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Merged
wkliao merged 19 commits into from
Nov 15, 2025
Merged

Hint consistency check #195

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775e6b6
new error core NC_EMULTIDEFINE_HINTS for inconsistent I/O hints set b…
wkliao Nov 8, 2025
1709e89
rename hint variables used internally
wkliao Nov 8, 2025
af3f095
One Bcast and Allreduce to check consistency of all I/O hints
wkliao Nov 8, 2025
831402e
move setting is_open inside of open call
wkliao Nov 9, 2025
9d678d8
parallel_run.sh run ncmpidiff based on driver mode
wkliao Nov 9, 2025
c5b7853
make ncmpi_close() returns the same error code
wkliao Nov 15, 2025
726f693
duplicate MPI info for non-INA aggregators in case later switch to in…
wkliao Nov 15, 2025
a00ae89
pncio_write_str_naive.c assert disp and offset are 0s
wkliao Nov 15, 2025
64bb6f7
benchmarks/C/aggregation.c add indep I/O mode option
wkliao Nov 15, 2025
1e575dd
benchmarks/C/pnetcdf_put_vara.c add indep I/O mode option
wkliao Nov 15, 2025
80141cd
benchmarks/C/write_block_read_column.c add indep I/O mode option
wkliao Nov 15, 2025
73f0f11
benchmarks/C make ptest problem size larger
wkliao Nov 15, 2025
6889bbc
FLASH-IO/parallel_run.sh separate cases for running ncmpidiff
wkliao Nov 15, 2025
66764a1
test/C add an option to run in indep I/O mode
wkliao Nov 15, 2025
995bcac
test/nonblocking/bput_varn.m4 add an option to put multiple variables
wkliao Nov 15, 2025
97b0c2f
column_wise.m4 add testing for indep I/O mode
wkliao Nov 15, 2025
b72b67f
flexible_bput.c add testing for indep I/O mode
wkliao Nov 15, 2025
a532d59
testcases/alignment_test.c increases problem size
wkliao Nov 15, 2025
4aea2f2
tst_multi_redefine.c tests entering define mode multiple times
wkliao Nov 15, 2025
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118 changes: 85 additions & 33 deletions benchmarks/C/aggregation.c
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,7 @@ typedef struct {
int star_block;
int blocking_io;
int double_xtype;
int indep_io;
MPI_Offset len;
MPI_Offset w_size;
MPI_Offset r_size;
Expand Down Expand Up @@ -287,6 +288,11 @@ int benchmark_write(char *filename,
sts = (int*) malloc(sizeof(int) * num_reqs);

err = ncmpi_enddef(ncid); ERR(err)
if (cfg->indep_io) {
err = ncmpi_begin_indep_data(ncid);
ERR(err)
}

