Creating initial reader for netcdf
This commit is contained in:
Mark Berrill
parent
865726d3c0
commit
b5da224624
@ -105,6 +105,7 @@ IF ( NOT ONLY_BUILD_DOCS )
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CONFIGURE_MPI() # MPI must be before other libraries
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CONFIGURE_CUDA()
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CONFIGURE_MIC()
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CONFIGURE_NETCDF()
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CONFIGURE_LBPM()
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CONFIGURE_TIMER( 0 "${${PROJ}_INSTALL_DIR}/null_timer" )
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CONFIGURE_LINE_COVERAGE()
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288
IO/netcdf.cpp
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288
IO/netcdf.cpp
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@ -0,0 +1,288 @@
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#include "IO/netcdf.h"
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#include "common/Utilities.h"
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#include "ProfilerApp.h"
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#ifdef USE_NETCDF
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#include <netcdf.h>
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#define CHECK_NC_ERR( ERR ) \
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do { \
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if ( ERR != NC_NOERR ) { \
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std::string msg = "Error calling netcdf routine: "; \
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msg += nc_strerror( ERR ); \
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ERROR( msg ); \
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} \
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} while (0)
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namespace netcdf {
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// Function to reverse an array
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template<class TYPE>
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inline std::vector<TYPE> reverse( const std::vector<TYPE>& x )
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{
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std::vector<TYPE> y(x.size());
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for (size_t i=0; i<x.size(); i++)
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y[i] = x[x.size()-i-1];
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return y;
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}
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/****************************************************
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* Open/close a file *
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****************************************************/
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int open( const std::string& filename )
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{
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int fid = 0;
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int err = nc_open( filename.c_str(), NC_NOWRITE, &fid );
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CHECK_NC_ERR( err );
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return fid;
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}
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void close( int fid )
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{
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int err = nc_close( fid );
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if ( err != NC_NOERR )
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ERROR("Error closing file");
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}
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/****************************************************
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* Query basic properties *
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****************************************************/
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static std::vector<size_t> getDimVar( int fid, int varid )
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{
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int ndim = 0;
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int err = nc_inq_varndims( fid, varid, &ndim );
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CHECK_NC_ERR( err );
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std::vector<size_t> dims(ndim,0);
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int dimid[64] = {-1};
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err = nc_inq_vardimid( fid, varid, dimid );
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CHECK_NC_ERR( err );
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for (int i=0; i<ndim; i++) {
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err = nc_inq_dimlen( fid, dimid[i], &dims[i] );
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CHECK_NC_ERR( err );
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}
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return dims;
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}
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static int getVarID( int fid, const std::string& var )
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{
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int id = -1;
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int err = nc_inq_varid( fid, var.c_str(), &id );
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CHECK_NC_ERR( err );
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return id;
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}
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std::vector<size_t> getVarDim( int fid, const std::string& var )
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{
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return getDimVar( fid, getVarID( fid, var ) );
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}
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std::vector<size_t> getAttDim( int fid, const std::string& att )
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{
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std::vector<size_t> dim(1,0);
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int err = nc_inq_attlen( fid, NC_GLOBAL, att.c_str(), dim.data() );
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return dim;
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}
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std::vector<std::string> getVarNames( int fid )
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{
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int nvar;
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int err = nc_inq( fid, NULL, &nvar, NULL, NULL );
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CHECK_NC_ERR( err );
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std::vector<std::string> vars(nvar);
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for (int i=0; i<nvar; i++) {
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char name[NC_MAX_NAME+1];
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err = nc_inq_varname( fid, i, name );
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CHECK_NC_ERR( err );
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vars[i] = name;
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}
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return vars;
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}
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std::vector<std::string> getAttNames( int fid )
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{
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int natt;
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int err = nc_inq( fid, NULL, NULL, &natt, NULL );
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CHECK_NC_ERR( err );
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std::vector<std::string> att(natt);
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for (int i=0; i<natt; i++) {
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char name[NC_MAX_NAME+1];
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err = nc_inq_attname( fid, NC_GLOBAL, i, name );
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CHECK_NC_ERR( err );
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att[i] = name;
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}
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return att;
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}
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static inline VariableType convertType( nc_type type )
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{
