auto& var : vars ) {
pass = pass && static_cast<int>(var->type)>=1 && static_cast<int>(var->type)<=3;
pass = pass && !var->data.empty();
for ( const auto &var : vars ) {
checkResult( var->type == VariableType::NodeVariable ||
var->type == VariableType::EdgeVariable ||
var->type == VariableType::SurfaceVariable ||
var->type == VariableType::VolumeVariable,
"Invalid data type" );
checkResult( !var->data.empty(), "Variable data is empty" );
}
if ( !pass )
return false;
const std::string& meshClass = mesh->className();
const std::string &meshClass = mesh->className();
if ( meshClass == "PointList" ) {
const auto mesh2 = dynamic_cast<IO::PointList*>( mesh.get() );
if ( mesh2 == nullptr )
return false;
for ( const auto& var : vars ) {
auto mesh2 = dynamic_cast<IO::PointList *>( mesh.get() );
ASSERT( mesh2 );
for ( const auto &var : vars ) {
if ( var->type == IO::VariableType::NodeVariable ) {
pass = pass && var->data.size(0)==mesh2->points.size() && var->data.size(1)==var->dim;
size_t N_points = mesh2->points.size();
checkResult( var->data.size( 0 ) == N_points, "sizeof NodeVariable" );
checkResult( var->data.size( 1 ) == var->dim, "sizeof NodeVariable" );
} else if ( var->type == IO::VariableType::EdgeVariable ) {
ERROR("Invalid type for PointList");
ERROR( "Invalid type for PointList" );
} else if ( var->type == IO::VariableType::SurfaceVariable ) {
ERROR("Invalid type for PointList");
ERROR( "Invalid type for PointList" );
} else if ( var->type == IO::VariableType::VolumeVariable ) {
ERROR("Invalid type for PointList");
ERROR( "Invalid type for PointList" );
} else {
ERROR("Invalid variable type");
ERROR( "Invalid variable type" );
}
}
} else if ( meshClass == "TriMesh" || meshClass == "TriList" ) {
const auto mesh2 = getTriMesh( mesh );
if ( mesh2 == nullptr )
return false;
for ( const auto& var : vars ) {
auto mesh2 = getTriMesh( mesh );
ASSERT( mesh2 );
for ( const auto &var : vars ) {
if ( var->type == IO::VariableType::NodeVariable ) {
pass = pass && var->data.size(0)==mesh2->vertices->points.size() && var->data.size(1)==var->dim;
size_t N_points = mesh2->vertices->points.size();
checkResult( var->data.size( 0 ) == N_points, "sizeof NodeVariable" );
checkResult( var->data.size( 1 ) == var->dim, "sizeof NodeVariable" );
} else if ( var->type == IO::VariableType::EdgeVariable ) {
ERROR("Not finished");
ERROR( "Not finished" );
} else if ( var->type == IO::VariableType::SurfaceVariable ) {
ERROR("Not finished");
ERROR( "Not finished" );
} else if ( var->type == IO::VariableType::VolumeVariable ) {
pass = pass && var->data.size(0)==mesh2->A.size() && var->data.size(1)==var->dim;
checkResult( var->data.size( 0 ) == mesh2->A.size(), "sizeof VolumeVariable" );
checkResult( var->data.size( 1 ) == var->dim, "sizeof VolumeVariable" );
} else {
ERROR("Invalid variable type");
ERROR( "Invalid variable type" );
}
}
} else if ( meshClass == "DomainMesh" ) {
const auto mesh2 = dynamic_cast<IO::DomainMesh*>( mesh.get() );
if ( mesh2 == nullptr )
return false;
for ( const auto& var : vars ) {
auto mesh2 = dynamic_cast<IO::DomainMesh *>( mesh.get() );
ASSERT( mesh2 );
for ( const auto &var : vars ) {
ArraySize varSize;
if ( var->type == IO::VariableType::NodeVariable ) {
pass = pass && (int) var->data.size(0)==(mesh2->nx+1) && (int) var->data.size(1)==(mesh2->ny+1)
&& (int) var->data.size(2)==(mesh2->nz+1) && var->data.size(3)==var->dim;
varSize = ArraySize( mesh2->nx + 1, mesh2->ny + 1, mesh2->nz + 1, var->dim );
} else if ( var->type == IO::VariableType::EdgeVariable ) {
ERROR("Not finished");
ERROR( "Not finished" );
} else if ( var->type == IO::VariableType::SurfaceVariable ) {
ERROR("Not finished");
ERROR( "Not finished" );
} else if ( var->type == IO::VariableType::VolumeVariable ) {
pass = pass && (int) var->data.size(0)==mesh2->nx && (int) var->data.size(1)==mesh2->ny
&& (int) var->data.size(2)==mesh2->nz && var->data.size(3)==var->dim;
varSize = ArraySize( mesh2->nx, mesh2->ny, mesh2->nz, var->dim );
} else {
ERROR("Invalid variable type");
ERROR( "Invalid variable type" );
}
if ( var->data.size( 0 ) == varSize[0] * varSize[1] * varSize[2] &&
var->data.size( 1 ) == varSize[3] )
var->data.resize( varSize );
for ( int d = 0; d < 4; d++ )
checkResult( var->data.size( d ) == varSize[d], "DomainMesh Variable" );
}
} else {
ERROR("Unknown mesh class: "+mesh->className());
ERROR( "Unknown mesh class: " + mesh->className() );
}
return pass;
return true;
}
/****************************************************
* PointList *
****************************************************/
PointList::PointList( )
{
}
* PointList *
****************************************************/
PointList::PointList() {}
PointList::PointList( size_t N )
{
Point tmp = nullPoint();
points.resize(N,tmp);
}
PointList::~PointList( )
{
points.resize( N, tmp );
}
PointList::~PointList() {}
size_t PointList::numberPointsVar( VariableType type ) const
{
size_t N = 0;
@ -124,174 +131,168 @@ size_t PointList::numberPointsVar( VariableType type ) const
N = points.size();
return N;
}
std::pair<size_t,void*> PointList::pack( int level ) const
std::pair<size_t, void *> PointList::pack( int level ) const
{
std::pair<size_t,void*> data_out(0,NULL);
if ( level==0 ) {
data_out.first = (2+3*points.size())*sizeof(double);
double *data_ptr = new double[2+3*points.size()];
data_out.second = data_ptr;
uint64_t *data_int = reinterpret_cast<uint64_t*>(data_ptr);
data_int[0] = level;
data_int[1] = points.size();
double *data = &data_ptr[2];
for (size_t i=0; i<points.size(); i++) {
data[3*i+0] = points[i].x;
data[3*i+1] = points[i].y;
data[3*i+2] = points[i].z;
std::pair<size_t, void *> data_out( 0, NULL );
if ( level == 0 ) {
data_out.first = ( 2 + 3 * points.size() ) * sizeof( double );
double *data_ptr = new double[2 + 3 * points.size()];
data_out.second = data_ptr;
uint64_t *data_int = reinterpret_cast<uint64_t *>( data_ptr );
data_int[0] = level;
data_int[1] = points.size();
double *data = &data_ptr[2];
for ( size_t i = 0; i < points.size(); i++ ) {
data[3 * i + 0] = points[i].x;
data[3 * i + 1] = points[i].y;
data[3 * i + 2] = points[i].z;
}
}
return data_out;
}
void PointList::unpack( const std::pair<size_t,void*>& data_in )
void PointList::unpack( const std::pair<size_t, void *> &data_in )
{
uint64_t *data_int = reinterpret_cast<uint64_t*>(data_in.second);
const double *data = reinterpret_cast<const double*>(data_in.second);
int level = data_int[0];
uint64_t N = data_int[1];
data = &data[2];
if ( level==0 ) {
ASSERT((2+3*N)*sizeof(double)==data_in.first);
points.resize(N);
for (size_t i=0; i<points.size(); i++) {
points[i].x = data[3*i+0];
points[i].y = data[3*i+1];
points[i].z = data[3*i+2];
uint64_t *data_int = reinterpret_cast<uint64_t *>( data_in.second );
const double *data = reinterpret_cast<const double *>( data_in.second );
int level = data_int[0];
uint64_t N = data_int[1];
data = &data[2];
if ( level == 0 ) {
ASSERT( ( 2 + 3 * N ) * sizeof( double ) == data_in.first );
points.resize( N );
for ( size_t i = 0; i < points.size(); i++ ) {
points[i].x = data[3 * i + 0];
points[i].y = data[3 * i + 1];
points[i].z = data[3 * i + 2];
}
}
}
/****************************************************
* TriList *
****************************************************/
TriList::TriList( )
{
}
* TriList *
****************************************************/
TriList::TriList() {}
TriList::TriList( size_t N_tri )
{
Point tmp = nullPoint();
A.resize(N_tri,tmp);
B.resize(N_tri,tmp);
C.resize(N_tri,tmp);
A.resize( N_tri, tmp );
B.resize( N_tri, tmp );
C.resize( N_tri, tmp );
}
TriList::TriList( const TriMesh& mesh )
TriList::TriList( const TriMesh &mesh )
{
Point tmp = nullPoint();
A.resize(mesh.A.size(),tmp);
B.resize(mesh.B.size(),tmp);
C.resize(mesh.C.size(),tmp);
ASSERT(mesh.vertices.get()!=NULL);
const std::vector<Point>& P = mesh.vertices->points;
for (size_t i=0; i<A.size(); i++)
A.resize( mesh.A.size(), tmp );
B.resize( mesh.B.size(), tmp );
C.resize( mesh.C.size(), tmp );
ASSERT( mesh.vertices.get() != NULL );
const std::vector<Point> &P = mesh.vertices->points;
for ( size_t i = 0; i < A.size(); i++ )
A[i] = P[mesh.A[i]];
for (size_t i=0; i<B.size(); i++)
for ( size_t i = 0; i < B.size(); i++ )
B[i] = P[mesh.B[i]];
for (size_t i=0; i<C.size(); i++)
for ( size_t i = 0; i < C.size(); i++ )
C[i] = P[mesh.C[i]];
}
TriList::~TriList( )
{
}
TriList::~TriList() {}
size_t TriList::numberPointsVar( VariableType type ) const
{
size_t N = 0;
if ( type==VariableType::NodeVariable )
N = 3*A.size();
else if ( type==VariableType::SurfaceVariable || type==VariableType::VolumeVariable )
if ( type == VariableType::NodeVariable )
N = 3 * A.size();
else if ( type == VariableType::SurfaceVariable || type == VariableType::VolumeVariable )
N = A.size();
return N;
}
std::pair<size_t,void*> TriList::pack( int level ) const
std::pair<size_t, void *> TriList::pack( int level ) const
{
std::pair<size_t,void*> data_out(0,NULL);
if ( level==0 ) {
data_out.first = (2+9*A.size())*sizeof(double);
double *data_ptr = new double[2+9*A.size()];
data_out.second = data_ptr;
uint64_t *data_int = reinterpret_cast<uint64_t*>(data_ptr);
data_int[0] = level;
data_int[1] = A.size();
double *data = &data_ptr[2];
for (size_t i=0; i<A.size(); i++) {
data[9*i+0] = A[i].x;
data[9*i+1] = A[i].y;
data[9*i+2] = A[i].z;
data[9*i+3] = B[i].x;
data[9*i+4] = B[i].y;
data[9*i+5] = B[i].z;
data[9*i+6] = C[i].x;
data[9*i+7] = C[i].y;
data[9*i+8] = C[i].z;
std::pair<size_t, void *> data_out( 0, NULL );
if ( level == 0 ) {
data_out.first = ( 2 + 9 * A.size() ) * sizeof( double );
double *data_ptr = new double[2 + 9 * A.size()];
data_out.second = data_ptr;
uint64_t *data_int = reinterpret_cast<uint64_t *>( data_ptr );
data_int[0] = level;
data_int[1] = A.size();
double *data = &data_ptr[2];
for ( size_t i = 0; i < A.size(); i++ ) {
data[9 * i + 0] = A[i].x;
data[9 * i + 1] = A[i].y;
data[9 * i + 2] = A[i].z;
data[9 * i + 3] = B[i].x;
data[9 * i + 4] = B[i].y;
data[9 * i + 5] = B[i].z;
data[9 * i + 6] = C[i].x;
data[9 * i + 7] = C[i].y;
data[9 * i + 8] = C[i].z;
}
}
return data_out;
}
void TriList::unpack( const std::pair<size_t,void*>& data_in )
void TriList::unpack( const std::pair<size_t, void *> &data_in )
{
uint64_t *data_int = reinterpret_cast<uint64_t*>(data_in.second);
const double *data = reinterpret_cast<const double*>(data_in.second);
int level = data_int[0];
uint64_t N = data_int[1];
data = &data[2];
if ( level==0 ) {
ASSERT((2+9*N)*sizeof(double)==data_in.first);
A.resize(N);
B.resize(N);
C.resize(N);
for (size_t i=0; i<A.size(); i++) {
A[i].x = data[9*i+0];
A[i].y = data[9*i+1];
A[i].z = data[9*i+2];
B[i].x = data[9*i+3];
B[i].y = data[9*i+4];
B[i].z = data[9*i+5];
C[i].x = data[9*i+6];
C[i].y = data[9*i+7];
C[i].z = data[9*i+8];
uint64_t *data_int = reinterpret_cast<uint64_t *>( data_in.second );
const double *data = reinterpret_cast<const double *>( data_in.second );
int level = data_int[0];
uint64_t N = data_int[1];
data = &data[2];
if ( level == 0 ) {
ASSERT( ( 2 + 9 * N ) * sizeof( double ) == data_in.first );
A.resize( N );
B.resize( N );
C.resize( N );
for ( size_t i = 0; i < A.size(); i++ ) {
A[i].x = data[9 * i + 0];
A[i].y = data[9 * i + 1];
A[i].z = data[9 * i + 2];
B[i].x = data[9 * i + 3];
B[i].y = data[9 * i + 4];
B[i].z = data[9 * i + 5];
C[i].x = data[9 * i + 6];
C[i].y = data[9 * i + 7];
C[i].z = data[9 * i + 8];
}
}
}
/****************************************************
* TriMesh *
****************************************************/
TriMesh::TriMesh( )
{
}
* TriMesh *
****************************************************/
TriMesh::TriMesh() {}
TriMesh::TriMesh( size_t N_tri, size_t N_point )
{
vertices.reset( new PointList(N_point) );
A.resize(N_tri,-1);
B.resize(N_tri,-1);
C.resize(N_tri,-1);
vertices.reset( new PointList( N_point ) );
A.resize( N_tri, -1 );
B.resize( N_tri, -1 );
C.resize( N_tri, -1 );
}
TriMesh::TriMesh( size_t N_tri, std::shared_ptr<PointList> points )
{
vertices = points;
A.resize(N_tri,-1);
B.resize(N_tri,-1);
C.resize(N_tri,-1);
A.resize( N_tri, -1 );
B.resize( N_tri, -1 );
C.resize( N_tri, -1 );
}
TriMesh::TriMesh( const TriList& mesh )
TriMesh::TriMesh( const TriList &mesh )
{
// For simlicity we will just create a mesh with ~3x the verticies for now
ASSERT(mesh.A.size()==mesh.B.size()&&mesh.A.size()==mesh.C.size());
A.resize(mesh.A.size());
B.resize(mesh.B.size());
C.resize(mesh.C.size());
vertices.reset( new PointList(3*mesh.A.size()) );
for (size_t i=0; i<A.size(); i++) {
A[i] = 3*i+0;
B[i] = 3*i+1;
C[i] = 3*i+2;
ASSERT( mesh.A.size() == mesh.B.size() && mesh.A.size() == mesh.C.size() );
A.resize( mesh.A.size() );
B.resize( mesh.B.size() );
C.resize( mesh.C.size() );
vertices.reset( new PointList( 3 * mesh.A.size() ) );
for ( size_t i = 0; i < A.size(); i++ ) {
A[i] = 3 * i + 0;
B[i] = 3 * i + 1;
C[i] = 3 * i + 2;
vertices->points[A[i]] = mesh.A[i];
vertices->points[B[i]] = mesh.B[i];
vertices->points[C[i]] = mesh.C[i];
}
}
TriMesh::~TriMesh( )
TriMesh::~TriMesh()
{
vertices.reset();
A.clear();
@ -301,181 +302,319 @@ TriMesh::~TriMesh( )
size_t TriMesh::numberPointsVar( VariableType type ) const
{
size_t N = 0;
if ( type==VariableType::NodeVariable )
if ( type == VariableType::NodeVariable )
N = vertices->points.size();
else if ( type==VariableType::SurfaceVariable || type==VariableType::VolumeVariable )
else if ( type == VariableType::SurfaceVariable || type == VariableType::VolumeVariable )
N = A.size();
return N;
}
std::pair<size_t,void*> TriMesh::pack( int level ) const
std::pair<size_t, void *> TriMesh::pack( int level ) const
{
std::pair<size_t,void*> data_out(0,NULL);
if ( level==0 ) {
const std::vector<Point>& points = vertices->points;
data_out.first = (3+3*points.size())*sizeof(double) + 3*A.size()*sizeof(int);
double *data_ptr = new double[4+3*points.size()+(3*A.size()*sizeof(int))/sizeof(double)];
data_out.second = data_ptr;
uint64_t *data_int64 = reinterpret_cast<uint64_t*>(data_ptr);
data_int64[0] = level;
data_int64[1] = points.size();
data_int64[2] = A.size();
double *data = &data_ptr[3];
for (size_t i=0; i<points.size(); i++) {
data[3*i+0] = points[i].x;
data[3*i+1] = points[i].y;
data[3*i+2] = points[i].z;
std::pair<size_t, void *> data_out( 0, NULL );
if ( level == 0 ) {
const std::vector<Point> &points = vertices->points;
data_out.first =
( 3 + 3 * points.size() ) * sizeof( double ) + 3 * A.size() * sizeof( int );
double *data_ptr =
new double[4 + 3 * points.size() + ( 3 * A.size() * sizeof( int ) ) / sizeof( double )];
data_out.second = data_ptr;
uint64_t *data_int64 = reinterpret_cast<uint64_t *>( data_ptr );
data_int64[0] = level;
data_int64[1] = points.size();
data_int64[2] = A.size();
double *data = &data_ptr[3];
for ( size_t i = 0; i < points.size(); i++ ) {
data[3 * i + 0] = points[i].x;
data[3 * i + 1] = points[i].y;
data[3 * i + 2] = points[i].z;
}
int *data_int = reinterpret_cast<int*>(&data[3*points.size()]);
for (size_t i=0; i<A.size(); i++) {
data_int[3*i+0] = A[i];
data_int[3*i+1] = B[i];
data_int[3*i+2] = C[i];
int *data_int = reinterpret_cast<int *>( &data[3 * points.size()] );
for ( size_t i = 0; i < A.size(); i++ ) {
data_int[3 * i + 0] = A[i];
data_int[3 * i + 1] = B[i];
data_int[3 * i + 2] = C[i];
}
}
return data_out;
}
void TriMesh::unpack( const std::pair<size_t,void*>& data_in )
void TriMesh::unpack( const std::pair<size_t, void *> &data_in )
{
uint64_t *data_int64 = reinterpret_cast<uint64_t*>(data_in.second);
const double *data = reinterpret_cast<const double*>(data_in.second);
int level = data_int64[0];
uint64_t N_P = data_int64[1];
uint64_t N_A = data_int64[2];
data = &data[3];
if ( level==0 ) {
size_t size = (3+3*N_P)*sizeof(double)+3*N_A*sizeof(int);
ASSERT(size==data_in.first);
vertices.reset( new PointList(N_P) );
std::vector<Point>& points = vertices->points;
for (size_t i=0; i<points.size(); i++) {
points[i].x = data[3*i+0];
points[i].y = data[3*i+1];
points[i].z = data[3*i+2];
uint64_t *data_int64 = reinterpret_cast<uint64_t *>( data_in.second );
const double *data = reinterpret_cast<const double *>( data_in.second );
int level = data_int64[0];
uint64_t N_P = data_int64[1];
uint64_t N_A = data_int64[2];
data = &data[3];
if ( level == 0 ) {
size_t size = ( 3 + 3 * N_P ) * sizeof( double ) + 3 * N_A * sizeof( int );
ASSERT( size == data_in.first );
vertices.reset( new PointList( N_P ) );
std::vector<Point> &points = vertices->points;
for ( size_t i = 0; i < points.size(); i++ ) {
points[i].x = data[3 * i + 0];
points[i].y = data[3 * i + 1];
points[i].z = data[3 * i + 2];
}
const int *data_int = reinterpret_cast<const int*>(&data[3*N_P]);
A.resize(N_A);
B.resize(N_A);
C.resize(N_A);
for (size_t i=0; i<A.size(); i++) {
A[i] = data_int[3*i+0];
B[i] = data_int[3*i+1];
C[i] = data_int[3*i+2];
const int *data_int = reinterpret_cast<const int *>( &data[3 * N_P] );
A.resize( N_A );
B.resize( N_A );
C.resize( N_A );
for ( size_t i = 0; i < A.size(); i++ ) {
A[i] = data_int[3 * i + 0];
B[i] = data_int[3 * i + 1];
C[i] = data_int[3 * i + 2];
}
}
}
/****************************************************
* Domain mesh *
****************************************************/
DomainMesh::DomainMesh():
nprocx(0), nprocy(0), nprocz(0), rank(0),
nx(0), ny(0), nz(0),
Lx(0), Ly(0), Lz(0)
* Domain mesh *
****************************************************/
DomainMesh::DomainMesh()
: nprocx( 0 ),
nprocy( 0 ),
nprocz( 0 ),
rank( 0 ),
nx( 0 ),
ny( 0 ),
nz( 0 ),
Lx( 0 ),
Ly( 0 ),
Lz( 0 )
{
}
DomainMesh::DomainMesh( RankInfoStruct data,
int nx2, int ny2, int nz2, double Lx2, double Ly2, double Lz2 ):
nprocx(data.nx), nprocy(data.ny), nprocz(data.nz), rank(data.rank[1][1][1]),
nx(nx2), ny(ny2), nz(nz2),
Lx(Lx2), Ly(Ly2), Lz(Lz2)
{
}
DomainMesh::~DomainMesh()
DomainMesh::DomainMesh(
RankInfoStruct data, int nx2, int ny2, int nz2, double Lx2, double Ly2, double Lz2 )
: nprocx( data.nx ),
nprocy( data.ny ),
nprocz( data.nz ),
rank( data.rank[1][1][1] ),
nx( nx2 ),
ny( ny2 ),
nz( nz2 ),
Lx( Lx2 ),
Ly( Ly2 ),
Lz( Lz2 )
{
}
DomainMesh::~DomainMesh() {}
size_t DomainMesh::numberPointsVar( VariableType type ) const
{
size_t N = 0;
if ( type==VariableType::NodeVariable )
N = (nx+1)*(ny+1)*(nz+1);
else if ( type==VariableType::SurfaceVariable )
N = (nx+1)*ny*nz + nx*(ny+1)*nz + nx*ny*(nz+1);
else if ( type==VariableType::VolumeVariable )
N = nx*ny*nz;
if ( type == VariableType::NodeVariable )
N = ( nx + 1 ) * ( ny + 1 ) * ( nz + 1 );
else if ( type == VariableType::SurfaceVariable )
N = ( nx + 1 ) * ny * nz + nx * ( ny + 1 ) * nz + nx * ny * ( nz + 1 );
else if ( type == VariableType::VolumeVariable )
N = nx * ny * nz;
return N;
}
std::pair<size_t,void*> DomainMesh::pack( int level ) const
std::pair<size_t, void *> DomainMesh::pack( int level ) const
{
std::pair<size_t,void*> data(0,NULL);
data.first = 7*sizeof(double);
std::pair<size_t, void *> data( 0, NULL );
data.first = 7 * sizeof( double );
data.second = new double[7];
memset(data.second,0,7*sizeof(double));
int *data_int = reinterpret_cast<int*>(data.second);
double *data_double = &reinterpret_cast<double*>(data.second)[4];
data_int[0] = nprocx;
data_int[1] = nprocy;
data_int[2] = nprocz;
data_int[3] = rank;
data_int[4] = nx;
data_int[5] = ny;
data_int[6] = nz;
data_double[0] = Lx;
data_double[1] = Ly;
data_double[2] = Lz;
memset( data.second, 0, 7 * sizeof( double ) );
int *data_int = reinterpret_cast<int *>( data.second );
double *data_double = &reinterpret_cast<double *>( data.second )[4];
data_int[0] = nprocx;
data_int[1] = nprocy;
data_int[2] = nprocz;
data_int[3] = rank;
data_int[4] = nx;
data_int[5] = ny;
data_int[6] = nz;
data_double[0] = Lx;
data_double[1] = Ly;
data_double[2] = Lz;
return data;
}
void DomainMesh::unpack( const std::pair<size_t,void*>& data )
void DomainMesh::unpack( const std::pair<size_t, void *> &data )
{
const int *data_int = reinterpret_cast<const int*>(data.second);
const double *data_double = &reinterpret_cast<const double*>(data.second)[4];
nprocx = data_int[0];
nprocy = data_int[1];
nprocz = data_int[2];
rank = data_int[3];
nx = data_int[4];
ny = data_int[5];
nz = data_int[6];
Lx = data_double[0];
Ly = data_double[1];
Lz = data_double[2];
const int *data_int = reinterpret_cast<const int *>( data.second );
const double *data_double = &reinterpret_cast<const double *>( data.second )[4];
nprocx = data_int[0];
nprocy = data_int[1];
nprocz = data_int[2];
rank = data_int[3];
nx = data_int[4];
ny = data_int[5];
nz = data_int[6];
Lx = data_double[0];
Ly = data_double[1];
Lz = data_double[2];
}
/****************************************************
* Converters *
****************************************************/
* Converters *
****************************************************/
std::shared_ptr<PointList> getPointList( std::shared_ptr<Mesh> mesh )
{
return std::dynamic_pointer_cast<PointList>(mesh);
return std::dynamic_pointer_cast<PointList>( mesh );
}
std::shared_ptr<TriMesh> getTriMesh( std::shared_ptr<Mesh> mesh )
{
std::shared_ptr<TriMesh> mesh2;
if ( std::dynamic_pointer_cast<TriMesh>(mesh).get() != NULL ) {
mesh2 = std::dynamic_pointer_cast<TriMesh>(mesh);
} else if ( std::dynamic_pointer_cast<TriList>(mesh).get() != NULL ) {
std::shared_ptr<TriList> trilist = std::dynamic_pointer_cast<TriList>(mesh);
ASSERT(trilist.get()!=NULL);
mesh2.reset( new TriMesh(*trilist) );
if ( std::dynamic_pointer_cast<TriMesh>( mesh ).get() != NULL ) {
mesh2 = std::dynamic_pointer_cast<TriMesh>( mesh );
} else if ( std::dynamic_pointer_cast<TriList>( mesh ).get() != NULL ) {
std::shared_ptr<TriList> trilist = std::dynamic_pointer_cast<TriList>( mesh );
ASSERT( trilist.get() != NULL );
mesh2.reset( new TriMesh( *trilist ) );
}
return mesh2;
}
std::shared_ptr<TriList> getTriList( std::shared_ptr<Mesh> mesh )
{
std::shared_ptr<TriList> mesh2;
if ( std::dynamic_pointer_cast<TriList>(mesh).get() != NULL ) {
mesh2 = std::dynamic_pointer_cast<TriList>(mesh);
} else if ( std::dynamic_pointer_cast<TriMesh>(mesh).get() != NULL ) {
std::shared_ptr<TriMesh> trimesh = std::dynamic_pointer_cast<TriMesh>(mesh);
ASSERT(trimesh.get()!=NULL);
mesh2.reset( new TriList(*trimesh) );
if ( std::dynamic_pointer_cast<TriList>( mesh ).get() != NULL ) {
mesh2 = std::dynamic_pointer_cast<TriList>( mesh );
} else if ( std::dynamic_pointer_cast<TriMesh>( mesh ).get() != NULL ) {
std::shared_ptr<TriMesh> trimesh = std::dynamic_pointer_cast<TriMesh>( mesh );
ASSERT( trimesh.get() != NULL );
mesh2.reset( new TriList( *trimesh ) );
}
return mesh2;
}
std::shared_ptr<const PointList> getPointList( std::shared_ptr<const Mesh> mesh )
{
return getPointList( std::const_pointer_cast<Mesh>(mesh) );
return getPointList( std::const_pointer_cast<Mesh>( mesh ) );
}
std::shared_ptr<const TriMesh> getTriMesh( std::shared_ptr<const Mesh> mesh )
{
return getTriMesh( std::const_pointer_cast<Mesh>(mesh) );
return getTriMesh( std::const_pointer_cast<Mesh>( mesh ) );
}
std::shared_ptr<const TriList> getTriList( std::shared_ptr<const Mesh> mesh )
{
return getTriList( std::const_pointer_cast<Mesh>(mesh) );
return getTriList( std::const_pointer_cast<Mesh>( mesh ) );
}
} // IO namespace
/****************************************************
* Convert enum values *
****************************************************/
std::string getString( VariableType type )
{
if ( type == VariableType::NodeVariable )
return "node";
else if ( type == VariableType::EdgeVariable )
return "edge";
else if ( type == VariableType::SurfaceVariable )
return "face";
else if ( type == VariableType::VolumeVariable )
return "cell";
else if ( type == VariableType::NullVariable )
return "null";
else
ERROR( "Invalid type" );
return "";
}
VariableType getVariableType( const std::string &type_in )
{
auto type = deblank( type_in );
if ( type == "node" )
return VariableType::NodeVariable;
else if ( type == "edge" || type == "1" )
return VariableType::EdgeVariable;
else if ( type == "face" )
return VariableType::SurfaceVariable;
else if ( type == "cell" || type == "3" )
return VariableType::VolumeVariable;
else if ( type == "null" )
return VariableType::NullVariable;
else
ERROR( "Invalid type: " + type );
return VariableType::NullVariable;
}
std::string getString( DataType type )
{
if ( type == DataType::Double )
return "double";
else if ( type == DataType::Float )
return "float";
else if ( type == DataType::Int )
return "int";
else if ( type == DataType::Null )
return "null";
else
ERROR( "Invalid type" );
return "";
}
DataType getDataType( const std::string &type_in )
{
auto type = deblank( type_in );
if ( type == "double" )
return DataType::Double;
else if ( type == "float" )
return DataType::Float;
else if ( type == "int" )
return DataType::Int;
else if ( type == "null" )
return DataType::Null;
else
ERROR( "Invalid type: " + type );
return DataType::Null;
}
std::string getString( MeshType type )
{
if ( type == MeshType::PointMesh )
return "PointMesh";
else if ( type == MeshType::SurfaceMesh )
return "SurfaceMesh";
else if ( type == MeshType::VolumeMesh )
return "VolumeMesh";
else if ( type == MeshType::Unknown )
return "unknown";
else
ERROR( "Invalid type" );
return "";
}
MeshType getMeshType( const std::string &type_in )
{
auto type = deblank( type_in );
if ( type == "PointMesh" || type == "1" )
return MeshType::PointMesh;
else if ( type == "SurfaceMesh" || type == "2" )
return MeshType::SurfaceMesh;
else if ( type == "VolumeMesh" || type == "3" )
return MeshType::VolumeMesh;
else if ( type == "unknown" || type == "-1" )
return MeshType::Unknown;
else
ERROR( "Invalid type: " + type );
return MeshType::Unknown;
}
std::string getString( FileFormat type )
{
if ( type == FileFormat::OLD )
return "old";
else if ( type == FileFormat::NEW )
return "new";
else if ( type == FileFormat::NEW_SINGLE )
return "new(single)";
else if ( type == FileFormat::SILO )
return "silo";
else
ERROR( "Invalid type" );
return "";
}
FileFormat getFileFormat( const std::string &type_in )
{
auto type = deblank( type_in );
if ( type == "old" || type == "1" )
return FileFormat::OLD;
else if ( type == "new" || type == "2" )
return FileFormat::NEW;
else if ( type == "new(single)" || type == "3" )
return FileFormat::NEW_SINGLE;
else if ( type == "silo" || type == "4" )
return FileFormat::SILO;
else
ERROR( "Invalid type: " + type );
return FileFormat::SILO;
}
} // namespace IO

133
IO/Mesh.h
View File

@ -6,17 +6,36 @@
#include <string.h>
#include <vector>
#include "analysis/PointList.h"
#include "common/Array.h"
#include "common/Communication.h"
#include "analysis/PointList.h"
namespace IO {
//! Possible variable types
enum class VariableType: unsigned char { NodeVariable=1, EdgeVariable=2, SurfaceVariable=2, VolumeVariable=3, NullVariable=0 };
enum class DataType: unsigned char { Double=1, Float=2, Int=2, Null=0 };
//! Enums to define types
enum class VariableType {
NodeVariable,
EdgeVariable,
SurfaceVariable,
VolumeVariable,
NullVariable
};
enum class DataType { Double, Float, Int, Null };
enum class MeshType { PointMesh, SurfaceMesh, VolumeMesh, Unknown };
enum class FileFormat { OLD, NEW, NEW_SINGLE, SILO };
//! Convert enums to/from strings (more future-proof than static_cast<int>)
std::string getString( VariableType );
std::string getString( DataType );
std::string getString( MeshType );
std::string getString( FileFormat );
VariableType getVariableType( const std::string & );
DataType getDataType( const std::string & );
MeshType getMeshType( const std::string & );
FileFormat getFileFormat( const std::string & );
/*! \class Mesh
@ -32,21 +51,22 @@ public:
//! Number of points for the given variable type
virtual size_t numberPointsVar( VariableType type ) const = 0;
//! Pack the data
virtual std::pair<size_t,void*> pack( int level ) const = 0;
virtual std::pair<size_t, void *> pack( int level ) const = 0;
//! Unpack the data
virtual void unpack( const std::pair<size_t,void*>& data ) = 0;
virtual void unpack( const std::pair<size_t, void *> &data ) = 0;
protected:
//! Empty constructor
Mesh();
Mesh(const Mesh&);
Mesh& operator=(const Mesh&);
Mesh( const Mesh & );
Mesh &operator=( const Mesh & );
};
/*! \class PointList
\brief A class used to hold a list of verticies
*/
class PointList: public Mesh
class PointList : public Mesh
{
public:
//! Empty constructor
@ -60,13 +80,14 @@ public:
//! Number of points for the given variable type
virtual size_t numberPointsVar( VariableType type ) const;
//! Pack the data
virtual std::pair<size_t,void*> pack( int level ) const;
virtual std::pair<size_t, void *> pack( int level ) const;
//! Unpack the data
virtual void unpack( const std::pair<size_t,void*>& data );
virtual void unpack( const std::pair<size_t, void *> &data );
//! Access the points
const std::vector<Point>& getPoints() const { return points; }
const std::vector<Point> &getPoints() const { return points; }
public:
std::vector<Point> points; //!< List of points vertex
std::vector<Point> points; //!< List of points vertex
};
@ -74,7 +95,7 @@ public:
\brief A class used to hold a list of triangles specified by their vertex coordinates
*/
class TriMesh;
class TriList: public Mesh
class TriList : public Mesh
{
public:
//! Empty constructor
@ -82,7 +103,7 @@ public:
//! Constructor for N triangles
TriList( size_t N_tri );
//! Constructor from TriMesh
TriList( const TriMesh& );
TriList( const TriMesh & );
//! Destructor
virtual ~TriList();
//! Mesh class name
@ -90,20 +111,22 @@ public:
//! Number of points for the given variable type
virtual size_t numberPointsVar( VariableType type ) const;
//! Pack the data
virtual std::pair<size_t,void*> pack( int level ) const;
virtual std::pair<size_t, void *> pack( int level ) const;
//! Unpack the data
virtual void unpack( const std::pair<size_t,void*>& data );
virtual void unpack( const std::pair<size_t, void *> &data );
public:
std::vector<Point> A; //!< First vertex
std::vector<Point> B; //!< Second vertex
std::vector<Point> C; //!< Third vertex
std::vector<Point> A; //!< First vertex
std::vector<Point> B; //!< Second vertex
std::vector<Point> C; //!< Third vertex
};
/*! \class TriMesh
\brief A class used to hold a list of trianges specified by their vertex number and list of coordiantes
\brief A class used to hold a list of trianges specified by their vertex number and list of
coordiantes
*/
class TriMesh: public Mesh
class TriMesh : public Mesh
{
public:
//! TriMesh constructor
@ -113,7 +136,7 @@ public:
//! Constructor for Nt triangles and the given points
TriMesh( size_t N_tri, std::shared_ptr<PointList> points );
//! Constructor from TriList
TriMesh( const TriList& );
TriMesh( const TriList & );
//! Destructor
virtual ~TriMesh();
//! Mesh class name
@ -121,21 +144,22 @@ public:
//! Number of points for the given variable type
virtual size_t numberPointsVar( VariableType type ) const;
//! Pack the data
virtual std::pair<size_t,void*> pack( int level ) const;
virtual std::pair<size_t, void *> pack( int level ) const;
//! Unpack the data
virtual void unpack( const std::pair<size_t,void*>& data );
virtual void unpack( const std::pair<size_t, void *> &data );
public:
std::shared_ptr<PointList> vertices; //!< List of verticies
std::vector<int> A; //!< First vertex
std::vector<int> B; //!< Second vertex
std::vector<int> C; //!< Third vertex
std::shared_ptr<PointList> vertices; //!< List of verticies
std::vector<int> A; //!< First vertex
std::vector<int> B; //!< Second vertex
std::vector<int> C; //!< Third vertex
};
/*! \class Domain
\brief A class used to hold the domain
*/
class DomainMesh: public Mesh
class DomainMesh : public Mesh
{
public:
//! Empty constructor
@ -149,9 +173,10 @@ public:
//! Number of points for the given variable type
virtual size_t numberPointsVar( VariableType type ) const;
//! Pack the data
virtual std::pair<size_t,void*> pack( int level ) const;
virtual std::pair<size_t, void *> pack( int level ) const;
//! Unpack the data
virtual void unpack( const std::pair<size_t,void*>& data );
virtual void unpack( const std::pair<size_t, void *> &data );
public:
int nprocx, nprocy, nprocz, rank;
int nx, ny, nz;
@ -159,37 +184,40 @@ public:
};
/*! \class Variable
\brief A base class for variables
*/
struct Variable
{
struct Variable {
public:
// Internal variables
unsigned char dim; //!< Number of points per grid point (1: scalar, 3: vector, ...)
VariableType type; //!< Variable type
DataType precision; //!< Variable precision to use for IO
std::string name; //!< Variable name
Array<double> data; //!< Variable data
unsigned char dim; //!< Number of points per grid point (1: scalar, 3: vector, ...)
VariableType type; //!< Variable type
DataType precision; //!< Variable precision to use for IO
std::string name; //!< Variable name
Array<double> data; //!< Variable data
//! Empty constructor
Variable(): dim(0), type(VariableType::NullVariable), precision(DataType::Double) {}
Variable() : dim( 0 ), type( VariableType::NullVariable ), precision( DataType::Double ) {}
//! Constructor
Variable( int dim_, IO::VariableType type_, const std::string& name_ ):
dim(dim_), type(type_), precision(DataType::Double), name(name_) {}
Variable( int dim_, IO::VariableType type_, const std::string &name_ )
: dim( dim_ ), type( type_ ), precision( DataType::Double ), name( name_ )
{
}
//! Constructor
Variable( int dim_, IO::VariableType type_, const std::string& name_, const Array<double>& data_ ):
dim(dim_), type(type_), precision(DataType::Double), name(name_), data(data_) {}
Variable(
int dim_, IO::VariableType type_, const std::string &name_, const Array<double> &data_ )
: dim( dim_ ), type( type_ ), precision( DataType::Double ), name( name_ ), data( data_ )
{
}
//! Destructor
virtual ~Variable() {}
protected:
//! Empty constructor
Variable(const Variable&);
Variable& operator=(const Variable&);
Variable( const Variable & );
Variable &operator=( const Variable & );
};
/*! \class MeshDataStruct
\brief A class used to hold database info for saving a mesh
*/
@ -197,11 +225,11 @@ struct MeshDataStruct {
DataType precision; //!< Precision to use for IO (mesh)
std::string meshName; //!< Mesh name
std::shared_ptr<Mesh> mesh; //!< Mesh data
std::vector<std::shared_ptr<Variable> > vars;
std::vector<std::shared_ptr<Variable>> vars;
//! Empty constructor
MeshDataStruct(): precision(DataType::Double) {}
MeshDataStruct() : precision( DataType::Double ) {}
//! Check the data
bool check() const;
bool check( bool abort = true ) const;
};
@ -214,7 +242,6 @@ std::shared_ptr<const TriMesh> getTriMesh( std::shared_ptr<const Mesh> mesh );
std::shared_ptr<const TriList> getTriList( std::shared_ptr<const Mesh> mesh );
} // IO namespace
} // namespace IO
#endif