err = ncmpi_inq_header_size(ncid, &cfg->header_size); ERR(err)
err = ncmpi_inq_header_extent(ncid, &cfg->header_extent); ERR(err)
end_t = MPI_Wtime();
Expand All @@ -306,12 +312,17 @@ int benchmark_write(char *filename,
start[1] = cfg->len * (rank / psizes[1]);
count[1] = cfg->len;
count[2] = cfg->len;
if (cfg->blocking_io)
err = ncmpi_put_vara_double_all(ncid, varid[v], start,
if (cfg->blocking_io) {
if (cfg->indep_io)
err = ncmpi_put_vara_double(ncid, varid[v], start,
count, buf[v]);
else
err = ncmpi_put_vara_double_all(ncid, varid[v], start,
count, buf[v]);
}
else
err = ncmpi_iput_vara_double(ncid, varid[v], start, count,
buf[v], &reqs[k++]);
buf[v], &reqs[k++]);
ERR(err)
if (debug) DBG_PRINT("block-block", n, i);
v++;
Expand All @@ -323,9 +334,14 @@ int benchmark_write(char *filename,
count[2] = cfg->len;
stride[1] = 1;
stride[2] = nprocs;
if (cfg->blocking_io)
err = ncmpi_put_vars_double_all(ncid, varid[v], start,
if (cfg->blocking_io) {
if (cfg->indep_io)
err = ncmpi_put_vars_double(ncid, varid[v], start,
count, stride, buf[v]);
else
err = ncmpi_put_vars_double_all(ncid, varid[v], start,
count, stride, buf[v]);
}
else
err = ncmpi_iput_vars_double(ncid, varid[v], start, count,
stride, buf[v], &reqs[k++]);
Expand All @@ -338,9 +354,14 @@ int benchmark_write(char *filename,
start[2] = 0;
count[1] = cfg->len;
count[2] = bs_gsizes[2];
if (cfg->blocking_io)
err = ncmpi_put_vara_double_all(ncid, varid[v], start,
if (cfg->blocking_io) {
if (cfg->indep_io)
err = ncmpi_put_vara_double(ncid, varid[v], start,
count, buf[v]);
else
err = ncmpi_put_vara_double_all(ncid, varid[v], start,
count, buf[v]);
}
else
err = ncmpi_iput_vara_double(ncid, varid[v], start, count,
buf[v], &reqs[k++]);
Expand All @@ -353,9 +374,14 @@ int benchmark_write(char *filename,
start[2] = cfg->len * rank;
count[1] = sb_gsizes[1];
count[2] = cfg->len;
if (cfg->blocking_io)
err = ncmpi_put_vara_double_all(ncid, varid[v], start,
if (cfg->blocking_io) {
if (cfg->indep_io)
err = ncmpi_put_vara_double(ncid, varid[v], start,
count, buf[v]);
else
err = ncmpi_put_vara_double_all(ncid, varid[v], start,
count, buf[v]);
}
else
err = ncmpi_iput_vara_double(ncid, varid[v], start, count,
buf[v], &reqs[k++]);
Expand All @@ -372,13 +398,13 @@ int benchmark_write(char *filename,

if (!cfg->blocking_io) {
start_t = end_t;
#ifdef USE_INDEP_MODE
err = ncmpi_begin_indep_data(ncid); ERR(err)
err = ncmpi_wait(ncid, num_reqs, reqs, sts); ERR(err)
err = ncmpi_end_indep_data(ncid); ERR(err)
#else
err = ncmpi_wait_all(ncid, num_reqs, reqs, sts); ERR(err)
#endif

if (cfg->indep_io)
err = ncmpi_wait(ncid, num_reqs, reqs, sts);
else
err = ncmpi_wait_all(ncid, num_reqs, reqs, sts);
ERR(err)

/* check status of all requests */
for (i=0; i<num_reqs; i++) ERR(sts[i])

Expand Down Expand Up @@ -452,6 +478,11 @@ int benchmark_read(char *filename,
start_t = MPI_Wtime();
timing[1] = start_t - timing[0];