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VariableType type2;
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if ( type == NC_BYTE )
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type2 = BYTE;
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else if ( type == NC_CHAR )
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type2 = STRING;
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else if ( type == NC_SHORT )
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type2 = SHORT;
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else if ( type == NC_USHORT )
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type2 = USHORT;
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else if ( type == NC_INT )
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type2 = INT;
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else if ( type == NC_UINT )
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type2 = UINT;
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else if ( type == NC_INT64 )
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type2 = INT64;
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else if ( type == NC_UINT64 )
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type2 = UINT64;
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else if ( type == NC_FLOAT )
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type2 = FLOAT;
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else if ( type == NC_DOUBLE )
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type2 = DOUBLE;
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else
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ERROR("Unknown type");
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return type2;
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}
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VariableType getVarType( int fid, const std::string& var )
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{
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int varid = -1;
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int err = nc_inq_varid( fid, var.c_str(), &varid );
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CHECK_NC_ERR( err );
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nc_type type;
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err = nc_inq_vartype( fid, varid, &type );
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CHECK_NC_ERR( err );
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return convertType(type);
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}
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VariableType getAttType( int fid, const std::string& att )
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{
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nc_type type;
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int err = nc_inq_atttype( fid, NC_GLOBAL, att.c_str(), &type );
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CHECK_NC_ERR( err );
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return convertType(type);
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}
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/****************************************************
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* Read a variable *
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****************************************************/
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template<>
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Array<unsigned short> getVar<unsigned short>( int fid, const std::string& var )
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{
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PROFILE_START("getVar<unsigned short>");
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Array<unsigned short> x( reverse(getVarDim(fid,var)) );
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int err = nc_get_var_ushort( fid, getVarID(fid,var), x.get() );
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CHECK_NC_ERR( err );
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PROFILE_STOP("getVar<unsigned short>");
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return x;
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}
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template<>
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Array<short> getVar<short>( int fid, const std::string& var )
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{
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PROFILE_START("getVar<short>");
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Array<short> x( reverse(getVarDim(fid,var)) );
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int err = nc_get_var_short( fid, getVarID(fid,var), x.get() );
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CHECK_NC_ERR( err );
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PROFILE_STOP("getVar<short>");
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return x;
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}
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template<>
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Array<unsigned int> getVar<unsigned int>( int fid, const std::string& var )
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{
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PROFILE_START("getVar<unsigned int>");
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Array<unsigned int> x( reverse(getVarDim(fid,var)) );
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int err = nc_get_var_uint( fid, getVarID(fid,var), x.get() );
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CHECK_NC_ERR( err );
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PROFILE_STOP("getVar<unsigned int>");
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return x;
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}
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template<>
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Array<int> getVar<int>( int fid, const std::string& var )
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{
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PROFILE_START("getVar<int>");
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Array<int> x( reverse(getVarDim(fid,var)) );
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int err = nc_get_var_int( fid, getVarID(fid,var), x.get() );
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CHECK_NC_ERR( err );
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PROFILE_STOP("getVar<int>");
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return x;
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}
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template<>
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Array<float> getVar<float>( int fid, const std::string& var )
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{
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PROFILE_START("getVar<float>");
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Array<float> x( reverse(getVarDim(fid,var)) );
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int err = nc_get_var_float( fid, getVarID(fid,var), x.get() );
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CHECK_NC_ERR( err );
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PROFILE_STOP("getVar<float>");
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return x;
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}
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template<>
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Array<double> getVar<double>( int fid, const std::string& var )
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{
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PROFILE_START("getVar<double>");
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Array<double> x( reverse(getVarDim(fid,var)) );
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int err = nc_get_var_double( fid, getVarID(fid,var), x.get() );
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CHECK_NC_ERR( err );
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PROFILE_STOP("getVar<double>");
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return x;
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}
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template<>
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Array<char> getVar<char>( int fid, const std::string& var )
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{
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PROFILE_START("getVar<char>");
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Array<char> x( reverse(getVarDim(fid,var)) );
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int err = nc_get_var_text( fid, getVarID(fid,var), x.get() );
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CHECK_NC_ERR( err );