541
IO/MeshDatabase.cpp
View File

@ -1,130 +1,144 @@
#include "IO/MeshDatabase.h"
#include "IO/IOHelpers.h"
#include "IO/Mesh.h"
#include "IO/PackData.h"
#include "IO/IOHelpers.h"
#include "common/MPI.h"
#include "common/Utilities.h"
#include <vector>
#include <cstdio>
#include <map>
#include <set>
#include <cstdio>
#include <vector>
#include <ProfilerApp.h>
// Default pack/unpack
// clang-format off
#define INSTANTIATE_PACK( TYPE ) \
template<> \
size_t packsize<TYPE>( const TYPE &rhs ) \
{ \
return sizeof( TYPE ); \
} \
template<> \
void pack<TYPE>( const TYPE &rhs, char *buffer ) \
{ \
memcpy( buffer, &rhs, sizeof( IO::MeshType ) ); \
} \
template<> \
void unpack<TYPE>( TYPE &data, const char *buffer ) \
{ \
memcpy( &data, buffer, sizeof( IO::MeshType ) ); \
}
INSTANTIATE_PACK( IO::VariableType )
INSTANTIATE_PACK( IO::DataType )
INSTANTIATE_PACK( IO::MeshType )
INSTANTIATE_PACK( IO::FileFormat )
// clang-format on
// MeshType
template<>
size_t packsize<IO::MeshType>( const IO::MeshType& rhs )
{
return sizeof(IO::MeshType);
}
template<>
void pack<IO::MeshType>( const IO::MeshType& rhs, char *buffer )
{
memcpy(buffer,&rhs,sizeof(IO::MeshType));
}
template<>
void unpack<IO::MeshType>( IO::MeshType& data, const char *buffer )
{
memcpy(&data,buffer,sizeof(IO::MeshType));
}
// Variable::VariableType
template<>
size_t packsize<IO::VariableType>( const IO::VariableType& rhs )
{
return sizeof(IO::VariableType);
}
template<>
void pack<IO::VariableType>( const IO::VariableType& rhs, char *buffer )
{
memcpy(buffer,&rhs,sizeof(IO::VariableType));
}
template<>
void unpack<IO::VariableType>( IO::VariableType& data, const char *buffer )
{
memcpy(&data,buffer,sizeof(IO::VariableType));
}
// DatabaseEntry
template<>
size_t packsize<IO::DatabaseEntry>( const IO::DatabaseEntry& rhs )
size_t packsize<IO::DatabaseEntry>( const IO::DatabaseEntry &rhs )
{
return packsize(rhs.name)+packsize(rhs.file)+packsize(rhs.offset);
return packsize( rhs.name ) + packsize( rhs.file ) + packsize( rhs.offset );
}
template<>
void pack<IO::DatabaseEntry>( const IO::DatabaseEntry& rhs, char *buffer )
void pack<IO::DatabaseEntry>( const IO::DatabaseEntry &rhs, char *buffer )
{
size_t i=0;
pack(rhs.name,&buffer[i]); i+=packsize(rhs.name);
pack(rhs.file,&buffer[i]); i+=packsize(rhs.file);
pack(rhs.offset,&buffer[i]); i+=packsize(rhs.offset);
size_t i = 0;
pack( rhs.name, &buffer[i] );
i += packsize( rhs.name );
pack( rhs.file, &buffer[i] );
i += packsize( rhs.file );
pack( rhs.offset, &buffer[i] );
i += packsize( rhs.offset );
}
template<>
void unpack<IO::DatabaseEntry>( IO::DatabaseEntry& data, const char *buffer )
void unpack<IO::DatabaseEntry>( IO::DatabaseEntry &data, const char *buffer )
{
size_t i=0;
unpack(data.name,&buffer[i]); i+=packsize(data.name);
unpack(data.file,&buffer[i]); i+=packsize(data.file);
unpack(data.offset,&buffer[i]); i+=packsize(data.offset);
size_t i = 0;
unpack( data.name, &buffer[i] );
i += packsize( data.name );
unpack( data.file, &buffer[i] );
i += packsize( data.file );
unpack( data.offset, &buffer[i] );
i += packsize( data.offset );
}
// VariableDatabase
template<>
size_t packsize<IO::VariableDatabase>( const IO::VariableDatabase& rhs )
size_t packsize<IO::VariableDatabase>( const IO::VariableDatabase &rhs )
{
return packsize(rhs.name)+packsize(rhs.type)+packsize(rhs.dim);
return packsize( rhs.name ) + packsize( rhs.type ) + packsize( rhs.dim );
}
template<>
void pack<IO::VariableDatabase>( const IO::VariableDatabase& rhs, char *buffer )
void pack<IO::VariableDatabase>( const IO::VariableDatabase &rhs, char *buffer )
{
size_t i=0;
pack(rhs.name,&buffer[i]); i+=packsize(rhs.name);
pack(rhs.type,&buffer[i]); i+=packsize(rhs.type);
pack(rhs.dim,&buffer[i]); i+=packsize(rhs.dim);
size_t i = 0;
pack( rhs.name, &buffer[i] );
i += packsize( rhs.name );
pack( rhs.type, &buffer[i] );
i += packsize( rhs.type );
pack( rhs.dim, &buffer[i] );
i += packsize( rhs.dim );
}
template<>
void unpack<IO::VariableDatabase>( IO::VariableDatabase& data, const char *buffer )
void unpack<IO::VariableDatabase>( IO::VariableDatabase &data, const char *buffer )
{
size_t i=0;
unpack(data.name,&buffer[i]); i+=packsize(data.name);
unpack(data.type,&buffer[i]); i+=packsize(data.type);
unpack(data.dim,&buffer[i]); i+=packsize(data.dim);
size_t i = 0;
unpack( data.name, &buffer[i] );
i += packsize( data.name );
unpack( data.type, &buffer[i] );
i += packsize( data.type );
unpack( data.dim, &buffer[i] );
i += packsize( data.dim );
}
// MeshDatabase
template<>
size_t packsize<IO::MeshDatabase>( const IO::MeshDatabase& data )
size_t packsize<IO::MeshDatabase>( const IO::MeshDatabase &data )
{
return packsize(data.name)
+ packsize(data.type)
+ packsize(data.meshClass)
+ packsize(data.format)
+ packsize(data.domains)
+ packsize(data.variables)
+ packsize(data.variable_data);
return packsize( data.name ) + packsize( data.type ) + packsize( data.meshClass ) +
packsize( data.format ) + packsize( data.domains ) + packsize( data.variables ) +
packsize( data.variable_data );
}
template<>
void pack<IO::MeshDatabase>( const IO::MeshDatabase& rhs, char *buffer )
void pack<IO::MeshDatabase>( const IO::MeshDatabase &rhs, char *buffer )
{
size_t i = 0;
pack(rhs.name,&buffer[i]); i+=packsize(rhs.name);
pack(rhs.type,&buffer[i]); i+=packsize(rhs.type);
pack(rhs.meshClass,&buffer[i]); i+=packsize(rhs.meshClass);
pack(rhs.format,&buffer[i]); i+=packsize(rhs.format);
pack(rhs.domains,&buffer[i]); i+=packsize(rhs.domains);
pack(rhs.variables,&buffer[i]); i+=packsize(rhs.variables);
pack(rhs.variable_data,&buffer[i]); i+=packsize(rhs.variable_data);
pack( rhs.name, &buffer[i] );
i += packsize( rhs.name );
pack( rhs.type, &buffer[i] );
i += packsize( rhs.type );
pack( rhs.meshClass, &buffer[i] );
i += packsize( rhs.meshClass );
pack( rhs.format, &buffer[i] );
i += packsize( rhs.format );
pack( rhs.domains, &buffer[i] );
i += packsize( rhs.domains );
pack( rhs.variables, &buffer[i] );
i += packsize( rhs.variables );
pack( rhs.variable_data, &buffer[i] );
i += packsize( rhs.variable_data );
}
template<>
void unpack<IO::MeshDatabase>( IO::MeshDatabase& data, const char *buffer )
void unpack<IO::MeshDatabase>( IO::MeshDatabase &data, const char *buffer )
{
size_t i=0;
unpack(data.name,&buffer[i]); i+=packsize(data.name);
unpack(data.type,&buffer[i]); i+=packsize(data.type);
unpack(data.meshClass,&buffer[i]); i+=packsize(data.meshClass);
unpack(data.format,&buffer[i]); i+=packsize(data.format);
unpack(data.domains,&buffer[i]); i+=packsize(data.domains);
unpack(data.variables,&buffer[i]); i+=packsize(data.variables);
unpack(data.variable_data,&buffer[i]); i+=packsize(data.variable_data);
size_t i = 0;
unpack( data.name, &buffer[i] );
i += packsize( data.name );
unpack( data.type, &buffer[i] );
i += packsize( data.type );
unpack( data.meshClass, &buffer[i] );
i += packsize( data.meshClass );
unpack( data.format, &buffer[i] );
i += packsize( data.format );
unpack( data.domains, &buffer[i] );
i += packsize( data.domains );
unpack( data.variables, &buffer[i] );
i += packsize( data.variables );
unpack( data.variable_data, &buffer[i] );
i += packsize( data.variable_data );
}
@ -132,79 +146,72 @@ namespace IO {
/****************************************************
* VariableDatabase *
****************************************************/
bool VariableDatabase::operator==(const VariableDatabase& rhs ) const
* VariableDatabase *
****************************************************/
bool VariableDatabase::operator==( const VariableDatabase &rhs ) const
{
return type==rhs.type && dim==rhs.dim && name==rhs.name;
return type == rhs.type && dim == rhs.dim && name == rhs.name;
}
bool VariableDatabase::operator!=(const VariableDatabase& rhs ) const
bool VariableDatabase::operator!=( const VariableDatabase &rhs ) const
{
return type!=rhs.type || dim!=rhs.dim || name!=rhs.name;
return type != rhs.type || dim != rhs.dim || name != rhs.name;
}
bool VariableDatabase::operator>=(const VariableDatabase& rhs ) const
bool VariableDatabase::operator>=( const VariableDatabase &rhs ) const
{
return operator>(rhs) || operator==(rhs);
return operator>( rhs ) || operator==( rhs );
}
bool VariableDatabase::operator<=(const VariableDatabase& rhs ) const
bool VariableDatabase::operator<=( const VariableDatabase &rhs ) const { return !operator>( rhs ); }
bool VariableDatabase::operator>( const VariableDatabase &rhs ) const
{
return !operator>(rhs);
}
bool VariableDatabase::operator>(const VariableDatabase& rhs ) const
{
if ( name>rhs.name )
if ( name > rhs.name )
return true;
else if ( name<rhs.name )
else if ( name < rhs.name )
return false;
if ( type>rhs.type )
if ( type > rhs.type )
return true;
else if ( type<rhs.type )
else if ( type < rhs.type )
return false;
if ( dim>rhs.dim )
if ( dim > rhs.dim )
return true;
else if ( dim<rhs.dim )
else if ( dim < rhs.dim )
return false;
return false;
}
bool VariableDatabase::operator<(const VariableDatabase& rhs ) const
bool VariableDatabase::operator<( const VariableDatabase &rhs ) const
{
return !operator>(rhs) && operator!=(rhs);
return !operator>( rhs ) && operator!=( rhs );
}
/****************************************************
* MeshDatabase *
****************************************************/
MeshDatabase::MeshDatabase()
* MeshDatabase *
****************************************************/
MeshDatabase::MeshDatabase() {}
MeshDatabase::~MeshDatabase() {}
MeshDatabase::MeshDatabase( const MeshDatabase &rhs )
{
}
MeshDatabase::~MeshDatabase()
{
}
MeshDatabase::MeshDatabase(const MeshDatabase& rhs)
{
name = rhs.name;
type = rhs.type;
meshClass = rhs.meshClass;
format = rhs.format;
domains = rhs.domains;
variables = rhs.variables;
name = rhs.name;
type = rhs.type;
meshClass = rhs.meshClass;
format = rhs.format;
domains = rhs.domains;
variables = rhs.variables;
variable_data = rhs.variable_data;
}
MeshDatabase& MeshDatabase::operator=(const MeshDatabase& rhs)
MeshDatabase &MeshDatabase::operator=( const MeshDatabase &rhs )
{
this->name = rhs.name;
this->type = rhs.type;
this->meshClass = rhs.meshClass;
this->format = rhs.format;
this->domains = rhs.domains;
this->variables = rhs.variables;
this->name = rhs.name;
this->type = rhs.type;
this->meshClass = rhs.meshClass;
this->format = rhs.format;
this->domains = rhs.domains;
this->variables = rhs.variables;
this->variable_data = rhs.variable_data;
return *this;
}
VariableDatabase MeshDatabase::getVariableDatabase( const std::string& varname ) const
VariableDatabase MeshDatabase::getVariableDatabase( const std::string &varname ) const
{
for (size_t i=0; i<variables.size(); i++) {
for ( size_t i = 0; i < variables.size(); i++ ) {
if ( variables[i].name == varname )
return variables[i];
}
@ -213,217 +220,219 @@ VariableDatabase MeshDatabase::getVariableDatabase( const std::string& varname )
/****************************************************
* DatabaseEntry *
****************************************************/
std::string DatabaseEntry::write( ) const
* DatabaseEntry *
****************************************************/
std::string DatabaseEntry::write() const
{
char tmp[1000];
sprintf(tmp,"%s; %s; %lu",name.c_str(),file.c_str(),offset);
return std::string(tmp);
sprintf( tmp, "%s; %s; %lu", name.c_str(), file.c_str(), offset );
return std::string( tmp );
}
DatabaseEntry::DatabaseEntry( const char* line )
DatabaseEntry::DatabaseEntry( const char *line )
{
std::vector<std::string> list = splitList(line,';');
name = list[0];
file = list[1];
offset = atol(list[2].c_str());
auto list = splitList( line, ';' );
name = list[0];
file = list[1];
offset = atol( list[2].c_str() );
}
void DatabaseEntry::read( const char* line )
void DatabaseEntry::read( const char *line )
{
std::vector<std::string> list = splitList(line,';');
name = list[0];
file = list[1];
offset = atol(list[2].c_str());
auto list = splitList( line, ';' );
name = list[0];
file = list[1];
offset = atol( list[2].c_str() );
}
void DatabaseEntry::read( const std::string& line )
void DatabaseEntry::read( const std::string &line )
{
std::vector<std::string> list = splitList(line.c_str(),';');
name = list[0];
file = list[1];
offset = atol(list[2].c_str());
auto list = splitList( line.c_str(), ';' );
name = list[0];
file = list[1];
offset = atol( list[2].c_str() );
}
// Gather the mesh databases from all processors
inline int tod( int N ) { return (N+7)/sizeof(double); }
std::vector<MeshDatabase> gatherAll( const std::vector<MeshDatabase>& meshes, const Utilities::MPI& comm )
inline int tod( int N ) { return ( N + 7 ) / sizeof( double ); }
std::vector<MeshDatabase> gatherAll(
const std::vector<MeshDatabase> &meshes, const Utilities::MPI &comm )
{
if ( comm.getSize() == 1 )
return meshes;
PROFILE_START("gatherAll");
PROFILE_START("gatherAll-pack",2);
PROFILE_START( "gatherAll" );
PROFILE_START( "gatherAll-pack", 2 );
int size = comm.getSize();
// First pack the mesh data to local buffers
int localsize = 0;
for (size_t i=0; i<meshes.size(); i++)
localsize += tod(packsize(meshes[i]));
for ( size_t i = 0; i < meshes.size(); i++ )
localsize += tod( packsize( meshes[i] ) );
auto localbuf = new double[localsize];
int pos = 0;
for (size_t i=0; i<meshes.size(); i++) {
pack( meshes[i], (char*) &localbuf[pos] );
pos += tod(packsize(meshes[i]));
int pos = 0;
for ( size_t i = 0; i < meshes.size(); i++ ) {
pack( meshes[i], (char *) &localbuf[pos] );
pos += tod( packsize( meshes[i] ) );
}
PROFILE_STOP("gatherAll-pack",2);
PROFILE_STOP( "gatherAll-pack", 2 );
// Get the number of bytes each processor will be sending/recieving
PROFILE_START("gatherAll-send1",2);
auto recvsize = comm.allGather( localsize );
PROFILE_START( "gatherAll-send1", 2 );
auto recvsize = comm.allGather( localsize );
int globalsize = recvsize[0];
auto disp = new int[size];
disp[0] = 0;
for (int i=1; i<size; i++) {
disp[i] = disp[i-1] + recvsize[i];
auto disp = new int[size];
disp[0] = 0;
for ( int i = 1; i < size; i++ ) {
disp[i] = disp[i - 1] + recvsize[i];
globalsize += recvsize[i];
}
PROFILE_STOP("gatherAll-send1",2);
PROFILE_STOP( "gatherAll-send1", 2 );
// Send/recv the global data
PROFILE_START("gatherAll-send2",2);
PROFILE_START( "gatherAll-send2", 2 );
auto globalbuf = new double[globalsize];
comm.allGather(localbuf,localsize,globalbuf,recvsize.data(),disp,true);
PROFILE_STOP("gatherAll-send2",2);
comm.allGather( localbuf, localsize, globalbuf, recvsize.data(), disp, true );
PROFILE_STOP( "gatherAll-send2", 2 );
// Unpack the data
PROFILE_START("gatherAll-unpack",2);
std::map<std::string,MeshDatabase> data;
PROFILE_START( "gatherAll-unpack", 2 );
std::map<std::string, MeshDatabase> data;
pos = 0;
while ( pos < globalsize ) {
MeshDatabase tmp;
unpack(tmp,(char*)&globalbuf[pos]);
pos += tod(packsize(tmp));
std::map<std::string,MeshDatabase>::iterator it = data.find(tmp.name);
if ( it==data.end() ) {
unpack( tmp, (char *) &globalbuf[pos] );
pos += tod( packsize( tmp ) );
std::map<std::string, MeshDatabase>::iterator it = data.find( tmp.name );
if ( it == data.end() ) {
data[tmp.name] = tmp;
} else {
for (size_t i=0; i<tmp.domains.size(); i++)
it->second.domains.push_back(tmp.domains[i]);
for (size_t i=0; i<tmp.variables.size(); i++)
it->second.variables.push_back(tmp.variables[i]);
it->second.variable_data.insert(tmp.variable_data.begin(),tmp.variable_data.end());
for ( size_t i = 0; i < tmp.domains.size(); i++ )
it->second.domains.push_back( tmp.domains[i] );
for ( size_t i = 0; i < tmp.variables.size(); i++ )
it->second.variables.push_back( tmp.variables[i] );
it->second.variable_data.insert( tmp.variable_data.begin(), tmp.variable_data.end() );
}
}
for (auto it=data.begin(); it!=data.end(); ++it) {
for ( auto it = data.begin(); it != data.end(); ++it ) {
// Get the unique variables
std::set<VariableDatabase> data2(it->second.variables.begin(),it->second.variables.end());
it->second.variables = std::vector<VariableDatabase>(data2.begin(),data2.end());
std::set<VariableDatabase> data2(
it->second.variables.begin(), it->second.variables.end() );
it->second.variables = std::vector<VariableDatabase>( data2.begin(), data2.end() );
}
// Free temporary memory
delete [] localbuf;
delete [] disp;
delete [] globalbuf;
delete[] localbuf;
delete[] disp;
delete[] globalbuf;
// Return the results
std::vector<MeshDatabase> data2(data.size());
size_t i=0;
for (std::map<std::string,MeshDatabase>::iterator it=data.begin(); it!=data.end(); ++it, ++i)
std::vector<MeshDatabase> data2( data.size() );
size_t i = 0;
for ( auto it = data.begin(); it != data.end(); ++it, ++i )
data2[i] = it->second;
PROFILE_STOP("gatherAll-unpack",2);
PROFILE_STOP("gatherAll");
PROFILE_STOP( "gatherAll-unpack", 2 );
PROFILE_STOP( "gatherAll" );
return data2;
}
//! Write the mesh databases to a file
void write( const std::vector<MeshDatabase>& meshes, const std::string& filename )
void write( const std::vector<MeshDatabase> &meshes, const std::string &filename )
{
PROFILE_START("write");
FILE *fid = fopen(filename.c_str(),"wb");
for (size_t i=0; i<meshes.size(); i++) {
fprintf(fid,"%s\n",meshes[i].name.c_str());
fprintf(fid," type: %i\n",static_cast<int>(meshes[i].type));
fprintf(fid," meshClass: %s\n",meshes[i].meshClass.c_str());
fprintf(fid," format: %i\n",static_cast<int>(meshes[i].format));
for (size_t j=0; j<meshes[i].domains.size(); j++)
fprintf(fid," domain: %s\n",meshes[i].domains[j].write().c_str());
fprintf(fid," variables: ");
for (size_t j=0; j<meshes[i].variables.size(); j++) {
const VariableDatabase& var = meshes[i].variables[j];
fprintf(fid,"%s|%i|%i; ",var.name.c_str(),static_cast<int>(var.type),var.dim);
PROFILE_START( "write" );
FILE *fid = fopen( filename.c_str(), "wb" );
for ( size_t i = 0; i < meshes.size(); i++ ) {
fprintf( fid, "%s\n", meshes[i].name.c_str() );
fprintf( fid, " type: %s\n", getString( meshes[i].type ).data() );
fprintf( fid, " meshClass: %s\n", meshes[i].meshClass.c_str() );
fprintf( fid, " format: %s\n", getString( meshes[i].format ).data() );
for ( size_t j = 0; j < meshes[i].domains.size(); j++ )
fprintf( fid, " domain: %s\n", meshes[i].domains[j].write().c_str() );
fprintf( fid, " variables: " );
for ( size_t j = 0; j < meshes[i].variables.size(); j++ ) {
const VariableDatabase &var = meshes[i].variables[j];
fprintf( fid, "%s|%s|%i; ", var.name.data(), getString( var.type ).data(), var.dim );
}
fprintf(fid,"\n");
std::map<std::pair<std::string,std::string>,DatabaseEntry>::const_iterator it;
for (it=meshes[i].variable_data.begin(); it!=meshes[i].variable_data.end(); ++it) {
const char* domain = it->first.first.c_str();
const char* variable = it->first.second.c_str();
fprintf(fid," variable(%s,%s): %s\n",domain,variable,it->second.write().c_str());
fprintf( fid, "\n" );
for ( auto it = meshes[i].variable_data.begin(); it != meshes[i].variable_data.end();
++it ) {
const char *domain = it->first.first.c_str();
const char *variable = it->first.second.c_str();
fprintf(
fid, " variable(%s,%s): %s\n", domain, variable, it->second.write().c_str() );
}
}
fclose(fid);
PROFILE_STOP("write");
fclose( fid );
PROFILE_STOP( "write" );
}
//! Read the mesh databases from a file
std::vector<MeshDatabase> read( const std::string& filename )
std::vector<MeshDatabase> read( const std::string &filename )
{
std::vector<MeshDatabase> meshes;
PROFILE_START("read");
FILE *fid = fopen(filename.c_str(),"rb");
if ( fid==NULL )
ERROR("Error opening file");
PROFILE_START( "read" );
FILE *fid = fopen( filename.c_str(), "rb" );
if ( fid == NULL )
ERROR( "Error opening file" );
char *line = new char[10000];
while ( std::fgets(line,1000,fid) != NULL ) {
if ( line[0]<32 ) {
while ( std::fgets( line, 1000, fid ) != NULL ) {
if ( line[0] < 32 ) {
// Empty line
continue;
} else if ( line[0] != ' ' ) {
meshes.resize(meshes.size()+1);
std::string name(line);
name.resize(name.size()-1);
meshes.resize( meshes.size() + 1 );
std::string name( line );
name.resize( name.size() - 1 );
meshes.back().name = name;
} else if ( strncmp(line," format:",10)==0 ) {
meshes.back().format = static_cast<unsigned char>(atoi(&line[10]));
} else if ( strncmp(line," type:",8)==0 ) {
meshes.back().type = static_cast<MeshType>(atoi(&line[8]));
} else if ( strncmp(line," meshClass:",13)==0 ) {
meshes.back().meshClass = deblank(std::string(&line[13]));
} else if ( strncmp(line," domain:",10)==0 ) {
DatabaseEntry data(&line[10]);
meshes.back().domains.push_back(data);
} else if ( strncmp(line," variables:",13)==0 ) {
MeshDatabase& mesh = meshes.back();
std::vector<std::string> variables = splitList(&line[13],';');
mesh.variables.resize(variables.size());
for (size_t i=0; i<variables.size(); i++) {
std::vector<std::string> tmp = splitList(variables[i].c_str(),'|');
ASSERT(tmp.size()==3);
} else if ( strncmp( line, " format:", 10 ) == 0 ) {
meshes.back().format = getFileFormat( &line[10] );
} else if ( strncmp( line, " type:", 8 ) == 0 ) {
meshes.back().type = getMeshType( &line[8] );
} else if ( strncmp( line, " meshClass:", 13 ) == 0 ) {
meshes.back().meshClass = deblank( std::string( &line[13] ) );
} else if ( strncmp( line, " domain:", 10 ) == 0 ) {
DatabaseEntry data( &line[10] );
meshes.back().domains.push_back( data );
} else if ( strncmp( line, " variables:", 13 ) == 0 ) {
MeshDatabase &mesh = meshes.back();
std::vector<std::string> variables = splitList( &line[13], ';' );
mesh.variables.resize( variables.size() );
for ( size_t i = 0; i < variables.size(); i++ ) {
std::vector<std::string> tmp = splitList( variables[i].c_str(), '|' );
ASSERT( tmp.size() == 3 );
mesh.variables[i].name = tmp[0];
mesh.variables[i].type = static_cast<VariableType>(atoi(tmp[1].c_str()));
mesh.variables[i].dim = atoi(tmp[2].c_str());
mesh.variables[i].type = getVariableType( tmp[1] );
mesh.variables[i].dim = atoi( tmp[2].c_str() );
}
} else if ( strncmp(line," variable(",12)==0 ) {
size_t i1 = find(line,',');
size_t i2 = find(line,':');
std::string domain = deblank(std::string(line,12,i1-12));
std::string variable = deblank(std::string(line,i1+1,i2-i1-2));
std::pair<std::string,std::string> key(domain,variable);
DatabaseEntry data(&line[i2+1]);
meshes.back().variable_data.insert(
std::pair<std::pair<std::string,std::string>,DatabaseEntry>(key,data) );
} else if ( strncmp( line, " variable(", 12 ) == 0 ) {
size_t i1 = find( line, ',' );
size_t i2 = find( line, ':' );
std::string domain = deblank( std::string( line, 12, i1 - 12 ) );
std::string variable = deblank( std::string( line, i1 + 1, i2 - i1 - 2 ) );
std::pair<std::string, std::string> key( domain, variable );
DatabaseEntry data( &line[i2 + 1] );
meshes.back().variable_data.insert(
std::pair<std::pair<std::string, std::string>, DatabaseEntry>( key, data ) );
} else {
ERROR("Error reading line");
ERROR( "Error reading line" );
}
}
fclose(fid);
delete [] line;
PROFILE_STOP("read");
fclose( fid );
delete[] line;
PROFILE_STOP( "read" );
return meshes;
}
// Return the mesh type
IO::MeshType meshType( const IO::Mesh& mesh )
IO::MeshType meshType( const IO::Mesh &mesh )
{
IO::MeshType type = IO::Unknown;
IO::MeshType type = IO::MeshType::Unknown;
const std::string meshClass = mesh.className();
if ( meshClass=="PointList" ) {
type = IO::PointMesh;
} else if ( meshClass=="TriList" || meshClass=="TriMesh" ) {
type = IO::SurfaceMesh;
} else if ( meshClass=="DomainMesh" ) {
type = IO::VolumeMesh;
if ( meshClass == "PointList" ) {
type = IO::MeshType::PointMesh;
} else if ( meshClass == "TriList" || meshClass == "TriMesh" ) {
type = IO::MeshType::SurfaceMesh;
} else if ( meshClass == "DomainMesh" ) {
type = IO::MeshType::VolumeMesh;
} else {
ERROR("Unknown mesh");
ERROR( "Unknown mesh" );
}
return type;
}
} // IO namespace
} // namespace IO

73
IO/MeshDatabase.h
View File

@ -1,90 +1,85 @@
#ifndef MeshDatabase_INC
#define MeshDatabase_INC
#include "IO/Mesh.h"
#include "IO/Mesh.h"
#include "common/MPI.h"
#include <iostream>
#include <map>
#include <memory>
#include <string.h>
#include <vector>
#include <map>
namespace IO {
class Mesh;
//! Enum to identify mesh type
//enum class MeshType : char { PointMesh=1, SurfaceMesh=2, VolumeMesh=3, Unknown=-1 };
enum MeshType { PointMesh=1, SurfaceMesh=2, VolumeMesh=3, Unknown=-1 };
//! Helper struct for containing offsets for the mesh info
struct DatabaseEntry {
std::string name; //!< Name of the entry
std::string file; //!< Name of the file containing the entry
size_t offset; //!< Offset in the file to start reading
std::string write( ) const; //!< Convert the data to a string
void read( const char* line ); //!< Convert the string to data
void read( const std::string& line ); //!< Convert the string to data
DatabaseEntry( ) {} //!< Empty constructor
DatabaseEntry( const char* line ); //!< Convert the string to data
~DatabaseEntry() {} //!< Destructor
std::string name; //!< Name of the entry
std::string file; //!< Name of the file containing the entry
size_t offset; //!< Offset in the file to start reading
std::string write() const; //!< Convert the data to a string
void read( const char *line ); //!< Convert the string to data
void read( const std::string &line ); //!< Convert the string to data
DatabaseEntry() {} //!< Empty constructor
DatabaseEntry( const char *line ); //!< Convert the string to data
~DatabaseEntry() {} //!< Destructor
};
//! Structure to hold the info about the variables
struct VariableDatabase {
std::string name; //!< Name of the variable
IO::VariableType type; //!< Variable
unsigned int dim; //!< Number of points per grid point (1: scalar, 3: vector, ...)
std::string name; //!< Name of the variable
IO::VariableType type; //!< Variable
unsigned int dim; //!< Number of points per grid point (1: scalar, 3: vector, ...)
// Overload key operators
bool operator==(const VariableDatabase& rhs ) const;
bool operator!=(const VariableDatabase& rhs ) const;
bool operator>=(const VariableDatabase& rhs ) const;
bool operator<=(const VariableDatabase& rhs ) const;
bool operator> (const VariableDatabase& rhs ) const;
bool operator< (const VariableDatabase& rhs ) const;
bool operator==( const VariableDatabase &rhs ) const;
bool operator!=( const VariableDatabase &rhs ) const;
bool operator>=( const VariableDatabase &rhs ) const;
bool operator<=( const VariableDatabase &rhs ) const;
bool operator>( const VariableDatabase &rhs ) const;
bool operator<( const VariableDatabase &rhs ) const;
};
//! Structure to hold the info about the meshes
struct MeshDatabase {
typedef std::pair<std::string,std::string> variable_id;
typedef std::pair<std::string, std::string> variable_id;
std::string name; //!< Name of the mesh
MeshType type; //!< Mesh type
std::string meshClass; //!< Mesh class
unsigned char format; //!< Data format (1: old, 2: new, 3: new (single), 4: silo)
FileFormat format; //!< Data format (1: old, 2: new, 3: new (single), 4: silo)
std::vector<DatabaseEntry> domains; //!< List of the domains
std::vector<VariableDatabase> variables; //!< List of the variables
std::map<variable_id,DatabaseEntry> variable_data; //!< Data for the variables
VariableDatabase getVariableDatabase( const std::string& varname ) const;
std::vector<VariableDatabase> variables; //!< List of the variables
std::map<variable_id, DatabaseEntry> variable_data; //!< Data for the variables
VariableDatabase getVariableDatabase( const std::string &varname ) const;
public:
MeshDatabase();
~MeshDatabase();
MeshDatabase(const MeshDatabase&);
MeshDatabase& operator=(const MeshDatabase&);
MeshDatabase( const MeshDatabase & );
MeshDatabase &operator=( const MeshDatabase & );
};
//! Gather the mesh databases from all processors
std::vector<MeshDatabase> gatherAll( const std::vector<MeshDatabase>& meshes, const Utilities::MPI& comm );
std::vector<MeshDatabase> gatherAll(
const std::vector<MeshDatabase> &meshes, const Utilities::MPI &comm );
//! Write the mesh databases to a file
void write( const std::vector<MeshDatabase>& meshes, const std::string& filename );
void write( const std::vector<MeshDatabase> &meshes, const std::string &filename );
//! Read the mesh databases from a file
std::vector<MeshDatabase> read( const std::string& filename );
std::vector<MeshDatabase> read( const std::string &filename );
//! Return the mesh type
IO::MeshType meshType( const IO::Mesh& mesh );
IO::MeshType meshType( const IO::Mesh &mesh );
} // IO namespace
} // namespace IO
#endif

