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fix failed merge

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This commit is contained in:
JamesEMcclure
2020-03-17 21:44:45 -04:00
parent 9f5b44dfe4
commit 05cafcb525
125 changed files with 2544 additions and 8538 deletions
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145
IO/MeshDatabase.cpp
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@@ -1,8 +1,7 @@
#include "IO/MeshDatabase.h"
#include "IO/Mesh.h"
#include "IO/PackData.h"
#include "IO/IOHelpers.h"
#include "common/MPI.h"
#include "common/MPI_Helpers.h"
#include "common/Utilities.h"
#include <vector>
@@ -14,6 +13,8 @@
/****************************************************
****************************************************/
// MeshType
template<>
size_t packsize<IO::MeshType>( const IO::MeshType& rhs )
@@ -246,76 +247,80 @@ void DatabaseEntry::read( const std::string& line )
// 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 )
std::vector<MeshDatabase> gatherAll( const std::vector<MeshDatabase>& meshes, MPI_Comm comm )
{
if ( comm.getSize() == 1 )
return meshes;
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]));
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]));
}
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 );
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];
globalsize += recvsize[i];
}
PROFILE_STOP("gatherAll-send1",2);
// Send/recv the global data
PROFILE_START("gatherAll-send2",2);
auto globalbuf = new double[globalsize];
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;
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() ) {
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());
#ifdef USE_MPI
PROFILE_START("gatherAll");
PROFILE_START("gatherAll-pack",2);
int size = MPI_WORLD_SIZE();
// 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]));
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]));
}
}
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());
}
// Free temporary memory
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)
data2[i] = it->second;
PROFILE_STOP("gatherAll-unpack",2);
PROFILE_STOP("gatherAll");
return data2;
PROFILE_STOP("gatherAll-pack",2);
// Get the number of bytes each processor will be sending/recieving
PROFILE_START("gatherAll-send1",2);
auto recvsize = new int[size];
MPI_Allgather(&localsize,1,MPI_INT,recvsize,1,MPI_INT,comm);
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];
globalsize += recvsize[i];
}
PROFILE_STOP("gatherAll-send1",2);
// Send/recv the global data
PROFILE_START("gatherAll-send2",2);
auto globalbuf = new double[globalsize];
MPI_Allgatherv(localbuf,localsize,MPI_DOUBLE,globalbuf,recvsize,disp,MPI_DOUBLE,comm);
PROFILE_STOP("gatherAll-send2",2);
// Unpack the 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() ) {
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 (std::map<std::string,MeshDatabase>::iterator 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());
}
// Free temporary memory
delete [] localbuf;
delete [] recvsize;
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)
data2[i] = it->second;
PROFILE_STOP("gatherAll-unpack",2);
PROFILE_STOP("gatherAll");
return data2;
#else
return meshes;
#endif
}