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-rw-r--r--perform/pio_engine.c230
-rw-r--r--perform/pio_perf.c38
-rw-r--r--perform/pio_perf.h1
3 files changed, 176 insertions, 93 deletions
diff --git a/perform/pio_engine.c b/perform/pio_engine.c
index ca3ceeb..a9499d3 100644
--- a/perform/pio_engine.c
+++ b/perform/pio_engine.c
@@ -464,7 +464,6 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
size_t nelmts_in_buf; /*how many element the buffer holds */
off_t elmts_begin; /*first elmt this process transfer */
off_t elmts_count; /*number of elmts this process transfer */
- hid_t dcpl = -1; /* Dataset creation property list */
/* HDF5 variables */
herr_t hrc; /*HDF5 return code */
@@ -472,17 +471,12 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
hid_t h5dset_space_id = -1; /*dataset space ID */
hid_t h5mem_space_id = -1; /*memory dataspace ID */
hid_t h5ds_id = -1; /*dataset handle */
- hsize_t h5mem_block[1]; /*memory space selection */
- hsize_t h5mem_stride[1];
- hsize_t h5mem_count[1];
- hssize_t h5mem_start[1];
-#if 0
- /* for future implementation */
- hsize_t h5dset_block[1]; /*dset space selection */
- hsize_t h5dset_stride[1];
- hsize_t h5dset_count[1];
- hssize_t h5dset_start[1];
-#endif
+ hsize_t h5block[1]; /*dataspace selection */
+ hsize_t h5stride[1];
+ hsize_t h5count[1];
+ hssize_t h5start[1];
+ hid_t h5dcpl = -1; /* Dataset creation property list */
+ hid_t h5dxpl = -1; /* Dataset transfer property list */
/* calculate dataset parameters. data type is always native C int */
dset_size = nelmts * (off_t)ELMT_SIZE;
@@ -501,7 +495,7 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
VRFY((h5dset_space_id >= 0), "H5Screate");
} /* end else */
- /* create the memory dataspace that corresponds to the xfer buffer */
+ /* Create the memory dataspace that corresponds to the xfer buffer */
if(nelmts_in_buf>0) {
h5dims[0] = nelmts_in_buf;
h5mem_space_id = H5Screate_simple(1, h5dims, NULL);
@@ -511,6 +505,22 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
h5mem_space_id = H5Screate(H5S_SCALAR);
VRFY((h5mem_space_id >= 0), "H5Screate");
} /* end else */
+
+ /* Create the dataset transfer property list */
+ h5dxpl = H5Pcreate(H5P_DATASET_XFER);
+ if (h5dxpl < 0) {
+ fprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ /* Change to collective I/O, if asked */
+ if(parms->collective) {
+ hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE);
+ if (hrc < 0) {
+ fprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ } /* end if */
+ } /* end if */
}
for (ndset = 1; ndset <= ndsets; ++ndset) {
@@ -526,8 +536,8 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
break;
case PHDF5:
- dcpl = H5Pcreate(H5P_DATASET_CREATE);
- if (dcpl < 0) {
+ h5dcpl = H5Pcreate(H5P_DATASET_CREATE);
+ if (h5dcpl < 0) {
fprintf(stderr, "HDF5 Property List Create failed\n");
GOTOERROR(FAIL);
}
@@ -536,7 +546,7 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
if(parms->h5_use_chunks) {
/* Set the chunk size to be the same as the buffer size */
h5dims[0] = nelmts_in_buf;
- hrc = H5Pset_chunk(dcpl, 1, h5dims);
+ hrc = H5Pset_chunk(h5dcpl, 1, h5dims);
if (hrc < 0) {
fprintf(stderr, "HDF5 Property List Set failed\n");
GOTOERROR(FAIL);
@@ -546,7 +556,7 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
#ifdef H5_HAVE_NOFILL
/* Disable writing fill values if asked */