131
IO/PIO.cpp
View File

@ -1,10 +1,10 @@
#include "IO/PIO.h"
#include "common/Utilities.h"
#include "common/MPI.h"
#include "common/Utilities.h"
#include <cstring>
#include <fstream>
#include <string>
#include <cstring>
namespace IO {
@ -15,19 +15,18 @@ static ParallelStreamBuffer perr_buffer;
static ParallelStreamBuffer plog_buffer;
std::ostream pout(&pout_buffer);
std::ostream perr(&perr_buffer);
std::ostream plog(&plog_buffer);
std::ostream pout( &pout_buffer );
std::ostream perr( &perr_buffer );
std::ostream plog( &plog_buffer );
/****************************************************************************
* Functions to control logging *
****************************************************************************/
std::ofstream *global_filestream=NULL;
static void shutdownFilestream( )
* Functions to control logging *
****************************************************************************/
std::ofstream *global_filestream = NULL;
static void shutdownFilestream()
{
if ( global_filestream!=NULL ) {
if ( global_filestream != NULL ) {
global_filestream->flush();
global_filestream->close();
delete global_filestream;
@ -37,16 +36,16 @@ static void shutdownFilestream( )
void Utilities::logOnlyNodeZero( const std::string &filename )
{
int rank = 0;
#ifdef USE_MPI
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
#endif
#ifdef USE_MPI
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
#endif
if ( rank == 0 )
logAllNodes(filename,true);
logAllNodes( filename, true );
}
void Utilities::logAllNodes( const std::string &filename, bool singleStream )
{
if ( singleStream )
ERROR("Not implimented yet");
ERROR( "Not implimented yet" );
// If the filestream was open, then close it and reset streams
shutdownFilestream();
@ -55,33 +54,33 @@ void Utilities::logAllNodes( const std::string &filename, bool singleStream )
std::string full_filename = filename;
if ( !singleStream ) {
int rank = 0;
#ifdef USE_MPI
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
#endif
#ifdef USE_MPI
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
#endif
char tmp[100];
sprintf(tmp,".%04i",rank);
full_filename += std::string(tmp);
sprintf( tmp, ".%04i", rank );
full_filename += std::string( tmp );
}
global_filestream = new std::ofstream(full_filename.c_str());
global_filestream = new std::ofstream( full_filename.c_str() );
if ( !(*global_filestream) ) {
if ( !( *global_filestream ) ) {
delete global_filestream;
global_filestream = NULL;
perr << "PIO: Could not open log file ``" << full_filename << "''\n";
} else {
pout_buffer.setOutputStream(global_filestream);
pout_buffer.setOutputStream(&std::cout);
perr_buffer.setOutputStream(global_filestream);
perr_buffer.setOutputStream(&std::cerr);
plog_buffer.setOutputStream(global_filestream);
pout_buffer.setOutputStream( global_filestream );
pout_buffer.setOutputStream( &std::cout );
perr_buffer.setOutputStream( global_filestream );
perr_buffer.setOutputStream( &std::cerr );
plog_buffer.setOutputStream( global_filestream );
}
}
/****************************************************************************
* ParallelStreamBuffer class *
****************************************************************************/
void Utilities::stopLogging( )
* ParallelStreamBuffer class *
****************************************************************************/
void Utilities::stopLogging()
{
pout_buffer.reset();
perr_buffer.reset();
@ -93,77 +92,71 @@ void Utilities::stopLogging( )
/****************************************************************************
* ParallelStreamBuffer class *
****************************************************************************/
ParallelStreamBuffer::ParallelStreamBuffer( ):
d_rank(0), d_size(0), d_buffer_size(0), d_buffer(NULL)
* ParallelStreamBuffer class *
****************************************************************************/
ParallelStreamBuffer::ParallelStreamBuffer()
: d_rank( 0 ), d_size( 0 ), d_buffer_size( 0 ), d_buffer( NULL )
{
}
ParallelStreamBuffer:: ~ParallelStreamBuffer()
{
delete [] d_buffer;
}
void ParallelStreamBuffer::setOutputStream( std::ostream *stream )
{
d_stream.push_back( stream );
}
ParallelStreamBuffer::~ParallelStreamBuffer() { delete[] d_buffer; }
void ParallelStreamBuffer::setOutputStream( std::ostream *stream ) { d_stream.push_back( stream ); }
int ParallelStreamBuffer::sync()
{
for (size_t i=0; i<d_stream.size(); i++) {
std::ostream& stream = *d_stream[i];
for ( size_t i = 0; i < d_stream.size(); i++ ) {
std::ostream &stream = *d_stream[i];
stream << d_buffer;
}
d_size = 0;
memset(d_buffer,0,d_buffer_size);
memset( d_buffer, 0, d_buffer_size );
return 0;
}
void ParallelStreamBuffer::reserve( size_t size )
{
if ( size > d_buffer_size ) {
if ( d_buffer_size==0 ) {
if ( d_buffer_size == 0 ) {
d_buffer_size = 1024;
d_buffer = new char[d_buffer_size];
memset(d_buffer,0,d_buffer_size);
d_buffer = new char[d_buffer_size];
memset( d_buffer, 0, d_buffer_size );
}
while ( size > d_buffer_size ) {
char *tmp = d_buffer;
d_buffer_size *= 2;
d_buffer = new char[d_buffer_size];
memset(d_buffer,0,d_buffer_size);
memcpy(d_buffer,tmp,d_size);
delete [] tmp;
memset( d_buffer, 0, d_buffer_size );
memcpy( d_buffer, tmp, d_size );
delete[] tmp;
}
}
}
std::streamsize ParallelStreamBuffer::xsputn( const char* text, std::streamsize n )
std::streamsize ParallelStreamBuffer::xsputn( const char *text, std::streamsize n )
{
reserve(d_size+n);
memcpy(&d_buffer[d_size],text,n);
reserve( d_size + n );
memcpy( &d_buffer[d_size], text, n );
d_size += n;
if ( text[n-1]==0 || text[n-1]==10 ) { sync(); }
if ( text[n - 1] == 0 || text[n - 1] == 10 ) {
sync();
}
return n;
}
int ParallelStreamBuffer::overflow(int ch)
int ParallelStreamBuffer::overflow( int ch )
{
reserve(d_size+1);
reserve( d_size + 1 );
d_buffer[d_size] = ch;
d_size++;
if ( ch==0 || ch==10 ) { sync(); }
return std::char_traits<char>::to_int_type(ch);
if ( ch == 0 || ch == 10 ) {
sync();
}
return std::char_traits<char>::to_int_type( ch );
}
int ParallelStreamBuffer::underflow()
{
return -1;
}
void ParallelStreamBuffer::reset()
int ParallelStreamBuffer::underflow() { return -1; }
void ParallelStreamBuffer::reset()
{
sync();
d_stream.clear();
delete [] d_buffer;
d_buffer = NULL;
delete[] d_buffer;
d_buffer = NULL;
d_buffer_size = 0;
}
} // IO namespace
} // namespace IO

47
IO/PIO.h
View File

@ -17,7 +17,7 @@ extern std::ostream pout;
/*!
* Parallel output stream perr writes to the standard error from all nodes.
* Output is prepended with the processor number.
* Output is prepended with the processor number.
*/
extern std::ostream perr;
@ -45,12 +45,11 @@ inline int printp( const char *format, ... );
class ParallelStreamBuffer : public std::streambuf
{
public:
/*!
* Create a parallel buffer class. The object will require further
* initialization to set up the I/O streams and prefix string.
*/
ParallelStreamBuffer( );
ParallelStreamBuffer();
/*!
* Set the output file stream (multiple output streams are supported)
@ -60,26 +59,26 @@ public:
/*!
* The destructor simply deallocates any internal data
* buffers. It does not modify the output streams.
* buffers. It does not modify the output streams.
*/
virtual ~ParallelStreamBuffer();
/*!
* Synchronize the parallel buffer (called from streambuf).
*/
virtual int sync();
virtual int sync();
/**
* Write the specified number of characters into the output stream (called
* from streambuf).
*/
virtual std::streamsize xsputn(const char* text, std::streamsize n);
*/
virtual std::streamsize xsputn( const char *text, std::streamsize n );
/*!
* Write an overflow character into the parallel buffer (called from
* streambuf).
*/
virtual int overflow(int ch);
virtual int overflow( int ch );
/*!
* Read an overflow character from the parallel buffer (called from
@ -98,30 +97,30 @@ private:
size_t d_size;
size_t d_buffer_size;
char *d_buffer;
std::vector<std::ostream*> d_stream;
std::vector<std::ostream *> d_stream;
inline void reserve( size_t size );
};
namespace Utilities {
/*!
* Log messages for node zero only to the specified filename. All output
* to pout, perr, and plog on node zero will go to the log file.
*/
void logOnlyNodeZero( const std::string &filename );
/*!
* Log messages for node zero only to the specified filename. All output
* to pout, perr, and plog on node zero will go to the log file.
*/
void logOnlyNodeZero( const std::string &filename );
/*!
* Log messages from all nodes. The diagnostic data for processor XXXXX
* will be sent to a file with the name filename.XXXXX, where filename is
* the function argument.
*/
void logAllNodes( const std::string &filename, bool singleStream=false );
/*!
* Log messages from all nodes. The diagnostic data for processor XXXXX
* will be sent to a file with the name filename.XXXXX, where filename is
* the function argument.
*/
void logAllNodes( const std::string &filename, bool singleStream = false );
/*!
* Stop logging messages, flush buffers, and reset memory.
*/
void stopLogging( );
/*!
* Stop logging messages, flush buffers, and reset memory.
*/
void stopLogging();
} // namespace Utilities

12
IO/PIO.hpp
View File

@ -3,9 +3,9 @@
#include "IO/PIO.h"
#include <cstdio>
#include <iostream>
#include <stdarg.h>
#include <cstdio>
namespace IO {
@ -13,17 +13,17 @@ namespace IO {
inline int printp( const char *format, ... )
{
va_list ap;
va_start(ap,format);
va_list ap;
va_start( ap, format );
char tmp[1024];
int n = vsprintf(tmp,format,ap);
va_end(ap);
int n = vsprintf( tmp, format, ap );
va_end( ap );
pout << tmp;
pout.flush();
return n;
}
} // IO namespace
} // namespace IO
#endif

77
IO/PackData.cpp
View File

@ -4,102 +4,101 @@
/********************************************************
* Concrete implimentations for packing/unpacking *
********************************************************/
* Concrete implimentations for packing/unpacking *
********************************************************/
// unsigned char
template<>
size_t packsize<unsigned char>( const unsigned char& rhs )
size_t packsize<unsigned char>( const unsigned char &rhs )
{
return sizeof(unsigned char);
return sizeof( unsigned char );
}
template<>
void pack<unsigned char>( const unsigned char& rhs, char *buffer )
void pack<unsigned char>( const unsigned char &rhs, char *buffer )
{
memcpy(buffer,&rhs,sizeof(unsigned char));
memcpy( buffer, &rhs, sizeof( unsigned char ) );
}
template<>
void unpack<unsigned char>( unsigned char& data, const char *buffer )
void unpack<unsigned char>( unsigned char &data, const char *buffer )
{
memcpy(&data,buffer,sizeof(unsigned char));
memcpy( &data, buffer, sizeof( unsigned char ) );
}
// char
template<>
size_t packsize<char>( const char& rhs )
size_t packsize<char>( const char &rhs )
{
return sizeof(char);
return sizeof( char );
}
template<>
void pack<char>( const char& rhs, char *buffer )
void pack<char>( const char &rhs, char *buffer )
{
memcpy(buffer,&rhs,sizeof(char));
memcpy( buffer, &rhs, sizeof( char ) );
}
template<>
void unpack<char>( char& data, const char *buffer )
void unpack<char>( char &data, const char *buffer )
{
memcpy(&data,buffer,sizeof(char));
memcpy( &data, buffer, sizeof( char ) );
}
// int
template<>
size_t packsize<int>( const int& rhs )
size_t packsize<int>( const int &rhs )
{
return sizeof(int);
return sizeof( int );
}
template<>
void pack<int>( const int& rhs, char *buffer )
void pack<int>( const int &rhs, char *buffer )
{
memcpy(buffer,&rhs,sizeof(int));
memcpy( buffer, &rhs, sizeof( int ) );
}
template<>
void unpack<int>( int& data, const char *buffer )
void unpack<int>( int &data, const char *buffer )
{
memcpy(&data,buffer,sizeof(int));
memcpy( &data, buffer, sizeof( int ) );
}
// unsigned int
template<>
size_t packsize<unsigned int>( const unsigned int& rhs )
size_t packsize<unsigned int>( const unsigned int &rhs )
{
return sizeof(unsigned int);
return sizeof( unsigned int );
}
template<>
void pack<unsigned int>( const unsigned int& rhs, char *buffer )
void pack<unsigned int>( const unsigned int &rhs, char *buffer )
{
memcpy(buffer,&rhs,sizeof(int));
memcpy( buffer, &rhs, sizeof( int ) );
}
template<>
void unpack<unsigned int>( unsigned int& data, const char *buffer )
void unpack<unsigned int>( unsigned int &data, const char *buffer )
{
memcpy(&data,buffer,sizeof(int));
memcpy( &data, buffer, sizeof( int ) );
}
// size_t
template<>
size_t packsize<size_t>( const size_t& rhs )
size_t packsize<size_t>( const size_t &rhs )
{
return sizeof(size_t);
return sizeof( size_t );
}
template<>
void pack<size_t>( const size_t& rhs, char *buffer )
void pack<size_t>( const size_t &rhs, char *buffer )
{
memcpy(buffer,&rhs,sizeof(size_t));
memcpy( buffer, &rhs, sizeof( size_t ) );
}
template<>
void unpack<size_t>( size_t& data, const char *buffer )
void unpack<size_t>( size_t &data, const char *buffer )
{
memcpy(&data,buffer,sizeof(size_t));
memcpy( &data, buffer, sizeof( size_t ) );
}
// std::string
template<>
size_t packsize<std::string>( const std::string& rhs )
size_t packsize<std::string>( const std::string &rhs )
{
return rhs.size()+1;
return rhs.size() + 1;
}
template<>
void pack<std::string>( const std::string& rhs, char *buffer )
void pack<std::string>( const std::string &rhs, char *buffer )
{
memcpy(buffer,rhs.c_str(),rhs.size()+1);
memcpy( buffer, rhs.c_str(), rhs.size() + 1 );
}
template<>
void unpack<std::string>( std::string& data, const char *buffer )
void unpack<std::string>( std::string &data, const char *buffer )
{
data = std::string(buffer);
data = std::string( buffer );
}

35
IO/PackData.h
View File

@ -2,77 +2,76 @@
#ifndef included_PackData
#define included_PackData
#include <vector>
#include <set>
#include <map>
#include <set>
#include <vector>
//! Template function to return the buffer size required to pack a class
template<class TYPE>
size_t packsize( const TYPE& rhs );
size_t packsize( const TYPE &rhs );
//! Template function to pack a class to a buffer
template<class TYPE>
void pack( const TYPE& rhs, char *buffer );
void pack( const TYPE &rhs, char *buffer );
//! Template function to unpack a class from a buffer
template<class TYPE>
void unpack( TYPE& data, const char *buffer );
void unpack( TYPE &data, const char *buffer );
//! Template function to return the buffer size required to pack a std::vector
template<class TYPE>
size_t packsize( const std::vector<TYPE>& rhs );
size_t packsize( const std::vector<TYPE> &rhs );
//! Template function to pack a class to a buffer
template<class TYPE>
void pack( const std::vector<TYPE>& rhs, char *buffer );
void pack( const std::vector<TYPE> &rhs, char *buffer );
//! Template function to pack a class to a buffer
template<class TYPE>
void unpack( std::vector<TYPE>& data, const char *buffer );
void unpack( std::vector<TYPE> &data, const char *buffer );
//! Template function to return the buffer size required to pack a std::pair
template<class TYPE1, class TYPE2>
size_t packsize( const std::pair<TYPE1,TYPE2>& rhs );
size_t packsize( const std::pair<TYPE1, TYPE2> &rhs );
//! Template function to pack a class to a buffer
template<class TYPE1, class TYPE2>
void pack( const std::pair<TYPE1,TYPE2>& rhs, char *buffer );
void pack( const std::pair<TYPE1, TYPE2> &rhs, char *buffer );
//! Template function to pack a class to a buffer
template<class TYPE1, class TYPE2>
void unpack( std::pair<TYPE1,TYPE2>& data, const char *buffer );
void unpack( std::pair<TYPE1, TYPE2> &data, const char *buffer );
//! Template function to return the buffer size required to pack a std::map
template<class TYPE1, class TYPE2>
size_t packsize( const std::map<TYPE1,TYPE2>& rhs );
size_t packsize( const std::map<TYPE1, TYPE2> &rhs );
//! Template function to pack a class to a buffer
template<class TYPE1, class TYPE2>
void pack( const std::map<TYPE1,TYPE2>& rhs, char *buffer );
void pack( const std::map<TYPE1, TYPE2> &rhs, char *buffer );
//! Template function to pack a class to a buffer
template<class TYPE1, class TYPE2>
void unpack( std::map<TYPE1,TYPE2>& data, const char *buffer );
void unpack( std::map<TYPE1, TYPE2> &data, const char *buffer );
//! Template function to return the buffer size required to pack a std::set
template<class TYPE>
size_t packsize( const std::set<TYPE>& rhs );
size_t packsize( const std::set<TYPE> &rhs );
//! Template function to pack a class to a buffer
template<class TYPE>
void pack( const std::set<TYPE>& rhs, char *buffer );
void pack( const std::set<TYPE> &rhs, char *buffer );
//! Template function to pack a class to a buffer
template<class TYPE>
void unpack( std::set<TYPE>& data, const char *buffer );
void unpack( std::set<TYPE> &data, const char *buffer );
#include "IO/PackData.hpp"
#endif

150
IO/PackData.hpp
View File

@ -4,152 +4,156 @@
#include "IO/PackData.h"
#include <map>
#include <set>
#include <string.h>
#include <vector>
#include <set>
#include <map>
/********************************************************
* Default instantiations for std::vector *
********************************************************/
* Default instantiations for std::vector *
********************************************************/
template<class TYPE>
size_t packsize( const std::vector<TYPE>& rhs )
size_t packsize( const std::vector<TYPE> &rhs )
{
size_t bytes = sizeof(size_t);
for (size_t i=0; i<rhs.size(); i++)
bytes += packsize(rhs[i]);
size_t bytes = sizeof( size_t );
for ( size_t i = 0; i < rhs.size(); i++ )
bytes += packsize( rhs[i] );
return bytes;
}
template<class TYPE>
void pack( const std::vector<TYPE>& rhs, char *buffer )
void pack( const std::vector<TYPE> &rhs, char *buffer )
{
size_t size = rhs.size();
memcpy(buffer,&size,sizeof(size_t));
size_t pos = sizeof(size_t);
for (size_t i=0; i<rhs.size(); i++) {
pack(rhs[i],&buffer[pos]);
pos += packsize(rhs[i]);
memcpy( buffer, &size, sizeof( size_t ) );
size_t pos = sizeof( size_t );
for ( size_t i = 0; i < rhs.size(); i++ ) {
pack( rhs[i], &buffer[pos] );
pos += packsize( rhs[i] );
}
}
template<class TYPE>
void unpack( std::vector<TYPE>& data, const char *buffer )
void unpack( std::vector<TYPE> &data, const char *buffer )
{
size_t size;
memcpy(&size,buffer,sizeof(size_t));
memcpy( &size, buffer, sizeof( size_t ) );
data.clear();
data.resize(size);
size_t pos = sizeof(size_t);
for (size_t i=0; i<data.size(); i++) {
unpack(data[i],&buffer[pos]);
pos += packsize(data[i]);
data.resize( size );
size_t pos = sizeof( size_t );
for ( size_t i = 0; i < data.size(); i++ ) {
unpack( data[i], &buffer[pos] );
pos += packsize( data[i] );
}
}
/********************************************************
* Default instantiations for std::pair *
********************************************************/
* Default instantiations for std::pair *
********************************************************/
template<class TYPE1, class TYPE2>
size_t packsize( const std::pair<TYPE1,TYPE2>& rhs )
size_t packsize( const std::pair<TYPE1, TYPE2> &rhs )
{
return packsize(rhs.first)+packsize(rhs.second);
return packsize( rhs.first ) + packsize( rhs.second );
}
template<class TYPE1, class TYPE2>
void pack( const std::pair<TYPE1,TYPE2>& rhs, char *buffer )
void pack( const std::pair<TYPE1, TYPE2> &rhs, char *buffer )
{
pack(rhs.first,buffer);
pack(rhs.second,&buffer[packsize(rhs.first)]);
pack( rhs.first, buffer );
pack( rhs.second, &buffer[packsize( rhs.first )] );
}
template<class TYPE1, class TYPE2>
void unpack( std::pair<TYPE1,TYPE2>& data, const char *buffer )
void unpack( std::pair<TYPE1, TYPE2> &data, const char *buffer )
{
unpack(data.first,buffer);
unpack(data.second,&buffer[packsize(data.first)]);
unpack( data.first, buffer );
unpack( data.second, &buffer[packsize( data.first )] );
}
/********************************************************
* Default instantiations for std::map *
********************************************************/
* Default instantiations for std::map *
********************************************************/
template<class TYPE1, class TYPE2>
size_t packsize( const std::map<TYPE1,TYPE2>& rhs )
size_t packsize( const std::map<TYPE1, TYPE2> &rhs )
{
size_t bytes = sizeof(size_t);
typename std::map<TYPE1,TYPE2>::const_iterator it;
for (it=rhs.begin(); it!=rhs.end(); ++it) {
bytes += packsize(it->first);
bytes += packsize(it->second);
size_t bytes = sizeof( size_t );
typename std::map<TYPE1, TYPE2>::const_iterator it;
for ( it = rhs.begin(); it != rhs.end(); ++it ) {
bytes += packsize( it->first );
bytes += packsize( it->second );
}
return bytes;
}
template<class TYPE1, class TYPE2>
void pack( const std::map<TYPE1,TYPE2>& rhs, char *buffer )
void pack( const std::map<TYPE1, TYPE2> &rhs, char *buffer )
{
size_t N = rhs.size();
pack(N,buffer);
size_t pos = sizeof(size_t);
typename std::map<TYPE1,TYPE2>::const_iterator it;
for (it=rhs.begin(); it!=rhs.end(); ++it) {
pack(it->first,&buffer[pos]); pos+=packsize(it->first);
pack(it->second,&buffer[pos]); pos+=packsize(it->second);
pack( N, buffer );
size_t pos = sizeof( size_t );
typename std::map<TYPE1, TYPE2>::const_iterator it;
for ( it = rhs.begin(); it != rhs.end(); ++it ) {
pack( it->first, &buffer[pos] );
pos += packsize( it->first );
pack( it->second, &buffer[pos] );
pos += packsize( it->second );
}
}
template<class TYPE1, class TYPE2>
void unpack( std::map<TYPE1,TYPE2>& data, const char *buffer )
void unpack( std::map<TYPE1, TYPE2> &data, const char *buffer )
{
size_t N = 0;
unpack(N,buffer);
size_t pos = sizeof(size_t);
unpack( N, buffer );
size_t pos = sizeof( size_t );
data.clear();
for (size_t i=0; i<N; i++) {
std::pair<TYPE1,TYPE2> tmp;
unpack(tmp.first,&buffer[pos]); pos+=packsize(tmp.first);
unpack(tmp.second,&buffer[pos]); pos+=packsize(tmp.second);
data.insert(tmp);
for ( size_t i = 0; i < N; i++ ) {
std::pair<TYPE1, TYPE2> tmp;
unpack( tmp.first, &buffer[pos] );
pos += packsize( tmp.first );
unpack( tmp.second, &buffer[pos] );
pos += packsize( tmp.second );
data.insert( tmp );
}
}
/********************************************************
* Default instantiations for std::set *
********************************************************/
* Default instantiations for std::set *
********************************************************/
template<class TYPE>
size_t packsize( const std::set<TYPE>& rhs )
size_t packsize( const std::set<TYPE> &rhs )
{
size_t bytes = sizeof(size_t);
size_t bytes = sizeof( size_t );
typename std::set<TYPE>::const_iterator it;
for (it=rhs.begin(); it!=rhs.end(); ++it) {
bytes += packsize(*it);
for ( it = rhs.begin(); it != rhs.end(); ++it ) {
bytes += packsize( *it );
}
return bytes;
}
template<class TYPE>
void pack( const std::set<TYPE>& rhs, char *buffer )
void pack( const std::set<TYPE> &rhs, char *buffer )
{
size_t N = rhs.size();
pack(N,buffer);
size_t pos = sizeof(size_t);
pack( N, buffer );
size_t pos = sizeof( size_t );
typename std::set<TYPE>::const_iterator it;
for (it=rhs.begin(); it!=rhs.end(); ++it) {
pack(*it); pos+=packsize(*it);
for ( it = rhs.begin(); it != rhs.end(); ++it ) {
pack( *it );
pos += packsize( *it );
}
}
template<class TYPE>
void unpack( std::set<TYPE>& data, const char *buffer )
void unpack( std::set<TYPE> &data, const char *buffer )
{
size_t N = 0;
unpack(N,buffer);
size_t pos = sizeof(size_t);
unpack( N, buffer );
size_t pos = sizeof( size_t );
data.clear();
for (size_t i=0; i<N; i++) {
for ( size_t i = 0; i < N; i++ ) {
TYPE tmp;
unpack(tmp,&buffer[pos]); pos+=packsize(tmp);
data.insert(tmp);
unpack( tmp, &buffer[pos] );
pos += packsize( tmp );
data.insert( tmp );
}
}
#endif