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PROFILE_STOP("getVar<char>");
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return x;
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}
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template<>
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Array<std::string> getVar<std::string>( int fid, const std::string& var )
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{
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PROFILE_START("getVar<std::string>");
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Array<char> tmp = getVar<char>( fid, var );
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std::vector<size_t> dim = tmp.size();
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if ( dim.size() == 1 )
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dim[0] = 1;
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else
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dim.erase( dim.begin() );
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Array<std::string> text(dim);
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for (size_t i=0; i<text.length(); i++)
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text(i) = &(tmp(0,i));
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PROFILE_STOP("getVar<std::string>");
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return text;
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}
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/****************************************************
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* Read an attribute *
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****************************************************/
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template<>
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Array<double> getAtt<double>( int fid, const std::string& att )
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{
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PROFILE_START("getAtt<double>");
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Array<double> x( getAttDim(fid,att) );
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int err = nc_get_att_double( fid, NC_GLOBAL, att.c_str(), x.get() );
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CHECK_NC_ERR( err );
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PROFILE_STOP("getAtt<double>");
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return x;
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}
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template<>
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Array<std::string> getAtt<std::string>( int fid, const std::string& att )
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{
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PROFILE_START("getAtt<std::string>");
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char *tmp = new char[getAttDim(fid,att)[0]];
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Array<std::string> x(1);
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x(0) = tmp;
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delete [] tmp;
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PROFILE_STOP("getAtt<std::string>");
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return x;
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}
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}; // netcdf namespace
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#else
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#endif
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98
IO/netcdf.h
Normal file
98
IO/netcdf.h
Normal file
@ -0,0 +1,98 @@
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#ifndef NETCDF_READER
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#define NETCDF_READER
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#include <string>
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#include <vector>
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#include "common/Array.h"
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namespace netcdf {
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//! Enum to hold variable type
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enum VariableType { BYTE, SHORT, USHORT, INT, UINT, INT64, UINT64, FLOAT, DOUBLE, STRING };
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/*!
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* @brief Open netcdf file
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* @detailed This function opens a netcdf file
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* @return This function returns a handle to the file
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* @param filename File to open
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*/
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int open( const std::string& filename );
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/*!
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* @brief Close netcdf file
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* @detailed This function closes a netcdf file
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* @param fid Handle to the open file
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*/
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void close( int fid );
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/*!
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* @brief Read the variable names
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* @detailed This function reads a list of the variable names in the file
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* @param fid Handle to the open file
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*/
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std::vector<std::string> getVarNames( int fid );
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/*!
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* @brief Read the attribute names
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* @detailed This function reads a list of the attribute names in the file
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* @param fid Handle to the open file
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*/
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std::vector<std::string> getAttNames( int fid );
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/*!
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* @brief Return the variable type
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* @detailed This function returns the type for a variable
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* @param fid Handle to the open file
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* @param var Variable to read
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*/
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VariableType getVarType( int fid, const std::string& var );
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/*!
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* @brief Return the attribute type
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* @detailed This function returns the type for an attribute
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* @param fid Handle to the open file
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* @param att Attribute to read
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*/
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VariableType getAttType( int fid, const std::string& att );
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/*!
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* @brief Return the variable dimensions
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* @detailed This function returns the die for a variable
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* @param fid Handle to the open file
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* @param var Variable to read
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*/
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std::vector<size_t> getVarDim( int fid, const std::string& var );
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/*!
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* @brief Read a variable
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* @detailed This function reads a variable with the given name from the file
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* @param fid Handle to the open file
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* @param var Variable to read
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*/
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template<class TYPE>
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Array<TYPE> getVar( int fid, const std::string& var );
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/*!