if(parms->h5_no_fill) {
- hrc = H5Pset_fill_time(dcpl, H5D_FILL_TIME_NEVER);
+ hrc = H5Pset_fill_time(h5dcpl, H5D_FILL_TIME_NEVER);
if (hrc < 0) {
fprintf(stderr, "HDF5 Property List Set failed\n");
GOTOERROR(FAIL);
@@ -556,14 +566,14 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
sprintf(dname, "Dataset_%ld", ndset);
h5ds_id = H5Dcreate(fd->h5fd, dname, ELMT_H5_TYPE,
- h5dset_space_id, dcpl);
+ h5dset_space_id, h5dcpl);
if (h5ds_id < 0) {
fprintf(stderr, "HDF5 Dataset Create failed\n");
GOTOERROR(FAIL);
}
- hrc = H5Pclose(dcpl);
+ hrc = H5Pclose(h5dcpl);
/* verifying the close of the dcpl */
if (hrc < 0) {
fprintf(stderr, "HDF5 Property List Close failed\n");
@@ -718,44 +728,54 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
mpi_offset = dset_offset + (elmts_begin + (nelmts_xfer*pio_mpi_nprocs_g))*(off_t)ELMT_SIZE;
} /* end else */
- mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buffer,
- (int)nelmts_toxfer, ELMT_MPI_TYPE,
- &mpi_status);
- VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE");
+ if(parms->collective==0) {
+ mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buffer,
+ (int)nelmts_toxfer, ELMT_MPI_TYPE,
+ &mpi_status);
+ VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE");
+ } /* end if */
+ else {
+ mrc = MPI_File_write_at_all(fd->mpifd, mpi_offset, buffer,
+ (int)nelmts_toxfer, ELMT_MPI_TYPE,
+ &mpi_status);
+ VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE");
+ } /* end else */
break;
case PHDF5:
- /*set up the dset space id to select the segment to process */
- {
- if (parms->interleaved==0){
- /* Contiguous pattern */
- h5mem_start[0] = elmts_begin + nelmts_xfer;
- } /* end if */
- else {
- /* Interleaved access pattern */
- /* Skip offset over blocks of other processes */
- h5mem_start[0] = elmts_begin + (nelmts_xfer*pio_mpi_nprocs_g);
- } /* end else */
- h5mem_stride[0] = h5mem_block[0] = nelmts_toxfer;
- h5mem_count[0] = 1;
- hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
- h5mem_start, h5mem_stride, h5mem_count, h5mem_block);
- VRFY((hrc >= 0), "H5Sset_hyperslab");
-
- /*setup the memory space id too. Only start is different */
- h5mem_start[0] = 0;
+ /* Set up the file dset space id to select the segment to process */
+ if (parms->interleaved==0){
+ /* Contiguous pattern */
+ h5start[0] = elmts_begin + nelmts_xfer;
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5start[0] = elmts_begin + (nelmts_xfer*pio_mpi_nprocs_g);
+ } /* end else */
+ h5stride[0] = h5block[0] = nelmts_toxfer;
+ h5count[0] = 1;
+ hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
+ h5start, h5stride, h5count, h5block);
+ VRFY((hrc >= 0), "H5Sset_hyperslab");
+
+ /* Only need selection in memory dataset if it is smaller than the whole buffer */
+ if(nelmts_toxfer<nelmts_in_buf) {
+ /* Setup the memory space id too. Only start is different */
+ h5start[0] = 0;
hrc = H5Sselect_hyperslab(h5mem_space_id, H5S_SELECT_SET,
- h5mem_start, h5mem_stride, h5mem_count, h5mem_block);
+ h5start, h5stride, h5count, h5block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
- }
+ } /* end if */
/* set write time here */
hrc = H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id,
- h5dset_space_id, H5P_DEFAULT, buffer);
+ h5dset_space_id, h5dxpl, buffer);
VRFY((hrc >= 0), "H5Dwrite");
break;
- }
+ } /* switch (parms->io_type) */