468
IO/Reader.cpp
View File

@ -1,7 +1,7 @@
#include "IO/Reader.h"
#include "IO/IOHelpers.h"
#include "IO/Mesh.h"
#include "IO/MeshDatabase.h"
#include "IO/IOHelpers.h"
#include "common/Utilities.h"
#ifdef USE_SILO
@ -10,60 +10,139 @@
#include <ProfilerApp.h>
#include <cstdio>
#include <fstream>
#include <iostream>
#include <map>
#include <string.h>
#include <vector>
#include <map>
#include <cstdio>
// Inline function to read line without a return argument
static inline void fgetl( char * str, int num, FILE * stream )
static inline void fgetl( char *str, int num, FILE *stream )
{
char* ptr = fgets( str, num, stream );
if ( 0 ) {char *temp = (char *)&ptr; temp++;}
char *ptr = fgets( str, num, stream );
if ( 0 ) {
char *temp = (char *) &ptr;
temp++;
}
}
// Check if the file exists
bool fileExists( const std::string &filename )
{
std::ifstream ifile( filename.c_str() );
return ifile.good();
}
// Get the path to a file
std::string IO::getPath( const std::string& filename )
std::string IO::getPath( const std::string &filename )
{
std::string file(filename);
size_t k1 = file.rfind(47);
size_t k2 = file.rfind(92);
if ( k1==std::string::npos ) { k1=0; }
if ( k2==std::string::npos ) { k2=0; }
return file.substr(0,std::max(k1,k2));
std::string file( filename );
size_t k1 = file.rfind( 47 );
size_t k2 = file.rfind( 92 );
if ( k1 == std::string::npos ) {
k1 = 0;
}
if ( k2 == std::string::npos ) {
k2 = 0;
}
return file.substr( 0, std::max( k1, k2 ) );
}
// List the timesteps in the given directors (dumps.LBPM)
std::vector<std::string> IO::readTimesteps( const std::string& filename )
// List the timesteps in the given directory (dumps.LBPM)
std::vector<std::string> IO::readTimesteps( const std::string &path, const std::string &format )
{
PROFILE_START("readTimesteps");
FILE *fid= fopen(filename.c_str(),"rb");
if ( fid==NULL )
ERROR("Error opening file");
// Get the name of the summary filename
std::string filename = path + "/";
if ( format == "old" || format == "new" ) {
filename += "summary.LBM";
} else if ( format == "silo" ) {
filename += "LBM.visit";
} else if ( format == "auto" ) {
bool test_old = fileExists( path + "/summary.LBM" );
bool test_silo = fileExists( path + "/LBM.visit" );
if ( test_old && test_silo ) {
ERROR( "Unable to determine format (both summary.LBM and LBM.visit exist)" );
} else if ( test_old ) {
filename += "summary.LBM";
} else if ( test_silo ) {
filename += "LBM.visit";
} else {
ERROR( "Unable to determine format (neither summary.LBM or LBM.visit exist)" );
}
} else {
ERROR( "Unknown format: " + format );
}
PROFILE_START( "readTimesteps" );
// Read the data
FILE *fid = fopen( filename.c_str(), "rb" );
if ( fid == NULL )
ERROR( "Error opening file" );
std::vector<std::string> timesteps;
char buf[1000];
while (fgets(buf,sizeof(buf),fid) != NULL) {
std::string line(buf);
line.resize(line.size()-1);
while ( fgets( buf, sizeof( buf ), fid ) != NULL ) {
std::string line( buf );
line.resize( line.size() - 1 );
auto pos = line.find( "summary.silo" );
if ( pos != std::string::npos )
line.resize(pos);
line.resize( pos );
if ( line.empty() )
continue;
timesteps.push_back(line);
timesteps.push_back( line );
}
fclose(fid);
PROFILE_STOP("readTimesteps");
fclose( fid );
PROFILE_STOP( "readTimesteps" );
return timesteps;
return timesteps;
}
// Get the maximum number of domains
int IO::maxDomains( const std::string &path, const std::string &format, const Utilities::MPI &comm )
{
int rank = comm.getRank();
int n_domains = 0;
if ( rank == 0 ) {
// Get the timesteps
auto timesteps = IO::readTimesteps( path, format );
ASSERT( !timesteps.empty() );
// Get the database for the first domain
auto db = IO::getMeshList( path, timesteps[0] );
for ( size_t i = 0; i < db.size(); i++ )
n_domains = std::max<int>( n_domains, db[i].domains.size() );
}
return comm.bcast( n_domains, 0 );
}
// Read the data for the given timestep
std::vector<IO::MeshDataStruct> IO::readData(
const std::string &path, const std::string &timestep, int rank )
{
// Get the mesh databases
auto db = IO::getMeshList( path, timestep );
// Create the data
std::vector<IO::MeshDataStruct> data( db.size() );
for ( size_t i = 0; i < data.size(); i++ ) {
data[i].precision = IO::DataType::Double;
data[i].meshName = db[i].name;
data[i].mesh = getMesh( path, timestep, db[i], rank );
data[i].vars.resize( db[i].variables.size() );
for ( size_t j = 0; j < db[i].variables.size(); j++ )
data[i].vars[j] = getVariable( path, timestep, db[i], rank, db[i].variables[j].name );
INSIST( data[i].check(), "Failed check of " + data[i].meshName );
}
return data;
}
// Read the list of variables for the given timestep
std::vector<IO::MeshDatabase> IO::getMeshList( const std::string& path, const std::string& timestep )
std::vector<IO::MeshDatabase> IO::getMeshList(
const std::string &path, const std::string &timestep )
{
std::string filename = path + "/" + timestep + "/LBM.summary";
return IO::read( filename );
@ -71,270 +150,271 @@ std::vector<IO::MeshDatabase> IO::getMeshList( const std::string& path, const st
// Read the given mesh domain
std::shared_ptr<IO::Mesh> IO::getMesh( const std::string& path, const std::string& timestep,
const IO::MeshDatabase& meshDatabase, int domain )
std::shared_ptr<IO::Mesh> IO::getMesh( const std::string &path, const std::string &timestep,
const IO::MeshDatabase &meshDatabase, int domain )
{
PROFILE_START("getMesh");
PROFILE_START( "getMesh" );
std::shared_ptr<IO::Mesh> mesh;
if ( meshDatabase.format==1 ) {
if ( meshDatabase.format == FileFormat::OLD ) {
// Old format (binary doubles)
std::string filename = path + "/" + timestep + "/" + meshDatabase.domains[domain].file;
FILE *fid = fopen(filename.c_str(),"rb");
INSIST(fid!=NULL,"Error opening file");
FILE *fid = fopen( filename.c_str(), "rb" );
INSIST( fid != NULL, "Error opening file" );
fseek( fid, 0, SEEK_END );
size_t bytes = ftell(fid);
size_t N_max = bytes/sizeof(double)+1000;
size_t bytes = ftell( fid );
size_t N_max = bytes / sizeof( double ) + 1000;
double *data = new double[N_max];
fseek(fid,0,SEEK_SET);
size_t count = fread(data,sizeof(double),N_max,fid);
fclose(fid);
if ( count%3 != 0 )
ERROR("Error reading file");
if ( meshDatabase.type==IO::PointMesh ) {
size_t N = count/3;
std::shared_ptr<PointList> pointlist( new PointList(N) );
std::vector<Point>& P = pointlist->points;
for (size_t i=0; i<N; i++) {
P[i].x = data[3*i+0];
P[i].y = data[3*i+1];
P[i].z = data[3*i+2];
fseek( fid, 0, SEEK_SET );
size_t count = fread( data, sizeof( double ), N_max, fid );
fclose( fid );
if ( count % 3 != 0 )
ERROR( "Error reading file" );
if ( meshDatabase.type == IO::MeshType::PointMesh ) {
size_t N = count / 3;
std::shared_ptr<PointList> pointlist( new PointList( N ) );
std::vector<Point> &P = pointlist->points;
for ( size_t i = 0; i < N; i++ ) {
P[i].x = data[3 * i + 0];
P[i].y = data[3 * i + 1];
P[i].z = data[3 * i + 2];
}
mesh = pointlist;
} else if ( meshDatabase.type==IO::SurfaceMesh ) {
if ( count%9 != 0 )
ERROR("Error reading file (2)");
size_t N_tri = count/9;
std::shared_ptr<TriList> trilist( new TriList(N_tri) );
std::vector<Point>& A = trilist->A;
std::vector<Point>& B = trilist->B;
std::vector<Point>& C = trilist->C;
for (size_t i=0; i<N_tri; i++) {
A[i].x = data[9*i+0];
A[i].y = data[9*i+1];
A[i].z = data[9*i+2];
B[i].x = data[9*i+3];
B[i].y = data[9*i+4];
B[i].z = data[9*i+5];
C[i].x = data[9*i+6];
C[i].y = data[9*i+7];
C[i].z = data[9*i+8];
} else if ( meshDatabase.type == IO::MeshType::SurfaceMesh ) {
if ( count % 9 != 0 )
ERROR( "Error reading file (2)" );
size_t N_tri = count / 9;
std::shared_ptr<TriList> trilist( new TriList( N_tri ) );
std::vector<Point> &A = trilist->A;
std::vector<Point> &B = trilist->B;
std::vector<Point> &C = trilist->C;
for ( size_t i = 0; i < N_tri; i++ ) {
A[i].x = data[9 * i + 0];
A[i].y = data[9 * i + 1];
A[i].z = data[9 * i + 2];
B[i].x = data[9 * i + 3];
B[i].y = data[9 * i + 4];
B[i].z = data[9 * i + 5];
C[i].x = data[9 * i + 6];
C[i].y = data[9 * i + 7];
C[i].z = data[9 * i + 8];
}
mesh = trilist;
} else if ( meshDatabase.type==IO::VolumeMesh ) {
} else if ( meshDatabase.type == IO::MeshType::VolumeMesh ) {
// this was never supported in the old format
mesh = std::shared_ptr<DomainMesh>( new DomainMesh() );
} else {
ERROR("Unknown mesh type");
ERROR( "Unknown mesh type" );
}
delete [] data;
} else if ( meshDatabase.format==2 ) {
const DatabaseEntry& database = meshDatabase.domains[domain];
std::string filename = path + "/" + timestep + "/" + database.file;
FILE *fid = fopen(filename.c_str(),"rb");
fseek(fid,database.offset,SEEK_SET);
delete[] data;
} else if ( meshDatabase.format == FileFormat::NEW ||
meshDatabase.format == FileFormat::NEW_SINGLE ) {
const DatabaseEntry &database = meshDatabase.domains[domain];
std::string filename = path + "/" + timestep + "/" + database.file;
FILE *fid = fopen( filename.c_str(), "rb" );
fseek( fid, database.offset, SEEK_SET );
char line[1000];
fgetl(line,1000,fid);
size_t i1 = find(line,':');
size_t i2 = find(&line[i1+1],':')+i1+1;
size_t bytes = atol(&line[i2+1]);
char *data = new char[bytes];
size_t count = fread(data,1,bytes,fid);
fclose(fid);
ASSERT(count==bytes);
if ( meshDatabase.meshClass=="PointList" ) {
fgetl( line, 1000, fid );
size_t i1 = find( line, ':' );
size_t i2 = find( &line[i1 + 1], ':' ) + i1 + 1;
size_t bytes = atol( &line[i2 + 1] );
char *data = new char[bytes];
size_t count = fread( data, 1, bytes, fid );
fclose( fid );
ASSERT( count == bytes );
if ( meshDatabase.meshClass == "PointList" ) {
mesh.reset( new IO::PointList() );
} else if ( meshDatabase.meshClass=="TriMesh" ) {
} else if ( meshDatabase.meshClass == "TriMesh" ) {
mesh.reset( new IO::TriMesh() );
} else if ( meshDatabase.meshClass=="TriList" ) {
} else if ( meshDatabase.meshClass == "TriList" ) {
mesh.reset( new IO::TriList() );
} else if ( meshDatabase.meshClass=="DomainMesh" ) {
} else if ( meshDatabase.meshClass == "DomainMesh" ) {
mesh.reset( new IO::DomainMesh() );
} else {
ERROR("Unknown mesh class");
ERROR( "Unknown mesh class" );
}
mesh->unpack( std::pair<size_t,void*>(bytes,data) );
delete [] data;
} else if ( meshDatabase.format==4 ) {
mesh->unpack( std::pair<size_t, void *>( bytes, data ) );
delete[] data;
} else if ( meshDatabase.format == FileFormat::SILO ) {
// Reading a silo file
#ifdef USE_SILO
const DatabaseEntry& database = meshDatabase.domains[domain];
std::string filename = path + "/" + timestep + "/" + database.file;
auto fid = silo::open( filename, silo::READ );
if ( meshDatabase.meshClass=="PointList" ) {
const DatabaseEntry &database = meshDatabase.domains[domain];
std::string filename = path + "/" + timestep + "/" + database.file;
auto fid = silo::open( filename, silo::READ );
if ( meshDatabase.meshClass == "PointList" ) {
Array<double> coords = silo::readPointMesh<double>( fid, database.name );
ASSERT(coords.size(1)==3);
std::shared_ptr<IO::PointList> mesh2( new IO::PointList( coords.size(0) ) );
for (size_t i=0; i<coords.size(1); i++) {
mesh2->points[i].x = coords(i,0);
mesh2->points[i].y = coords(i,1);
mesh2->points[i].z = coords(i,2);
ASSERT( coords.size( 1 ) == 3 );
std::shared_ptr<IO::PointList> mesh2( new IO::PointList( coords.size( 0 ) ) );
for ( size_t i = 0; i < coords.size( 1 ); i++ ) {
mesh2->points[i].x = coords( i, 0 );
mesh2->points[i].y = coords( i, 1 );
mesh2->points[i].z = coords( i, 2 );
}
mesh = mesh2;
} else if ( meshDatabase.meshClass=="TriMesh" || meshDatabase.meshClass=="TriList" ) {
} else if ( meshDatabase.meshClass == "TriMesh" || meshDatabase.meshClass == "TriList" ) {
Array<double> coords;
Array<int> tri;
silo::readTriMesh( fid, database.name, coords, tri );
ASSERT( tri.size(1)==3 && coords.size(1)==3 );
int N_tri = tri.size(0);
int N_point = coords.size(0);
ASSERT( tri.size( 1 ) == 3 && coords.size( 1 ) == 3 );
int N_tri = tri.size( 0 );
int N_point = coords.size( 0 );
std::shared_ptr<IO::TriMesh> mesh2( new IO::TriMesh( N_tri, N_point ) );
for (int i=0; i<N_point; i++) {
mesh2->vertices->points[i].x = coords(i,0);
mesh2->vertices->points[i].y = coords(i,1);
mesh2->vertices->points[i].z = coords(i,2);
for ( int i = 0; i < N_point; i++ ) {
mesh2->vertices->points[i].x = coords( i, 0 );
mesh2->vertices->points[i].y = coords( i, 1 );
mesh2->vertices->points[i].z = coords( i, 2 );
}
for (int i=0; i<N_tri; i++) {
mesh2->A[i] = tri(i,0);
mesh2->B[i] = tri(i,1);
mesh2->C[i] = tri(i,2);
for ( int i = 0; i < N_tri; i++ ) {
mesh2->A[i] = tri( i, 0 );
mesh2->B[i] = tri( i, 1 );
mesh2->C[i] = tri( i, 2 );
}
if ( meshDatabase.meshClass=="TriMesh" ) {
if ( meshDatabase.meshClass == "TriMesh" ) {
mesh = mesh2;
} else if ( meshDatabase.meshClass=="TriList" ) {
} else if ( meshDatabase.meshClass == "TriList" ) {
auto trilist = IO::getTriList( std::dynamic_pointer_cast<IO::Mesh>( mesh2 ) );
mesh = trilist;
mesh = trilist;
}
} else if ( meshDatabase.meshClass=="DomainMesh" ) {
} else if ( meshDatabase.meshClass == "DomainMesh" ) {
std::vector<double> range;
std::vector<int> N;
silo::readUniformMesh( fid, database.name, range, N );
auto rankinfo = silo::read<int>( fid, database.name+"_rankinfo" );
auto rankinfo = silo::read<int>( fid, database.name + "_rankinfo" );
RankInfoStruct rank_data( rankinfo[0], rankinfo[1], rankinfo[2], rankinfo[3] );
mesh.reset( new IO::DomainMesh( rank_data, N[0], N[1], N[2], range[1]-range[0], range[3]-range[2], range[5]-range[4] ) );
mesh.reset( new IO::DomainMesh( rank_data, N[0], N[1], N[2], range[1] - range[0],
range[3] - range[2], range[5] - range[4] ) );
} else {
ERROR("Unknown mesh class");
ERROR( "Unknown mesh class" );
}
silo::close( fid );
#else
ERROR("Build without silo support");
ERROR( "Build without silo support" );
#endif
} else {
ERROR("Unknown format");
ERROR( "Unknown format" );
}
PROFILE_STOP("getMesh");
PROFILE_STOP( "getMesh" );
return mesh;
}
// Read the given variable for the given mesh domain
std::shared_ptr<IO::Variable> IO::getVariable( const std::string& path, const std::string& timestep,
const MeshDatabase& meshDatabase, int domain, const std::string& variable )
std::shared_ptr<IO::Variable> IO::getVariable( const std::string &path, const std::string &timestep,
const MeshDatabase &meshDatabase, int domain, const std::string &variable )
{
std::pair<std::string,std::string> key(meshDatabase.domains[domain].name,variable);
std::map<std::pair<std::string,std::string>,DatabaseEntry>::const_iterator it;
it = meshDatabase.variable_data.find(key);
if ( it==meshDatabase.variable_data.end() )
std::pair<std::string, std::string> key( meshDatabase.domains[domain].name, variable );
auto it = meshDatabase.variable_data.find( key );
if ( it == meshDatabase.variable_data.end() )
return std::shared_ptr<IO::Variable>();
std::shared_ptr<IO::Variable> var;
if ( meshDatabase.format == 2 ) {
const DatabaseEntry& database = it->second;
std::string filename = path + "/" + timestep + "/" + database.file;
FILE *fid = fopen(filename.c_str(),"rb");
fseek(fid,database.offset,SEEK_SET);
if ( meshDatabase.format == FileFormat::NEW || meshDatabase.format == FileFormat::NEW_SINGLE ) {
const DatabaseEntry &database = it->second;
std::string filename = path + "/" + timestep + "/" + database.file;
FILE *fid = fopen( filename.c_str(), "rb" );
fseek( fid, database.offset, SEEK_SET );
char line[1000];
fgetl(line,1000,fid);
size_t i1 = find(line,':');
size_t i2 = find(&line[i1+1],':')+i1+1;
std::vector<std::string> values = splitList(&line[i2+1],',');
ASSERT(values.size()==5);
int dim = atoi(values[0].c_str());
int type = atoi(values[1].c_str());
size_t N = atol(values[2].c_str());
size_t bytes = atol(values[3].c_str());
std::string precision = values[4];
var = std::shared_ptr<IO::Variable>( new IO::Variable() );
var->dim = dim;
var->type = static_cast<IO::VariableType>(type);
var->name = variable;
var->data.resize(N*dim);
if ( precision=="double" ) {
size_t count = fread(var->data.data(),sizeof(double),N*dim,fid);
ASSERT(count*sizeof(double)==bytes);
fgetl( line, 1000, fid );
size_t i1 = find( line, ':' );
size_t i2 = find( &line[i1 + 1], ':' ) + i1 + 1;
std::vector<std::string> values = splitList( &line[i2 + 1], ',' );
ASSERT( values.size() == 5 );
int dim = atoi( values[0].c_str() );
auto type = values[1];
size_t N = atol( values[2].c_str() );
size_t bytes = atol( values[3].c_str() );
std::string precision = values[4];
var = std::shared_ptr<IO::Variable>( new IO::Variable() );
var->dim = dim;
var->type = getVariableType( type );
var->name = variable;
var->data.resize( N, dim );
if ( precision == "double" ) {
size_t count = fread( var->data.data(), sizeof( double ), N * dim, fid );
ASSERT( count * sizeof( double ) == bytes );
} else {
ERROR("Format not implimented");
ERROR( "Format not implimented" );
}
fclose(fid);
} else if ( meshDatabase.format == 4 ) {
fclose( fid );
} else if ( meshDatabase.format == FileFormat::SILO ) {
// Reading a silo file
#ifdef USE_SILO
const auto& database = meshDatabase.domains[domain];
const auto &database = meshDatabase.domains[domain];
auto variableDatabase = meshDatabase.getVariableDatabase( variable );
std::string filename = path + "/" + timestep + "/" + database.file;
auto fid = silo::open( filename, silo::READ );
std::string filename = path + "/" + timestep + "/" + database.file;
auto fid = silo::open( filename, silo::READ );
var.reset( new Variable( variableDatabase.dim, variableDatabase.type, variable ) );
if ( meshDatabase.meshClass=="PointList" ) {
if ( meshDatabase.meshClass == "PointList" ) {
var->data = silo::readPointMeshVariable<double>( fid, variable );
} else if ( meshDatabase.meshClass=="TriMesh" || meshDatabase.meshClass=="TriList" ) {
} else if ( meshDatabase.meshClass == "TriMesh" || meshDatabase.meshClass == "TriList" ) {
var->data = silo::readTriMeshVariable<double>( fid, variable );
} else if ( meshDatabase.meshClass=="DomainMesh" ) {
} else if ( meshDatabase.meshClass == "DomainMesh" ) {
var->data = silo::readUniformMeshVariable<double>( fid, variable );
} else {
ERROR("Unknown mesh class");
ERROR( "Unknown mesh class" );
}
silo::close( fid );
#else
ERROR("Build without silo support");
ERROR( "Build without silo support" );
#endif
} else {
ERROR("Unknown format");
ERROR( "Unknown format" );
}
return var;
}
/****************************************************
* Reformat the variable to match the mesh *
****************************************************/
void IO::reformatVariable( const IO::Mesh& mesh, IO::Variable& var )
* Reformat the variable to match the mesh *
****************************************************/
void IO::reformatVariable( const IO::Mesh &mesh, IO::Variable &var )
{
if ( mesh.className() == "DomainMesh" ) {
const IO::DomainMesh& mesh2 = dynamic_cast<const IO::DomainMesh&>( mesh );
const IO::DomainMesh &mesh2 = dynamic_cast<const IO::DomainMesh &>( mesh );
if ( var.type == VariableType::NodeVariable ) {
size_t N2 = var.data.length() / ((mesh2.nx+1)*(mesh2.ny+1)*(mesh2.nz+1));
ASSERT( (mesh2.nx+1)*(mesh2.ny+1)*(mesh2.nz+1)*N2 == var.data.length() );
var.data.reshape( { (size_t) mesh2.nx+1, (size_t) mesh2.ny+1, (size_t) mesh2.nz+1, N2 } );
size_t N2 =
var.data.length() / ( ( mesh2.nx + 1 ) * ( mesh2.ny + 1 ) * ( mesh2.nz + 1 ) );
ASSERT(
( mesh2.nx + 1 ) * ( mesh2.ny + 1 ) * ( mesh2.nz + 1 ) * N2 == var.data.length() );
var.data.reshape(
{ (size_t) mesh2.nx + 1, (size_t) mesh2.ny + 1, (size_t) mesh2.nz + 1, N2 } );
} else if ( var.type == VariableType::EdgeVariable ) {
ERROR("Not finished");
ERROR( "Not finished" );
} else if ( var.type == VariableType::SurfaceVariable ) {
ERROR("Not finished");
ERROR( "Not finished" );
} else if ( var.type == VariableType::VolumeVariable ) {
size_t N2 = var.data.length() / (mesh2.nx*mesh2.ny*mesh2.nz);
ASSERT( mesh2.nx*mesh2.ny*mesh2.nz*N2 == var.data.length() );
size_t N2 = var.data.length() / ( mesh2.nx * mesh2.ny * mesh2.nz );
ASSERT( mesh2.nx * mesh2.ny * mesh2.nz * N2 == var.data.length() );
var.data.reshape( { (size_t) mesh2.nx, (size_t) mesh2.ny, (size_t) mesh2.nz, N2 } );
} else {
ERROR("Invalid variable type");
ERROR( "Invalid variable type" );
}
} else if ( mesh.className() == "PointList" ) {
const IO::PointList& mesh2 = dynamic_cast<const IO::PointList&>( mesh );
size_t N = mesh2.points.size();
size_t N_var = var.data.length()/N;
ASSERT( N*N_var == var.data.length() );
const IO::PointList &mesh2 = dynamic_cast<const IO::PointList &>( mesh );
size_t N = mesh2.points.size();
size_t N_var = var.data.length() / N;
ASSERT( N * N_var == var.data.length() );
var.data.reshape( { N, N_var } );
} else if ( mesh.className()=="TriMesh" || mesh.className() == "TriList" ) {
std::shared_ptr<Mesh> mesh_ptr( const_cast<Mesh*>(&mesh), []( void* ) {} );
} else if ( mesh.className() == "TriMesh" || mesh.className() == "TriList" ) {
std::shared_ptr<Mesh> mesh_ptr( const_cast<Mesh *>( &mesh ), []( void * ) {} );
std::shared_ptr<TriMesh> mesh2 = getTriMesh( mesh_ptr );
if ( var.type == VariableType::NodeVariable ) {
size_t N = mesh2->vertices->points.size();
size_t N_var = var.data.length()/N;
ASSERT( N*N_var == var.data.length() );
size_t N = mesh2->vertices->points.size();
size_t N_var = var.data.length() / N;
ASSERT( N * N_var == var.data.length() );
var.data.reshape( { N, N_var } );
} else if ( var.type == VariableType::EdgeVariable ) {
ERROR("Not finished");
ERROR( "Not finished" );
} else if ( var.type == VariableType::SurfaceVariable ) {
ERROR("Not finished");
ERROR( "Not finished" );
} else if ( var.type == VariableType::VolumeVariable ) {
size_t N = mesh2->A.size();
size_t N_var = var.data.length()/N;
ASSERT( N*N_var == var.data.length() );
size_t N = mesh2->A.size();
size_t N_var = var.data.length() / N;
ASSERT( N * N_var == var.data.length() );
var.data.reshape( { N, N_var } );
} else {
ERROR("Invalid variable type");
ERROR( "Invalid variable type" );
}
} else {
ERROR("Unknown mesh type");
ERROR( "Unknown mesh type" );
}
}

59
IO/Reader.h
View File

@ -14,20 +14,59 @@ namespace IO {
//! Get the path to a file
std::string getPath( const std::string& filename );
std::string getPath( const std::string &filename );
//! List the timesteps in the given directors (dumps.LBPM)
std::vector<std::string> readTimesteps( const std::string& filename );
/*!
* @brief Get the maximum number of domains written
* @details This function reads the summary files to determine the maximum
* number of domains in the output.
* @param[in] path The path to use for reading
* @param[in] format The data format to use:
* old - Old mesh format (provided for backward compatibility)
* new - New format, 1 file/process
* silo - Silo
* auto - Auto-determin the format
* @param[in] comm Optional comm to use to reduce IO load by
* reading on rank 0 and then communicating the result
*/
int maxDomains( const std::string &path, const std::string &format = "auto",
const Utilities::MPI &comm = MPI_COMM_SELF );
/*!
* @brief Read the timestep list
* @details This function reads the timestep list from the summary file.
* @param[in] path The path to use for reading
* @param[in] format The data format to use:
* old - Old mesh format (provided for backward compatibility)
* new - New format, 1 file/process
* silo - Silo
* auto - Auto-determin the format
* @return append Append any existing data (default is false)
*/
std::vector<std::string> readTimesteps(
const std::string &path, const std::string &format = "auto" );
/*!
* @brief Read the data for the timestep
* @details This function reads the mesh and variable data provided for the given timestep.
* @param[in] path The path to use for reading
* @param[in] timestep The timestep iteration
* @param[in] domain The desired domain to read
*/
std::vector<IO::MeshDataStruct> readData(
const std::string &path, const std::string &timestep, int domain );
//! Read the list of mesh databases for the given timestep
std::vector<IO::MeshDatabase> getMeshList( const std::string& path, const std::string& timestep );
std::vector<IO::MeshDatabase> getMeshList( const std::string &path, const std::string &timestep );
//! Read the given mesh domain
std::shared_ptr<IO::Mesh> getMesh( const std::string& path, const std::string& timestep,
const MeshDatabase& meshDatabase, int domain );
std::shared_ptr<IO::Mesh> getMesh( const std::string &path, const std::string &timestep,
const MeshDatabase &meshDatabase, int domain );
/*!
@ -40,8 +79,8 @@ std::shared_ptr<IO::Mesh> getMesh( const std::string& path, const std::string& t
* @param[in] variable The variable name to read
* @return Returns the variable data as a linear array
*/
std::shared_ptr<IO::Variable> getVariable( const std::string& path, const std::string& timestep,
const MeshDatabase& meshDatabase, int domain, const std::string& variable );
std::shared_ptr<IO::Variable> getVariable( const std::string &path, const std::string &timestep,
const MeshDatabase &meshDatabase, int domain, const std::string &variable );
/*!
@ -50,9 +89,9 @@ std::shared_ptr<IO::Variable> getVariable( const std::string& path, const std::s
* @param[in] mesh The underlying mesh
* @param[in/out] variable The variable name to read
*/
void reformatVariable( const IO::Mesh& mesh, IO::Variable& var );
void reformatVariable( const IO::Mesh &mesh, IO::Variable &var );
} // IO namespace
} // namespace IO
#endif

524
IO/Writer.cpp
View File

@ -1,28 +1,69 @@
#include "IO/Writer.h"
#include "IO/MeshDatabase.h"
#include "IO/IOHelpers.h"
#include "IO/MeshDatabase.h"
#include "IO/silo.h"
#include "common/MPI.h"
#include "common/Utilities.h"
#include <sys/stat.h>
#include <algorithm>
#include <vector>
#include <set>
#include <memory>
#include <set>
#include <sys/stat.h>
#include <vector>
enum class Format { OLD, NEW, SILO, UNKNOWN };
enum class Format { OLD, NEW, SILO, UNKNOWN };
/****************************************************
* Initialize the writer *
****************************************************/
* Recursively create the subdirectory *
****************************************************/
static void recursiveMkdir( const std::string &path, mode_t mode )
{
// Iterate through the root directories until we create the desired path
for ( size_t pos = 0; pos < path.size(); ) {
// slide backwards in string until next slash found
pos++;
for ( ; pos < path.size(); pos++ ) {
if ( path[pos] == '/' || path[pos] == 92 )
break;
}
// Create the temporary path
auto path2 = path.substr( 0, pos );
// Check if the temporary path exists
struct stat status;
int result = stat( path2.data(), &status );
if ( result == 0 ) {
// if there is a part of the path that already exists make sure it is really a directory
if ( !S_ISDIR( status.st_mode ) ) {
ERROR(
"Error in recursiveMkdir...\n"
" Cannot create directories in path = " +
path +
"\n because some intermediate item in path exists and is NOT a directory" );
}
continue;
}
// Create the directory and test the result
result = mkdir( path2.data(), mode );
if ( result != 0 ) {
// Maybe another rank created the directory, check
int result = stat( path2.data(), &status );
if ( result != 0 && !S_ISDIR( status.st_mode ) )
ERROR( "Error in Utilities::recursiveMkdir...\n"
" Cannot create directory = " +
path2 );
}
}
}
/****************************************************
* Initialize the writer *
****************************************************/
static std::string global_IO_path;
static Format global_IO_format = Format::UNKNOWN;
void IO::initialize( const std::string& path, const std::string& format, bool append )
void IO::initialize( const std::string &path, const std::string &format, bool append )
{
if ( path.empty() )
global_IO_path = ".";
@ -35,161 +76,168 @@ void IO::initialize( const std::string& path, const std::string& format, bool ap
else if ( format == "silo" )
global_IO_format = Format::SILO;
else
ERROR("Unknown format");
int rank = Utilities::MPI(MPI_COMM_WORLD).getRank();
if ( !append && rank==0 ) {
mkdir(path.c_str(),S_IRWXU|S_IRGRP);
ERROR( "Unknown format" );
int rank = Utilities::MPI( MPI_COMM_WORLD ).getRank();
if ( !append && rank == 0 ) {
recursiveMkdir( path, S_IRWXU | S_IRGRP );
std::string filename;
if ( global_IO_format==Format::OLD || global_IO_format==Format::NEW )
if ( global_IO_format == Format::OLD || global_IO_format == Format::NEW )
filename = global_IO_path + "/summary.LBM";
else if ( global_IO_format==Format::SILO )
else if ( global_IO_format == Format::SILO )
filename = global_IO_path + "/LBM.visit";
else
ERROR("Unknown format");
auto fid = fopen(filename.c_str(),"wb");
fclose(fid);
ERROR( "Unknown format" );
auto fid = fopen( filename.c_str(), "wb" );
fclose( fid );
}
}
// Write the mesh data in the original format
static std::vector<IO::MeshDatabase> writeMeshesOrigFormat( const std::vector<IO::MeshDataStruct>& meshData, const std::string& path )
static std::vector<IO::MeshDatabase> writeMeshesOrigFormat(
const std::vector<IO::MeshDataStruct> &meshData, const std::string &path, int rank )
{
int rank = Utilities::MPI(MPI_COMM_WORLD).getRank();
std::vector<IO::MeshDatabase> meshes_written;
for (size_t i=0; i<meshData.size(); i++) {
for ( size_t i = 0; i < meshData.size(); i++ ) {
char domainname[100], filename[100], fullpath[200];
sprintf(domainname,"%05i",rank);
sprintf(filename,"%s.%05i",meshData[i].meshName.c_str(),rank);
sprintf(fullpath,"%s/%s",path.c_str(),filename);
FILE *fid = fopen(fullpath,"wb");
INSIST(fid!=NULL,std::string("Error opening file: ")+fullpath);
sprintf( domainname, "%05i", rank );
sprintf( filename, "%s.%05i", meshData[i].meshName.c_str(), rank );
sprintf( fullpath, "%s/%s", path.c_str(), filename );
FILE *fid = fopen( fullpath, "wb" );
INSIST( fid != NULL, std::string( "Error opening file: " ) + fullpath );
std::shared_ptr<IO::Mesh> mesh = meshData[i].mesh;
IO::MeshDatabase mesh_entry;
mesh_entry.name = meshData[i].meshName;
mesh_entry.type = meshType(*mesh);
mesh_entry.name = meshData[i].meshName;
mesh_entry.type = meshType( *mesh );
mesh_entry.meshClass = meshData[i].mesh->className();
mesh_entry.format = 1;
mesh_entry.format = IO::FileFormat::OLD;
IO::DatabaseEntry domain;
domain.name = domainname;
domain.file = filename;
domain.name = domainname;
domain.file = filename;
domain.offset = 0;
mesh_entry.domains.push_back(domain);
mesh_entry.domains.push_back( domain );
if ( !meshData[i].vars.empty() ) {
printf("Warning: variables are not supported with this format\n");
//for (size_t j=0; j<meshData[i].vars.size(); j++)
printf( "Warning: variables are not supported with this format (original)\n" );
// for (size_t j=0; j<meshData[i].vars.size(); j++)
// mesh_entry.variables.push_back( meshData[i].vars[j]->name );
}
const std::string meshClass = mesh->className();
if ( meshClass=="PointList" ) {
if ( meshClass == "PointList" ) {
// List of points
std::shared_ptr<IO::PointList> pointlist = std::dynamic_pointer_cast<IO::PointList>(mesh);
const std::vector<Point>& P = pointlist->points;
for (size_t i=0; i<P.size(); i++) {
std::shared_ptr<IO::PointList> pointlist =
std::dynamic_pointer_cast<IO::PointList>( mesh );
const std::vector<Point> &P = pointlist->points;
for ( size_t i = 0; i < P.size(); i++ ) {
double x[3];
x[0] = P[i].x; x[1] = P[i].y; x[2] = P[i].z;
fwrite(x,sizeof(double),3,fid);
x[0] = P[i].x;
x[1] = P[i].y;
x[2] = P[i].z;
fwrite( x, sizeof( double ), 3, fid );
}
} else if ( meshClass=="TriList" || meshClass=="TriMesh" ) {
} else if ( meshClass == "TriList" || meshClass == "TriMesh" ) {
// Triangle mesh
std::shared_ptr<IO::TriList> trilist = IO::getTriList(mesh);
const std::vector<Point>& A = trilist->A;
const std::vector<Point>& B = trilist->B;
const std::vector<Point>& C = trilist->C;
for (size_t i=0; i<A.size(); i++) {
std::shared_ptr<IO::TriList> trilist = IO::getTriList( mesh );
const std::vector<Point> &A = trilist->A;
const std::vector<Point> &B = trilist->B;
const std::vector<Point> &C = trilist->C;
for ( size_t i = 0; i < A.size(); i++ ) {
double tri[9];
tri[0] = A[i].x; tri[1] = A[i].y; tri[2] = A[i].z;
tri[3] = B[i].x; tri[4] = B[i].y; tri[5] = B[i].z;
tri[6] = C[i].x; tri[7] = C[i].y; tri[8] = C[i].z;
fwrite(tri,sizeof(double),9,fid);
tri[0] = A[i].x;
tri[1] = A[i].y;
tri[2] = A[i].z;
tri[3] = B[i].x;
tri[4] = B[i].y;
tri[5] = B[i].z;
tri[6] = C[i].x;
tri[7] = C[i].y;
tri[8] = C[i].z;
fwrite( tri, sizeof( double ), 9, fid );
}
} else if ( meshClass=="DomainMesh" ) {
} else if ( meshClass == "DomainMesh" ) {
// This format was never supported with the old format
} else {
ERROR("Unknown mesh");
ERROR( "Unknown mesh" );
}
fclose(fid);
fclose( fid );
std::sort( mesh_entry.variables.begin(), mesh_entry.variables.end() );
mesh_entry.variables.erase( std::unique( mesh_entry.variables.begin(), mesh_entry.variables.end() ), mesh_entry.variables.end() );
meshes_written.push_back(mesh_entry);
mesh_entry.variables.erase(
std::unique( mesh_entry.variables.begin(), mesh_entry.variables.end() ),
mesh_entry.variables.end() );
meshes_written.push_back( mesh_entry );
}
return meshes_written;
}
// Create the database entry for the mesh data
static IO::MeshDatabase getDatabase( const std::string& filename, const IO::MeshDataStruct& mesh, int format )
static IO::MeshDatabase getDatabase(
const std::string &filename, const IO::MeshDataStruct &mesh, IO::FileFormat format, int rank )
{
int rank = Utilities::MPI(MPI_COMM_WORLD).getRank();
char domainname[100];
sprintf(domainname,"%s_%05i",mesh.meshName.c_str(),rank);
sprintf( domainname, "%s_%05i", mesh.meshName.c_str(), rank );
// Create the MeshDatabase
IO::MeshDatabase database;
database.name = mesh.meshName;
database.type = meshType(*(mesh.mesh));
database.name = mesh.meshName;
database.type = meshType( *( mesh.mesh ) );
database.meshClass = mesh.mesh->className();
database.format = format;
database.format = format;
// Write the mesh
IO::DatabaseEntry domain;
domain.name = domainname;
domain.file = filename;
domain.name = domainname;
domain.file = filename;
domain.offset = -1;
database.domains.push_back(domain);
database.domains.push_back( domain );
// Write the variables
for (size_t i=0; i<mesh.vars.size(); i++) {
for ( size_t i = 0; i < mesh.vars.size(); i++ ) {
// Add basic variable info
IO::VariableDatabase info;
info.name = mesh.vars[i]->name;
info.type = mesh.vars[i]->type;
info.dim = mesh.vars[i]->dim;
database.variables.push_back(info);
info.dim = mesh.vars[i]->dim;
database.variables.push_back( info );
// Add domain variable info
IO::DatabaseEntry variable;
variable.name = mesh.vars[i]->name;
variable.file = filename;
variable.name = mesh.vars[i]->name;
variable.file = filename;
variable.offset = -1;
std::pair<std::string,std::string> key(domain.name,mesh.vars[i]->name);
database.variable_data.insert(
std::pair<std::pair<std::string,std::string>,IO::DatabaseEntry>(key,variable) );
std::pair<std::string, std::string> key( domain.name, mesh.vars[i]->name );
database.variable_data.insert(
std::pair<std::pair<std::string, std::string>, IO::DatabaseEntry>( key, variable ) );
}
return database;
}
// Write a mesh (and variables) to a file
static IO::MeshDatabase write_domain( FILE *fid, const std::string& filename,
const IO::MeshDataStruct& mesh, int format )
static IO::MeshDatabase write_domain( FILE *fid, const std::string &filename,
const IO::MeshDataStruct &mesh, IO::FileFormat format, int rank )
{
const int level = 0;
int rank = Utilities::MPI(MPI_COMM_WORLD).getRank();
// Create the MeshDatabase
IO::MeshDatabase database = getDatabase( filename, mesh, format );
IO::MeshDatabase database = getDatabase( filename, mesh, format, rank );
// Write the mesh
IO::DatabaseEntry& domain = database.domains[0];
domain.offset = ftell(fid);
std::pair<size_t,void*> data = mesh.mesh->pack(level);
fprintf(fid,"Mesh: %s-%05i: %lu\n",mesh.meshName.c_str(),rank,data.first);
fwrite(data.second,1,data.first,fid);
fprintf(fid,"\n");
delete [] (char*) data.second;
IO::DatabaseEntry &domain = database.domains[0];
domain.offset = ftell( fid );
std::pair<size_t, void *> data = mesh.mesh->pack( level );
fprintf( fid, "Mesh: %s-%05i: %lu\n", mesh.meshName.c_str(), rank, data.first );
fwrite( data.second, 1, data.first, fid );
fprintf( fid, "\n" );
delete[]( char * ) data.second;
// Write the variables
for (size_t i=0; i<mesh.vars.size(); i++) {
std::pair<std::string,std::string> key(domain.name,mesh.vars[i]->name);
IO::DatabaseEntry& variable = database.variable_data[key];
variable.offset = ftell(fid);
int dim = mesh.vars[i]->dim;
int type = static_cast<int>(mesh.vars[i]->type);
size_t N = mesh.vars[i]->data.length();
if ( type == static_cast<int>(IO::VariableType::NullVariable) ) {
ERROR("Variable type not set");
}
size_t N_mesh = mesh.mesh->numberPointsVar(mesh.vars[i]->type);
ASSERT(N==dim*N_mesh);
fprintf(fid,"Var: %s-%05i-%s: %i, %i, %lu, %lu, double\n",
database.name.c_str(), rank, variable.name.c_str(),
dim, type, N_mesh, N*sizeof(double) );
fwrite(mesh.vars[i]->data.data(),sizeof(double),N,fid);
fprintf(fid,"\n");
for ( size_t i = 0; i < mesh.vars.size(); i++ ) {
ASSERT( mesh.vars[i]->type != IO::VariableType::NullVariable );
std::pair<std::string, std::string> key( domain.name, mesh.vars[i]->name );
auto &variable = database.variable_data[key];
variable.offset = ftell( fid );
int dim = mesh.vars[i]->dim;
auto type = getString( mesh.vars[i]->type );
size_t N = mesh.vars[i]->data.length();
size_t N_mesh = mesh.mesh->numberPointsVar( mesh.vars[i]->type );
ASSERT( N == dim * N_mesh );
fprintf( fid, "Var: %s-%05i-%s: %i, %s, %lu, %lu, double\n", database.name.c_str(), rank,
variable.name.c_str(), dim, type.data(), N_mesh, N * sizeof( double ) );
fwrite( mesh.vars[i]->data.data(), sizeof( double ), N, fid );
fprintf( fid, "\n" );
}
return database;
}
@ -198,72 +246,74 @@ static IO::MeshDatabase write_domain( FILE *fid, const std::string& filename,
#ifdef USE_SILO
// Write a PointList mesh (and variables) to a file
template<class TYPE>
static void writeSiloPointMesh( DBfile *fid, const IO::PointList& mesh, const std::string& meshname )
static void writeSiloPointMesh(
DBfile *fid, const IO::PointList &mesh, const std::string &meshname )
{
const auto& points = mesh.getPoints();
std::vector<TYPE> x(points.size()), y(points.size()), z(points.size());
for (size_t i=0; i<x.size(); i++) {
const auto &points = mesh.getPoints();
std::vector<TYPE> x( points.size() ), y( points.size() ), z( points.size() );
for ( size_t i = 0; i < x.size(); i++ ) {
x[i] = points[i].x;
y[i] = points[i].y;
z[i] = points[i].z;
}
const TYPE *coords[] = { x.data(), y.data(), z.data() };
silo::writePointMesh<TYPE>( fid, meshname, 3, points.size(), coords );
IO::silo::writePointMesh<TYPE>( fid, meshname, 3, points.size(), coords );
}
static void writeSiloPointList( DBfile *fid, const IO::MeshDataStruct& meshData, IO::MeshDatabase database )
static void writeSiloPointList(
DBfile *fid, const IO::MeshDataStruct &meshData, IO::MeshDatabase database )
{
const IO::PointList& mesh = dynamic_cast<IO::PointList&>( *meshData.mesh );
const IO::PointList &mesh = dynamic_cast<IO::PointList &>( *meshData.mesh );
const std::string meshname = database.domains[0].name;
if ( meshData.precision == IO::DataType::Double ) {
writeSiloPointMesh<double>( fid, mesh, meshname );
} else if ( meshData.precision == IO::DataType::Float ) {
writeSiloPointMesh<float>( fid, mesh, meshname );
} else {
ERROR("Unsupported format");
ERROR( "Unsupported format" );
}
const auto& points = mesh.getPoints();
std::vector<double> x(points.size()), y(points.size()), z(points.size());
for (size_t i=0; i<x.size(); i++) {
const auto &points = mesh.getPoints();
std::vector<double> x( points.size() ), y( points.size() ), z( points.size() );
for ( size_t i = 0; i < x.size(); i++ ) {
x[i] = points[i].x;
y[i] = points[i].y;
z[i] = points[i].z;
}
const double *coords[] = { x.data(), y.data(), z.data() };
silo::writePointMesh( fid, meshname, 3, points.size(), coords );
for (size_t i=0; i<meshData.vars.size(); i++) {
const IO::Variable& var = *meshData.vars[i];
IO::silo::writePointMesh( fid, meshname, 3, points.size(), coords );
for ( size_t i = 0; i < meshData.vars.size(); i++ ) {
const IO::Variable &var = *meshData.vars[i];
if ( var.precision == IO::DataType::Double ) {
silo::writePointMeshVariable( fid, meshname, var.name, var.data );
IO::silo::writePointMeshVariable( fid, meshname, var.name, var.data );
} else if ( var.precision == IO::DataType::Float ) {
Array<float> data2( var.data.size() );
data2.copy( var.data );
silo::writePointMeshVariable( fid, meshname, var.name, data2 );
IO::silo::writePointMeshVariable( fid, meshname, var.name, data2 );
} else if ( var.precision == IO::DataType::Int ) {
Array<int> data2( var.data.size() );
data2.copy( var.data );
silo::writePointMeshVariable( fid, meshname, var.name, data2 );
IO::silo::writePointMeshVariable( fid, meshname, var.name, data2 );
} else {
ERROR("Unsupported format");
ERROR( "Unsupported format" );
}
}
}
// Write a TriMesh mesh (and variables) to a file
template<class TYPE>
static void writeSiloTriMesh( DBfile *fid, const IO::TriMesh& mesh, const std::string& meshname )
static void writeSiloTriMesh( DBfile *fid, const IO::TriMesh &mesh, const std::string &meshname )
{
const auto& points = mesh.vertices->getPoints();
std::vector<TYPE> x(points.size()), y(points.size()), z(points.size());
for (size_t i=0; i<x.size(); i++) {
const auto &points = mesh.vertices->getPoints();
std::vector<TYPE> x( points.size() ), y( points.size() ), z( points.size() );
for ( size_t i = 0; i < x.size(); i++ ) {
x[i] = points[i].x;
y[i] = points[i].y;
z[i] = points[i].z;
}
const TYPE *coords[] = { x.data(), y.data(), z.data() };
const int *tri[] = { mesh.A.data(), mesh.B.data(), mesh.C.data() };
silo::writeTriMesh<TYPE>( fid, meshname, 3, 2, points.size(), coords, mesh.A.size(), tri );
const int *tri[] = { mesh.A.data(), mesh.B.data(), mesh.C.data() };
IO::silo::writeTriMesh<TYPE>( fid, meshname, 3, 2, points.size(), coords, mesh.A.size(), tri );
}
static void writeSiloTriMesh2( DBfile *fid, const IO::MeshDataStruct& meshData,
const IO::TriMesh& mesh, IO::MeshDatabase database )
static void writeSiloTriMesh2( DBfile *fid, const IO::MeshDataStruct &meshData,
const IO::TriMesh &mesh, IO::MeshDatabase database )
{
const std::string meshname = database.domains[0].name;
if ( meshData.precision == IO::DataType::Double ) {
@ -271,238 +321,240 @@ static void writeSiloTriMesh2( DBfile *fid, const IO::MeshDataStruct& meshData,
} else if ( meshData.precision == IO::DataType::Float ) {
writeSiloTriMesh<float>( fid, mesh, meshname );
} else {
ERROR("Unsupported format");
ERROR( "Unsupported format" );
}
for (size_t i=0; i<meshData.vars.size(); i++) {
const IO::Variable& var = *meshData.vars[i];
auto type = static_cast<silo::VariableType>( var.type );
for ( size_t i = 0; i < meshData.vars.size(); i++ ) {
const IO::Variable &var = *meshData.vars[i];
if ( var.precision == IO::DataType::Double ) {
silo::writeTriMeshVariable( fid, 3, meshname, var.name, var.data, type );
IO::silo::writeTriMeshVariable( fid, 3, meshname, var.name, var.data, var.type );
} else if ( var.precision == IO::DataType::Float ) {
Array<float> data2( var.data.size() );
data2.copy( var.data );
silo::writeTriMeshVariable( fid, 3, meshname, var.name, data2, type );
IO::silo::writeTriMeshVariable( fid, 3, meshname, var.name, data2, var.type );
} else if ( var.precision == IO::DataType::Int ) {
Array<int> data2( var.data.size() );
data2.copy( var.data );
silo::writeTriMeshVariable( fid, 3, meshname, var.name, data2, type );
IO::silo::writeTriMeshVariable( fid, 3, meshname, var.name, data2, var.type );
} else {
ERROR("Unsupported format");
ERROR( "Unsupported format" );
}
}
}
static void writeSiloTriMesh( DBfile *fid, const IO::MeshDataStruct& meshData, IO::MeshDatabase database )
static void writeSiloTriMesh(
DBfile *fid, const IO::MeshDataStruct &meshData, IO::MeshDatabase database )
{
const IO::TriMesh& mesh = dynamic_cast<IO::TriMesh&>( *meshData.mesh );
const IO::TriMesh &mesh = dynamic_cast<IO::TriMesh &>( *meshData.mesh );
writeSiloTriMesh2( fid, meshData, mesh, database );
}
static void writeSiloTriList( DBfile *fid, const IO::MeshDataStruct& meshData, IO::MeshDatabase database )
static void writeSiloTriList(
DBfile *fid, const IO::MeshDataStruct &meshData, IO::MeshDatabase database )
{
auto mesh = getTriMesh( meshData.mesh );
writeSiloTriMesh2( fid, meshData, *mesh, database );
}
// Write a DomainMesh mesh (and variables) to a file
static void writeSiloDomainMesh( DBfile *fid, const IO::MeshDataStruct& meshData, IO::MeshDatabase database )
static void writeSiloDomainMesh(
DBfile *fid, const IO::MeshDataStruct &meshData, IO::MeshDatabase database )
{
const IO::DomainMesh& mesh = dynamic_cast<IO::DomainMesh&>( *meshData.mesh );
const IO::DomainMesh &mesh = dynamic_cast<IO::DomainMesh &>( *meshData.mesh );
RankInfoStruct info( mesh.rank, mesh.nprocx, mesh.nprocy, mesh.nprocz );
std::array<double,6> range = { info.ix*mesh.Lx/info.nx, (info.ix+1)*mesh.Lx/info.nx,
info.jy*mesh.Ly/info.ny, (info.jy+1)*mesh.Ly/info.ny,
info.kz*mesh.Lz/info.nz, (info.kz+1)*mesh.Lz/info.nz };
std::array<int,3> N = { mesh.nx, mesh.ny, mesh.nz };
auto meshname = database.domains[0].name;
silo::writeUniformMesh<3>( fid, meshname, range, N );
silo::write<int>( fid, meshname+"_rankinfo", { mesh.rank, mesh.nprocx, mesh.nprocy, mesh.nprocz } );
for (size_t i=0; i<meshData.vars.size(); i++) {
const auto& var = *meshData.vars[i];
auto type = static_cast<silo::VariableType>( var.type );
std::array<double, 6> range = { info.ix * mesh.Lx / info.nx,
( info.ix + 1 ) * mesh.Lx / info.nx, info.jy * mesh.Ly / info.ny,
( info.jy + 1 ) * mesh.Ly / info.ny, info.kz * mesh.Lz / info.nz,
( info.kz + 1 ) * mesh.Lz / info.nz };
std::array<int, 3> N = { mesh.nx, mesh.ny, mesh.nz };
auto meshname = database.domains[0].name;
IO::silo::writeUniformMesh<3>( fid, meshname, range, N );
IO::silo::write<int>(
fid, meshname + "_rankinfo", { mesh.rank, mesh.nprocx, mesh.nprocy, mesh.nprocz } );
for ( size_t i = 0; i < meshData.vars.size(); i++ ) {
const auto &var = *meshData.vars[i];
if ( var.precision == IO::DataType::Double ) {
silo::writeUniformMeshVariable<3>( fid, meshname, N, var.name, var.data, type );
IO::silo::writeUniformMeshVariable<3>( fid, meshname, N, var.name, var.data, var.type );
} else if ( var.precision == IO::DataType::Float ) {
Array<float> data2( var.data.size() );
data2.copy( var.data );
silo::writeUniformMeshVariable<3>( fid, meshname, N, var.name, data2, type );
IO::silo::writeUniformMeshVariable<3>( fid, meshname, N, var.name, data2, var.type );
} else if ( var.precision == IO::DataType::Int ) {
Array<int> data2( var.data.size() );
data2.copy( var.data );
silo::writeUniformMeshVariable<3>( fid, meshname, N, var.name, data2, type );
IO::silo::writeUniformMeshVariable<3>( fid, meshname, N, var.name, data2, var.type );
} else {
ERROR("Unsupported format");
ERROR( "Unsupported format" );
}
}
}
// Write a mesh (and variables) to a file
static IO::MeshDatabase write_domain_silo( DBfile *fid, const std::string& filename,
const IO::MeshDataStruct& mesh, int format )
static IO::MeshDatabase write_domain_silo( DBfile *fid, const std::string &filename,
const IO::MeshDataStruct &mesh, IO::FileFormat format, int rank )
{
// Create the MeshDatabase
auto database = getDatabase( filename, mesh, format );
if ( database.meshClass=="PointList" ) {
auto database = getDatabase( filename, mesh, format, rank );
if ( database.meshClass == "PointList" ) {
writeSiloPointList( fid, mesh, database );
} else if ( database.meshClass=="TriMesh" ) {
} else if ( database.meshClass == "TriMesh" ) {
writeSiloTriMesh( fid, mesh, database );
} else if ( database.meshClass=="TriList" ) {
} else if ( database.meshClass == "TriList" ) {
writeSiloTriList( fid, mesh, database );
} else if ( database.meshClass=="DomainMesh" ) {
} else if ( database.meshClass == "DomainMesh" ) {
writeSiloDomainMesh( fid, mesh, database );
} else {
ERROR("Unknown mesh class");
ERROR( "Unknown mesh class" );
}
return database;
}
// Write the summary file for silo
std::pair<int,int> getSiloMeshType( const std::string& meshClass )
std::pair<int, int> getSiloMeshType( const std::string &meshClass )
{
int meshType = 0;
int varType = 0;
if ( meshClass=="PointList" ) {
int varType = 0;
if ( meshClass == "PointList" ) {
meshType = DB_POINTMESH;
varType = DB_POINTVAR;
} else if ( meshClass=="TriMesh" ) {
} else if ( meshClass == "TriMesh" ) {
meshType = DB_UCDMESH;
varType = DB_UCDVAR;
} else if ( meshClass=="TriList" ) {
} else if ( meshClass == "TriList" ) {
meshType = DB_UCDMESH;
varType = DB_UCDVAR;
} else if ( meshClass=="DomainMesh" ) {
} else if ( meshClass == "DomainMesh" ) {
meshType = DB_QUAD_RECT;
varType = DB_QUADVAR;
} else {
ERROR("Unknown mesh class");
ERROR( "Unknown mesh class" );
}
return std::make_pair( meshType, varType );
}
void writeSiloSummary( const std::vector<IO::MeshDatabase>& meshes_written, const std::string& filename )
void writeSiloSummary(
const std::vector<IO::MeshDatabase> &meshes_written, const std::string &filename )
{
auto fid = silo::open( filename, silo::CREATE );
for ( const auto& data : meshes_written ) {
auto fid = IO::silo::open( filename, IO::silo::CREATE );
for ( const auto &data : meshes_written ) {
auto type = getSiloMeshType( data.meshClass );
std::vector<int> meshTypes( data.domains.size(), type.first );
std::vector<int> varTypes( data.domains.size(), type.second );
std::vector<std::string> meshNames;
for ( const auto& tmp : data.domains )
for ( const auto &tmp : data.domains )
meshNames.push_back( tmp.file + ":" + tmp.name );
silo::writeMultiMesh( fid, data.name, meshNames, meshTypes );
for (const auto& variable : data.variables ) {
IO::silo::writeMultiMesh( fid, data.name, meshNames, meshTypes );
for ( const auto &variable : data.variables ) {
std::vector<std::string> varnames;
for ( const auto& tmp : data.domains )
for ( const auto &tmp : data.domains )
varnames.push_back( tmp.file + ":" + variable.name );
silo::writeMultiVar( fid, variable.name, varnames, varTypes );
IO::silo::writeMultiVar( fid, variable.name, varnames, varTypes );
}
}
silo::close( fid );
IO::silo::close( fid );
}
#endif
// Write the mesh data in the new format
static std::vector<IO::MeshDatabase> writeMeshesNewFormat(
const std::vector<IO::MeshDataStruct>& meshData, const std::string& path, int format )
static std::vector<IO::MeshDatabase> writeMeshesNewFormat(
const std::vector<IO::MeshDataStruct> &meshData, const std::string &path, IO::FileFormat format,
int rank )
{
int rank = Utilities::MPI(MPI_COMM_WORLD).getRank();
std::vector<IO::MeshDatabase> meshes_written;
char filename[100], fullpath[200];
sprintf(filename,"%05i",rank);
sprintf(fullpath,"%s/%s",path.c_str(),filename);
FILE *fid = fopen(fullpath,"wb");
for (size_t i=0; i<meshData.size(); i++) {
sprintf( filename, "%05i", rank );
sprintf( fullpath, "%s/%s", path.c_str(), filename );
FILE *fid = fopen( fullpath, "wb" );
for ( size_t i = 0; i < meshData.size(); i++ ) {
std::shared_ptr<IO::Mesh> mesh = meshData[i].mesh;
meshes_written.push_back( write_domain(fid,filename,meshData[i],format) );
meshes_written.push_back( write_domain( fid, filename, meshData[i], format, rank ) );
}
fclose(fid);
fclose( fid );
return meshes_written;
}
// Write the mesh data to silo
static std::vector<IO::MeshDatabase> writeMeshesSilo(
const std::vector<IO::MeshDataStruct>& meshData, const std::string& path, int format )
static std::vector<IO::MeshDatabase> writeMeshesSilo(
const std::vector<IO::MeshDataStruct> &meshData, const std::string &path, IO::FileFormat format,
int rank )
{
#ifdef USE_SILO
int rank = Utilities::MPI(MPI_COMM_WORLD).getRank();
std::vector<IO::MeshDatabase> meshes_written;
char filename[100], fullpath[200];
sprintf(filename,"%05i.silo",rank);
sprintf(fullpath,"%s/%s",path.c_str(),filename);
auto fid = silo::open( fullpath, silo::CREATE );
for (size_t i=0; i<meshData.size(); i++) {
sprintf( filename, "%05i.silo", rank );
sprintf( fullpath, "%s/%s", path.c_str(), filename );
auto fid = IO::silo::open( fullpath, IO::silo::CREATE );
for ( size_t i = 0; i < meshData.size(); i++ ) {
auto mesh = meshData[i].mesh;
meshes_written.push_back( write_domain_silo(fid,filename,meshData[i],format) );
meshes_written.push_back( write_domain_silo( fid, filename, meshData[i], format, rank ) );
}
silo::close( fid );
IO::silo::close( fid );
return meshes_written;
#else
ERROR("Application built without silo support");
NULL_USE( meshData );
NULL_USE( path );
NULL_USE( format );
NULL_USE( rank );
ERROR( "Application built without silo support" );
return std::vector<IO::MeshDatabase>();
#endif
}
}
/****************************************************
* Write the mesh data *
****************************************************/
void IO::writeData( const std::string& subdir, const std::vector<IO::MeshDataStruct>& meshData, const Utilities::MPI& comm )
* Write the mesh data *
****************************************************/
void IO::writeData( const std::string &subdir, const std::vector<IO::MeshDataStruct> &meshData,
const Utilities::MPI &comm )
{
if ( global_IO_path.empty() )
IO::initialize( );
PROFILE_START("writeData");
int rank = Utilities::MPI(MPI_COMM_WORLD).getRank();
IO::initialize();
PROFILE_START( "writeData" );
int rank = Utilities::MPI( MPI_COMM_WORLD ).getRank();
// Check the meshData before writing
for ( const auto& data : meshData ) {
if ( !data.check() )
ERROR("Error in meshData");
}
for ( const auto &data : meshData )
ASSERT( data.check() );
// Create the output directory
std::string path = global_IO_path + "/" + subdir;
if ( rank == 0 ) {
mkdir(path.c_str(),S_IRWXU|S_IRGRP);
}
comm.barrier();
recursiveMkdir( path, S_IRWXU | S_IRGRP );
// Write the mesh files
std::vector<IO::MeshDatabase> meshes_written;
if ( global_IO_format == Format::OLD ) {
// Write the original triangle format
meshes_written = writeMeshesOrigFormat( meshData, path );
meshes_written = writeMeshesOrigFormat( meshData, path, rank );
} else if ( global_IO_format == Format::NEW ) {
// Write the new format (double precision)
meshes_written = writeMeshesNewFormat( meshData, path, 2 );
meshes_written = writeMeshesNewFormat( meshData, path, IO::FileFormat::NEW, rank );
} else if ( global_IO_format == Format::SILO ) {
// Write silo
meshes_written = writeMeshesSilo( meshData, path, 4 );
meshes_written = writeMeshesSilo( meshData, path, IO::FileFormat::SILO, rank );
} else {
ERROR("Unknown format");
ERROR( "Unknown format" );
}
// Gather a complete list of files on rank 0
meshes_written = gatherAll(meshes_written,comm);
meshes_written = gatherAll( meshes_written, comm );
// Write the summary files
if ( rank == 0 ) {
// Write the summary file for the current timestep
char filename[200];
sprintf(filename,"%s/LBM.summary",path.c_str());
write(meshes_written,filename);
// Write summary silo file if needed
#ifdef USE_SILO
sprintf( filename, "%s/LBM.summary", path.c_str() );
write( meshes_written, filename );
// Write summary silo file if needed
#ifdef USE_SILO
if ( global_IO_format == Format::SILO ) {
sprintf(filename,"%s/summary.silo",path.c_str());
writeSiloSummary(meshes_written,filename);
sprintf( filename, "%s/summary.silo", path.c_str() );
writeSiloSummary( meshes_written, filename );
}
#endif
#endif
// Add the timestep to the global summary file
if ( global_IO_format == Format::OLD || global_IO_format == Format::NEW ) {
auto filename = global_IO_path+"/summary.LBM";
FILE *fid = fopen(filename.c_str(),"ab");
fprintf(fid,"%s/\n",subdir.c_str());
fclose(fid);
auto filename = global_IO_path + "/summary.LBM";
FILE *fid = fopen( filename.c_str(), "ab" );
fprintf( fid, "%s/\n", subdir.c_str() );
fclose( fid );
} else if ( global_IO_format == Format::SILO ) {
auto filename = global_IO_path+"/LBM.visit";
FILE *fid = fopen(filename.c_str(),"ab");
fprintf(fid,"%s/summary.silo\n",subdir.c_str());
fclose(fid);
auto filename = global_IO_path + "/LBM.visit";
FILE *fid = fopen( filename.c_str(), "ab" );
fprintf( fid, "%s/summary.silo\n", subdir.c_str() );
fclose( fid );
} else {
ERROR("Unknown format");
ERROR( "Unknown format" );
}
}
PROFILE_STOP("writeData");
PROFILE_STOP( "writeData" );
}

