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-rw-r--r--perform/Makefile.in1
-rw-r--r--perform/benchpar.c20
-rw-r--r--perform/perf_meta.c59
-rw-r--r--perform/pio_engine.c800
-rw-r--r--perform/pio_perf.c44
-rw-r--r--perform/pio_perf.h1
-rw-r--r--perform/sio_engine.c461
-rw-r--r--perform/sio_perf.c15
-rw-r--r--perform/sio_perf.h1
9 files changed, 193 insertions, 1209 deletions
diff --git a/perform/Makefile.in b/perform/Makefile.in
index 091f4f1..fe9d184 100644
--- a/perform/Makefile.in
+++ b/perform/Makefile.in
@@ -254,7 +254,6 @@ FC_VERSION = @FC_VERSION@
FGREP = @FGREP@
FILTERS = @FILTERS@
FSEARCH_DIRS = @FSEARCH_DIRS@
-GPFS = @GPFS@
GREP = @GREP@
H5_CFLAGS = @H5_CFLAGS@
H5_CPPFLAGS = @H5_CPPFLAGS@
diff --git a/perform/benchpar.c b/perform/benchpar.c
index 24146e4..b75006a 100644
--- a/perform/benchpar.c
+++ b/perform/benchpar.c
@@ -44,7 +44,6 @@
/* defines for type of VFL driver to use */
#define FACC_DEFAULT 0
#define FACC_MPIO 1
-#define FACC_MPIPOSIX 2
/* Defines for computing performance information */
#define ONE_KB 1024
@@ -78,7 +77,7 @@ char mpi_name[MPI_MAX_PROCESSOR_NAME];
static void usage(void)
{
printf("usage: benchpar [-d <# of dims>] [-s <dim_size>] [-f <file name>] [-h]\n");
- printf(" [-S <slice dim>] [-p] [-I] [-c] [-i <# of iterations>\n");
+ printf(" [-S <slice dim>] [-I] [-c] [-i <# of iterations>\n");
printf(" -c - Use chunked storage for dataset with 1-1 exact\n");
printf(" mapping of chunks to hyperslabs\n");
printf(" Default: off (i.e. contiguous storage)\n");
@@ -91,8 +90,6 @@ static void usage(void)
printf(" Default: 3\n");
printf(" -I - Use independent parallel I/O\n");
printf(" Default: use collective parallel I/O\n");
- printf(" -p - Use MPI-posix VFL driver\n");
- printf(" Default: use MPI-I/O VFL driver\n");
printf(" -s <dim_size> - Set the size of each of the dataset's dimensions\n");
printf(" Default: 1024\n");
printf(" -S <slice dim> - Set the dimension to slice the dataset along\n");
@@ -114,7 +111,6 @@ static hid_t create_fcpl(void)
static hid_t create_fapl(MPI_Comm comm, MPI_Info info, int acc_type )
{
hid_t fapl; /* File access property list */
- hbool_t use_gpfs = FALSE; /* Use GPFS hints */
herr_t ret; /* Generic return value */
fapl = H5Pcreate (H5P_FILE_ACCESS);
@@ -122,13 +118,7 @@ static hid_t create_fapl(MPI_Comm comm, MPI_Info info, int acc_type )
/* set parallel access with communicator, using MPI-I/O driver */
if (acc_type == FACC_MPIO) {
- ret = H5Pset_fapl_mpio(fapl, comm, info);
- assert(ret>=0);
- } /* end if */
-
- /* set parallel access with communicator, using MPI-posix driver */
- if (acc_type == FACC_MPIPOSIX) {
- ret = H5Pset_fapl_mpiposix(fapl, comm, use_gpfs);
+ ret = H5Pset_fapl_mpio(fapl, comm, info);
assert(ret>=0);
} /* end if */
@@ -279,10 +269,6 @@ int main(int argc, char *argv[])
par_mode=H5FD_MPIO_INDEPENDENT;
break;
- case 'p': /* Use MPI-posix VFL driver */
- vfl_type=FACC_MPIPOSIX;
- break;
-
case 's': /* Change dimension size */
/* Get new dimension size */
dim_size=atoi(argv[curr_arg]);
@@ -469,7 +455,7 @@ int main(int argc, char *argv[])
/* Only print information from one node */
if(mpi_rank==0) {
/* Print information about test */
- printf("File driver used: %s\n",vfl_type==FACC_MPIO ? "MPI-I/O" : "MPI-posix");
+ printf("File driver used: %s\n",vfl_type==FACC_MPIO ? "MPI-I/O" : "Unknown");
printf("Type of parallel access: %s\n",par_mode==H5FD_MPIO_COLLECTIVE ? "Collective" : "Independent");
printf("Type of dataset storage: %s\n",use_chunks ? "Chunked" : "Contiguous");
printf("Number of processes: %d\n",mpi_size);
diff --git a/perform/perf_meta.c b/perform/perf_meta.c
index 8c3b06f..b52871e 100644