if (cfg->indep_io) {
err = ncmpi_begin_indep_data(ncid);
ERR(err)
}

/* Note that PnetCDF read the file in chunks of size 256KB, thus the read
* amount may be more than the file header size
*/
Expand Down Expand Up @@ -518,8 +549,12 @@ int benchmark_read(char *filename,
start[1] = cfg->len * (rank / psizes[1]);
count[1] = cfg->len;
count[2] = cfg->len;
if (cfg->blocking_io)
err = ncmpi_get_vara_double_all(ncid, v, start, count, buf[v]);
if (cfg->blocking_io) {
if (cfg->indep_io)
err = ncmpi_get_vara_double(ncid, v, start, count, buf[v]);
else
err = ncmpi_get_vara_double_all(ncid, v, start, count, buf[v]);
}
else
err = ncmpi_iget_vara_double(ncid, v, start, count, buf[v],
&reqs[k++]);
Expand All @@ -533,9 +568,14 @@ int benchmark_read(char *filename,
count[2] = cfg->len;
stride[1] = 1;
stride[2] = nprocs;
if (cfg->blocking_io)
err = ncmpi_get_vars_double_all(ncid, v, start, count,
if (cfg->blocking_io) {
if (cfg->indep_io)
err = ncmpi_get_vars_double(ncid, v, start, count,
stride, buf[v]);
else
err = ncmpi_get_vars_double_all(ncid, v, start, count,
stride, buf[v]);
}
else
err = ncmpi_iget_vars_double(ncid, v, start, count, stride,
buf[v], &reqs[k++]);
Expand All @@ -547,8 +587,12 @@ int benchmark_read(char *filename,
start[2] = 0;
count[1] = cfg->len;
count[2] = bs_gsizes[2];
if (cfg->blocking_io)
err = ncmpi_get_vara_double_all(ncid, v, start, count, buf[v]);
if (cfg->blocking_io) {
if (cfg->indep_io)
err = ncmpi_get_vara_double(ncid, v, start, count, buf[v]);
else
err = ncmpi_get_vara_double_all(ncid, v, start, count, buf[v]);
}
else
err = ncmpi_iget_vara_double(ncid, v, start, count, buf[v],
&reqs[k++]);
Expand All @@ -560,8 +604,12 @@ int benchmark_read(char *filename,
start[2] = cfg->len * rank;
count[1] = sb_gsizes[1];
count[2] = cfg->len;
if (cfg->blocking_io)
err = ncmpi_get_vara_double_all(ncid, v, start, count, buf[v]);
if (cfg->blocking_io) {
if (cfg->indep_io)
err = ncmpi_get_vara_double(ncid, v, start, count, buf[v]);
else
err = ncmpi_get_vara_double_all(ncid, v, start, count, buf[v]);
}
else
err = ncmpi_iget_vara_double(ncid, v, start, count, buf[v],
&reqs[k++]);
Expand All @@ -578,13 +626,12 @@ int benchmark_read(char *filename,
if (!cfg->blocking_io) {
start_t = end_t;

#ifdef USE_INDEP_MODE
err = ncmpi_begin_indep_data(ncid); ERR(err)
err = ncmpi_wait(ncid, num_reqs, reqs, sts); ERR(err)
err = ncmpi_end_indep_data(ncid); ERR(err)
#else
err = ncmpi_wait_all(ncid, num_reqs, reqs, sts); ERR(err)
#endif
if (cfg->indep_io)
err = ncmpi_wait(ncid, num_reqs, reqs, sts);
else
err = ncmpi_wait_all(ncid, num_reqs, reqs, sts);
ERR(err)

/* check status of all requests */
for (i=0; i<num_reqs; i++) ERR(sts[i])

Expand Down Expand Up @@ -629,6 +676,7 @@ usage(char *argv0)
" [-c] *-cyclic partitioning pattern\n"
" [-i] block-* partitioning pattern\n"
" [-j] *-block partitioning pattern\n"
" [-a] use independent I/O\n"
" [-m] use double type in both memory buffer and file\n"
" [-l len]: local variable of size len x len (default 10)\n"
" [-n num]: number of variables each pattern (default 1)\n"
Expand All @@ -646,7 +694,7 @@ int main(int argc, char** argv) {
char filename[256];
int i, rank, nprocs, verbose=1, nerrs=0, enable_read, enable_write;
int nvars, block_block, star_cyclic, block_star, star_block, num_records;
int blocking_io, double_xtype;
int blocking_io, double_xtype, indep_io;
double timing[11], max_t[11];
MPI_Offset len=0, sum_w_size, sum_r_size;
MPI_Comm comm=MPI_COMM_WORLD;
Expand All @@ -666,10 +714,11 @@ int main(int argc, char** argv) {
num_records = 1;
blocking_io = 0;
double_xtype = 0;
indep_io = 0;