25
IO/Writer.h
View File

@ -14,17 +14,18 @@ namespace IO {
/*!
* @brief Initialize the writer
* @details This function initializes the writer to the given path. All subsequent
* writes will occur in this directory. If this is not called, then it will default
* to the current path.
* @details This function initializes the writer to the given path.
* All subsequent writes will occur in this directory.
* If this is not called, then it will default to the current path.
* @param[in] path The path to use for writes
* @param[in] format The data format to use:
* old - Old mesh format (provided for backward compatibility, cannot write variables)
* new - New format, 1 file/process
* silo - Silo
* old - Old mesh format
* (provided for backward compatibility, cannot write variables)
* new - New format, 1 file/process silo - Silo
* @param[in] append Append any existing data (default is false)
*/
void initialize( const std::string& path="", const std::string& format="silo", bool append=false );
void initialize(
const std::string &path = "", const std::string &format = "silo", bool append = false );
/*!
@ -34,7 +35,8 @@ void initialize( const std::string& path="", const std::string& format="silo", b
* @param[in] meshData The data to write
* @param[in] comm The comm to use for writing (usually MPI_COMM_WORLD or a dup thereof)
*/
void writeData( const std::string& subdir, const std::vector<IO::MeshDataStruct>& meshData, const Utilities::MPI& comm );
void writeData( const std::string &subdir, const std::vector<IO::MeshDataStruct> &meshData,
const Utilities::MPI &comm );
/*!
@ -44,14 +46,15 @@ void writeData( const std::string& subdir, const std::vector<IO::MeshDataStruct>
* @param[in] meshData The data to write
* @param[in] comm The comm to use for writing (usually MPI_COMM_WORLD or a dup thereof)
*/
inline void writeData( int timestep, const std::vector<IO::MeshDataStruct>& meshData, const Utilities::MPI& comm )
inline void writeData(
int timestep, const std::vector<IO::MeshDataStruct> &meshData, const Utilities::MPI &comm )
{
char subdir[100];
sprintf(subdir,"vis%03i",timestep);
sprintf( subdir, "vis%03i", timestep );
writeData( subdir, meshData, comm );
}
} // IO namespace
} // namespace IO
#endif

385
IO/netcdf.cpp
View File

@ -1,6 +1,6 @@
#include "IO/netcdf.h"
#include "common/Utilities.h"
#include "common/MPI.h"
#include "common/Utilities.h"
#include "ProfilerApp.h"
@ -12,14 +12,14 @@
#include <netcdf_par.h>
#define CHECK_NC_ERR( ERR ) \
do { \
if ( ERR != NC_NOERR ) { \
#define CHECK_NC_ERR( ERR ) \
do { \
if ( ERR != NC_NOERR ) { \
std::string msg = "Error calling netcdf routine: "; \
msg += nc_strerror( ERR ); \
ERROR( msg ); \
} \
} while (0)
msg += nc_strerror( ERR ); \
ERROR( msg ); \
} \
} while ( 0 )
namespace netcdf {
@ -50,43 +50,64 @@ static inline VariableType convertType( nc_type type )
else if ( type == NC_DOUBLE )
type2 = DOUBLE;
else
ERROR("Unknown type");
ERROR( "Unknown type" );
return type2;
}
// Get nc_type from the template
template<class T> inline nc_type getType();
template<> inline nc_type getType<char>() { return NC_CHAR; }
template<> inline nc_type getType<short>() { return NC_SHORT; }
template<> inline nc_type getType<int>() { return NC_INT; }
template<> inline nc_type getType<float>() { return NC_FLOAT; }
template<> inline nc_type getType<double>() { return NC_DOUBLE; }
template<class T>
inline nc_type getType();
template<>
inline nc_type getType<char>()
{
return NC_CHAR;
}
template<>
inline nc_type getType<short>()
{
return NC_SHORT;
}
template<>
inline nc_type getType<int>()
{
return NC_INT;
}
template<>
inline nc_type getType<float>()
{
return NC_FLOAT;
}
template<>
inline nc_type getType<double>()
{
return NC_DOUBLE;
}
// Function to reverse an array
template<class TYPE>
inline std::vector<TYPE> reverse( const std::vector<TYPE>& x )
inline std::vector<TYPE> reverse( const std::vector<TYPE> &x )
{
std::vector<TYPE> y(x.size());
for (size_t i=0; i<x.size(); i++)
y[i] = x[x.size()-i-1];
std::vector<TYPE> y( x.size() );
for ( size_t i = 0; i < x.size(); i++ )
y[i] = x[x.size() - i - 1];
return y;
}
// Function to reverse an array
template<class TYPE1, class TYPE2>
inline std::vector<TYPE2> convert( const std::vector<TYPE1>& x )
inline std::vector<TYPE2> convert( const std::vector<TYPE1> &x )
{
std::vector<TYPE2> y(x.size());
for (size_t i=0; i<x.size(); i++)
y[i] = static_cast<TYPE2>(x[i]);
std::vector<TYPE2> y( x.size() );
for ( size_t i = 0; i < x.size(); i++ )
y[i] = static_cast<TYPE2>( x[i] );
return y;
}
/****************************************************
* Convert the VariableType to a string *
****************************************************/
* Convert the VariableType to a string *
****************************************************/
std::string VariableTypeName( VariableType type )
{
if ( type == BYTE )
@ -114,9 +135,9 @@ std::string VariableTypeName( VariableType type )
/****************************************************
* Open/close a file *
****************************************************/
int open( const std::string& filename, FileMode mode, const Utilities::MPI& comm )
* Open/close a file *
****************************************************/
int open( const std::string &filename, FileMode mode, const Utilities::MPI &comm )
{
int fid = 0;
if ( comm.isNull() ) {
@ -127,23 +148,26 @@ int open( const std::string& filename, FileMode mode, const Utilities::MPI& comm
int err = nc_open( filename.c_str(), NC_WRITE, &fid );
CHECK_NC_ERR( err );
} else if ( mode == CREATE ) {
int err = nc_create( filename.c_str(), NC_SHARE|NC_64BIT_OFFSET, &fid );
int err = nc_create( filename.c_str(), NC_SHARE | NC_64BIT_OFFSET, &fid );
CHECK_NC_ERR( err );
} else {
ERROR("Unknown file mode");
ERROR( "Unknown file mode" );
}
} else {
if ( mode == READ ) {
int err = nc_open_par( filename.c_str(), NC_MPIPOSIX, comm.getCommunicator(), MPI_INFO_NULL, &fid );
int err = nc_open_par(
filename.c_str(), NC_MPIPOSIX, comm.getCommunicator(), MPI_INFO_NULL, &fid );
CHECK_NC_ERR( err );
} else if ( mode == WRITE ) {
int err = nc_open_par( filename.c_str(), NC_WRITE|NC_MPIPOSIX, comm.getCommunicator(), MPI_INFO_NULL, &fid );
int err = nc_open_par( filename.c_str(), NC_WRITE | NC_MPIPOSIX, comm.getCommunicator(),
MPI_INFO_NULL, &fid );
CHECK_NC_ERR( err );
} else if ( mode == CREATE ) {
int err = nc_create_par( filename.c_str(), NC_NETCDF4|NC_MPIIO, comm.getCommunicator(), MPI_INFO_NULL, &fid );
int err = nc_create_par( filename.c_str(), NC_NETCDF4 | NC_MPIIO,
comm.getCommunicator(), MPI_INFO_NULL, &fid );
CHECK_NC_ERR( err );
} else {
ERROR("Unknown file mode");
ERROR( "Unknown file mode" );
}
}
return fid;
@ -152,42 +176,42 @@ void close( int fid )
{
int err = nc_close( fid );
if ( err != NC_NOERR )
ERROR("Error closing file");
ERROR( "Error closing file" );
}
/****************************************************
* Query basic properties *
****************************************************/
* Query basic properties *
****************************************************/
static std::vector<size_t> getDimVar( int fid, int varid )
{
int ndim = 0;
int err = nc_inq_varndims( fid, varid, &ndim );
int err = nc_inq_varndims( fid, varid, &ndim );
CHECK_NC_ERR( err );
std::vector<size_t> dims(ndim,0);
int dimid[64] = {-1};
err = nc_inq_vardimid( fid, varid, dimid );
std::vector<size_t> dims( ndim, 0 );
int dimid[64] = { -1 };
err = nc_inq_vardimid( fid, varid, dimid );
CHECK_NC_ERR( err );
for (int i=0; i<ndim; i++) {
for ( int i = 0; i < ndim; i++ ) {
err = nc_inq_dimlen( fid, dimid[i], &dims[i] );
CHECK_NC_ERR( err );
}
return dims;
}
static int getVarID( int fid, const std::string& var )
static int getVarID( int fid, const std::string &var )
{
int id = -1;
int id = -1;
int err = nc_inq_varid( fid, var.c_str(), &id );
CHECK_NC_ERR( err );
return id;
}
std::vector<size_t> getVarDim( int fid, const std::string& var )
std::vector<size_t> getVarDim( int fid, const std::string &var )
{
return getDimVar( fid, getVarID( fid, var ) );
}
std::vector<size_t> getAttDim( int fid, const std::string& att )
std::vector<size_t> getAttDim( int fid, const std::string &att )
{
std::vector<size_t> dim(1,0);
std::vector<size_t> dim( 1, 0 );
int err = nc_inq_attlen( fid, NC_GLOBAL, att.c_str(), dim.data() );
CHECK_NC_ERR( err );
return dim;
@ -197,9 +221,9 @@ std::vector<std::string> getVarNames( int fid )
int nvar;
int err = nc_inq( fid, NULL, &nvar, NULL, NULL );
CHECK_NC_ERR( err );
std::vector<std::string> vars(nvar);
for (int i=0; i<nvar; i++) {
char name[NC_MAX_NAME+1];
std::vector<std::string> vars( nvar );
for ( int i = 0; i < nvar; i++ ) {
char name[NC_MAX_NAME + 1];
err = nc_inq_varname( fid, i, name );
CHECK_NC_ERR( err );
vars[i] = name;
@ -211,262 +235,269 @@ std::vector<std::string> getAttNames( int fid )
int natt;
int err = nc_inq( fid, NULL, NULL, &natt, NULL );
CHECK_NC_ERR( err );
std::vector<std::string> att(natt);
for (int i=0; i<natt; i++) {
char name[NC_MAX_NAME+1];
err = nc_inq_attname( fid, NC_GLOBAL, i, name );
std::vector<std::string> att( natt );
for ( int i = 0; i < natt; i++ ) {
char name[NC_MAX_NAME + 1];
err = nc_inq_attname( fid, NC_GLOBAL, i, name );
CHECK_NC_ERR( err );
att[i] = name;
}
return att;
}
VariableType getVarType( int fid, const std::string& var )
VariableType getVarType( int fid, const std::string &var )
{
int varid = -1;
int err = nc_inq_varid( fid, var.c_str(), &varid );
int err = nc_inq_varid( fid, var.c_str(), &varid );
CHECK_NC_ERR( err );
nc_type type=0;
err = nc_inq_vartype( fid, varid, &type );
nc_type type = 0;
err = nc_inq_vartype( fid, varid, &type );
CHECK_NC_ERR( err );
return convertType(type);
return convertType( type );
}
VariableType getAttType( int fid, const std::string& att )
VariableType getAttType( int fid, const std::string &att )
{
nc_type type=0;
int err = nc_inq_atttype( fid, NC_GLOBAL, att.c_str(), &type );
nc_type type = 0;
int err = nc_inq_atttype( fid, NC_GLOBAL, att.c_str(), &type );
CHECK_NC_ERR( err );
return convertType(type);
return convertType( type );
}
/****************************************************
* Read a variable *
****************************************************/
* Read a variable *
****************************************************/
template<>
Array<unsigned short> getVar<unsigned short>( int fid, const std::string& var )
Array<unsigned short> getVar<unsigned short>( int fid, const std::string &var )
{
PROFILE_START("getVar<unsigned short>");
Array<unsigned short> x( reverse(getVarDim(fid,var)) );
int err = nc_get_var_ushort( fid, getVarID(fid,var), x.data() );
PROFILE_START( "getVar<unsigned short>" );
Array<unsigned short> x( reverse( getVarDim( fid, var ) ) );
int err = nc_get_var_ushort( fid, getVarID( fid, var ), x.data() );
CHECK_NC_ERR( err );
PROFILE_STOP("getVar<unsigned short>");
PROFILE_STOP( "getVar<unsigned short>" );
return x.reverseDim();
}
template<>
Array<short> getVar<short>( int fid, const std::string& var )
Array<short> getVar<short>( int fid, const std::string &var )
{
PROFILE_START("getVar<short>");
Array<short> x( reverse(getVarDim(fid,var)) );
int err = nc_get_var_short( fid, getVarID(fid,var), x.data() );
PROFILE_START( "getVar<short>" );
Array<short> x( reverse( getVarDim( fid, var ) ) );
int err = nc_get_var_short( fid, getVarID( fid, var ), x.data() );
CHECK_NC_ERR( err );
PROFILE_STOP("getVar<short>");
PROFILE_STOP( "getVar<short>" );
return x.reverseDim();
}
template<>
Array<unsigned int> getVar<unsigned int>( int fid, const std::string& var )
Array<unsigned int> getVar<unsigned int>( int fid, const std::string &var )
{
PROFILE_START("getVar<unsigned int>");
Array<unsigned int> x( reverse(getVarDim(fid,var)) );
int err = nc_get_var_uint( fid, getVarID(fid,var), x.data() );
PROFILE_START( "getVar<unsigned int>" );
Array<unsigned int> x( reverse( getVarDim( fid, var ) ) );
int err = nc_get_var_uint( fid, getVarID( fid, var ), x.data() );
CHECK_NC_ERR( err );
PROFILE_STOP("getVar<unsigned int>");
PROFILE_STOP( "getVar<unsigned int>" );
return x.reverseDim();
}
template<>
Array<int> getVar<int>( int fid, const std::string& var )
Array<int> getVar<int>( int fid, const std::string &var )
{
PROFILE_START("getVar<int>");
Array<int> x( reverse(getVarDim(fid,var)) );
int err = nc_get_var_int( fid, getVarID(fid,var), x.data() );
PROFILE_START( "getVar<int>" );
Array<int> x( reverse( getVarDim( fid, var ) ) );
int err = nc_get_var_int( fid, getVarID( fid, var ), x.data() );
CHECK_NC_ERR( err );
PROFILE_STOP("getVar<int>");
PROFILE_STOP( "getVar<int>" );
return x.reverseDim();
}
template<>
Array<float> getVar<float>( int fid, const std::string& var )
Array<float> getVar<float>( int fid, const std::string &var )
{
PROFILE_START("getVar<float>");
Array<float> x( reverse(getVarDim(fid,var)) );
int err = nc_get_var_float( fid, getVarID(fid,var), x.data() );
PROFILE_START( "getVar<float>" );
Array<float> x( reverse( getVarDim( fid, var ) ) );
int err = nc_get_var_float( fid, getVarID( fid, var ), x.data() );
CHECK_NC_ERR( err );
PROFILE_STOP("getVar<float>");
PROFILE_STOP( "getVar<float>" );
return x.reverseDim();
}
template<>
Array<double> getVar<double>( int fid, const std::string& var )
Array<double> getVar<double>( int fid, const std::string &var )
{
PROFILE_START("getVar<double>");
Array<double> x( reverse(getVarDim(fid,var)) );
int err = nc_get_var_double( fid, getVarID(fid,var), x.data() );
PROFILE_START( "getVar<double>" );
Array<double> x( reverse( getVarDim( fid, var ) ) );
int err = nc_get_var_double( fid, getVarID( fid, var ), x.data() );
CHECK_NC_ERR( err );
PROFILE_STOP("getVar<double>");
PROFILE_STOP( "getVar<double>" );
return x.reverseDim();
}
template<>
Array<char> getVar<char>( int fid, const std::string& var )
{
PROFILE_START("getVar<char>");
Array<char> x( reverse(getVarDim(fid,var)) );
int err = nc_get_var_text( fid, getVarID(fid,var), x.data() );
Array<char> getVar<char>( int fid, const std::string &var )
{
PROFILE_START( "getVar<char>" );
Array<char> x( reverse( getVarDim( fid, var ) ) );
int err = nc_get_var_text( fid, getVarID( fid, var ), x.data() );
CHECK_NC_ERR( err );
PROFILE_STOP("getVar<char>");
PROFILE_STOP( "getVar<char>" );
return x.reverseDim();
}
template<>
Array<std::string> getVar<std::string>( int fid, const std::string& var )
Array<std::string> getVar<std::string>( int fid, const std::string &var )
{
PROFILE_START("getVar<std::string>");
Array<char> tmp = getVar<char>( fid, var );
std::vector<size_t> dim = {tmp.size(0), tmp.size(1), tmp.size(2) };
PROFILE_START( "getVar<std::string>" );
Array<char> tmp = getVar<char>( fid, var );
std::vector<size_t> dim = { tmp.size( 0 ), tmp.size( 1 ), tmp.size( 2 ) };
if ( dim.size() == 1 )
dim[0] = 1;
else
dim.erase( dim.begin() );
Array<std::string> text(dim);
for (size_t i=0; i<text.length(); i++)
text(i) = &(tmp(0,i));
PROFILE_STOP("getVar<std::string>");
Array<std::string> text( dim );
for ( size_t i = 0; i < text.length(); i++ )
text( i ) = &( tmp( 0, i ) );
PROFILE_STOP( "getVar<std::string>" );
return text;
}
static inline void get_stride_args( const std::vector<int>& start,
const std::vector<int>& count, const std::vector<int>& stride,
size_t *startp, size_t *countp, ptrdiff_t *stridep )
static inline void get_stride_args( const std::vector<int> &start, const std::vector<int> &count,
const std::vector<int> &stride, size_t *startp, size_t *countp, ptrdiff_t *stridep )
{
for (size_t i=0; i<start.size(); i++)
for ( size_t i = 0; i < start.size(); i++ )
startp[i] = start[i];
for (size_t i=0; i<count.size(); i++)
for ( size_t i = 0; i < count.size(); i++ )
countp[i] = count[i];
for (size_t i=0; i<stride.size(); i++)
for ( size_t i = 0; i < stride.size(); i++ )
stridep[i] = stride[i];
}
template<class TYPE>
int nc_get_vars_TYPE( int fid, int varid, const size_t start[],
const size_t count[], const ptrdiff_t stride[], TYPE *ptr );
int nc_get_vars_TYPE( int fid, int varid, const size_t start[], const size_t count[],
const ptrdiff_t stride[], TYPE *ptr );
template<>
int nc_get_vars_TYPE<short>( int fid, int varid, const size_t start[],
const size_t count[], const ptrdiff_t stride[], short *ptr )
int nc_get_vars_TYPE<short>( int fid, int varid, const size_t start[], const size_t count[],
const ptrdiff_t stride[], short *ptr )
{
return nc_get_vars_short( fid, varid, start, count, stride, ptr );
}
template<>
int nc_get_vars_TYPE<int>( int fid, int varid, const size_t start[],
const size_t count[], const ptrdiff_t stride[], int *ptr )
int nc_get_vars_TYPE<int>( int fid, int varid, const size_t start[], const size_t count[],
const ptrdiff_t stride[], int *ptr )
{
return nc_get_vars_int( fid, varid, start, count, stride, ptr );
}
template<>
int nc_get_vars_TYPE<float>( int fid, int varid, const size_t start[],
const size_t count[], const ptrdiff_t stride[], float *ptr )
int nc_get_vars_TYPE<float>( int fid, int varid, const size_t start[], const size_t count[],
const ptrdiff_t stride[], float *ptr )
{
return nc_get_vars_float( fid, varid, start, count, stride, ptr );
}
template<>
int nc_get_vars_TYPE<double>( int fid, int varid, const size_t start[],
const size_t count[], const ptrdiff_t stride[], double *ptr )
int nc_get_vars_TYPE<double>( int fid, int varid, const size_t start[], const size_t count[],
const ptrdiff_t stride[], double *ptr )
{
return nc_get_vars_double( fid, varid, start, count, stride, ptr );
}
template<class TYPE>
Array<TYPE> getVar( int fid, const std::string& var, const std::vector<int>& start,
const std::vector<int>& count, const std::vector<int>& stride )
Array<TYPE> getVar( int fid, const std::string &var, const std::vector<int> &start,
const std::vector<int> &count, const std::vector<int> &stride )
{
PROFILE_START("getVar<> (strided)");
PROFILE_START( "getVar<> (strided)" );
std::vector<size_t> var_size = getVarDim( fid, var );
for (int d=0; d<(int)var_size.size(); d++) {
if ( start[d]<0 || start[d]+stride[d]*(count[d]-1)>(int)var_size[d] ) {
int rank = Utilities::MPI(MPI_COMM_WORLD).getRank();
for ( int d = 0; d < (int) var_size.size(); d++ ) {
if ( start[d] < 0 || start[d] + stride[d] * ( count[d] - 1 ) > (int) var_size[d] ) {
int rank = Utilities::MPI( MPI_COMM_WORLD ).getRank();
char tmp[1000];
sprintf(tmp,"%i: Range exceeded array dimension:\n"
sprintf( tmp,
"%i: Range exceeded array dimension:\n"
" start[%i]=%i, count[%i]=%i, stride[%i]=%i, var_size[%i]=%i",
rank,d,start[d],d,count[d],d,stride[d],d,(int)var_size[d]);
ERROR(tmp);
rank, d, start[d], d, count[d], d, stride[d], d, (int) var_size[d] );
ERROR( tmp );
}
}
Array<TYPE> x( reverse(convert<int,size_t>(count)) );
Array<TYPE> x( reverse( convert<int, size_t>( count ) ) );
size_t startp[10], countp[10];
ptrdiff_t stridep[10];
get_stride_args( start, count, stride, startp, countp, stridep );
int err = nc_get_vars_TYPE<TYPE>( fid, getVarID(fid,var), startp, countp, stridep, x.data() );
int err =
nc_get_vars_TYPE<TYPE>( fid, getVarID( fid, var ), startp, countp, stridep, x.data() );
CHECK_NC_ERR( err );
PROFILE_STOP("getVar<> (strided)");
PROFILE_STOP( "getVar<> (strided)" );
return x.reverseDim();
}
template Array<short> getVar<short>( int, const std::string&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>& );
template Array<int> getVar<int>( int, const std::string&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>& );
template Array<float> getVar<float>( int, const std::string&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>& );
template Array<double> getVar<double>( int, const std::string&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>& );
template Array<short> getVar<short>( int, const std::string &, const std::vector<int> &,
const std::vector<int> &, const std::vector<int> & );
template Array<int> getVar<int>( int, const std::string &, const std::vector<int> &,
const std::vector<int> &, const std::vector<int> & );
template Array<float> getVar<float>( int, const std::string &, const std::vector<int> &,
const std::vector<int> &, const std::vector<int> & );
template Array<double> getVar<double>( int, const std::string &, const std::vector<int> &,
const std::vector<int> &, const std::vector<int> & );
/****************************************************
* Read an attribute *
****************************************************/
* Read an attribute *
****************************************************/
template<>
Array<double> getAtt<double>( int fid, const std::string& att )
Array<double> getAtt<double>( int fid, const std::string &att )
{
PROFILE_START("getAtt<double>");
Array<double> x( getAttDim(fid,att) );
PROFILE_START( "getAtt<double>" );
Array<double> x( getAttDim( fid, att ) );
int err = nc_get_att_double( fid, NC_GLOBAL, att.c_str(), x.data() );
CHECK_NC_ERR( err );
PROFILE_STOP("getAtt<double>");
PROFILE_STOP( "getAtt<double>" );
return x;
}
template<>
Array<std::string> getAtt<std::string>( int fid, const std::string& att )
Array<std::string> getAtt<std::string>( int fid, const std::string &att )
{
PROFILE_START("getAtt<std::string>");
char *tmp = new char[getAttDim(fid,att)[0]];
Array<std::string> x(1);
x(0) = tmp;
delete [] tmp;
PROFILE_STOP("getAtt<std::string>");
PROFILE_START( "getAtt<std::string>" );
char *tmp = new char[getAttDim( fid, att )[0]];
Array<std::string> x( 1 );
x( 0 ) = tmp;
delete[] tmp;
PROFILE_STOP( "getAtt<std::string>" );
return x;
}
/****************************************************
* Write an array to a file *
****************************************************/
std::vector<int> defDim( int fid, const std::vector<std::string>& names, const std::vector<int>& dims )
* Write an array to a file *
****************************************************/
std::vector<int> defDim(
int fid, const std::vector<std::string> &names, const std::vector<int> &dims )
{
std::vector<int> dimid(names.size(),0);
for (size_t i=0; i<names.size(); i++) {
int err = nc_def_dim( fid, names[i].c_str(), dims[i], &dimid[i]);
std::vector<int> dimid( names.size(), 0 );
for ( size_t i = 0; i < names.size(); i++ ) {
int err = nc_def_dim( fid, names[i].c_str(), dims[i], &dimid[i] );
CHECK_NC_ERR( err );
}
return dimid;
}
template<class TYPE>
void write( int fid, const std::string& var, const std::vector<int>& dimids,
const Array<TYPE>& data, const RankInfoStruct& info )
void write( int fid, const std::string &var, const std::vector<int> &dimids,
const Array<TYPE> &data, const RankInfoStruct &info )
{
// Define the variable
int varid = 0;
int err = nc_def_var( fid, var.c_str(), getType<TYPE>(), data.ndim(), dimids.data(), &varid );
int err = nc_def_var( fid, var.c_str(), getType<TYPE>(), data.ndim(), dimids.data(), &varid );
CHECK_NC_ERR( err );
// exit define mode
// exit define mode
err = nc_enddef( fid );
CHECK_NC_ERR( err );
// set the access method to use MPI/PnetCDF collective I/O
// set the access method to use MPI/PnetCDF collective I/O
err = nc_var_par_access( fid, varid, NC_INDEPENDENT );
CHECK_NC_ERR( err );
// parallel write: each process writes its subarray to the file
auto x = data.reverseDim();
std::vector<size_t> count = { data.size(0), data.size(1), data.size(2) };
std::vector<size_t> start = { info.ix*data.size(0), info.jy*data.size(1), info.kz*data.size(2) };
auto x = data.reverseDim();
std::vector<size_t> count = { data.size( 0 ), data.size( 1 ), data.size( 2 ) };
std::vector<size_t> start = { info.ix * data.size( 0 ), info.jy * data.size( 1 ),
info.kz * data.size( 2 ) };
nc_put_vara( fid, varid, start.data(), count.data(), x.data() );
}
template void write<short>( int fid, const std::string& var, const std::vector<int>& dimids, const Array<short>& data, const RankInfoStruct& info );
template void write<int>( int fid, const std::string& var, const std::vector<int>& dimids, const Array<int>& data, const RankInfoStruct& info );
template void write<float>( int fid, const std::string& var, const std::vector<int>& dimids, const Array<float>& data, const RankInfoStruct& info );
template void write<double>( int fid, const std::string& var, const std::vector<int>& dimids, const Array<double>& data, const RankInfoStruct& info );
template void write<short>( int fid, const std::string &var, const std::vector<int> &dimids,
const Array<short> &data, const RankInfoStruct &info );
template void write<int>( int fid, const std::string &var, const std::vector<int> &dimids,
const Array<int> &data, const RankInfoStruct &info );
template void write<float>( int fid, const std::string &var, const std::vector<int> &dimids,
const Array<float> &data, const RankInfoStruct &info );
template void write<double>( int fid, const std::string &var, const std::vector<int> &dimids,
const Array<double> &data, const RankInfoStruct &info );
}; // netcdf namespace
}; // namespace netcdf
#else
#endif