+ /* Increment number of elements transferred */
nelmts_xfer += nelmts_toxfer;
}
@@ -799,6 +819,16 @@ done:
}
}
+ if (h5dxpl != -1) {
+ hrc = H5Pclose(h5dxpl);
+ if (hrc < 0) {
+ fprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n");
+ ret_code = FAIL;
+ } else {
+ h5dxpl = -1;
+ }
+ }
+
return ret_code;
}
@@ -835,17 +865,11 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets,
hid_t h5dset_space_id = -1; /*dataset space ID */
hid_t h5mem_space_id = -1; /*memory dataspace ID */
hid_t h5ds_id = -1; /*dataset handle */
- hsize_t h5mem_block[1]; /*memory space selection */
- hsize_t h5mem_stride[1];
- hsize_t h5mem_count[1];
- hssize_t h5mem_start[1];
-#if 0
- /* for future implementation */
- hsize_t h5dset_block[1]; /*dset space selection */
- hsize_t h5dset_stride[1];
- hsize_t h5dset_count[1];
- hssize_t h5dset_start[1];
-#endif
+ hsize_t h5block[1]; /*dataspace selection */
+ hsize_t h5stride[1];
+ hsize_t h5count[1];
+ hssize_t h5start[1];
+ hid_t h5dxpl = -1; /* Dataset transfer property list */
/* calculate dataset parameters. data type is always native C int */
dset_size = nelmts * (off_t)ELMT_SIZE;
@@ -864,7 +888,7 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets,
VRFY((h5dset_space_id >= 0), "H5Screate");
} /* end else */
- /* create the memory dataspace that corresponds to the xfer buffer */
+ /* Create the memory dataspace that corresponds to the xfer buffer */
if(nelmts_in_buf>0) {
h5dims[0] = nelmts_in_buf;
h5mem_space_id = H5Screate_simple(1, h5dims, NULL);
@@ -874,7 +898,23 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets,
h5mem_space_id = H5Screate(H5S_SCALAR);
VRFY((h5mem_space_id >= 0), "H5Screate");
} /* end else */
- }
+
+ /* Create the dataset transfer property list */
+ h5dxpl = H5Pcreate(H5P_DATASET_XFER);
+ if (h5dxpl < 0) {
+ fprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ /* Change to collective I/O, if asked */
+ if(parms->collective) {
+ hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE);
+ if (hrc < 0) {
+ fprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ } /* end if */
+ } /* end if */
+ } /* end if */
for (ndset = 1; ndset <= ndsets; ++ndset) {
/* Calculate dataset offset within a file */
@@ -1035,40 +1075,49 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets,
mpi_offset = dset_offset + (elmts_begin + (nelmts_xfer*pio_mpi_nprocs_g))*(off_t)ELMT_SIZE;
} /* end else */
- mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buffer,
- (int)nelmts_toxfer, ELMT_MPI_TYPE,
- &mpi_status);
- VRFY((mrc==MPI_SUCCESS), "MPIO_read");
+ if(parms->collective==0) {
+ mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buffer,
+ (int)nelmts_toxfer, ELMT_MPI_TYPE,
+ &mpi_status);
+ VRFY((mrc==MPI_SUCCESS), "MPIO_read");
+ } /* end if */
+ else {
+ mrc = MPI_File_read_at_all(fd->mpifd, mpi_offset, buffer,
+ (int)nelmts_toxfer, ELMT_MPI_TYPE,
+ &mpi_status);
+ VRFY((mrc==MPI_SUCCESS), "MPIO_read");
+ } /* end else */
break;
case PHDF5:
- /*set up the dset space id to select the segment to process */
- {
- if (parms->interleaved==0){
- /* Contiguous pattern */
- h5mem_start[0] = elmts_begin + nelmts_xfer;
- } /* end if */
- else {
- /* Interleaved access pattern */
- /* Skip offset over blocks of other processes */
- h5mem_start[0] = elmts_begin + (nelmts_xfer*pio_mpi_nprocs_g);
- } /* end else */