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* @brief Read an attribute
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* @detailed This function reads an attribute with the given name from the file
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* @param fid Handle to the open file
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* @param att Attribute to read
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*/
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template<class TYPE>
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Array<TYPE> getAtt( int fid, const std::string& att );
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}; // netcdf namespace
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#endif
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@ -75,7 +75,9 @@ ENDMACRO()
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# Macro to configure MIC
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MACRO( CONFIGURE_MIC )
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CHECK_ENABLE_FLAG( USE_MIC 0 )
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ADD_DEFINITIONS ( "-D USE_MIC" )
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IF ( USE_MIC )
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ADD_DEFINITIONS( "-D USE_MIC" )
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ENDIF()
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ENDMACRO()
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@ -173,6 +175,65 @@ MACRO( CONFIGURE_MPI )
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ENDMACRO()
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# Macro to find and configure hdf5
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MACRO ( CONFIGURE_HDF5 )
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CHECK_ENABLE_FLAG( USE_HDF5 0 )
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IF ( USE_HDF5 )
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# Check if we specified the silo directory
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IF ( HDF5_DIRECTORY )
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VERIFY_PATH ( ${HDF5_DIRECTORY} )
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INCLUDE_DIRECTORIES ( ${HDF5_DIRECTORY}/include )
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SET ( HDF5_INCLUDE ${HDF5_DIRECTORY}/include )
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FIND_LIBRARY ( HDF5_LIB NAMES hdf5 PATHS ${HDF5_DIRECTORY}/lib NO_DEFAULT_PATH )
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FIND_LIBRARY ( HDF5_HL_LIB NAMES hdf5_hl PATHS ${HDF5_DIRECTORY}/lib NO_DEFAULT_PATH )
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ELSE()
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MESSAGE( FATAL_ERROR "Default search for hdf5 is not yet supported. Use -D HDF5_DIRECTORY=" )
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ENDIF()
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SET ( HDF5_LIBS
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${HDF5_HL_LIB}
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${HDF5_LIB}
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)
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ADD_DEFINITIONS ( "-D USE_HDF5" )
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MESSAGE( "Using hdf5" )
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MESSAGE( " ${HDF5_LIB}" )
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ENDIF()
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ENDMACRO()
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# Macro to find and configure netcdf
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MACRO( CONFIGURE_NETCDF )
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CHECK_ENABLE_FLAG( USE_NETCDF 0 )
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IF ( USE_NETCDF )
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SET( USE_HDF5 1 )
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CONFIGURE_HDF5()
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IF ( NETCDF_DIRECTORY )
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VERIFY_PATH ( ${NETCDF_DIRECTORY} )
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INCLUDE_DIRECTORIES ( ${NETCDF_DIRECTORY}/include )
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SET ( NETCDF_INCLUDE ${NETCDF_DIRECTORY}/include )
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FIND_LIBRARY( NETCDF_NETCDF_LIB NAMES netcdf PATHS ${NETCDF_DIRECTORY}/lib NO_DEFAULT_PATH )