55
IO/netcdf.h
View File

@ -5,9 +5,8 @@
#include <vector>
#include "common/Array.h"
#include "common/MPI.h"
#include "common/Communication.h"
#include "common/MPI.h"
namespace netcdf {
@ -31,15 +30,15 @@ std::string VariableTypeName( VariableType type );
* @param filename File to open
* @param mode Open the file for reading or writing
* @param comm MPI communicator to use (MPI_COMM_WORLD: don't use parallel netcdf)
*/
int open( const std::string& filename, FileMode mode, const Utilities::MPI& comm=MPI_COMM_NULL );
*/
int open( const std::string &filename, FileMode mode, const Utilities::MPI &comm = MPI_COMM_NULL );
/*!
* @brief Close netcdf file
* @details This function closes a netcdf file
* @param fid Handle to the open file
*/
*/
void close( int fid );
@ -47,7 +46,7 @@ void close( int fid );
* @brief Read the variable names
* @details This function reads a list of the variable names in the file
* @param fid Handle to the open file
*/
*/
std::vector<std::string> getVarNames( int fid );
@ -55,7 +54,7 @@ std::vector<std::string> getVarNames( int fid );
* @brief Read the attribute names
* @details This function reads a list of the attribute names in the file
* @param fid Handle to the open file
*/
*/
std::vector<std::string> getAttNames( int fid );
@ -64,8 +63,8 @@ std::vector<std::string> getAttNames( int fid );
* @details This function returns the type for a variable
* @param fid Handle to the open file
* @param var Variable to read
*/
VariableType getVarType( int fid, const std::string& var );
*/
VariableType getVarType( int fid, const std::string &var );
/*!
@ -73,8 +72,8 @@ VariableType getVarType( int fid, const std::string& var );
* @details This function returns the type for an attribute
* @param fid Handle to the open file
* @param att Attribute to read
*/
VariableType getAttType( int fid, const std::string& att );
*/
VariableType getAttType( int fid, const std::string &att );
/*!
@ -82,8 +81,8 @@ VariableType getAttType( int fid, const std::string& att );
* @details This function returns the die for a variable
* @param fid Handle to the open file
* @param var Variable to read
*/
std::vector<size_t> getVarDim( int fid, const std::string& var );
*/
std::vector<size_t> getVarDim( int fid, const std::string &var );
/*!
@ -91,9 +90,9 @@ std::vector<size_t> getVarDim( int fid, const std::string& var );
* @details This function reads a variable with the given name from the file
* @param fid Handle to the open file
* @param var Variable to read
*/
*/
template<class TYPE>
Array<TYPE> getVar( int fid, const std::string& var );
Array<TYPE> getVar( int fid, const std::string &var );
/*!
@ -104,10 +103,10 @@ Array<TYPE> getVar( int fid, const std::string& var );
* @param start Starting corner for the read
* @param count Number of elements to read
* @param stride Stride size for the read
*/
*/
template<class TYPE>
Array<TYPE> getVar( int fid, const std::string& var, const std::vector<int>& start,
const std::vector<int>& count, const std::vector<int>& stride );
Array<TYPE> getVar( int fid, const std::string &var, const std::vector<int> &start,
const std::vector<int> &count, const std::vector<int> &stride );
/*!
@ -115,27 +114,29 @@ Array<TYPE> getVar( int fid, const std::string& var, const std::vector<int>& sta
* @details This function reads an attribute with the given name from the file
* @param fid Handle to the open file
* @param att Attribute to read
*/
*/
template<class TYPE>
Array<TYPE> getAtt( int fid, const std::string& att );
Array<TYPE> getAtt( int fid, const std::string &att );
/*!
* @brief Write the dimensions
* @details This function writes the grid dimensions to netcdf.
* @details This function writes the grid dimensions to netcdf.
* @param fid Handle to the open file
*/
std::vector<int> defDim( int fid, const std::vector<std::string>& names, const std::vector<int>& dims );
*/
std::vector<int> defDim(
int fid, const std::vector<std::string> &names, const std::vector<int> &dims );
/*!
* @brief Write a variable
* @details This function writes a variable to netcdf.
* @details This function writes a variable to netcdf.
* @param fid Handle to the open file
*/
*/
template<class TYPE>
void write( int fid, const std::string& var, const std::vector<int>& dimids, const Array<TYPE>& data, const RankInfoStruct& rank_info );
void write( int fid, const std::string &var, const std::vector<int> &dimids,
const Array<TYPE> &data, const RankInfoStruct &rank_info );
}; // netcdf namespace
}; // namespace netcdf
#endif

91
IO/silo.cpp
View File

@ -1,6 +1,6 @@
#include "IO/silo.h"
#include "common/Utilities.h"
#include "common/MPI.h"
#include "common/Utilities.h"
#include "ProfilerApp.h"
@ -10,14 +10,13 @@
#include <silo.h>
namespace silo {
namespace IO::silo {
/****************************************************
* Open/close a file *
****************************************************/
DBfile* open( const std::string& filename, FileMode mode )
* Open/close a file *
****************************************************/
DBfile *open( const std::string &filename, FileMode mode )
{
DBfile *fid = nullptr;
if ( mode == CREATE ) {
@ -29,82 +28,78 @@ DBfile* open( const std::string& filename, FileMode mode )
}
return fid;
}
void close( DBfile* fid )
{
DBClose( fid );
}
void close( DBfile *fid ) { DBClose( fid ); }
/****************************************************
* Helper functions *
****************************************************/
VariableDataType varDataType( DBfile *fid, const std::string& name )
* Helper functions *
****************************************************/
DataType varDataType( DBfile *fid, const std::string &name )
{
auto type = DBGetVarType( fid, name.c_str() );
VariableDataType type2 = VariableDataType::UNKNOWN;
auto type = DBGetVarType( fid, name.c_str() );
DataType type2 = DataType::Null;
if ( type == DB_DOUBLE )
type2 = VariableDataType::DOUBLE;
type2 = DataType::Double;
else if ( type == DB_FLOAT )
type2 = VariableDataType::FLOAT;
type2 = DataType::Float;
else if ( type == DB_INT )
type2 = VariableDataType::INT;
type2 = DataType::Int;
return type2;
}
/****************************************************
* Write/read a uniform mesh to silo *
****************************************************/
void readUniformMesh( DBfile* fid, const std::string& meshname,
std::vector<double>& range, std::vector<int>& N )
* Write/read a uniform mesh to silo *
****************************************************/
void readUniformMesh(
DBfile *fid, const std::string &meshname, std::vector<double> &range, std::vector<int> &N )
{
DBquadmesh* mesh = DBGetQuadmesh( fid, meshname.c_str() );
int ndim = mesh->ndims;
range.resize(2*ndim);
N.resize(ndim);
for (int d=0; d<ndim; d++) {
N[d] = mesh->dims[d]-1;
range[2*d+0] = mesh->min_extents[d];
range[2*d+1] = mesh->max_extents[d];
DBquadmesh *mesh = DBGetQuadmesh( fid, meshname.c_str() );
int ndim = mesh->ndims;
range.resize( 2 * ndim );
N.resize( ndim );
for ( int d = 0; d < ndim; d++ ) {
N[d] = mesh->dims[d] - 1;
range[2 * d + 0] = mesh->min_extents[d];
range[2 * d + 1] = mesh->max_extents[d];
}
DBFreeQuadmesh( mesh );
}
/****************************************************
* Write a multimesh *
****************************************************/
void writeMultiMesh( DBfile* fid, const std::string& meshname,
const std::vector<std::string>& meshNames,
const std::vector<int>& meshTypes )
* Write a multimesh *
****************************************************/
void writeMultiMesh( DBfile *fid, const std::string &meshname,
const std::vector<std::string> &meshNames, const std::vector<int> &meshTypes )
{
std::vector<char*> meshnames(meshNames.size());
std::vector<char *> meshnames( meshNames.size() );
for ( size_t i = 0; i < meshNames.size(); ++i )
meshnames[i] = (char *) meshNames[i].c_str();
std::string tree_name = meshname + "_tree";
DBoptlist *optList = DBMakeOptlist( 1 );
DBAddOption( optList, DBOPT_MRGTREE_NAME, (char *) tree_name.c_str() );
DBPutMultimesh( fid, meshname.c_str(), meshNames.size(), meshnames.data(), (int*) meshTypes.data(), nullptr );
DBPutMultimesh( fid, meshname.c_str(), meshNames.size(), meshnames.data(),
(int *) meshTypes.data(), nullptr );
DBFreeOptlist( optList );
}
/****************************************************
* Write a multivariable *
****************************************************/
void writeMultiVar( DBfile* fid, const std::string& varname,
const std::vector<std::string>& varNames,
const std::vector<int>& varTypes )
* Write a multivariable *
****************************************************/
void writeMultiVar( DBfile *fid, const std::string &varname,
const std::vector<std::string> &varNames, const std::vector<int> &varTypes )
{
std::vector<char*> varnames(varNames.size(),nullptr);
for (size_t j=0; j<varNames.size(); j++)
varnames[j] = const_cast<char*>(varNames[j].c_str());
DBPutMultivar( fid, varname.c_str(), varNames.size(), varnames.data(), (int*) varTypes.data(), nullptr );
std::vector<char *> varnames( varNames.size(), nullptr );
for ( size_t j = 0; j < varNames.size(); j++ )
varnames[j] = const_cast<char *>( varNames[j].c_str() );
DBPutMultivar(
fid, varname.c_str(), varNames.size(), varnames.data(), (int *) varTypes.data(), nullptr );
}
}; // silo namespace
}; // namespace IO::silo
#else

120
IO/silo.h
View File

@ -1,32 +1,28 @@
#ifndef SILO_INTERFACE
#define SILO_INTERFACE
#include <array>
#include <string>
#include <vector>
#include <array>
#include "IO/Mesh.h"
#include "common/Array.h"
#include "common/MPI.h"
#include "common/Communication.h"
#include "common/MPI.h"
#ifdef USE_SILO
#include <silo.h>
#include <silo.h>
#else
typedef int DBfile;
typedef int DBfile;
#endif
namespace silo {
namespace IO::silo {
enum FileMode { READ, WRITE, CREATE };
enum class VariableType : int { NodeVariable=1, EdgeVariable=2, SurfaceVariable=2, VolumeVariable=3, NullVariable=0 };
enum class VariableDataType { DOUBLE, FLOAT, INT, UNKNOWN };
/*!
* @brief Open silo file
@ -34,16 +30,16 @@ enum class VariableDataType { DOUBLE, FLOAT, INT, UNKNOWN };
* @param[in] filename File to open
* @param[in] mode Open the file for reading or writing
* @return This function returns a handle to the file
*/
DBfile* open( const std::string& filename, FileMode mode );
*/
DBfile *open( const std::string &filename, FileMode mode );
/*!
* @brief Close silo file
* @details This function closes a silo file
* @param[in] fid Handle to the open file
*/
void close( DBfile* fid );
*/
void close( DBfile *fid );
/*!
@ -51,8 +47,8 @@ void close( DBfile* fid );
* @details This function returns the type of variable data
* @param[in] fid Handle to the open file
* @param[in] name Name of variable
*/
VariableDataType varDataType( DBfile *dbfile, const std::string& name );
*/
DataType varDataType( DBfile *dbfile, const std::string &name );
/*!
@ -61,9 +57,9 @@ VariableDataType varDataType( DBfile *dbfile, const std::string& name );
* @param[in] fid Handle to the open file
* @param[in] varname Variable name
* @param[in] data Data to write
*/
*/
template<class TYPE>
void write( DBfile* fid, const std::string& varname, const std::vector<TYPE>& data );
void write( DBfile *fid, const std::string &varname, const std::vector<TYPE> &data );
/*!
@ -72,9 +68,9 @@ void write( DBfile* fid, const std::string& varname, const std::vector<TYPE>& da
* @param[in] fid Handle to the open file
* @param[in] varname Variable name
* @return Data read
*/
*/
template<class TYPE>
std::vector<TYPE> read( DBfile* fid, const std::string& varname );
std::vector<TYPE> read( DBfile *fid, const std::string &varname );
/*!
@ -84,10 +80,10 @@ std::vector<TYPE> read( DBfile* fid, const std::string& varname );
* @param[in] meshname Mesh name
* @param[in] range Range of mesh { xmin, xmax, ymin, ymax, zmin, zmax }
* @param[in] N Number of cells in each direction
*/
*/
template<int NDIM>
void writeUniformMesh( DBfile* fid, const std::string& meshname,
const std::array<double,2*NDIM>& range, const std::array<int,NDIM>& N );
void writeUniformMesh( DBfile *fid, const std::string &meshname,
const std::array<double, 2 * NDIM> &range, const std::array<int, NDIM> &N );
/*!
@ -97,9 +93,9 @@ void writeUniformMesh( DBfile* fid, const std::string& meshname,
* @param[in] meshname Mesh name
* @param[out] range Range of mesh { xmin, xmax, ymin, ymax, zmin, zmax }
* @param[out] N Number of cells in each direction
*/
void readUniformMesh( DBfile* fid, const std::string& meshname,
std::vector<double>& range, std::vector<int>& N );
*/
void readUniformMesh(
DBfile *fid, const std::string &meshname, std::vector<double> &range, std::vector<int> &N );
/*!
@ -111,10 +107,11 @@ void readUniformMesh( DBfile* fid, const std::string& meshname,
* @param[in] varname Variable name
* @param[in] data Variable data
* @param[in] type Variable type
*/
template< int NDIM, class TYPE >
void writeUniformMeshVariable( DBfile* fid, const std::string& meshname, const std::array<int,NDIM>& N,
const std::string& varname, const Array<TYPE>& data, VariableType type );
*/
template<int NDIM, class TYPE>
void writeUniformMeshVariable( DBfile *fid, const std::string &meshname,
const std::array<int, NDIM> &N, const std::string &varname, const Array<TYPE> &data,
VariableType type );
/*!
@ -123,9 +120,9 @@ void writeUniformMeshVariable( DBfile* fid, const std::string& meshname, const s
* @param[in] fid Handle to the open file
* @param[in] varname Variable name
* @return Variable data
*/
*/
template<class TYPE>
Array<TYPE> readUniformMeshVariable( DBfile* fid, const std::string& varname );
Array<TYPE> readUniformMeshVariable( DBfile *fid, const std::string &varname );
/*!
@ -136,10 +133,10 @@ Array<TYPE> readUniformMeshVariable( DBfile* fid, const std::string& varname );
* @param[in] ndim Number of dimensions
* @param[in] N Number of points
* @param[in] coords Coordinates of the points
*/
*/
template<class TYPE>
void writePointMesh( DBfile* fid, const std::string& meshname,
int ndim, int N, const TYPE *coords[] );
void writePointMesh(
DBfile *fid, const std::string &meshname, int ndim, int N, const TYPE *coords[] );
/*!
@ -147,10 +144,10 @@ void writePointMesh( DBfile* fid, const std::string& meshname,
* @details This function reads a pointmesh from silo
* @param[in] fid Handle to the open file
* @param[in] meshname Mesh name
* @return Returns the coordinates as a N x ndim array
*/
* @return Returns the coordinates as a N x ndim array
*/
template<class TYPE>
Array<TYPE> readPointMesh( DBfile* fid, const std::string& meshname );
Array<TYPE> readPointMesh( DBfile *fid, const std::string &meshname );
/*!
@ -160,10 +157,10 @@ Array<TYPE> readPointMesh( DBfile* fid, const std::string& meshname );
* @param[in] meshname Mesh name
* @param[in] varname Variable name
* @param[in] data Variable data
*/
*/
template<class TYPE>
void writePointMeshVariable( DBfile* fid, const std::string& meshname,
const std::string& varname, const Array<TYPE>& data );
void writePointMeshVariable(
DBfile *fid, const std::string &meshname, const std::string &varname, const Array<TYPE> &data );
/*!
@ -172,9 +169,9 @@ void writePointMeshVariable( DBfile* fid, const std::string& meshname,
* @param[in] fid Handle to the open file
* @param[in] varname Variable name
* @return Variable data
*/
*/
template<class TYPE>
Array<TYPE> readPointMeshVariable( DBfile* fid, const std::string& varname );
Array<TYPE> readPointMeshVariable( DBfile *fid, const std::string &varname );
/*!
@ -188,10 +185,10 @@ Array<TYPE> readPointMeshVariable( DBfile* fid, const std::string& varname );
* @param[in] coords Coordinates of the points
* @param[in] N_tri Number of triangles
* @param[in] tri Coordinates of the points
*/
*/
template<class TYPE>
void writeTriMesh( DBfile* fid, const std::string& meshname,
int ndim, int ndim_tri, int N, const TYPE *coords[], int N_tri, const int *tri[] );
void writeTriMesh( DBfile *fid, const std::string &meshname, int ndim, int ndim_tri, int N,
const TYPE *coords[], int N_tri, const int *tri[] );
/*!
@ -201,9 +198,9 @@ void writeTriMesh( DBfile* fid, const std::string& meshname,
* @param[in] meshname Mesh name
* @param[in] coords Coordinates of the points
* @param[in] tri Coordinates of the points
*/
*/
template<class TYPE>
void readTriMesh( DBfile* fid, const std::string& meshname, Array<TYPE>& coords, Array<int>& tri );
void readTriMesh( DBfile *fid, const std::string &meshname, Array<TYPE> &coords, Array<int> &tri );
/*!
@ -215,10 +212,10 @@ void readTriMesh( DBfile* fid, const std::string& meshname, Array<TYPE>& coords,
* @param[in] varname Variable name
* @param[in] data Variable data
* @param[in] type Variable type
*/
*/
template<class TYPE>
void writeTriMeshVariable( DBfile* fid, int ndim, const std::string& meshname,
const std::string& varname, const Array<TYPE>& data, VariableType type );
void writeTriMeshVariable( DBfile *fid, int ndim, const std::string &meshname,
const std::string &varname, const Array<TYPE> &data, VariableType type );
/*!
@ -227,9 +224,9 @@ void writeTriMeshVariable( DBfile* fid, int ndim, const std::string& meshname,
* @param[in] fid Handle to the open file
* @param[in] varname Variable name
* @return Variable data
*/
*/
template<class TYPE>
Array<TYPE> readTriMeshVariable( DBfile* fid, const std::string& varname );
Array<TYPE> readTriMeshVariable( DBfile *fid, const std::string &varname );
/*!
@ -239,10 +236,9 @@ Array<TYPE> readTriMeshVariable( DBfile* fid, const std::string& varname );
* @param[in] meshname Mesh name
* @param[in] subMeshNames Names of the sub meshes in the form "filename:meshname"
* @param[in] subMeshTypes Type of each submesh
*/
void writeMultiMesh( DBfile* fid, const std::string& meshname,
const std::vector<std::string>& subMeshNames,
const std::vector<int>& subMeshTypes );
*/
void writeMultiMesh( DBfile *fid, const std::string &meshname,
const std::vector<std::string> &subMeshNames, const std::vector<int> &subMeshTypes );
/*!
@ -255,14 +251,12 @@ void writeMultiMesh( DBfile* fid, const std::string& meshname,
* @param[in] subVarTypes Type of each submesh
* @param[in] ndim Dimension of variable (used to determine suffix)
* @param[in] nvar Number of subvariables (used to determine suffix)
*/
void writeMultiVar( DBfile* fid, const std::string& varname,
const std::vector<std::string>& subVarNames,
const std::vector<int>& subVarTypes );
*/
void writeMultiVar( DBfile *fid, const std::string &varname,
const std::vector<std::string> &subVarNames, const std::vector<int> &subVarTypes );
}; // silo namespace
}; // namespace IO::silo
#endif
#include "IO/silo.hpp"

4
IO/silo.hpp
View File

@ -13,7 +13,7 @@
#include <silo.h>
namespace silo {
namespace IO::silo {
/****************************************************
@ -413,7 +413,7 @@ Array<TYPE> readTriMeshVariable( DBfile *fid, const std::string &varname )
}
}; // namespace silo
}; // namespace IO::silo
#endif

1
README.titan
View File

@ -26,7 +26,6 @@ cmake \
-D CMAKE_CXX_COMPILER:PATH=CC \
-D CFLAGS="-DCBUB" \
-D CXXFLAGS="-DCBUB" \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=aprun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Debug \