- h5mem_stride[0] = h5mem_block[0] = nelmts_toxfer;
- h5mem_count[0] = 1;
- hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
- h5mem_start, h5mem_stride, h5mem_count, h5mem_block);
- VRFY((hrc >= 0), "H5Sset_hyperslab");
-
- /*setup the memory space id too. Only start is different */
- h5mem_start[0] = 0;
+ /* Set up the dset space id to select the segment to process */
+ if (parms->interleaved==0){
+ /* Contiguous pattern */
+ h5start[0] = elmts_begin + nelmts_xfer;
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5start[0] = elmts_begin + (nelmts_xfer*pio_mpi_nprocs_g);
+ } /* end else */
+ h5stride[0] = h5block[0] = nelmts_toxfer;
+ h5count[0] = 1;
+ hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
+ h5start, h5stride, h5count, h5block);
+ VRFY((hrc >= 0), "H5Sset_hyperslab");
+
+ /* Only need selection in memory dataset if it is smaller than the whole buffer */
+ if(nelmts_toxfer<nelmts_in_buf) {
+ /* Setup the memory space id too. Only start is different */
+ h5start[0] = 0;
hrc = H5Sselect_hyperslab(h5mem_space_id, H5S_SELECT_SET,
- h5mem_start, h5mem_stride, h5mem_count, h5mem_block);
+ h5start, h5stride, h5count, h5block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
- }
+ } /* end if */
/* set read time here */
hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id,
- h5dset_space_id, H5P_DEFAULT, buffer);
+ h5dset_space_id, h5dxpl, buffer);
VRFY((hrc >= 0), "H5Dread");
break;
} /* switch (parms->io_type) */
@@ -1099,6 +1148,7 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets,
}
} /* if (parms->verify) */
+ /* Increment number of elements transferred */
nelmts_xfer += nelmts_toxfer;
}
@@ -1142,6 +1192,16 @@ done:
}
}
+ if (h5dxpl != -1) {
+ hrc = H5Pclose(h5dxpl);
+ if (hrc < 0) {
+ fprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n");
+ ret_code = FAIL;
+ } else {
+ h5dxpl = -1;
+ }
+ }
+
return ret_code;
}
diff --git a/perform/pio_perf.c b/perform/pio_perf.c
index f2fb52f..0f43f15 100644
--- a/perform/pio_perf.c
+++ b/perform/pio_perf.c
@@ -117,9 +117,9 @@ static const char *progname = "pio_perf";
* adding more, make sure that they don't clash with each other.
*/
#if 1
-static const char *s_opts = "ha:A:cD:f:P:p:X:x:nd:F:i:Io:stT:w";
+static const char *s_opts = "ha:A:cCD:f:P:p:X:x:nd:F:i:Io:stT:w";
#else
-static const char *s_opts = "ha:A:bcD:f:P:p:X:x:nd:F:i:Io:stT:w";
+static const char *s_opts = "ha:A:bcCD:f:P:p:X:x:nd:F:i:Io:stT:w";
#endif /* 1 */
static struct long_options l_opts[] = {
{ "help", no_arg, 'h' },
@@ -143,6 +143,15 @@ static struct long_options l_opts[] = {
{ "chun", no_arg, 'c' },
{ "chu", no_arg, 'c' },
{ "ch", no_arg, 'c' },
+ { "collective", no_arg, 'C' },
+ { "collectiv", no_arg, 'C' },
+ { "collecti", no_arg, 'C' },
+ { "collect", no_arg, 'C' },
+ { "collec", no_arg, 'C' },
+ { "colle", no_arg, 'C' },
+ { "coll", no_arg, 'C' },
+ { "col", no_arg, 'C' },
+ { "co", no_arg, 'C' },
{ "debug", require_arg, 'D' },
{ "debu", require_arg, 'D' },
{ "deb", require_arg, 'D' },
@@ -260,6 +269,7 @@ struct options {
size_t max_xfer_size; /* maximum transfer buffer size */
size_t min_xfer_size; /* minimum transfer buffer size */
unsigned interleaved; /* Interleaved vs. contiguous blocks */
+ unsigned collective; /* Collective vs. independent I/O */
int print_times; /* print times as well as throughputs */
int print_raw; /* print raw data throughput info */