/* get command-line arguments */
debug = 0;
while ((i = getopt(argc, argv, "hqdbcijmrwxl:n:t:")) != EOF)
while ((i = getopt(argc, argv, "hqdabcijkmrwxl:n:t:")) != EOF)
switch(i) {
case 'q': verbose = 0;
break;
Expand All @@ -683,6 +732,8 @@ int main(int argc, char** argv) {
break;
case 'j': star_block = 1;
break;
case 'a': indep_io = 1;
break;
case 'm': double_xtype = 1;
break;
case 'x': blocking_io = 1;
Expand Down Expand Up @@ -720,6 +771,7 @@ int main(int argc, char** argv) {
cfg.num_records = num_records;
cfg.blocking_io = blocking_io;
cfg.double_xtype = double_xtype;
cfg.indep_io = indep_io;

if (enable_read == 0 && enable_write == 0)
enable_read = enable_write = 1;
Expand Down
22 changes: 13 additions & 9 deletions benchmarks/C/parallel_run.sh
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,8 @@ unset PNETCDF_HINTS

fixed_length=23

TEST_MPIIO_MODES="0 1"

for i in ${check_PROGRAMS} ; do

for j in ${safe_modes} ; do
Expand All @@ -44,7 +46,7 @@ for i in ${check_PROGRAMS} ; do
fi
OUT_PREFIX="${TESTOUTDIR}/$i"

for mpiio_mode in 0 1 ; do
for mpiio_mode in ${TEST_MPIIO_MODES} ; do
if test "$mpiio_mode" = 1 ; then
USEMPIO_HINTS="nc_pncio=disable"
DRIVER_OUT_FILE="${OUT_PREFIX}.mpio"
Expand Down Expand Up @@ -83,9 +85,9 @@ for i in ${check_PROGRAMS} ; do
export PNETCDF_SAFE_MODE=$j
# echo "PNETCDF_SAFE_MODE=$PNETCDF_SAFE_MODE PNETCDF_HINTS=$PNETCDF_HINTS"

CMD_OPTS="-q -l 10"
CMD_OPTS="-q -l 500"
if test "$i" = "aggregation" ; then
CMD_OPTS+=" -b -c -i -j"
CMD_OPTS+=" -b -a -x -n 12 -t 2"
fi

# echo "${LINENO}: ${MPIRUN} ./$i $CMD_OPTS ${OUT_FILE}.nc"
Expand Down Expand Up @@ -128,12 +130,14 @@ for i in ${check_PROGRAMS} ; do
done # mpiio_mode

DIFF_OPT="-q"
# echo "${LINENO}: --- ncmpidiff $OUT_PREFIX.mpio.nc $OUT_PREFIX.mpio.ina.nc ---"
$MPIRUN $NCMPIDIFF $DIFF_OPT $OUT_PREFIX.mpio.nc $OUT_PREFIX.mpio.ina.nc
# echo "${LINENO}: --- ncmpidiff $OUT_PREFIX.mpio.nc $OUT_PREFIX.pncio.nc ---"
$MPIRUN $NCMPIDIFF $DIFF_OPT $OUT_PREFIX.mpio.nc $OUT_PREFIX.pncio.nc
# echo "${LINENO}: --- ncmpidiff $OUT_PREFIX.mpio.nc $OUT_PREFIX.pncio.ina.nc ---"
$MPIRUN $NCMPIDIFF $DIFF_OPT $OUT_PREFIX.mpio.nc $OUT_PREFIX.pncio.ina.nc
if test "x$TEST_MPIIO_MODES" = "x0 1" ; then
# echo "${LINENO}: --- ncmpidiff $OUT_PREFIX.mpio.nc $OUT_PREFIX.mpio.ina.nc ---"
$MPIRUN $NCMPIDIFF $DIFF_OPT $OUT_PREFIX.mpio.nc $OUT_PREFIX.mpio.ina.nc
# echo "${LINENO}: --- ncmpidiff $OUT_PREFIX.mpio.nc $OUT_PREFIX.pncio.nc ---"
$MPIRUN $NCMPIDIFF $DIFF_OPT $OUT_PREFIX.mpio.nc $OUT_PREFIX.pncio.nc
fi
# echo "${LINENO}: --- ncmpidiff $OUT_PREFIX.pncio.nc $OUT_PREFIX.pncio.ina.nc ---"
$MPIRUN $NCMPIDIFF $DIFF_OPT $OUT_PREFIX.pncio.nc $OUT_PREFIX.pncio.ina.nc