362
cmake/FindMPI.cmake
View File

@ -1,362 +0,0 @@
# - Message Passing Interface (MPI) module.
#
# The Message Passing Interface (MPI) is a library used to write
# high-performance parallel applications that use message passing, and
# is typically deployed on a cluster. MPI is a standard interface
# (defined by the MPI forum) for which many implementations are
# available. All of these implementations have somewhat different
# compilation approaches (different include paths, libraries to link
# against, etc.), and this module tries to smooth out those differences.
#
# This module will set the following variables:
# MPI_FOUND TRUE if we have found MPI
# MPI_COMPILE_FLAGS Compilation flags for MPI programs
# MPI_INCLUDE_PATH Include path(s) for MPI header
# MPI_LINK_FLAGS Linking flags for MPI programs
# MPI_LIBRARY First MPI library to link against (cached)
# MPI_EXTRA_LIBRARY Extra MPI libraries to link against (cached)
# MPI_LIBRARIES All libraries to link MPI programs against
# MPIEXEC Executable for running MPI programs
# MPIEXEC_NUMPROC_FLAG Flag to pass to MPIEXEC before giving it the
# number of processors to run on
# MPIEXEC_PREFLAGS Flags to pass to MPIEXEC directly before the
# executable to run.
# MPIEXEC_POSTFLAGS Flags to pass to MPIEXEC after all other flags.
#
# This module will attempt to auto-detect these settings, first by
# looking for a MPI compiler, which many MPI implementations provide
# as a pass-through to the native compiler to simplify the compilation
# of MPI programs. The MPI compiler is stored in the cache variable
# MPI_COMPILER, and will attempt to look for commonly-named drivers
# mpic++, mpicxx, mpiCC, or mpicc. If the compiler driver is found and
# recognized, it will be used to set all of the module variables. To
# skip this auto-detection, set MPI_LIBRARY and MPI_INCLUDE_PATH in
# the CMake cache.
#
# If no compiler driver is found or the compiler driver is not
# recognized, this module will then search for common include paths
# and library names to try to detect MPI.
#
# If CMake initially finds a different MPI than was intended, and you
# want to use the MPI compiler auto-detection for a different MPI
# implementation, set MPI_COMPILER to the MPI compiler driver you want
# to use (e.g., mpicxx) and then set MPI_LIBRARY to the string
# MPI_LIBRARY-NOTFOUND. When you re-configure, auto-detection of MPI
# will run again with the newly-specified MPI_COMPILER.
#
# When using MPIEXEC to execute MPI applications, you should typically
# use all of the MPIEXEC flags as follows:
# ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} PROCS ${MPIEXEC_PREFLAGS} EXECUTABLE
# ${MPIEXEC_POSTFLAGS} ARGS
# where PROCS is the number of processors on which to execute the program,
# EXECUTABLE is the MPI program, and ARGS are the arguments to pass to the
# MPI program.
#=============================================================================
# Copyright 2001-2009 Kitware, Inc.
#
# Distributed under the OSI-approved BSD License (the "License");
# see accompanying file Copyright.txt for details.
#
# This software is distributed WITHOUT ANY WARRANTY; without even the
# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the License for more information.
#=============================================================================
# (To distribute this file outside of CMake, substitute the full
# License text for the above reference.)
# This module is maintained by David Partyka <dave.partyka@kitware.com>.
# A set of directories to search through in addition to the standard system paths
# that find_program will search through.
# Microsoft HPC SDK is automatically added to the system path
# Argonne National Labs MPICH2 sets a registry key that we can use.
set(_MPI_PACKAGE_DIR
mpi
mpich
openmpi
lib/mpi
lib/mpich
lib/openmpi
"MPICH/SDK"
"Microsoft Compute Cluster Pack"
"Microsoft HPC Pack 2008 R2"
)
set(_MPI_PREFIX_PATH)
if(WIN32)
list(APPEND _MPI_PREFIX_PATH "[HKEY_LOCAL_MACHINE\\SOFTWARE\\MPICH\\SMPD;binary]/..")
list(APPEND _MPI_PREFIX_PATH "[HKEY_LOCAL_MACHINE\\SOFTWARE\\MPICH2;Path]")
endif()
foreach(SystemPrefixDir ${CMAKE_SYSTEM_PREFIX_PATH})
foreach(MpiPackageDir ${_MPI_PREFIX_PATH})
if(EXISTS ${SystemPrefixDir}/${MpiPackageDir})
list(APPEND _MPI_PREFIX_PATH "${SystemPrefixDir}/${MpiPackageDir}")
endif()
endforeach(MpiPackageDir)
endforeach(SystemPrefixDir)
# Most mpi distros have some form of mpiexec which gives us something we can reliably look for.
find_program(MPIEXEC
NAMES mpiexec mpirun lamexec
PATHS ${_MPI_PREFIX_PATH}
PATH_SUFFIXES bin
DOC "Executable for running MPI programs."
)
# call get_filename_component twice to remove mpiexec and the directory it exists in (typically bin).
# This gives us a fairly reliable base directory to search for /bin /lib and /include from.
get_filename_component(_MPI_BASE_DIR "${MPIEXEC}" PATH)
get_filename_component(_MPI_BASE_DIR "${_MPI_BASE_DIR}" PATH)
# If there is an mpi compiler find it and interogate (farther below) it for the include
# and lib dirs otherwise we will continue to search from ${_MPI_BASE_DIR}.
find_program(MPI_COMPILER
NAMES mpic++ mpicxx mpiCC mpicc
HINTS "${_MPI_BASE_DIR}"
PATH_SUFFIXES bin
DOC "MPI compiler. Used only to detect MPI compilation flags.")
mark_as_advanced(MPI_COMPILER)
set(MPIEXEC_NUMPROC_FLAG "-np" CACHE STRING "Flag used by MPI to specify the number of processes for MPIEXEC; the next option will be the number of processes.")
set(MPIEXEC_PREFLAGS "" CACHE STRING "These flags will be directly before the executable that is being run by MPIEXEC.")
set(MPIEXEC_POSTFLAGS "" CACHE STRING "These flags will come after all flags given to MPIEXEC.")
set(MPIEXEC_MAX_NUMPROCS "2" CACHE STRING "Maximum number of processors available to run MPI applications.")
mark_as_advanced(MPIEXEC MPIEXEC_NUMPROC_FLAG MPIEXEC_PREFLAGS
MPIEXEC_POSTFLAGS MPIEXEC_MAX_NUMPROCS)
if (MPI_INCLUDE_PATH AND MPI_LIBRARY)
# Do nothing: we already have MPI_INCLUDE_PATH and MPI_LIBRARY in
# the cache, and we don't want to override those settings.
elseif (MPI_COMPILER)
# Check whether the -showme:compile option works. This indicates
# that we have either Open MPI or a newer version of LAM-MPI, and
# implies that -showme:link will also work.
# Note that Windows distros do not have an mpi compiler to interogate.
exec_program(${MPI_COMPILER}
ARGS -showme:compile
OUTPUT_VARIABLE MPI_COMPILE_CMDLINE
RETURN_VALUE MPI_COMPILER_RETURN)
if (MPI_COMPILER_RETURN EQUAL 0)
# If we appear to have -showme:compile, then we should also have
# -showme:link. Try it.
exec_program(${MPI_COMPILER}
ARGS -showme:link
OUTPUT_VARIABLE MPI_LINK_CMDLINE
RETURN_VALUE MPI_COMPILER_RETURN)
# Note that we probably have -showme:incdirs and -showme:libdirs
# as well.
set(MPI_COMPILER_MAY_HAVE_INCLIBDIRS TRUE)
endif (MPI_COMPILER_RETURN EQUAL 0)
if (MPI_COMPILER_RETURN EQUAL 0)
# Do nothing: we have our command lines now
else (MPI_COMPILER_RETURN EQUAL 0)
# Older versions of LAM-MPI have "-showme". Try it.
exec_program(${MPI_COMPILER}
ARGS -showme
OUTPUT_VARIABLE MPI_COMPILE_CMDLINE
RETURN_VALUE MPI_COMPILER_RETURN)
endif (MPI_COMPILER_RETURN EQUAL 0)
if (MPI_COMPILER_RETURN EQUAL 0)
# Do nothing: we have our command lines now
else (MPI_COMPILER_RETURN EQUAL 0)
# MPICH uses "-show". Try it.
exec_program(${MPI_COMPILER}
ARGS -show
OUTPUT_VARIABLE MPI_COMPILE_CMDLINE
RETURN_VALUE MPI_COMPILER_RETURN)
endif (MPI_COMPILER_RETURN EQUAL 0)
if (MPI_COMPILER_RETURN EQUAL 0)
# We have our command lines, but we might need to copy
# MPI_COMPILE_CMDLINE into MPI_LINK_CMDLINE, if the underlying
if (NOT MPI_LINK_CMDLINE)
SET(MPI_LINK_CMDLINE ${MPI_COMPILE_CMDLINE})
endif (NOT MPI_LINK_CMDLINE)
else (MPI_COMPILER_RETURN EQUAL 0)
message(STATUS "Unable to determine MPI from MPI driver ${MPI_COMPILER}")
endif (MPI_COMPILER_RETURN EQUAL 0)
endif (MPI_INCLUDE_PATH AND MPI_LIBRARY)
if (MPI_INCLUDE_PATH AND MPI_LIBRARY)
# Do nothing: we already have MPI_INCLUDE_PATH and MPI_LIBRARY in
# the cache, and we don't want to override those settings.
elseif (MPI_COMPILE_CMDLINE)
# Extract compile flags from the compile command line.
string(REGEX MATCHALL "(^| )-[Df]([^\" ]+|\"[^\"]+\")" MPI_ALL_COMPILE_FLAGS "${MPI_COMPILE_CMDLINE}")
set(MPI_COMPILE_FLAGS_WORK)
foreach(FLAG ${MPI_ALL_COMPILE_FLAGS})
if (MPI_COMPILE_FLAGS_WORK)
set(MPI_COMPILE_FLAGS_WORK "${MPI_COMPILE_FLAGS_WORK} ${FLAG}")
else(MPI_COMPILE_FLAGS_WORK)
set(MPI_COMPILE_FLAGS_WORK ${FLAG})
endif(MPI_COMPILE_FLAGS_WORK)
endforeach(FLAG)
# Extract include paths from compile command line
string(REGEX MATCHALL "(^| )-I([^\" ]+|\"[^\"]+\")" MPI_ALL_INCLUDE_PATHS "${MPI_COMPILE_CMDLINE}")
set(MPI_INCLUDE_PATH_WORK)
foreach(IPATH ${MPI_ALL_INCLUDE_PATHS})
string(REGEX REPLACE "^ ?-I" "" IPATH ${IPATH})
string(REGEX REPLACE "//" "/" IPATH ${IPATH})
list(APPEND MPI_INCLUDE_PATH_WORK ${IPATH})
endforeach(IPATH)
if (NOT MPI_INCLUDE_PATH_WORK)
if (MPI_COMPILER_MAY_HAVE_INCLIBDIRS)
# The compile command line didn't have any include paths on it,
# but we may have -showme:incdirs. Use it.
exec_program(${MPI_COMPILER}
ARGS -showme:incdirs
OUTPUT_VARIABLE MPI_INCLUDE_PATH_WORK
RETURN_VALUE MPI_COMPILER_RETURN)
separate_arguments(MPI_INCLUDE_PATH_WORK)
endif (MPI_COMPILER_MAY_HAVE_INCLIBDIRS)
endif (NOT MPI_INCLUDE_PATH_WORK)
if (NOT MPI_INCLUDE_PATH_WORK)
# If all else fails, just search for mpi.h in the normal include
# paths.
find_path(MPI_INCLUDE_PATH mpi.h
HINTS ${_MPI_BASE_DIR} ${_MPI_PREFIX_PATH}
PATH_SUFFIXES include
)
set(MPI_INCLUDE_PATH_WORK ${MPI_INCLUDE_PATH})
endif (NOT MPI_INCLUDE_PATH_WORK)
# Extract linker paths from the link command line
string(REGEX MATCHALL "(^| |-Wl,)-L([^\" ]+|\"[^\"]+\")" MPI_ALL_LINK_PATHS "${MPI_LINK_CMDLINE}")
set(MPI_LINK_PATH)
foreach(LPATH ${MPI_ALL_LINK_PATHS})
string(REGEX REPLACE "^(| |-Wl,)-L" "" LPATH ${LPATH})
string(REGEX REPLACE "//" "/" LPATH ${LPATH})
list(APPEND MPI_LINK_PATH ${LPATH})
endforeach(LPATH)
if (NOT MPI_LINK_PATH)
if (MPI_COMPILER_MAY_HAVE_INCLIBDIRS)
# The compile command line didn't have any linking paths on it,
# but we may have -showme:libdirs. Use it.
exec_program(${MPI_COMPILER}
ARGS -showme:libdirs
OUTPUT_VARIABLE MPI_LINK_PATH
RETURN_VALUE MPI_COMPILER_RETURN)
separate_arguments(MPI_LINK_PATH)
endif (MPI_COMPILER_MAY_HAVE_INCLIBDIRS)
endif (NOT MPI_LINK_PATH)
# Extract linker flags from the link command line
string(REGEX MATCHALL "(^| )-Wl,([^\" ]+|\"[^\"]+\")" MPI_ALL_LINK_FLAGS "${MPI_LINK_CMDLINE}")
set(MPI_LINK_FLAGS_WORK)
foreach(FLAG ${MPI_ALL_LINK_FLAGS})
if (MPI_LINK_FLAGS_WORK)
set(MPI_LINK_FLAGS_WORK "${MPI_LINK_FLAGS_WORK} ${FLAG}")
else(MPI_LINK_FLAGS_WORK)
set(MPI_LINK_FLAGS_WORK ${FLAG})
endif(MPI_LINK_FLAGS_WORK)
endforeach(FLAG)
if ( MPI_LINK_FLAGS_WORK )
string ( REGEX REPLACE "^ " "" MPI_LINK_FLAGS_WORK ${MPI_LINK_FLAGS_WORK} )
endif ()
# Extract the set of libraries to link against from the link command
# line
string(REGEX MATCHALL "(^| )-l([^\" ]+|\"[^\"]+\")" MPI_LIBNAMES "${MPI_LINK_CMDLINE}")
# Determine full path names for all of the libraries that one needs
# to link against in an MPI program
set(MPI_LIBRARIES)
foreach(LIB ${MPI_LIBNAMES})
string(REGEX REPLACE "^ ?-l" "" LIB ${LIB})
set(MPI_LIB "MPI_LIB-NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
find_library(MPI_LIB ${LIB} HINTS ${MPI_LINK_PATH})
if (MPI_LIB)
list(APPEND MPI_LIBRARIES ${MPI_LIB})
elseif (NOT MPI_FIND_QUIETLY)
message(WARNING "Unable to find MPI library ${LIB}")
endif ()
endforeach(LIB)
set(MPI_LIB "MPI_LIB-NOTFOUND" CACHE INTERNAL "Scratch variable for MPI detection" FORCE)
# Chop MPI_LIBRARIES into the old-style MPI_LIBRARY and
# MPI_EXTRA_LIBRARY.
list(LENGTH MPI_LIBRARIES MPI_NUMLIBS)
list(LENGTH MPI_LIBNAMES MPI_NUMLIBS_EXPECTED)
if (MPI_NUMLIBS EQUAL MPI_NUMLIBS_EXPECTED)
list(GET MPI_LIBRARIES 0 MPI_LIBRARY_WORK)
set(MPI_LIBRARY ${MPI_LIBRARY_WORK} CACHE FILEPATH "MPI library to link against" FORCE)
else (MPI_NUMLIBS EQUAL MPI_NUMLIBS_EXPECTED)
set(MPI_LIBRARY "MPI_LIBRARY-NOTFOUND" CACHE FILEPATH "MPI library to link against" FORCE)
endif (MPI_NUMLIBS EQUAL MPI_NUMLIBS_EXPECTED)
if (MPI_NUMLIBS GREATER 1)
set(MPI_EXTRA_LIBRARY_WORK ${MPI_LIBRARIES})
list(REMOVE_AT MPI_EXTRA_LIBRARY_WORK 0)
set(MPI_EXTRA_LIBRARY ${MPI_EXTRA_LIBRARY_WORK} CACHE STRING "Extra MPI libraries to link against" FORCE)
else (MPI_NUMLIBS GREATER 1)
set(MPI_EXTRA_LIBRARY "MPI_EXTRA_LIBRARY-NOTFOUND" CACHE STRING "Extra MPI libraries to link against" FORCE)
endif (MPI_NUMLIBS GREATER 1)
# Set up all of the appropriate cache entries
set(MPI_COMPILE_FLAGS ${MPI_COMPILE_FLAGS_WORK} CACHE STRING "MPI compilation flags" FORCE)
set(MPI_INCLUDE_PATH ${MPI_INCLUDE_PATH_WORK} CACHE STRING "MPI include path" FORCE)
set(MPI_LINK_FLAGS ${MPI_LINK_FLAGS_WORK} CACHE STRING "MPI linking flags" FORCE)
else (MPI_COMPILE_CMDLINE)
# No MPI compiler to interogate so attempt to find everything with find functions.
find_path(MPI_INCLUDE_PATH mpi.h
HINTS ${_MPI_BASE_DIR} ${_MPI_PREFIX_PATH}
PATH_SUFFIXES include Inc
)
# Decide between 32-bit and 64-bit libraries for Microsoft's MPI
if("${CMAKE_SIZEOF_VOID_P}" EQUAL 8)
set(MS_MPI_ARCH_DIR amd64)
else()
set(MS_MPI_ARCH_DIR i386)
endif()
find_library(MPI_LIBRARY
NAMES mpi mpich msmpi
HINTS ${_MPI_BASE_DIR} ${_MPI_PREFIX_PATH}
PATH_SUFFIXES lib lib/${MS_MPI_ARCH_DIR} Lib Lib/${MS_MPI_ARCH_DIR}
)
find_library(MPI_EXTRA_LIBRARY
NAMES mpi++
HINTS ${_MPI_BASE_DIR} ${_MPI_PREFIX_PATH}
PATH_SUFFIXES lib
DOC "Extra MPI libraries to link against.")
set(MPI_COMPILE_FLAGS "" CACHE STRING "MPI compilation flags")
set(MPI_LINK_FLAGS "" CACHE STRING "MPI linking flags")
endif (MPI_INCLUDE_PATH AND MPI_LIBRARY)
# Set up extra variables to conform to
if (MPI_EXTRA_LIBRARY)
set(MPI_LIBRARIES ${MPI_LIBRARY} ${MPI_EXTRA_LIBRARY})
else (MPI_EXTRA_LIBRARY)
set(MPI_LIBRARIES ${MPI_LIBRARY})
endif (MPI_EXTRA_LIBRARY)
if (MPI_INCLUDE_PATH AND MPI_LIBRARY)
set(MPI_FOUND TRUE)
else (MPI_INCLUDE_PATH AND MPI_LIBRARY)
set(MPI_FOUND FALSE)
endif (MPI_INCLUDE_PATH AND MPI_LIBRARY)
#include("${CMAKE_CURRENT_LIST_DIR}/FindPackageHandleStandardArgs.cmake")
# handle the QUIETLY and REQUIRED arguments
#find_package_handle_standard_args(MPI DEFAULT_MSG MPI_LIBRARY MPI_INCLUDE_PATH)
mark_as_advanced(MPI_INCLUDE_PATH MPI_COMPILE_FLAGS MPI_LINK_FLAGS MPI_LIBRARY
MPI_EXTRA_LIBRARY)
# unset to cleanup namespace
unset(_MPI_PACKAGE_DIR)
unset(_MPI_PREFIX_PATH)
unset(_MPI_BASE_DIR)

41
cmake/Find_TIMER.cmake
View File

@ -4,7 +4,7 @@
# CONFIGURE_TIMER( DEFAULT_USE_TIMER NULL_TIMER_DIR )
# This function assumes that USE_TIMER is set to indicate if the timer should be used
# If USE_TIMER is set, TIMER_DIRECTORY specifies the install path for the timer
# If USE_TIMER is not set we will create a summy timer that does nothing.
# If USE_TIMER is not set we will create a dummy timer that does nothing.
# The input argument DEFAULT_USE_TIMER specifies if the timer library is included by default.
# The input argument NULL_TIMER_DIR specifies the location to install the dummy timer.
# If it is an empty string, the default install path "${CMAKE_CURRENT_BINARY_DIR}/null_timer" is used.
@ -13,7 +13,7 @@
# TIMER_CXXFLAGS - C++ flags for the timer library
# TIMER_LDFLAGS - Linker flags to link the timer library
# TIMER_LDLIBS - Linker libraries to link the timer library
FUNCTION( CONFIGURE_TIMER DEFAULT_USE_TIMER NULL_TIMER_DIR )
FUNCTION( CONFIGURE_TIMER DEFAULT_USE_TIMER NULL_TIMER_DIR QUIET )
# Determine if we want to use the timer utility
CHECK_ENABLE_FLAG( USE_TIMER ${DEFAULT_USE_TIMER} )
SET( TIMER_INCLUDE )
@ -33,20 +33,23 @@ FUNCTION( CONFIGURE_TIMER DEFAULT_USE_TIMER NULL_TIMER_DIR )
FIND_LIBRARY( TIMER_LIBS NAMES timerutility PATHS ${TIMER_DIRECTORY}/lib NO_DEFAULT_PATH )
SET( TIMER_INCLUDE ${TIMER_DIRECTORY}/include )
SET( TIMER_CXXFLAGS "-DUSE_TIMER -I${TIMER_DIRECTORY}/include" )
SET( TIMER_LDFLAGS -L${TIMER_DIRECTORY}/lib )
SET( TIMER_LDLIBS -ltimerutility )
SET( TIMER_LDFLAGS )
SET( TIMER_LDLIBS "${TIMER_LIBS}" )
ELSE()
MESSAGE( FATAL_ERROR "Default search for TIMER is not yet supported. Use -D TIMER_DIRECTORY=" )
ENDIF()
SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_RPATH} "${TIMER_DIRECTORY}/lib" PARENT_SCOPE )
SET( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_RPATH} "${TIMER_DIRECTORY}/lib" PARENT_SCOPE )
INCLUDE_DIRECTORIES( "${TIMER_INCLUDE}" )
ADD_DEFINITIONS( -DUSE_TIMER )
MESSAGE( "Using timer utility" )
MESSAGE( " TIMER_LIBRARIES = ${TIMER_LIBS}" )
IF ( NOT QUIET )
MESSAGE( STATUS "Using timer utility" )
MESSAGE( STATUS " TIMER_LIBRARIES = ${TIMER_LIBS}" )
ENDIF()
ELSE()
IF ( "${NULL_TIMER_DIR}" STREQUAL "" )
SET( NULL_TIMER_DIR "${CMAKE_CURRENT_BINARY_DIR}/null_timer" )
ENDIF()
# Write ProfilerApp.h
FILE(WRITE "${NULL_TIMER_DIR}/ProfilerApp.h" "#define PROFILE_START(...) do {} while(0)\n" )
FILE(APPEND "${NULL_TIMER_DIR}/ProfilerApp.h" "#define PROFILE_STOP(...) do {} while(0)\n" )
FILE(APPEND "${NULL_TIMER_DIR}/ProfilerApp.h" "#define PROFILE_START2(...) do {} while(0)\n" )
@ -61,9 +64,25 @@ FUNCTION( CONFIGURE_TIMER DEFAULT_USE_TIMER NULL_TIMER_DIR )
FILE(APPEND "${NULL_TIMER_DIR}/ProfilerApp.h" "#define PROFILE_DISABLE_TRACE() do {} while(0)\n" )
FILE(APPEND "${NULL_TIMER_DIR}/ProfilerApp.h" "#define PROFILE_ENABLE_MEMORY() do {} while(0)\n" )
FILE(APPEND "${NULL_TIMER_DIR}/ProfilerApp.h" "#define PROFILE_DISABLE_MEMORY() do {} while(0)\n" )
# Write MemoryApp.h
FILE(WRITE "${NULL_TIMER_DIR}/MemoryApp.h" "#include <cstring>\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" "class MemoryApp final {\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" "public:\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" " struct MemoryStats {\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" " size_t bytes_new, bytes_delete, N_new, N_delete, tot_bytes_used, system_memory, stack_used, stack_size;\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" " MemoryStats() { memset(this,0,sizeof(MemoryStats)); }\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" " };\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" " static inline void print( std::ostream& ) {}\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" " static inline size_t getMemoryUsage() { return 0; }\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" " static inline size_t getTotalMemoryUsage() { return 0; }\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" " static inline size_t getSystemMemory() { return 0; }\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" " static inline MemoryStats getMemoryStats() { return MemoryStats(); }\n" )
FILE(APPEND "${NULL_TIMER_DIR}/MemoryApp.h" "};\n" )
SET( TIMER_INCLUDE "${NULL_TIMER_DIR}" )
INCLUDE_DIRECTORIES( "${TIMER_INCLUDE}" )
MESSAGE( "Disabling timer utility" )
IF ( NOT QUIET )
MESSAGE( STATUS "Disabling timer utility" )
ENDIF()
ENDIF()
SET( TIMER_INCLUDE "${TIMER_INCLUDE}" PARENT_SCOPE )
SET( TIMER_CXXFLAGS "${TIMER_CXXFLAGS}" PARENT_SCOPE )
@ -88,12 +107,12 @@ MACRO( CHECK_ENABLE_FLAG FLAG DEFAULT )
SET( ${FLAG} ${DEFAULT} )
ELSEIF( ${FLAG} STREQUAL "" )
SET( ${FLAG} ${DEFAULT} )
ELSEIF( ( ${${FLAG}} STREQUAL "false" ) OR ( ${${FLAG}} STREQUAL "0" ) OR ( ${${FLAG}} STREQUAL "OFF" ) )
ELSEIF( ( ${${FLAG}} STREQUAL "FALSE" ) OR ( ${${FLAG}} STREQUAL "false" ) OR ( ${${FLAG}} STREQUAL "0" ) OR ( ${${FLAG}} STREQUAL "OFF" ) )
SET( ${FLAG} 0 )
ELSEIF( ( ${${FLAG}} STREQUAL "true" ) OR ( ${${FLAG}} STREQUAL "1" ) OR ( ${${FLAG}} STREQUAL "ON" ) )
ELSEIF( ( ${${FLAG}} STREQUAL "TRUE" ) OR ( ${${FLAG}} STREQUAL "true" ) OR ( ${${FLAG}} STREQUAL "1" ) OR ( ${${FLAG}} STREQUAL "ON" ) )
SET( ${FLAG} 1 )
ELSE()
MESSAGE( "Bad value for ${FLAG} (${${FLAG}}); use true or false" )
MESSAGE( FATAL_ERROR "Bad value for ${FLAG} (${${FLAG}}); use true or false" )
ENDIF ()
ENDMACRO()

3
cmake/ctest_script.cmake
View File

@ -32,7 +32,6 @@ SET( CMAKE_MAKE_PROGRAM $ENV{CMAKE_MAKE_PROGRAM} )
SET( CTEST_CMAKE_GENERATOR $ENV{CTEST_CMAKE_GENERATOR} )
SET( LDLIBS $ENV{LDLIBS} )
SET( LDFLAGS $ENV{LDFLAGS} )
SET( MPI_COMPILER $ENV{MPI_COMPILER} )
SET( MPI_DIRECTORY $ENV{MPI_DIRECTORY} )
SET( MPI_INCLUDE $ENV{MPI_INCLUDE} )
SET( MPI_LINK_FLAGS $ENV{MPI_LINK_FLAGS} )
@ -198,7 +197,7 @@ SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DCMAKE_C_FLAGS='${CFLAGS}';-DCMAKE_CXX_FLA
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DLDFLAGS:STRING='${FLAGS}';-DLDLIBS:STRING='${LDLIBS}'" )
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DENABLE_GCOV:BOOL=${ENABLE_GCOV}" )
IF ( USE_MPI )
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DMPI_COMPILER:BOOL=true;-DMPIEXEC=${MPIEXEC}")
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DMPIEXEC=${MPIEXEC}")
IF ( NOT USE_VALGRIND )
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DUSE_MPI_FOR_SERIAL_TESTS:BOOL=true")
ENDIF()

132
cmake/libraries.cmake
View File

@ -41,93 +41,61 @@ ENDMACRO()
# Macro to find and configure the MPI libraries
MACRO( CONFIGURE_MPI )
# Determine if we want to use MPI
CHECK_ENABLE_FLAG(USE_MPI 1 )
CHECK_ENABLE_FLAG( USE_MPI 1 )
IF ( USE_MPI )
# Check if we specified the MPI directory
IF ( MPI_DIRECTORY )
# Check the provided MPI directory for include files
VERIFY_PATH( "${MPI_DIRECTORY}" )
IF ( EXISTS "${MPI_DIRECTORY}/include/mpi.h" )
SET( MPI_INCLUDE_PATH "${MPI_DIRECTORY}/include" )
ELSEIF ( EXISTS "${MPI_DIRECTORY}/Inc/mpi.h" )
SET( MPI_INCLUDE_PATH "${MPI_DIRECTORY}/Inc" )
ELSE()
MESSAGE( FATAL_ERROR "mpi.h not found in ${MPI_DIRECTORY}/include" )
ENDIF ()
INCLUDE_DIRECTORIES ( ${MPI_INCLUDE_PATH} )
SET ( MPI_INCLUDE ${MPI_INCLUDE_PATH} )
# Set MPI libraries
IF ( ${CMAKE_SYSTEM_NAME} STREQUAL "Windows" )
FIND_LIBRARY( MSMPI_LIB NAMES msmpi PATHS "${MPI_DIRECTORY}/Lib/x64" NO_DEFAULT_PATH )
FIND_LIBRARY( MSMPI_LIB NAMES msmpi PATHS "${MPI_DIRECTORY}/Lib/amd64" NO_DEFAULT_PATH )
FIND_LIBRARY( MSMPIFEC_LIB NAMES msmpifec PATHS "${MPI_DIRECTORY}/Lib/x64" NO_DEFAULT_PATH )
FIND_LIBRARY( MSMPIFEC_LIB NAMES msmpifec PATHS "${MPI_DIRECTORY}/Lib/amd64" NO_DEFAULT_PATH )
FIND_LIBRARY( MSMPIFMC_LIB NAMES msmpifmc PATHS "${MPI_DIRECTORY}/Lib/x64" NO_DEFAULT_PATH )
FIND_LIBRARY( MSMPIFMC_LIB NAMES msmpifmc PATHS "${MPI_DIRECTORY}/Lib/amd64" NO_DEFAULT_PATH )
SET( MPI_LIBRARIES ${MSMPI_LIB} ${MSMPIFEC_LIB} ${MSMPIFMC_LIB} )
ENDIF()
# Set the mpi executable
IF ( MPIEXEC )
# User specified the MPI command directly, use as is
ELSEIF ( MPIEXEC_CMD )
# User specified the name of the MPI executable
SET ( MPIEXEC ${MPI_DIRECTORY}/bin/${MPIEXEC_CMD} )
IF ( NOT EXISTS ${MPIEXEC} )
MESSAGE( FATAL_ERROR "${MPIEXEC_CMD} not found in ${MPI_DIRECTORY}/bin" )
ENDIF ()
ELSE ()
# Search for the MPI executable in the current directory
FIND_PROGRAM( MPIEXEC NAMES mpiexec mpirun lamexec PATHS ${MPI_DIRECTORY}/bin NO_DEFAULT_PATH )
IF ( NOT MPIEXEC )
MESSAGE( FATAL_ERROR "Could not locate mpi executable" )
ENDIF()
ENDIF ()
# Set MPI flags
IF ( NOT MPIEXEC_NUMPROC_FLAG )
SET( MPIEXEC_NUMPROC_FLAG "-np" )
ENDIF()
ELSEIF ( MPI_COMPILER )
# The mpi compiler should take care of everything
IF ( MPI_INCLUDE )
INCLUDE_DIRECTORIES( ${MPI_INCLUDE} )
ENDIF()
MESSAGE( "Configuring MPI" )
IF ( MPIEXEC )
SET( MPIEXEC_EXECUTABLE ${MPIEXEC} )
ENDIF()
IF ( NOT MPI_SKIP_SEARCH )
FIND_PACKAGE( MPI )
ELSE()
# Perform the default search for MPI
INCLUDE ( FindMPI )
IF ( NOT MPI_FOUND )
MESSAGE( " MPI_INCLUDE = ${MPI_INCLUDE}" )
MESSAGE( " MPI_LINK_FLAGS = ${MPI_LINK_FLAGS}" )
MESSAGE( " MPI_LIBRARIES = ${MPI_LIBRARIES}" )
MESSAGE( FATAL_ERROR "Did not find MPI" )
ENDIF ()
INCLUDE_DIRECTORIES( "${MPI_INCLUDE_PATH}" )
SET( MPI_INCLUDE "${MPI_INCLUDE_PATH}" )
# Write mpi test
SET( MPI_TEST_SRC "${CMAKE_CURRENT_BINARY_DIR}/test_mpi.cpp" )
FILE(WRITE ${MPI_TEST_SRC} "#include <mpi.h>\n" )
FILE(APPEND ${MPI_TEST_SRC} "int main(int argc, char** argv) {\n" )
FILE(APPEND ${MPI_TEST_SRC} " MPI_Init(NULL, NULL);\n")
FILE(APPEND ${MPI_TEST_SRC} " MPI_Finalize();\n" )
FILE(APPEND ${MPI_TEST_SRC} "}\n" )
# Test the compile
IF ( CMAKE_CXX_COMPILER )
SET( TMP_FLAGS -DINCLUDE_DIRECTORIES=${MPI_CXX_INCLUDE_PATH} )
TRY_COMPILE( MPI_TEST_CXX ${CMAKE_CURRENT_BINARY_DIR} ${MPI_TEST_SRC}
CMAKE_FLAGS ${TMP_FLAGS}
LINK_OPTIONS ${MPI_CXX_LINK_FLAGS}
LINK_LIBRARIES ${MPI_CXX_LIBRARIES}
OUTPUT_VARIABLE OUT_TXT)
IF ( NOT ${MPI_TEST} )
MESSAGE( FATAL_ERROR "Skipping MPI search and default compile fails:\n${OUT_TXT}" )
ENDIF()
SET( MPI_C_FOUND TRUE )
SET( MPI_CXX_FOUND TRUE )
SET( MPI_Fortran_FOUND TRUE )
ENDIF()
ENDIF()
# Check if we need to use MPI for serial tests
CHECK_ENABLE_FLAG( USE_MPI_FOR_SERIAL_TESTS 0 )
# Set defaults if they have not been set
IF ( NOT MPIEXEC )
SET( MPIEXEC mpirun )
STRING( STRIP "${MPI_CXX_COMPILE_FLAGS}" MPI_CXX_COMPILE_FLAGS )
STRING( STRIP "${MPI_CXX_LINK_FLAGS}" MPI_CXX_LINK_FLAGS )
STRING( STRIP "${MPI_CXX_LIBRARIES}" MPI_CXX_LIBRARIES )
MESSAGE( " MPI_CXX_FOUND = ${MPI_CXX_FOUND}" )
MESSAGE( " MPI_CXX_COMPILER = ${MPI_CXX_COMPILER}" )
MESSAGE( " MPI_CXX_COMPILE_FLAGS = ${MPI_CXX_COMPILE_FLAGS}" )
MESSAGE( " MPI_CXX_INCLUDE_PATH = ${MPI_CXX_INCLUDE_PATH}" )
MESSAGE( " MPI_CXX_LINK_FLAGS = ${MPI_CXX_LINK_FLAGS}" )
MESSAGE( " MPI_CXX_LIBRARIES = ${MPI_CXX_LIBRARIES}" )
MESSAGE( " MPIEXEC = ${MPIEXEC}" )
MESSAGE( " MPIEXEC_NUMPROC_FLAG = ${MPIEXEC_NUMPROC_FLAG}" )
MESSAGE( " MPIEXEC_PREFLAGS = ${MPIEXEC_PREFLAGS}" )
MESSAGE( " MPIEXEC_POSTFLAGS = ${MPIEXEC_POSTFLAGS}" )
ADD_DEFINITIONS( -DUSE_MPI )
INCLUDE_DIRECTORIES( ${MPI_CXX_INCLUDE_PATH} )
SET( MPI_LIBRARIES ${MPI_CXX_LIBRARIES} )
SET( MPI_LINK_FLAGS ${MPI_CXX_LINK_FLAGS} )
IF ( NOT MPI_CXX_FOUND )
MESSAGE( FATAL_ERROR "MPI not found" )
ENDIF()
IF ( NOT MPIEXEC_NUMPROC_FLAG )
SET( MPIEXEC_NUMPROC_FLAG "-np" )
IF ( USE_MPI AND NOT MPIEXEC )
MESSAGE( FATAL_ERROR "Unable to find MPIEXEC, please set it before continuing" )
ENDIF()
# Set the definitions
ADD_DEFINITIONS( "-DUSE_MPI" )
MESSAGE( "Using MPI" )
MESSAGE( " MPIEXEC = ${MPIEXEC}" )
MESSAGE( " MPIEXEC_NUMPROC_FLAG = ${MPIEXEC_NUMPROC_FLAG}" )
MESSAGE( " MPI_INCLUDE = ${MPI_INCLUDE}" )
MESSAGE( " MPI_LINK_FLAGS = ${MPI_LINK_FLAGS}" )
MESSAGE( " MPI_LIBRARIES = ${MPI_LIBRARIES}" )
ELSE()
SET( USE_MPI_FOR_SERIAL_TESTS 0 )
SET( MPIEXEC "" )
SET( MPIEXEC_NUMPROC_FLAG "" )
SET( MPI_INCLUDE "" )
SET( MPI_LINK_FLAGS "" )
SET( MPI_LIBRARIES "" )
MESSAGE( "Not using MPI, all parallel tests will be disabled" )
ENDIF()
ENDMACRO()

4
cmake/macros.cmake
View File

@ -681,8 +681,8 @@ MACRO( TARGET_LINK_EXTERNAL_LIBRARIES TARGET_NAME )
FOREACH ( tmp ${BLAS_LAPACK_LIBS} )
TARGET_LINK_LIBRARIES( ${TARGET_NAME} ${ARGN} ${tmp} )
ENDFOREACH()
FOREACH ( MPI_LIBRARIES )
TARGET_LINK_LIBRARIES( ${EXE} ${ARGN} ${tmp} )
FOREACH ( tmp ${MPI_LIBRARIES} )
TARGET_LINK_LIBRARIES( ${TARGET_NAME} ${ARGN} ${tmp} )
ENDFOREACH()
FOREACH ( tmp ${CMAKE_C_IMPLICIT_LINK_LIBRARIES}
${CMAKE_CXX_IMPLICIT_LINK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES} )

2
ctest_script.cmake
View File

@ -164,7 +164,7 @@ SET( CTEST_OPTIONS )
SET( CTEST_OPTIONS "-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}" )
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DCMAKE_C_COMPILER:PATH=${CC};-DCMAKE_C_FLAGS='${C_FLAGS}';" )
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DCMAKE_CXX_COMPILER:PATH=${CXX};-DCMAKE_CXX_FLAGS='${CXX_FLAGS}'" )
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DMPI_COMPILER:BOOL=true;-DMPIEXEC=${MPIEXEC};-DUSE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=true")
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DMPIEXEC=${MPIEXEC};-DUSE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=true")
IF ( USE_CUDA )
SET( CTEST_OPTIONS "${CTEST_OPTIONS};-DUSE_CUDA:BOOL=true;-DCUDA_NVCC_FLAGS='${CUDA_FLAGS}';-DCUDA_HOST_COMPILER=${CUDA_HOST_COMPILER}" )
ELSE()

1
sample_scripts/config_build_eos
View File

@ -33,7 +33,6 @@ cmake \
-D CMAKE_CXX_STANDARD=14 \
-D USE_TIMER=false \
-D TIMER_DIRECTORY=${HOME}/timerutility/build/opt \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=aprun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D USE_CUDA=0 \

1
sample_scripts/config_build_rhea
View File

@ -27,7 +27,6 @@ cmake \
-D CMAKE_CXX_STD=11 \
-D USE_TIMER=false \
-D TIMER_DIRECTORY=${HOME}/timerutility/build/opt \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=aprun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D USE_CUDA=0 \

1
sample_scripts/config_build_titan
View File

@ -25,7 +25,6 @@ cmake \
-D CMAKE_CUDA_FLAGS="-arch sm_35" \
-D CMAKE_CUDA_HOST_COMPILER="/opt/gcc/6.3.0/bin/gcc" \
-D USE_MPI=1 \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=aprun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D USE_SILO=1 \

1
sample_scripts/config_build_titan_silo
View File

@ -20,7 +20,6 @@ cmake \
-D CMAKE_CUDA_FLAGS="-arch sm_35" \
-D CMAKE_CUDA_HOST_COMPILER="/opt/gcc/6.3.0/bin/gcc" \
-D USE_MPI=1 \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=aprun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D USE_NETCDF=0 \

1
sample_scripts/config_poplar_hip
View File

@ -36,6 +36,5 @@ cmake \
# MPI_THREAD_MULTIPLE=1 MV2_USE_RDMA_CM=0 MV2_USE_RDMA_CM= MV2_NUM_HCAS=1 MV2_USE_CUDA=1 MV2_ENABLE_AFFINITY=0 srun -n 2 -N 1 --cpu-bind=v -c 1 ./test_MPI
# -D MPI_COMPILER:BOOL=TRUE \
# -D MPIEXEC=mpirun \
# -D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \

1
sample_scripts/config_summit_hip
View File

@ -21,7 +21,6 @@ cmake \
-D HIP_NVCC_OPTIONS="-arch sm_70" \
-D LINK_LIBRARIES="/sw/summit/cuda/9.2.148/lib64/libcudart.so" \
-D USE_MPI=1 \
-D MPI_COMPILER:BOOL=TRUE \
-D USE_NETCDF=0 \
-D USE_SILO=1 \
-D SILO_DIRECTORY=${TPL_DIR}/silo \

1
sample_scripts/config_titan
View File

@ -9,7 +9,6 @@ cmake \
-D CMAKE_CUDA_FLAGS="-arch sm_35" \
-D CMAKE_CUDA_HOST_COMPILER="/usr/bin/gcc" \
-D USE_MPI=1 \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=aprun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
${HOME}/LBPM-WIA

1
sample_scripts/configure_arc_cluster
View File

@ -10,7 +10,6 @@ cmake \
-D CMAKE_CXX_COMPILER:PATH=mpicxx \
-D CMAKE_C_FLAGS="" \
-D CMAKE_CXX_FLAGS="" \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Release \

1
sample_scripts/configure_arden
View File

@ -5,7 +5,6 @@ cmake -D CMAKE_C_COMPILER:PATH=/opt/arden/openmpi/3.1.2/bin/mpicc \
-D CMAKE_C_FLAGS="-O3 -fPIC" \
-D CMAKE_CXX_FLAGS="-O3 -fPIC " \
-D CMAKE_CXX_STANDARD=14 \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Release \

1
sample_scripts/configure_basic_cluster
View File

@ -8,7 +8,6 @@ cmake \
-D CMAKE_CXX_COMPILER:PATH=mpicxx \
-D CMAKE_C_FLAGS="" \
-D CMAKE_CXX_FLAGS="" \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Release \

1
sample_scripts/configure_blueridge
View File

@ -8,7 +8,6 @@ cmake \
-D CMAKE_CXX_COMPILER:PATH=mpicxx \
-D CMAKE_C_FLAGS="" \
-D CMAKE_CXX_FLAGS="" \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Release \

1
sample_scripts/configure_cascades_cpu
View File

@ -11,7 +11,6 @@ cmake \
-D CMAKE_CXX_COMPILER:PATH=mpicxx \
-D CMAKE_C_FLAGS="-fPIC" \
-D CMAKE_CXX_FLAGS="-fPIC" \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Release \

1
sample_scripts/configure_desktop
View File

@ -7,7 +7,6 @@ cmake \
-D CMAKE_C_FLAGS="-g " \
-D CMAKE_CXX_FLAGS="-g " \
-D CMAKE_CXX_STANDARD=14 \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Release \

1
sample_scripts/configure_huckleberry
View File

@ -12,7 +12,6 @@ cmake \
-D CMAKE_CXX_COMPILER:PATH=mpicxx \
-D CMAKE_C_FLAGS="-fPIC" \
-D CMAKE_CXX_FLAGS="-fPIC" \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Release \

1
sample_scripts/configure_summit
View File

@ -20,7 +20,6 @@ cmake \
-D CMAKE_CUDA_FLAGS="-arch sm_70 -Xptxas=-v -Xptxas -dlcm=cg -lineinfo" \
-D CMAKE_CUDA_HOST_COMPILER="/sw/summit/gcc/6.4.0/bin/gcc" \
-D USE_MPI=1 \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D USE_HDF5=1 \

1
sample_scripts/configure_titan_jem
View File

@ -15,7 +15,6 @@ cmake \
-D CMAKE_C_COMPILER:PATH=cc \
-D CMAKE_CXX_COMPILER:PATH=CC \
-D CMAKE_CXX_COMPILER:PATH=CC \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=aprun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Debug \

2
sample_scripts/configure_ubuntu
View File

@ -5,9 +5,7 @@ cmake -D CMAKE_C_COMPILER:PATH=/opt/arden/openmpi/3.1.2/bin/mpicc \
-D CMAKE_C_FLAGS="-O3 -fPIC" \
-D CMAKE_CXX_FLAGS="-O3 -fPIC " \
-D CMAKE_CXX_STANDARD=14 \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Release \
-D CUDA_FLAGS="-arch sm_35" \
-D CUDA_HOST_COMPILER="/usr/bin/gcc" \

