tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

ENH: Enable multi file writes.

Browse Source
This commit is contained in:
Lars Pastewka
2017-10-01 14:21:09 +02:00
parent 84378f8ae2
commit 100231bba8
2 changed files with 57 additions and 15 deletions
Download Patch File Download Diff File Expand all files Collapse all files

35
src/USER-NETCDF/dump_netcdf.cpp
View File

@ -88,8 +88,8 @@ DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
if (multiproc)
error->all(FLERR,"Multi-processor writes are not supported.");
if (multifile)
error->all(FLERR,"Multiple files are not supported.");
if (append_flag && multifile)
error->all(FLERR,"Cannot append when writing to multiple files.");
perat = new nc_perat_t[nfield];
@ -224,6 +224,24 @@ DumpNetCDF::~DumpNetCDF()
void DumpNetCDF::openfile()
{
char *filecurrent = filename;
if (multifile && !singlefile_opened) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
if (thermo && !singlefile_opened) {
if (thermovar) delete [] thermovar;
thermovar = new int[output->thermo->nfield];
@ -268,14 +286,14 @@ void DumpNetCDF::openfile()
ntotalgr = group->count(igroup);
if (filewriter) {
if (append_flag && access(filename, F_OK) != -1) {
if (append_flag && !multifile && access(filecurrent, F_OK) != -1) {
// Fixme! Perform checks if dimensions and variables conform with
// data structure standard.
if (singlefile_opened) return;
singlefile_opened = 1;
NCERRX( nc_open(filename, NC_WRITE, &ncid), filename );
NCERRX( nc_open(filecurrent, NC_WRITE, &ncid), filecurrent );
// dimensions
NCERRX( nc_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR );
@ -348,8 +366,8 @@ void DumpNetCDF::openfile()
if (singlefile_opened) return;
singlefile_opened = 1;
NCERRX( nc_create(filename, NC_64BIT_DATA, &ncid),
filename );
NCERRX( nc_create(filecurrent, NC_64BIT_DATA, &ncid),
filecurrent );
// dimensions
NCERRX( nc_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim),
@ -601,7 +619,10 @@ void DumpNetCDF::closefile()
// append next time DumpNetCDF::openfile is called
append_flag = 1;
// write to next frame upon next open
framei++;
if (multifile)
framei = 1;
else
framei++;
}
}

37
src/USER-NETCDF/dump_netcdf_mpiio.cpp
View File

@ -88,8 +88,8 @@ DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) :
if (multiproc)
error->all(FLERR,"Multi-processor writes are not supported.");
if (multifile)
error->all(FLERR,"Multiple files are not supported.");
if (append_flag && multifile)
error->all(FLERR,"Cannot append when writing to multiple files.");
perat = new nc_perat_t[nfield];
@ -217,6 +217,24 @@ DumpNetCDFMPIIO::~DumpNetCDFMPIIO()
void DumpNetCDFMPIIO::openfile()
{
char *filecurrent = filename;
if (multifile && !singlefile_opened) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
if (thermo && !singlefile_opened) {
if (thermovar) delete [] thermovar;
thermovar = new int[output->thermo->nfield];
@ -260,7 +278,7 @@ void DumpNetCDFMPIIO::openfile()
// get total number of atoms
ntotalgr = group->count(igroup);
if (append_flag && access(filename, F_OK) != -1) {
if (append_flag && !multifile && access(filecurrent, F_OK) != -1) {
// Fixme! Perform checks if dimensions and variables conform with
// data structure standard.
@ -270,8 +288,8 @@ void DumpNetCDFMPIIO::openfile()
if (singlefile_opened) return;
singlefile_opened = 1;
NCERRX( ncmpi_open(MPI_COMM_WORLD, filename, NC_WRITE, MPI_INFO_NULL,
&ncid), filename );
NCERRX( ncmpi_open(MPI_COMM_WORLD, filecurrent, NC_WRITE, MPI_INFO_NULL,
&ncid), filecurrent );
// dimensions
NCERRX( ncmpi_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR );
@ -344,8 +362,8 @@ void DumpNetCDFMPIIO::openfile()
if (singlefile_opened) return;
singlefile_opened = 1;
NCERRX( ncmpi_create(MPI_COMM_WORLD, filename, NC_64BIT_DATA,
MPI_INFO_NULL, &ncid), filename );
NCERRX( ncmpi_create(MPI_COMM_WORLD, filecurrent, NC_64BIT_DATA,
MPI_INFO_NULL, &ncid), filecurrent );
// dimensions
NCERRX( ncmpi_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim),
@ -577,7 +595,10 @@ void DumpNetCDFMPIIO::closefile()
// append next time DumpNetCDFMPIIO::openfile is called
append_flag = 1;
// write to next frame upon next open
framei++;
if (multifile)
framei = 1;
else
framei++;
}
}