off_t h5_alignment; /* alignment in HDF5 file */
@@ -401,6 +411,7 @@ run_test_loop(struct options *opts)
parms.num_dsets = opts->num_dsets;
parms.num_iters = opts->num_iters;
parms.interleaved = opts->interleaved;
+ parms.collective = opts->collective;
parms.h5_align = opts->h5_alignment;
parms.h5_thresh = opts->h5_threshold;
parms.h5_use_chunks = opts->h5_use_chunks;
@@ -1001,11 +1012,17 @@ report_parameters(struct options *opts)
recover_size_and_print((long_long)opts->min_xfer_size, ":");
recover_size_and_print((long_long)opts->max_xfer_size, "\n");
- HDfprintf(output, "rank %d: Block Pattern in Dataset:", rank);
+ HDfprintf(output, "rank %d: Block Pattern in Dataset=", rank);
if(opts->interleaved)
- HDfprintf(output, "Interleaved");
+ HDfprintf(output, "Interleaved\n");
else
- HDfprintf(output, "Contiguous");
+ HDfprintf(output, "Contiguous\n");
+
+ HDfprintf(output, "rank %d: I/O Method for MPI and HDF5=", rank);
+ if(opts->collective)
+ HDfprintf(output, "Collective\n");
+ else
+ HDfprintf(output, "Independent\n");
{
char *prefix = getenv("HDF5_PARAPREFIX");
@@ -1048,6 +1065,7 @@ parse_command_line(int argc, char *argv[])
cl_opts->max_xfer_size = 1 * ONE_MB;
cl_opts->min_xfer_size = 128 * ONE_KB;
cl_opts->interleaved = 0; /* Default to contiguous blocks in dataset */
+ cl_opts->collective = 0; /* Default to independent I/O access */
cl_opts->print_times = FALSE; /* Printing times is off by default */
cl_opts->print_raw = FALSE; /* Printing raw data throughput is off by default */
cl_opts->h5_alignment = 1; /* No alignment for HDF5 objects by default */
@@ -1105,6 +1123,9 @@ parse_command_line(int argc, char *argv[])
/* Turn on chunked HDF5 dataset creation */
cl_opts->h5_use_chunks = TRUE;
break;
+ case 'C':
+ cl_opts->collective = 1;
+ break;
case 'd':
cl_opts->num_dsets = atoi(opt_arg);
break;
@@ -1199,15 +1220,15 @@ parse_command_line(int argc, char *argv[])
case 'T':
cl_opts->h5_threshold = parse_size_directive(opt_arg);
break;
+ case 'w':
+ cl_opts->h5_write_only = TRUE;
+ break;
case 'x':
cl_opts->min_xfer_size = parse_size_directive(opt_arg);
break;
case 'X':
cl_opts->max_xfer_size = parse_size_directive(opt_arg);
break;
- case 'w':
- cl_opts->h5_write_only = TRUE;
- break;
case 'h':
case '?':
default:
@@ -1298,6 +1319,7 @@ usage(const char *prog)
printf(" -b, --binary The elusive binary option\n");
#endif /* 0 */
printf(" -c, --chunk Create HDF5 datasets chunked [default: off]\n");
+ printf(" -C, --collective Use collective I/O for MPI and HDF5 APIs [default: off (i.e. independent I/O)]\n");
printf(" -d N, --num-dsets=N Number of datasets per file [default:1]\n");
printf(" -D DL, --debug=DL Indicate the debugging level\n");
printf(" [default: no debugging]\n");
diff --git a/perform/pio_perf.h b/perform/pio_perf.h
index 53377e2..e245e8a 100644
--- a/perform/pio_perf.h
+++ b/perform/pio_perf.h
@@ -40,6 +40,7 @@ typedef struct parameters_ {
int num_iters; /* Number of times to loop doing the IO */
size_t buf_size; /* Buffer size */
unsigned interleaved; /* Interleaved vs. contiguous blocks */
+ unsigned collective; /* Collective vs. independent I/O */
hsize_t h5_align; /* HDF5 object alignment */
hsize_t h5_thresh; /* HDF5 object alignment threshold */
int h5_use_chunks; /* Make HDF5 dataset chunked */
generated by cgit v0.12 at 2024-12-26 09:05:23 (GMT)