--- a/perform/perf_meta.c
+++ b/perform/perf_meta.c
@@ -29,7 +29,6 @@
/* File_Access_type bits */
#define FACC_DEFAULT 0x0 /* serial as default */
#define FACC_MPIO 0x1 /* MPIO */
-#define FACC_MPIPOSIX 0x8 /* MPIPOSIX */
/* Which test to run */
int RUN_TEST = 0x0; /* all tests as default */
@@ -129,11 +128,7 @@ parse_options(int argc, char **argv)
}
break;
- case 'p': /* Use the MPI-POSIX driver access */
- facc_type = FACC_MPIPOSIX;
- break;
-
- case 'm': /* Use the MPI-POSIX driver access */
+ case 'm': /* Use the MPI-IO driver */
facc_type = FACC_MPIO;
break;
@@ -171,7 +166,7 @@ parse_options(int argc, char **argv)
/* Check valid values */
#ifndef H5_HAVE_PARALLEL
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX)
+ if(facc_type == FACC_MPIO)
{
nerrors++;
return(1);
@@ -215,19 +210,15 @@ parse_options(int argc, char **argv)
static void
usage(void)
{
- printf("Usage: perf_meta [-h] [-m] [-p] [-d<num_datasets>]"
+ printf("Usage: perf_meta [-h] [-m] [-d<num_datasets>]"
"[-a<num_attributes>]\n"
"\t[-n<batch_attributes>] [-f<option>] [-t<test>]\n");
printf("\t-h"
"\t\t\thelp page.\n");
printf("\t-m"
"\t\t\tset MPIO as the file driver when parallel HDF5\n"
- "\t\t\t\tis enabled. Either -m or -p has be to \n"
- "\t\t\t\tspecified when running parallel program.\n");
- printf("\t-p"
- "\t\t\tset MPI POSIX as the file driver when parallel \n"
- "\t\t\t\tHDF5 is enabled. Either -m or -p has be to \n"
- "\t\t\t\tspecified when running parallel program.\n");
+ "\t\t\t\tis enabled. -m must be specified\n"
+ "\t\t\t\twhen running parallel program.\n");
printf("\t-d<num_datasets>"
"\tset number of datasets for meta data \n"
"\t\t\t\tperformance test\n");
@@ -372,7 +363,7 @@ create_attrs_1(void)
#ifdef H5_HAVE_PARALLEL
/* need the rank for printing data */
int mpi_rank;
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX)
+ if(facc_type == FACC_MPIO)
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
#endif /*H5_HAVE_PARALLEL*/
@@ -416,7 +407,7 @@ create_attrs_1(void)
goto error;
} /* end for */
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX) {
+ if(facc_type == FACC_MPIO) {
#ifdef H5_HAVE_PARALLEL
MPI_Barrier(MPI_COMM_WORLD);
#endif /*H5_HAVE_PARALLEL*/
@@ -478,7 +469,7 @@ create_attrs_2(void)
#ifdef H5_HAVE_PARALLEL
/* need the rank for printing data */
int mpi_rank;
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX)
+ if(facc_type == FACC_MPIO)
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
#endif /*H5_HAVE_PARALLEL*/
@@ -519,11 +510,10 @@ create_attrs_2(void)
goto error;
} /* end for */
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX) {
#ifdef H5_HAVE_PARALLEL
- MPI_Barrier(MPI_COMM_WORLD);
+ if(facc_type == FACC_MPIO)
+ MPI_Barrier(MPI_COMM_WORLD);
#endif /*H5_HAVE_PARALLEL*/
- }
#ifdef H5_HAVE_PARALLEL
/* only process 0 reports if parallel */
@@ -584,7 +574,7 @@ create_attrs_3(void)
#ifdef H5_HAVE_PARALLEL
/* need the rank for printing data */
int mpi_rank;
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX)
+ if(facc_type == FACC_MPIO)
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
#endif /*H5_HAVE_PARALLEL*/
@@ -633,11 +623,10 @@ create_attrs_3(void)
} /* end for */
} /* end for */
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX) {
#ifdef H5_HAVE_PARALLEL
+ if(facc_type == FACC_MPIO)
MPI_Barrier(MPI_COMM_WORLD);
#endif /*H5_HAVE_PARALLEL*/
- }
#ifdef H5_HAVE_PARALLEL
/* only process 0 reports if parallel */
@@ -709,8 +698,8 @@ void perf(p_time *perf_t, double start_t, double end_t)
{
double t = end_t - start_t;
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX) {
#ifdef H5_HAVE_PARALLEL
+ if(facc_type == FACC_MPIO) {
double reduced_t;
