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Merge branch 'var_par_access' of https://github.com/wkliao/netcdf-c into pr-aggregation.wif

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This commit is contained in:
Ward Fisher 2018-07-31 11:33:05 -06:00
commit 4c0d32cf47
7 changed files with 77 additions and 36 deletions
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7
docs/tutorial.dox
View File

@ -815,8 +815,11 @@ independent (any processor may access the data without waiting for others). All
netCDF metadata writing operations are collective. That is, all creation of
groups, types, variables, dimensions, or attributes. Data reads and writes
(e.g. calls to nc_put_vara_int() and nc_get_vara_int()) may be independent, the
default) or collective. To make writes to a variable collective, call
nc_var_par_access().
default) or collective. To change from collective to independent mode or vis
versa, call nc_var_par_access() with argument 'access' set to either
NC_INDEPENDENT or NC_COLLECTIVE. Note when using PnetCDF, the argument 'varid'
is ignored, as PnetCDF does not support per-variable collective/independent
mode change.
\page tutorial_ncids Numbering of NetCDF IDs

4
examples/C/parallel_vara.c
View File

@ -150,7 +150,7 @@ int main(int argc, char** argv)
err = nc_enddef(ncid); ERR
/* set to use MPI/PnetCDF collective I/O */
err = nc_var_par_access(ncid, varid, NC_COLLECTIVE); ERR
err = nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE); ERR
/* now we are in data mode */
start[0] = 0;
@ -176,7 +176,7 @@ int main(int argc, char** argv)
err = nc_inq_varid(ncid, "var", &varid); ERR
/* set to use MPI/PnetCDF collective I/O */
err = nc_var_par_access(ncid, varid, NC_COLLECTIVE); ERR
err = nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE); ERR
/* each process reads its subarray from the file */
err = nc_get_vara_int(ncid, varid, start, count, &buf[0][0]); ERR

75
libsrcp/ncpdispatch.c
View File

@ -9,10 +9,14 @@
#include <mpi.h>
#include "nc.h"
#include "ncdispatch.h"
#include "fbits.h"
/* Must follow netcdf.h */
#include <pnetcdf.h>
#define NCP_MODE_DATA 0x0001
#define NCP_MODE_INDEP 0x0002
typedef struct NCP_INFO
{
/* pnetcdf_access_mode keeps track of whether independpent or collective
@ -85,7 +89,12 @@ NCP_create(const char *path, int cmode,
res = ncmpi_create(comm, path, cmode, info, &(nc->int_ncid));
if (res != NC_NOERR) free(nc5); /* reclaim allocated space */
/* Default to independent access, like netCDF-4/HDF5 files. */
fSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP);
if(res && nc5 != NULL) free(nc5); /* reclaim allocated space */
done:
return res;
}
@ -116,6 +125,9 @@ NCP_open(const char *path, int cmode,
nc5 = (NCP_INFO*)calloc(1,sizeof(NCP_INFO));
if(nc5 == NULL) {res = NC_ENOMEM; goto done;}
/* file open automatically enters data mode */
fSet(nc5->pnetcdf_access_mode, NCP_MODE_DATA);
/* Link nc5 and nc */
NCP_DATA_SET(nc,nc5);
@ -124,7 +136,7 @@ NCP_open(const char *path, int cmode,
/* Default to independent access, like netCDF-4/HDF5 files. */
if (res == NC_NOERR) {
res = ncmpi_begin_indep_data(nc->int_ncid);
nc5->pnetcdf_access_mode = NC_INDEPENDENT;
fSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP);
}
done:
return res;
@ -134,8 +146,14 @@ static int
NCP_redef(int ncid)
{
NC* nc;
NCP_INFO* nc5;
int status = NC_check_id(ncid, &nc);
if(status != NC_NOERR) return status;
nc5 = NCP_DATA(nc);
fClr(nc5->pnetcdf_access_mode, NCP_MODE_DATA);
return ncmpi_redef(nc->int_ncid);
}
@ -166,7 +184,8 @@ NCP__enddef(int ncid, size_t h_minfree, size_t v_align, size_t v_minfree, size_t
#endif
if(!status) {
if (nc5->pnetcdf_access_mode == NC_INDEPENDENT)
fSet(nc5->pnetcdf_access_mode, NCP_MODE_DATA);
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP))
status = ncmpi_begin_indep_data(nc->int_ncid);
}
return status;
@ -578,7 +597,7 @@ NCP_get_vara(int ncid,
if (status) return status;
}
if(nc5->pnetcdf_access_mode == NC_INDEPENDENT) {
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP)) {
switch(memtype) {
case NC_BYTE:
status=ncmpi_get_vara_schar(nc->int_ncid, varid, mpi_start, mpi_count, ip); break;
@ -672,7 +691,7 @@ NCP_put_vara(int ncid,
if (status) return status;
}
if(nc5->pnetcdf_access_mode == NC_INDEPENDENT) {
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP)) {
switch(memtype) {
case NC_BYTE:
status = ncmpi_put_vara_schar(nc->int_ncid, varid, mpi_start, mpi_count, ip); break;
@ -768,7 +787,7 @@ NCP_get_vars(int ncid,
if (status) return status;
}
if(nc5->pnetcdf_access_mode == NC_INDEPENDENT) {
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP)) {
switch(memtype) {
case NC_BYTE:
status=ncmpi_get_vars_schar(nc->int_ncid, varid, mpi_start, mpi_count, mpi_stride, ip); break;
@ -864,7 +883,7 @@ NCP_put_vars(int ncid,
if (status) return status;
}
if(nc5->pnetcdf_access_mode == NC_INDEPENDENT) {
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP)) {
switch(memtype) {
case NC_BYTE:
status = ncmpi_put_vars_schar(nc->int_ncid, varid, mpi_start, mpi_count, mpi_stride, ip); break;
@ -962,7 +981,7 @@ NCP_get_varm(int ncid,
if (status) return status;
}
if(nc5->pnetcdf_access_mode == NC_INDEPENDENT) {
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP)) {
switch(memtype) {
case NC_BYTE:
status=ncmpi_get_varm_schar(nc->int_ncid, varid, mpi_start, mpi_count, mpi_stride, mpi_imap, ip); break;
@ -1060,7 +1079,7 @@ NCP_put_varm(int ncid,
if (status) return status;
}
if(nc5->pnetcdf_access_mode == NC_INDEPENDENT) {
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP)) {
switch(memtype) {
case NC_BYTE:
status = ncmpi_put_varm_schar(nc->int_ncid, varid, mpi_start, mpi_count, mpi_stride, mpi_imap, ip); break;
@ -1176,19 +1195,43 @@ NCP_var_par_access(int ncid, int varid, int par_access)
if (par_access != NC_INDEPENDENT && par_access != NC_COLLECTIVE)
return NC_EINVAL;
#ifdef _DO_NOT_IGNORE_VARID_
if (varid != NC_GLOBAL) /* PnetCDF cannot do per-veriable mode change */
return NC_EINVAL;
#endif
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR) return status;
nc5 = NCP_DATA(nc);
assert(nc5);
if(par_access == nc5->pnetcdf_access_mode)
return NC_NOERR;
nc5->pnetcdf_access_mode = par_access;
if (par_access == NC_INDEPENDENT)
return ncmpi_begin_indep_data(nc->int_ncid);
else
return ncmpi_end_indep_data(nc->int_ncid);
/* if currently in data mode */
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_DATA)) {
if (par_access == NC_INDEPENDENT) {
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP))
return NC_NOERR;
else { /* currently in collective data mode */
fSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP);
return ncmpi_begin_indep_data(nc->int_ncid);
}
}
else { /* want to enter collective data mode */
if (fIsSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP)) {
fClr(nc5->pnetcdf_access_mode, NCP_MODE_INDEP);
return ncmpi_end_indep_data(nc->int_ncid);
}
else
return NC_NOERR;
}
}
else { /* currently in define mode */
if (par_access == NC_INDEPENDENT)
fSet(nc5->pnetcdf_access_mode, NCP_MODE_INDEP);
else
fClr(nc5->pnetcdf_access_mode, NCP_MODE_INDEP);
}
return NC_NOERR;
}
#ifdef USE_NETCDF4