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FIND_LIBRARY( NETCDF_HDF5_LIB NAMES hdf5 PATHS ${NETCDF_DIRECTORY}/lib NO_DEFAULT_PATH )
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FIND_LIBRARY( NETCDF_HL_LIB NAMES hl PATHS ${NETCDF_DIRECTORY}/lib NO_DEFAULT_PATH )
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IF ( NOT NETCDF_NETCDF_LIB )
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MESSAGE( FATAL_ERROR "Did not find library for netcdf" )
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ENDIF()
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SET ( NETCDF_LIBS ${NETCDF_NETCDF_LIB} )
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IF ( NETCDF_HDF5_LIB )
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SET ( NETCDF_LIBS ${NETCDF_LIBS} ${NETCDF_HDF5_LIB} )
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ENDIF()
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IF ( NETCDF_HL_LIB )
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SET ( NETCDF_LIBS ${NETCDF_LIBS} ${NETCDF_HL_LIB} )
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ENDIF()
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ELSE()
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MESSAGE( FATAL_ERROR "Default search for netcdf is not yet supported. Use -D NETCDF_DIRECTORY=" )
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ENDIF()
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SET( EXTERNAL_LIBS ${EXTERNAL_LIBS} ${NETCDF_LIBS} ${HDF5_LIBS} )
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ADD_DEFINITIONS ( "-D USE_NETCDF" )
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MESSAGE( "Using netcdf" )
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MESSAGE( " ${NETCDF_LIBS}" )
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ENDIF()
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ENDMACRO()
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# Macro to configure system-specific libraries and flags
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MACRO( CONFIGURE_SYSTEM )
|
||||
# First check/set the compile mode
|
||||
|
||||
@ -35,6 +35,9 @@ ADD_LBPM_TEST_PARALLEL( TestMassConservationD3Q7 1 )
|
||||
ADD_LBPM_TEST_1_2_4( testCommunication )
|
||||
ADD_LBPM_TEST_1_2_4( testUtilities )
|
||||
ADD_LBPM_TEST( TestWriter )
|
||||
IF ( USE_NETCDF )
|
||||
ADD_LBPM_PROVISIONAL_TEST( TestNetcdf )
|
||||
ENDIF()
|
||||
|
||||
# Sample test that will run with 1, 2, and 4 processors, failing with 4 or more procs
|
||||
ADD_LBPM_TEST_1_2_4( hello_world )
|
||||
|
||||
57
tests/TestNetcdf.cpp
Normal file
57
tests/TestNetcdf.cpp
Normal file
@ -0,0 +1,57 @@
|
||||
// Sequential blob analysis
|
||||
// Reads parallel simulation data and performs connectivity analysis
|
||||
// and averaging on a blob-by-blob basis
|
||||
// James E. McClure 2014
|
||||
|
||||
#include "IO/netcdf.h"
|
||||
|
||||
#include "ProfilerApp.h"
|
||||
|
||||
|
||||
void load( const std::string filename )
|
||||
{
|
||||
int fid = netcdf::open( filename );
|
||||
|
||||
std::vector<std::string> vars = netcdf::getVarNames( fid );
|
||||
for (size_t i=0; i<vars.size(); i++) {
|
||||
printf("Reading variable %s\n",vars[i].c_str());
|
||||
netcdf::VariableType type = netcdf::getVarType( fid, vars[i] );
|
||||
if ( type == netcdf::STRING )
|
||||
Array<std::string> tmp = netcdf::getVar<std::string>( fid, vars[i] );
|
||||
else if ( type == netcdf::SHORT )
|
||||
Array<short> tmp = netcdf::getVar<short>( fid, vars[i] );
|
||||
else
|
||||
Array<double> tmp = netcdf::getVar<double>( fid, vars[i] );
|
||||
}
|
||||
|
||||
std::vector<std::string> attr = netcdf::getAttNames( fid );
|
||||
for (size_t i=0; i<attr.size(); i++) {
|
||||
printf("Reading attribute %s\n",attr[i].c_str());
|
||||
netcdf::VariableType type = netcdf::getAttType( fid, attr[i] );
|
||||
if ( type == netcdf::STRING )
|
||||
Array<std::string> tmp = netcdf::getAtt<std::string>( fid, attr[i] );
|
||||
else
|
||||
Array<double> tmp = netcdf::getAtt<double>( fid, attr[i] );
|
||||
}
|
||||
netcdf::close( fid );
|
||||
}
|
||||
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
PROFILE_START("Main");
|
||||
|
||||
std::vector<std::string> filenames;
|
||||
|
||||
if ( argc==0 ) {
|
||||
printf("At least one filename must be specified\n");
|
||||
return 1;
|
||||
}
|
||||
|
||||
for (int i=1; i<argc; i++)
|
||||
load( argv[i] );
|
||||
|
||||
PROFILE_SAVE("TestNetcdf");
|
||||
return 0;
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user