1
sample_scripts/daedalus_config
View File

@ -12,7 +12,6 @@ i -D CMAKE_CXX_COMPILER:PATH=/home/christopher/openmpi/install_dir/bin/mpicxx
-D USE_DOXYGEN=false \
# -D CMAKE_C_FLAGS="-std=gnu++11 -w" \
# -D CMAKE_CXX_FLAGS="-std=gnu++11 -w" \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=/home/christopher/openmpi/install_dir/bin/mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Release \

1
sample_scripts/promethius_config
View File

@ -7,7 +7,6 @@ cmake \
-D CMAKE_C_FLAGS="-g " \
-D CMAKE_CXX_FLAGS="-g -Wno-deprecated-declarations" \
-D CXX_STD=11 \
-D MPI_COMPILER:BOOL=TRUE \
-D MPIEXEC=mpirun \
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
-D CMAKE_BUILD_TYPE:STRING=Debug \

4
tests/CMakeLists.txt
View File

@ -35,8 +35,8 @@ ADD_LBPM_EXECUTABLE( GenerateSphereTest )
#ADD_LBPM_EXECUTABLE( BlobAnalysis )
#ADD_LBPM_EXECUTABLE( BlobIdentify )
#ADD_LBPM_EXECUTABLE( BlobIdentifyParallel )
#ADD_LBPM_EXECUTABLE( convertIO )
#ADD_LBPM_EXECUTABLE( DataAggregator )
ADD_LBPM_EXECUTABLE( convertIO )
ADD_LBPM_EXECUTABLE( DataAggregator )
#ADD_LBPM_EXECUTABLE( BlobAnalyzeParallel )(
ADD_LBPM_EXECUTABLE( lbpm_minkowski_scalar )
ADD_LBPM_EXECUTABLE( TestPoissonSolver )

531
tests/TestWriter.cpp
View File

@ -1,219 +1,232 @@
#include <exception>
#include <fstream>
#include <iostream>
#include <memory>
#include <stdexcept>
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <exception>
#include <stdexcept>
#include <fstream>
#include <memory>
#include "common/UnitTest.h"
#include "common/Utilities.h"
#include "common/MPI.h"
#include "IO/MeshDatabase.h"
#include "IO/Reader.h"
#include "IO/Writer.h"
#include "ProfilerApp.h"
#include "common/MPI.h"
#include "common/UnitTest.h"
#include "common/Utilities.h"
inline bool approx_equal( const Point& A, const Point& B )
inline bool approx_equal( const Point &A, const Point &B )
{
double tol = 1e-7*sqrt(A.x*A.x+A.y*A.y+A.z*A.z);
return fabs(A.x-B.x)<=tol && fabs(A.y-B.y)<=tol && fabs(A.z-B.z)<=tol;
double tol = 1e-7 * sqrt( A.x * A.x + A.y * A.y + A.z * A.z );
return fabs( A.x - B.x ) <= tol && fabs( A.y - B.y ) <= tol && fabs( A.z - B.z ) <= tol;
}
inline bool approx_equal( const double& A, const double& B )
inline bool approx_equal( const double &A, const double &B )
{
return fabs(A-B) <= std::max<double>(1e-7*fabs(A+B),1e-20);
return fabs( A - B ) <= std::max<double>( 1e-7 * fabs( A + B ), 1e-20 );
}
inline double distance( const Point& p )
inline double distance( const Point &p ) { return sqrt( p.x * p.x + p.y * p.y + p.z * p.z ); }
bool checkMesh( const std::vector<IO::MeshDataStruct> &meshData, const std::string &format,
std::shared_ptr<IO::Mesh> mesh )
{
return sqrt(p.x*p.x+p.y*p.y+p.z*p.z);
// Get direct access to the meshes used to test the reader
const auto pointmesh = dynamic_cast<IO::PointList *>( meshData[0].mesh.get() );
const auto trimesh = dynamic_cast<IO::TriMesh *>( meshData[1].mesh.get() );
const auto trilist = dynamic_cast<IO::TriList *>( meshData[2].mesh.get() );
const auto domain = dynamic_cast<IO::DomainMesh *>( meshData[3].mesh.get() );
const size_t N_tri = trimesh->A.size();
if ( mesh->className() == "pointmesh" ) {
// Check the pointmesh
auto pmesh = IO::getPointList( mesh );
if ( pmesh.get() == NULL )
return false;
if ( pmesh->points.size() != pointmesh->points.size() )
return false;
}
if ( mesh->className() == "trimesh" || mesh->className() == "trilist" ) {
// Check the trimesh/trilist
auto mesh1 = IO::getTriMesh( mesh );
auto mesh2 = IO::getTriList( mesh );
if ( mesh1.get() == NULL || mesh2.get() == NULL )
return false;
if ( mesh1->A.size() != N_tri || mesh1->B.size() != N_tri || mesh1->C.size() != N_tri ||
mesh2->A.size() != N_tri || mesh2->B.size() != N_tri || mesh2->C.size() != N_tri )
return false;
const std::vector<Point> &P1 = mesh1->vertices->points;
const std::vector<int> &A1 = mesh1->A;
const std::vector<int> &B1 = mesh1->B;
const std::vector<int> &C1 = mesh1->C;
const std::vector<Point> &A2 = mesh2->A;
const std::vector<Point> &B2 = mesh2->B;
const std::vector<Point> &C2 = mesh2->C;
const std::vector<Point> &A = trilist->A;
const std::vector<Point> &B = trilist->B;
const std::vector<Point> &C = trilist->C;
for ( size_t i = 0; i < N_tri; i++ ) {
if ( !approx_equal( P1[A1[i]], A[i] ) || !approx_equal( P1[B1[i]], B[i] ) ||
!approx_equal( P1[C1[i]], C[i] ) )
return false;
if ( !approx_equal( A2[i], A[i] ) || !approx_equal( B2[i], B[i] ) ||
!approx_equal( C2[i], C[i] ) )
return false;
}
}
if ( mesh->className() == "domain" && format != "old" ) {
// Check the domain mesh
const IO::DomainMesh &mesh1 = *std::dynamic_pointer_cast<IO::DomainMesh>( mesh );
if ( mesh1.nprocx != domain->nprocx || mesh1.nprocy != domain->nprocy ||
mesh1.nprocz != domain->nprocz )
return false;
if ( mesh1.nx != domain->nx || mesh1.ny != domain->ny || mesh1.nz != domain->nz )
return false;
if ( mesh1.Lx != domain->Lx || mesh1.Ly != domain->Ly || mesh1.Lz != domain->Lz )
return false;
}
return true;
}
bool checkVar( const std::string &format, std::shared_ptr<IO::Mesh> mesh,
std::shared_ptr<IO::Variable> variable1, std::shared_ptr<IO::Variable> variable2 )
{
if ( format == "new" )
IO::reformatVariable( *mesh, *variable2 );
bool pass = true;
const IO::Variable &var1 = *variable1;
const IO::Variable &var2 = *variable2;
pass = var1.name == var2.name;
pass = pass && var1.dim == var2.dim;
pass = pass && var1.type == var2.type;
pass = pass && var1.data.length() == var2.data.length();
if ( pass ) {
for ( size_t m = 0; m < var1.data.length(); m++ )
pass = pass && approx_equal( var1.data( m ), var2.data( m ) );
}
return pass;
}
// Test writing and reading the given format
void testWriter( const std::string& format, std::vector<IO::MeshDataStruct>& meshData, UnitTest& ut )
void testWriter(
const std::string &format, std::vector<IO::MeshDataStruct> &meshData, UnitTest &ut )
{
PROFILE_SCOPED( path, 0, timer );
Utilities::MPI comm( MPI_COMM_WORLD );
int nprocs = comm.getSize();
comm.barrier();
// Set the path for the writer
std::string path = "test_" + format;
// Get the format
std::string format2 = format;
auto precision = IO::DataType::Double;
auto precision = IO::DataType::Double;
if ( format == "silo-double" ) {
format2 = "silo";
format2 = "silo";
precision = IO::DataType::Double;
} else if ( format == "silo-float" ) {
format2 = "silo";
format2 = "silo";
precision = IO::DataType::Float;
}
// Set the precision for the variables
for ( auto& data : meshData ) {
for ( auto &data : meshData ) {
data.precision = precision;
for ( auto& var : data.vars )
for ( auto &var : data.vars )
var->precision = precision;
}
// Write the data
PROFILE_START(format+"-write");
IO::initialize( "test_"+format, format2, false );
IO::initialize( path, format2, false );
IO::writeData( 0, meshData, comm );
IO::writeData( 3, meshData, comm );
comm.barrier();
PROFILE_STOP(format+"-write");
// Get the summary name for reading
std::string path = "test_" + format;
std::string summary_name;
if ( format=="old" || format=="new" )
summary_name = "summary.LBM";
else if ( format=="silo-float" || format=="silo-double" )
summary_name = "LBM.visit";
// Get a list of the timesteps
auto timesteps = IO::readTimesteps( path, format2 );
if ( timesteps.size() == 2 )
ut.passes( format + ": Corrent number of timesteps" );
else
ERROR("Unknown format");
ut.failure( format + ": Incorrent number of timesteps" );
// Get direct access to the meshes used to test the reader
const auto pointmesh = dynamic_cast<IO::PointList*>( meshData[0].mesh.get() );
const auto trimesh = dynamic_cast<IO::TriMesh*>( meshData[1].mesh.get() );
const auto trilist = dynamic_cast<IO::TriList*>( meshData[2].mesh.get() );
const auto domain = dynamic_cast<IO::DomainMesh*>( meshData[3].mesh.get() );
const size_t N_tri = trimesh->A.size();
// Get a list of the timesteps
PROFILE_START(format+"-read-timesteps");
auto timesteps = IO::readTimesteps( path + "/" + summary_name );
PROFILE_STOP(format+"-read-timesteps");
if ( timesteps.size()==2 )
ut.passes(format+": Corrent number of timesteps");
else
ut.failure(format+": Incorrent number of timesteps");
// Check the mesh lists
for ( const auto& timestep : timesteps ) {
// Load the list of meshes and check its size
PROFILE_START(format+"-read-getMeshList");
auto databaseList = IO::getMeshList(path,timestep);
PROFILE_STOP(format+"-read-getMeshList");
if ( databaseList.size()==meshData.size() )
ut.passes(format+": Corrent number of meshes found");
else
ut.failure(format+": Incorrent number of meshes found");
// Check the number of domains for each mesh
bool pass = true;
for ( const auto& database : databaseList )
pass = pass && (int)database.domains.size()==nprocs;
if ( pass ) {
ut.passes(format+": Corrent number of domains for mesh");
} else {
ut.failure(format+": Incorrent number of domains for mesh");
continue;
// Test the simple read interface
bool pass = true;
for ( const auto &timestep : timesteps ) {
auto data = IO::readData( path, timestep, comm.getRank() );
pass = pass && data.size() == meshData.size();
for ( size_t i = 0; i < data.size(); i++ ) {
pass = pass && checkMesh( meshData, format, data[i].mesh );
}
// For each domain, load the mesh and check its data
for ( const auto& database : databaseList ) {
pass = true;
for (size_t k=0; k<database.domains.size(); k++) {
PROFILE_START(format+"-read-getMesh");
auto mesh = IO::getMesh(path,timestep,database,k);
PROFILE_STOP(format+"-read-getMesh");
if ( mesh.get()==NULL ) {
printf("Failed to load %s\n",database.name.c_str());
}
if ( pass )
ut.passes( format + ": Simple read interface" );
else
ut.failure( format + ": Simple read interface" );
// Test reading each mesh domain
for ( const auto &timestep : timesteps ) {
// Load the list of meshes and check its size
auto databaseList = IO::getMeshList( path, timestep );
if ( databaseList.size() == meshData.size() )
ut.passes( format + ": Corrent number of meshes found" );
else
ut.failure( format + ": Incorrent number of meshes found" );
// Check the number of domains for each mesh
for ( const auto &database : databaseList ) {
int N_domains = database.domains.size();
if ( N_domains != nprocs ) {
ut.failure( format + ": Incorrent number of domains for mesh" );
continue;
}
// For each domain, load the mesh and check its data
bool pass = true;
for ( int k = 0; k < N_domains; k++ ) {
auto mesh = IO::getMesh( path, timestep, database, k );
if ( !mesh ) {
ut.failure( "Failed to load " + database.name );
pass = false;
break;
}
if ( database.name=="pointmesh" ) {
// Check the pointmesh
auto pmesh = IO::getPointList(mesh);
if ( pmesh.get()==NULL ) {
pass = false;
break;
}
if ( pmesh->points.size() != pointmesh->points.size() ) {
pass = false;
break;
}
}
if ( database.name=="trimesh" || database.name=="trilist" ) {
// Check the trimesh/trilist
auto mesh1 = IO::getTriMesh(mesh);
auto mesh2 = IO::getTriList(mesh);
if ( mesh1.get()==NULL || mesh2.get()==NULL ) {
pass = false;
break;
}
if ( mesh1->A.size()!=N_tri || mesh1->B.size()!=N_tri || mesh1->C.size()!=N_tri ||
mesh2->A.size()!=N_tri || mesh2->B.size()!=N_tri || mesh2->C.size()!=N_tri )
{
pass = false;
break;
}
const std::vector<Point>& P1 = mesh1->vertices->points;
const std::vector<int>& A1 = mesh1->A;
const std::vector<int>& B1 = mesh1->B;
const std::vector<int>& C1 = mesh1->C;
const std::vector<Point>& A2 = mesh2->A;
const std::vector<Point>& B2 = mesh2->B;
const std::vector<Point>& C2 = mesh2->C;
const std::vector<Point>& A = trilist->A;
const std::vector<Point>& B = trilist->B;
const std::vector<Point>& C = trilist->C;
for (size_t i=0; i<N_tri; i++) {
if ( !approx_equal(P1[A1[i]],A[i]) || !approx_equal(P1[B1[i]],B[i]) || !approx_equal(P1[C1[i]],C[i]) )
pass = false;
if ( !approx_equal(A2[i],A[i]) || !approx_equal(B2[i],B[i]) || !approx_equal(C2[i],C[i]) )
pass = false;
}
}
if ( database.name=="domain" && format!="old" ) {
// Check the domain mesh
const IO::DomainMesh& mesh1 = *std::dynamic_pointer_cast<IO::DomainMesh>(mesh);
if ( mesh1.nprocx!=domain->nprocx || mesh1.nprocy!=domain->nprocy || mesh1.nprocz!=domain->nprocz )
pass = false;
if ( mesh1.nx!=domain->nx || mesh1.ny!=domain->ny || mesh1.nz!=domain->nz )
pass = false;
if ( mesh1.Lx!=domain->Lx || mesh1.Ly!=domain->Ly || mesh1.Lz!=domain->Lz )
pass = false;
} else {
pass = pass && checkMesh( meshData, format, mesh );
}
}
if ( pass ) {
ut.passes(format+": Mesh \"" + database.name + "\" loaded correctly");
ut.passes( format + ": Mesh \"" + database.name + "\" loaded correctly" );
} else {
ut.failure(format+": Mesh \"" + database.name + "\" did not load correctly");
ut.failure( format + ": Mesh \"" + database.name + "\" did not load correctly" );
continue;
}
// Load the variables and check their data
if ( format=="old" )
continue; // Old format does not support variables
const IO::MeshDataStruct* mesh0 = NULL;
for (size_t k=0; k<meshData.size(); k++) {
if ( format == "old" )
continue; // Old format does not support variables
const IO::MeshDataStruct *mesh0 = nullptr;
for ( size_t k = 0; k < meshData.size(); k++ ) {
if ( meshData[k].meshName == database.name ) {
mesh0 = &meshData[k];
break;
}
}
for (size_t k=0; k<database.domains.size(); k++) {
auto mesh = IO::getMesh(path,timestep,database,k);
for (size_t v=0; v<mesh0->vars.size(); v++) {
PROFILE_START(format+"-read-getVariable");
auto variable = IO::getVariable(path,timestep,database,k,mesh0->vars[v]->name);
if ( format=="new" )
IO::reformatVariable( *mesh, *variable );
PROFILE_STOP(format+"-read-getVariable");
const IO::Variable& var1 = *mesh0->vars[v];
const IO::Variable& var2 = *variable;
pass = var1.name == var2.name;
pass = pass && var1.dim == var2.dim;
pass = pass && var1.type == var2.type;
pass = pass && var1.data.length() == var2.data.length();
for ( int k = 0; k < N_domains; k++ ) {
auto mesh = IO::getMesh( path, timestep, database, k );
for ( size_t v = 0; v < mesh0->vars.size(); v++ ) {
PROFILE_START( format + "-read-getVariable" );
auto variable =
IO::getVariable( path, timestep, database, k, mesh0->vars[v]->name );
pass = checkVar( format, mesh, mesh0->vars[v], variable );
if ( pass ) {
for (size_t m=0; m<var1.data.length(); m++)
pass = pass && approx_equal(var1.data(m),var2.data(m));
}
if ( pass ) {
ut.passes(format+": Variable \"" + variable->name + "\" matched");
ut.passes( format + ": Variable \"" + variable->name + "\" matched" );
} else {
ut.failure(format+": Variable \"" + variable->name + "\" did not match");
ut.failure(
format + ": Variable \"" + variable->name + "\" did not match" );
break;
}
}
@ -224,157 +237,161 @@ void testWriter( const std::string& format, std::vector<IO::MeshDataStruct>& mes
// Main
int main(int argc, char **argv)
int main( int argc, char **argv )
{
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int rank = comm.getRank();
int nprocs = comm.getSize();
Utilities::setAbortBehavior(true,2);
Utilities::setAbortBehavior( true, 2 );
Utilities::setErrorHandlers();
UnitTest ut;
// Create some points
const int N_points = 8;
const int N_tri = 12;
double x[8] = { 0, 1, 0, 1, 0, 1, 0, 1 };
double y[8] = { 0, 0, 1, 1, 0, 0, 1, 1 };
double z[8] = { 0, 0, 0, 0, 1, 1, 1, 1 };
int tri[N_tri][3] = {
{0,1,3}, {0,3,2}, {4,5,7}, {4,7,6}, // z faces
{0,1,4}, {1,4,5}, {2,3,6}, {3,6,7}, // y faces
{0,2,4}, {2,4,6}, {1,3,5}, {3,5,7} // x faces
const int N_tri = 12;
double x[8] = { 0, 1, 0, 1, 0, 1, 0, 1 };
double y[8] = { 0, 0, 1, 1, 0, 0, 1, 1 };
double z[8] = { 0, 0, 0, 0, 1, 1, 1, 1 };
int tri[N_tri][3] = {
{ 0, 1, 3 }, { 0, 3, 2 }, { 4, 5, 7 }, { 4, 7, 6 }, // z faces
{ 0, 1, 4 }, { 1, 4, 5 }, { 2, 3, 6 }, { 3, 6, 7 }, // y faces
{ 0, 2, 4 }, { 2, 4, 6 }, { 1, 3, 5 }, { 3, 5, 7 } // x faces
};
// Create the meshes
auto set1 = std::make_shared<IO::PointList>(N_points);
for (int i=0; i<N_points; i++) {
auto set1 = std::make_shared<IO::PointList>( N_points );
for ( int i = 0; i < N_points; i++ ) {
set1->points[i].x = x[i];
set1->points[i].y = y[i];
set1->points[i].z = z[i];
}
auto trimesh = std::make_shared<IO::TriMesh>(N_tri,set1);
for (int i=0; i<N_tri; i++) {
auto trimesh = std::make_shared<IO::TriMesh>( N_tri, set1 );
for ( int i = 0; i < N_tri; i++ ) {
trimesh->A[i] = tri[i][0];
trimesh->B[i] = tri[i][1];
trimesh->C[i] = tri[i][2];
}
auto trilist = std::make_shared<IO::TriList>(*trimesh);
for (int i=0; i<N_tri; i++) {
Point A(x[tri[i][0]],y[tri[i][0]],z[tri[i][0]]);
Point B(x[tri[i][1]],y[tri[i][1]],z[tri[i][1]]);
Point C(x[tri[i][2]],y[tri[i][2]],z[tri[i][2]]);
if ( !approx_equal(trilist->A[i],A) || !approx_equal(trilist->B[i],B) || !approx_equal(trilist->C[i],C) )
{
printf("Failed to create trilist\n");
auto trilist = std::make_shared<IO::TriList>( *trimesh );
for ( int i = 0; i < N_tri; i++ ) {
Point A( x[tri[i][0]], y[tri[i][0]], z[tri[i][0]] );
Point B( x[tri[i][1]], y[tri[i][1]], z[tri[i][1]] );
Point C( x[tri[i][2]], y[tri[i][2]], z[tri[i][2]] );
if ( !approx_equal( trilist->A[i], A ) || !approx_equal( trilist->B[i], B ) ||
!approx_equal( trilist->C[i], C ) ) {
printf( "Failed to create trilist\n" );
return -1;
}
}
RankInfoStruct rank_data( rank, nprocs, 1, 1 );
auto domain = std::make_shared<IO::DomainMesh>(rank_data,6,7,8,1.0,1.0,1.0);
auto domain = std::make_shared<IO::DomainMesh>( rank_data, 6, 7, 8, 1.0, 1.0, 1.0 );
// Create the variables
const auto NodeVar = IO::VariableType::NodeVariable;
const auto VolVar = IO::VariableType::VolumeVariable;
auto set_node_mag = std::make_shared<IO::Variable>(1,NodeVar,"Node_set_mag");
auto set_node_vec = std::make_shared<IO::Variable>(3,NodeVar,"Node_set_vec");
auto list_node_mag = std::make_shared<IO::Variable>(1,NodeVar,"Node_list_mag");
auto list_node_vec = std::make_shared<IO::Variable>(3,NodeVar,"Node_list_vec");
auto point_node_mag = std::make_shared<IO::Variable>(1,NodeVar,"Node_point_mag");
auto point_node_vec = std::make_shared<IO::Variable>(3,NodeVar,"Node_point_vec");
auto domain_node_mag = std::make_shared<IO::Variable>(1,NodeVar,"Node_domain_mag");
auto domain_node_vec = std::make_shared<IO::Variable>(3,NodeVar,"Node_domain_vec");
auto set_cell_mag = std::make_shared<IO::Variable>(1,VolVar,"Cell_set_mag");
auto set_cell_vec = std::make_shared<IO::Variable>(3,VolVar,"Cell_set_vec");
auto list_cell_mag = std::make_shared<IO::Variable>(1,VolVar,"Cell_list_mag");
auto list_cell_vec = std::make_shared<IO::Variable>(3,VolVar,"Cell_list_vec");
auto domain_cell_mag = std::make_shared<IO::Variable>(1,VolVar,"Cell_domain_mag");
auto domain_cell_vec = std::make_shared<IO::Variable>(3,VolVar,"Cell_domain_vec");
auto set_node_mag = std::make_shared<IO::Variable>( 1, NodeVar, "Node_set_mag" );
auto set_node_vec = std::make_shared<IO::Variable>( 3, NodeVar, "Node_set_vec" );
auto list_node_mag = std::make_shared<IO::Variable>( 1, NodeVar, "Node_list_mag" );
auto list_node_vec = std::make_shared<IO::Variable>( 3, NodeVar, "Node_list_vec" );
auto point_node_mag = std::make_shared<IO::Variable>( 1, NodeVar, "Node_point_mag" );
auto point_node_vec = std::make_shared<IO::Variable>( 3, NodeVar, "Node_point_vec" );
auto domain_node_mag = std::make_shared<IO::Variable>( 1, NodeVar, "Node_domain_mag" );
auto domain_node_vec = std::make_shared<IO::Variable>( 3, NodeVar, "Node_domain_vec" );
auto set_cell_mag = std::make_shared<IO::Variable>( 1, VolVar, "Cell_set_mag" );
auto set_cell_vec = std::make_shared<IO::Variable>( 3, VolVar, "Cell_set_vec" );
auto list_cell_mag = std::make_shared<IO::Variable>( 1, VolVar, "Cell_list_mag" );
auto list_cell_vec = std::make_shared<IO::Variable>( 3, VolVar, "Cell_list_vec" );
auto domain_cell_mag = std::make_shared<IO::Variable>( 1, VolVar, "Cell_domain_mag" );
auto domain_cell_vec = std::make_shared<IO::Variable>( 3, VolVar, "Cell_domain_vec" );
point_node_mag->data.resize( N_points );
point_node_vec->data.resize( N_points, 3 );
for (int i=0; i<N_points; i++) {
point_node_mag->data(i) = distance(set1->points[i]);
point_node_vec->data(i,0) = set1->points[i].x;
point_node_vec->data(i,1) = set1->points[i].y;
point_node_vec->data(i,2) = set1->points[i].z;
for ( int i = 0; i < N_points; i++ ) {
point_node_mag->data( i ) = distance( set1->points[i] );
point_node_vec->data( i, 0 ) = set1->points[i].x;
point_node_vec->data( i, 1 ) = set1->points[i].y;
point_node_vec->data( i, 2 ) = set1->points[i].z;
}
set_node_mag->data = point_node_mag->data;
set_node_vec->data = point_node_vec->data;
list_node_mag->data.resize( 3*N_tri );
list_node_vec->data.resize( 3*N_tri, 3 );
for (int i=0; i<N_points; i++) {
list_node_mag->data(3*i+0) = distance(trilist->A[i]);
list_node_mag->data(3*i+1) = distance(trilist->B[i]);
list_node_mag->data(3*i+2) = distance(trilist->C[i]);
list_node_vec->data(3*i+0,0) = trilist->A[i].x;
list_node_vec->data(3*i+0,1) = trilist->A[i].y;
list_node_vec->data(3*i+0,2) = trilist->A[i].z;
list_node_vec->data(3*i+1,0) = trilist->B[i].x;
list_node_vec->data(3*i+1,1) = trilist->B[i].y;
list_node_vec->data(3*i+1,2) = trilist->B[i].z;
list_node_vec->data(3*i+2,0) = trilist->C[i].x;
list_node_vec->data(3*i+2,1) = trilist->C[i].y;
list_node_vec->data(3*i+2,2) = trilist->C[i].z;
list_node_mag->data.resize( 3 * N_tri );
list_node_vec->data.resize( 3 * N_tri, 3 );
for ( int i = 0; i < N_points; i++ ) {
list_node_mag->data( 3 * i + 0 ) = distance( trilist->A[i] );
list_node_mag->data( 3 * i + 1 ) = distance( trilist->B[i] );
list_node_mag->data( 3 * i + 2 ) = distance( trilist->C[i] );
list_node_vec->data( 3 * i + 0, 0 ) = trilist->A[i].x;
list_node_vec->data( 3 * i + 0, 1 ) = trilist->A[i].y;
list_node_vec->data( 3 * i + 0, 2 ) = trilist->A[i].z;
list_node_vec->data( 3 * i + 1, 0 ) = trilist->B[i].x;
list_node_vec->data( 3 * i + 1, 1 ) = trilist->B[i].y;
list_node_vec->data( 3 * i + 1, 2 ) = trilist->B[i].z;
list_node_vec->data( 3 * i + 2, 0 ) = trilist->C[i].x;
list_node_vec->data( 3 * i + 2, 1 ) = trilist->C[i].y;
list_node_vec->data( 3 * i + 2, 2 ) = trilist->C[i].z;
}
domain_node_mag->data.resize(domain->nx+1,domain->ny+1,domain->nz+1);
domain_node_vec->data.resize({(size_t)domain->nx+1,(size_t)domain->ny+1,(size_t)domain->nz+1,3});
for (int i=0; i<domain->nx+1; i++) {
for (int j=0; j<domain->ny+1; j++) {
for (int k=0; k<domain->nz+1; k++) {
domain_node_mag->data(i,j,k) = distance(Point(i,j,k));
domain_node_vec->data(i,j,k,0) = Point(i,j,k).x;
domain_node_vec->data(i,j,k,1) = Point(i,j,k).y;
domain_node_vec->data(i,j,k,2) = Point(i,j,k).z;
domain_node_mag->data.resize( domain->nx + 1, domain->ny + 1, domain->nz + 1 );
domain_node_vec->data.resize(
{ (size_t) domain->nx + 1, (size_t) domain->ny + 1, (size_t) domain->nz + 1, 3 } );
for ( int i = 0; i < domain->nx + 1; i++ ) {
for ( int j = 0; j < domain->ny + 1; j++ ) {
for ( int k = 0; k < domain->nz + 1; k++ ) {
domain_node_mag->data( i, j, k ) = distance( Point( i, j, k ) );
domain_node_vec->data( i, j, k, 0 ) = Point( i, j, k ).x;
domain_node_vec->data( i, j, k, 1 ) = Point( i, j, k ).y;
domain_node_vec->data( i, j, k, 2 ) = Point( i, j, k ).z;
}
}
}
set_cell_mag->data.resize( N_tri );
set_cell_vec->data.resize( N_tri, 3 );
for (int i=0; i<N_tri; i++) {
set_cell_mag->data(i) = i;
set_cell_vec->data(i,0) = 3*i+0;
set_cell_vec->data(i,1) = 3*i+1;
set_cell_vec->data(i,2) = 3*i+2;
for ( int i = 0; i < N_tri; i++ ) {
set_cell_mag->data( i ) = i;
set_cell_vec->data( i, 0 ) = 3 * i + 0;
set_cell_vec->data( i, 1 ) = 3 * i + 1;
set_cell_vec->data( i, 2 ) = 3 * i + 2;
}
list_cell_mag->data = set_cell_mag->data;
list_cell_vec->data = set_cell_vec->data;
domain_cell_mag->data.resize(domain->nx,domain->ny,domain->nz);
domain_cell_vec->data.resize({(size_t)domain->nx,(size_t)domain->ny,(size_t)domain->nz,3});
for (int i=0; i<domain->nx; i++) {
for (int j=0; j<domain->ny; j++) {
for (int k=0; k<domain->nz; k++) {
domain_cell_mag->data(i,j,k) = distance(Point(i,j,k));
domain_cell_vec->data(i,j,k,0) = Point(i,j,k).x;
domain_cell_vec->data(i,j,k,1) = Point(i,j,k).y;
domain_cell_vec->data(i,j,k,2) = Point(i,j,k).z;
domain_cell_mag->data.resize( domain->nx, domain->ny, domain->nz );
domain_cell_vec->data.resize(
{ (size_t) domain->nx, (size_t) domain->ny, (size_t) domain->nz, 3 } );
for ( int i = 0; i < domain->nx; i++ ) {
for ( int j = 0; j < domain->ny; j++ ) {
for ( int k = 0; k < domain->nz; k++ ) {
domain_cell_mag->data( i, j, k ) = distance( Point( i, j, k ) );
domain_cell_vec->data( i, j, k, 0 ) = Point( i, j, k ).x;
domain_cell_vec->data( i, j, k, 1 ) = Point( i, j, k ).y;
domain_cell_vec->data( i, j, k, 2 ) = Point( i, j, k ).z;
}
}
}
// Create the MeshDataStruct
std::vector<IO::MeshDataStruct> meshData(4);
std::vector<IO::MeshDataStruct> meshData( 4 );
meshData[0].meshName = "pointmesh";
meshData[0].mesh = set1;
meshData[0].vars.push_back(point_node_mag);
meshData[0].vars.push_back(point_node_vec);
meshData[0].mesh = set1;
meshData[0].vars.push_back( point_node_mag );
meshData[0].vars.push_back( point_node_vec );
meshData[1].meshName = "trimesh";
meshData[1].mesh = trimesh;
meshData[1].vars.push_back(set_node_mag);
meshData[1].vars.push_back(set_node_vec);
meshData[1].vars.push_back(set_cell_mag);
meshData[1].vars.push_back(set_cell_vec);
meshData[1].mesh = trimesh;
meshData[1].vars.push_back( set_node_mag );
meshData[1].vars.push_back( set_node_vec );
meshData[1].vars.push_back( set_cell_mag );
meshData[1].vars.push_back( set_cell_vec );
meshData[2].meshName = "trilist";
meshData[2].mesh = trilist;
meshData[2].vars.push_back(list_node_mag);
meshData[2].vars.push_back(list_node_vec);
meshData[2].vars.push_back(list_cell_mag);
meshData[2].vars.push_back(list_cell_vec);
meshData[2].mesh = trilist;
meshData[2].vars.push_back( list_node_mag );
meshData[2].vars.push_back( list_node_vec );
meshData[2].vars.push_back( list_cell_mag );
meshData[2].vars.push_back( list_cell_vec );
meshData[3].meshName = "domain";
meshData[3].mesh = domain;
meshData[3].vars.push_back(domain_node_mag);
meshData[3].vars.push_back(domain_node_vec);
meshData[3].vars.push_back(domain_cell_mag);
meshData[3].vars.push_back(domain_cell_vec);
meshData[3].mesh = domain;
meshData[3].vars.push_back( domain_node_mag );
meshData[3].vars.push_back( domain_node_vec );
meshData[3].vars.push_back( domain_cell_mag );
meshData[3].vars.push_back( domain_cell_vec );
for ( const auto &data : meshData )
ASSERT( data.check( true ) );
// Run the tests
testWriter( "old", meshData, ut );
@ -384,11 +401,9 @@ int main(int argc, char **argv)
// Finished
ut.report();
PROFILE_SAVE("TestWriter",true);
PROFILE_SAVE( "TestWriter", true );
int N_errors = ut.NumFailGlobal();
comm.barrier();
Utilities::shutdown();
return N_errors;
}

113
tests/convertIO.cpp
View File

@ -5,85 +5,66 @@
#include <stdexcept>
#include <fstream>
#include "common/MPI_Helpers.h"
#include "common/Communication.h"
#include "common/MPI.h"
#include "common/Utilities.h"
#include "IO/Mesh.h"
#include "IO/Reader.h"
#include "IO/Writer.h"
#include "ProfilerApp.h"
int main(int argc, char **argv)
{
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
Utilities::setErrorHandlers();
PROFILE_ENABLE(2);
PROFILE_ENABLE_TRACE();
PROFILE_START("Main");
{ // Limit scope
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::setErrorHandlers();
PROFILE_ENABLE(2);
PROFILE_ENABLE_TRACE();
PROFILE_START("Main");
// Get inputs
if ( argc != 3 ) {
std::cerr << "Error calling convertIO:\n";
std::cerr << " convertIO input_file format\n";
return -1;
}
std::string filename = argv[1];
std::string format = argv[2];
std::string path = IO::getPath( filename );
{ // Limit scope
// Read the timesteps
auto timesteps = IO::readTimesteps( filename );
// Loop through the timesteps, reading/writing the data
IO::initialize( "", format, false );
for ( auto timestep : timesteps ) {
// Read the list of MeshDatabase
auto databases = IO::getMeshList( path, timestep );
// Build the MeshDataStruct
std::vector<IO::MeshDataStruct> meshData(databases.size());
// Loop through the database
int i = 0;
PROFILE_START("Read");
for ( const auto& database : databases ) {
// Read the appropriate mesh domain
ASSERT( (int) database.domains.size() == nprocs );
meshData[i].meshName = database.name;
meshData[i].mesh = IO::getMesh( path, timestep, database, rank );
// Read the variables
for ( auto var : database.variables ) {
auto varData = IO::getVariable( path, timestep, database, rank, var.name );
IO::reformatVariable( *meshData[i].mesh, *varData );
meshData[i].vars.push_back( varData );
}
i++;
Utilities::MPI comm( MPI_COMM_WORLD );
// Get inputs
if ( argc != 5 ) {
std::cerr << "Error calling convertIO:\n";
std::cerr << " convertIO <input_path> <input_format> <output_path> <output_format>\n";
return -1;
}
MPI_Barrier(comm);
PROFILE_STOP("Read");
std::string path_in = argv[1];
std::string format_in = argv[2];
std::string path_out = argv[3];
std::string format_out = argv[4];
// Save the mesh data to a new file
PROFILE_START("Write");
IO::writeData( timestep, meshData, MPI_COMM_WORLD );
MPI_Barrier(comm);
PROFILE_STOP("Write");
}
// Check that we have enough ranks to load and write the data
// This is really only a bottleneck for the writer
int N_domains = IO::maxDomains( path_in, format_in, comm );
ASSERT( comm.getSize() == N_domains );
} // Limit scope
PROFILE_STOP("Main");
PROFILE_SAVE("convertData",true);
comm.barrier();
Utilities::shutdown();
return 0;
// Read the timesteps
auto timesteps = IO::readTimesteps( path_in, format_in );
// Loop through the timesteps, reading/writing the data
IO::initialize( path_out, format_out, false );
for ( auto timestep : timesteps ) {
// Set the domain to read (needs to be the current rank for the writer to be valid)
int domain = comm.getRank();
// Get the maximum number of domains for the
auto data = IO::readData( path_in, timestep, domain );
// Save the mesh data to a new file
IO::writeData( timestep, data, comm );
}
} // Limit scope
// shutdown
PROFILE_STOP("Main");
PROFILE_SAVE("convertData",true);
Utilities::shutdown();
return 0;
}