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Fixing bug with netcdf writer

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This commit is contained in:
Mark Berrill
2016-06-28 16:00:30 -04:00
parent f0aa2724bc
commit a00979dd4d
5 changed files with 20 additions and 53 deletions
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49
IO/netcdf.cpp
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@@ -140,7 +140,7 @@ int open( const std::string& filename, FileMode mode, MPI_Comm comm )
int err = nc_open_par( filename.c_str(), NC_WRITE|NC_MPIPOSIX, comm, MPI_INFO_NULL, &fid );
CHECK_NC_ERR( err );
} else if ( mode == CREATE ) {
int err = nc_create_par( filename.c_str(), NC_MPIPOSIX, comm, MPI_INFO_NULL, &fid );
int err = nc_create_par( filename.c_str(), NC_NETCDF4|NC_MPIIO, comm, MPI_INFO_NULL, &fid );
CHECK_NC_ERR( err );
} else {
ERROR("Unknown file mode");
@@ -436,31 +436,8 @@ std::vector<int> defDim( int fid, const std::vector<std::string>& names, const s
return dimid;
}
template<class TYPE>
int nc_put_vars_TYPE( int, int, const size_t*, const size_t*, const ptrdiff_t*, const TYPE* );
template<>
int nc_put_vars_TYPE<short>( int fid, int varid, const size_t* start, const size_t* count, const ptrdiff_t* stride, const short* data )
{
return nc_put_vars_short( fid, varid, start, count, stride, data );
}
template<>
int nc_put_vars_TYPE<int>( int fid, int varid, const size_t* start, const size_t* count, const ptrdiff_t* stride, const int* data )
{
return nc_put_vars_int( fid, varid, start, count, stride, data );
}
template<>
int nc_put_vars_TYPE<float>( int fid, int varid, const size_t* start, const size_t* count, const ptrdiff_t* stride, const float* data )
{
return nc_put_vars_float( fid, varid, start, count, stride, data );
}
template<>
int nc_put_vars_TYPE<double>( int fid, int varid, const size_t* start, const size_t* count, const ptrdiff_t* stride, const double* data )
{
return nc_put_vars_double( fid, varid, start, count, stride, data );
}
template<class TYPE>
void write( int fid, const std::string& var, const std::vector<int>& dimids,
const Array<TYPE>& data, const std::vector<size_t>& start,
const std::vector<size_t>& count, const std::vector<size_t>& stride )
const Array<TYPE>& data, const RankInfoStruct& info )
{
// Define the variable
int varid = 0;
@@ -470,24 +447,18 @@ void write( int fid, const std::string& var, const std::vector<int>& dimids,
err = nc_enddef( fid );
CHECK_NC_ERR( err );
// set the access method to use MPI/PnetCDF collective I/O
err = nc_var_par_access( fid, varid, NC_COLLECTIVE );
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();
nc_put_vars_TYPE<TYPE>( fid, varid, start.data(), count.data(), (const ptrdiff_t*) stride.data(), x.data() );
std::vector<size_t> count = data.size();
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 std::vector<size_t>& start,
const std::vector<size_t>& count, const std::vector<size_t>& stride );
template void write<int>( int fid, const std::string& var, const std::vector<int>& dimids,
const Array<int>& data, const std::vector<size_t>& start,
const std::vector<size_t>& count, const std::vector<size_t>& stride );
template void write<float>( int fid, const std::string& var, const std::vector<int>& dimids,
const Array<float>& data, const std::vector<size_t>& start,
const std::vector<size_t>& count, const std::vector<size_t>& stride );
template void write<double>( int fid, const std::string& var, const std::vector<int>& dimids,
const Array<double>& data, const std::vector<size_t>& start,
const std::vector<size_t>& count, const std::vector<size_t>& stride );
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 );