done # safe_modes
rm -f ${OUTDIR}/$i*nc*
Expand Down
34 changes: 26 additions & 8 deletions benchmarks/C/pnetcdf_put_vara.c
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Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,8 @@ pnetcdf_io(char *filename,
int kind,
int len,
int nvars,
int ntimes)
int ntimes,
int indep_io)
{
char name[128], str_att[128], *file_kind;
int i, j, rank, nprocs, err, nerrs=0;
Expand Down Expand Up @@ -175,6 +176,11 @@ pnetcdf_io(char *filename,
/* exit define mode */
err = ncmpi_enddef(ncid); ERR

if (indep_io) {
err = ncmpi_begin_indep_data(ncid);
ERR
}

/* set up the access pattern */
start[0] = 0;
start[1] = len * (rank / psizes[1]);
Expand All @@ -190,14 +196,22 @@ pnetcdf_io(char *filename,
if (nonblocking)
err = ncmpi_iput_vara_float(ncid, varid[i], start,
count, buf[i], NULL);
else
err = ncmpi_put_vara_float_all(ncid, varid[i], start,
else {
if (indep_io)
err = ncmpi_put_vara_float(ncid, varid[i], start,
count, buf[i]);
else
err = ncmpi_put_vara_float_all(ncid, varid[i], start,
count, buf[i]);
}
ERR
}
}
if (nonblocking) {
err = ncmpi_wait_all(ncid, NC_REQ_ALL, NULL, NULL);
if (indep_io)
err = ncmpi_wait(ncid, NC_REQ_ALL, NULL, NULL);
else
err = ncmpi_wait_all(ncid, NC_REQ_ALL, NULL, NULL);
ERR
}
timing[1] = MPI_Wtime() - timing[1];
Expand Down Expand Up @@ -246,9 +260,10 @@ static void
usage(char *argv0)
{
char *help =
"Usage: %s [-h | -q | -i | -k num |-l num | -n num | -t num] [file_name]\n"
"Usage: %s [-h | -q | -a | -i | -k num |-l num | -n num | -t num] [file_name]\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [-a] Use PnetCDF independent APIs\n"
" [-i] Use PnetCDF nonblocking APIs\n"
" [-k format] file format: 1 for CDF-1,\n"
" 2 for CDF-2,\n"
Expand All @@ -266,7 +281,7 @@ int main(int argc, char** argv)
extern char *optarg;
char filename[512];
int i, rank, kind, nerrs=0;
int nonblocking, nvars, len, ntimes;
int nonblocking, nvars, len, ntimes, indep_io;

MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
Expand All @@ -277,12 +292,15 @@ int main(int argc, char** argv)
nvars = 4;
len = 32;
ntimes = 1;
indep_io = 0;

/* get command-line arguments */
while ((i = getopt(argc, argv, "hqik:l:n:t:")) != EOF)
while ((i = getopt(argc, argv, "hqaik:l:n:t:")) != EOF)
switch(i) {
case 'q': verbose = 0;
break;
case 'a': indep_io = 1;
break;
case 'i': nonblocking = 1;
break;
case 'k': kind = atoi(optarg);
Expand All @@ -303,7 +321,7 @@ int main(int argc, char** argv)

MPI_Bcast(filename, 512, MPI_CHAR, 0, MPI_COMM_WORLD);

nerrs += pnetcdf_io(filename, nonblocking, kind, len, nvars, ntimes);
nerrs += pnetcdf_io(filename, nonblocking, kind, len, nvars, ntimes, indep_io);

MPI_Finalize();
return (nerrs > 0);
Expand Down
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