5
nc_test/tst_parallel2.c
View File

@ -135,8 +135,13 @@ main(int argc, char **argv)
sleep(mpi_rank);
#endif /* USE_MPE */
#ifdef USE_PNETCDF
/* if (nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE)) ERR;*/
if (nc_var_par_access(ncid, NC_GLOBAL, NC_INDEPENDENT)) ERR;
#else
/* if (nc_var_par_access(ncid, varid, NC_COLLECTIVE)) ERR;*/
if (nc_var_par_access(ncid, varid, NC_INDEPENDENT)) ERR;
#endif
if (!mpi_rank)
start_time = MPI_Wtime();

6
nc_test/tst_pnetcdf.c
View File

@ -68,10 +68,8 @@ int main(int argc, char* argv[])
}
if (nc_enddef(ncid)) ERR;
for (i=0; i<NVARS; i++) {
/* Note NC_INDEPENDENT is the default */
if (nc_var_par_access(ncid, varid[i], NC_INDEPENDENT)) ERR;
}
/* Note NC_INDEPENDENT is the default */
if (nc_var_par_access(ncid, NC_GLOBAL, NC_INDEPENDENT)) ERR;
/* write all variables */
buf = (int*) malloc(NX * sizeof(int));

6
nc_test/tst_small.c
View File

@ -34,7 +34,7 @@
int format; \
nc_inq_format_extended(ncid,&format,NULL); \
if (format == NC_FORMATX_PNETCDF) { \
if (nc_var_par_access(ncid, varid, NC_COLLECTIVE)) ERR;\
if (nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE)) ERR;\
}\
}
#else
@ -425,9 +425,7 @@ test_two_growing_with_att(const char *testfile)
{int format;
nc_inq_format_extended(ncid,&format,NULL);
if (format == NC_FORMATX_PNETCDF) {
for (v = 0; v < NUM_VARS; v++) {
if (nc_var_par_access(ncid, varid[v], NC_COLLECTIVE)) ERR;
}
if (nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE)) ERR;
}}
#endif
count[0] = 1;

10
nc_test/util.c
View File

@ -927,14 +927,8 @@ write_file(char *filename)
error("nc_enddef: %s", nc_strerror(err));
#ifdef USE_PNETCDF
{ int i,format;
nc_inq_format_extended(ncid, &format, NULL);
if (format == NC_FORMATX_PNETCDF) {
for (i = 0; i < numVars; i++) {
err = nc_var_par_access(ncid, i, NC_COLLECTIVE);
IF (err) error("nc_var_par_access: %s", nc_strerror(err));
}
}}
err = nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE);
IF (err) error("nc_var_par_access: %s", nc_strerror(err));
#endif
put_vars(ncid);