double t_max, t_min;
int mpi_size, mpi_rank;
@@ -736,8 +725,9 @@ void perf(p_time *perf_t, double start_t, double end_t)
if(t_min < perf_t->min)
perf_t->min = t_min;
}
+ } else
#endif /*H5_HAVE_PARALLEL*/
- } else {
+ {
perf_t->total += t;
if(t > perf_t->max)
@@ -796,17 +786,17 @@ main(int argc, char **argv)
#endif /*H5_HAVE_PARALLEL*/
if(parse_options(argc, argv) != 0) {
- usage();
- return 0;
+ usage();
+ return 0;
}
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX) {
#ifdef H5_HAVE_PARALLEL
+ if(facc_type == FACC_MPIO) {
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
-#endif /*H5_HAVE_PARALLEL*/
}
+#endif /*H5_HAVE_PARALLEL*/
#ifdef H5_HAVE_PARALLEL
if (facc_type == FACC_DEFAULT || (facc_type != FACC_DEFAULT && MAINPROCESS))
@@ -814,14 +804,10 @@ main(int argc, char **argv)
fprintf(stderr, "\t\tPerformance result of metadata for datasets and attributes\n\n");
fapl = H5Pcreate (H5P_FILE_ACCESS);
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX) {
#ifdef H5_HAVE_PARALLEL
- if(facc_type == FACC_DEFAULT || facc_type == FACC_MPIO)
- H5Pset_fapl_mpio(fapl, MPI_COMM_WORLD, MPI_INFO_NULL);
- else if(facc_type == FACC_MPIPOSIX)
- H5Pset_fapl_mpiposix(fapl, MPI_COMM_WORLD, FALSE);
+ if(facc_type == FACC_MPIO)
+ H5Pset_fapl_mpio(fapl, MPI_COMM_WORLD, MPI_INFO_NULL);
#endif /*H5_HAVE_PARALLEL*/
- }
nerrors += create_dspace() < 0 ?1:0;
@@ -837,12 +823,11 @@ main(int argc, char **argv)
h5_cleanup(FILENAME, fapl);
- if(facc_type == FACC_MPIO || facc_type == FACC_MPIPOSIX) {
#ifdef H5_HAVE_PARALLEL
+ if(facc_type == FACC_MPIO)
/* MPI_Finalize must be called AFTER H5close which may use MPI calls */
MPI_Finalize();
#endif /*H5_HAVE_PARALLEL*/
- }
if (nerrors) goto error;
#ifdef H5_HAVE_PARALLEL
diff --git a/perform/pio_engine.c b/perform/pio_engine.c
index d34fe38..82d1bb8 100644
--- a/perform/pio_engine.c
+++ b/perform/pio_engine.c
@@ -37,10 +37,6 @@
# include <mpio.h>
#endif /* !MPI_FILE_NULL */
-#ifdef H5_HAVE_GPFS
-# include <gpfs_fcntl.h>
-#endif /* H5_HAVE_GPFS */
-
#include "pio_perf.h"
#include "pio_timer.h"
@@ -135,19 +131,6 @@ static herr_t do_fopen(parameters *param, char *fname, file_descr *fd /*out*/,
static herr_t do_fclose(iotype iot, file_descr *fd);
static void do_cleanupfile(iotype iot, char *fname);
-/* GPFS-specific functions */
-#ifdef H5_HAVE_GPFS
-static void gpfs_access_range(int handle, off_t start, off_t length, int is_write);
-static void gpfs_free_range(int handle, off_t start, off_t length);
-static void gpfs_clear_file_cache(int handle);
-static void gpfs_cancel_hints(int handle);
-static void gpfs_start_data_shipping(int handle, int num_insts);
-static void gpfs_start_data_ship_map(int handle, int partition_size,
- int agent_count, int *agent_node_num);
-static void gpfs_stop_data_shipping(int handle);
-static void gpfs_invalidate_file_cache(const char *filename);
-#endif /* H5_HAVE_GPFS */
-
/*
* Function: do_pio
* Purpose: PIO Engine where Parallel IO are executed.
@@ -189,22 +172,22 @@ do_pio(parameters param)
iot = param.io_type;
switch (iot) {
- case MPIO:
- fd.mpifd = MPI_FILE_NULL;
- res.timers = pio_time_new(MPI_TIMER);
- break;
- case POSIXIO:
- fd.posixfd = -1;
- res.timers = pio_time_new(MPI_TIMER);
- break;
- case PHDF5:
- fd.h5fd = -1;
- res.timers = pio_time_new(MPI_TIMER);
- break;
- default:
- /* unknown request */
- fprintf(stderr, "Unknown IO type request (%d)\n", iot);
- GOTOERROR(FAIL);
+ case MPIO:
+ fd.mpifd = MPI_FILE_NULL;
+ res.timers = pio_time_new(MPI_TIMER);
+ break;
+ case POSIXIO:
+ fd.posixfd = -1;
+ res.timers = pio_time_new(MPI_TIMER);
+ break;
+ case PHDF5:
+ fd.h5fd = -1;
+ res.timers = pio_time_new(MPI_TIMER);
+ break;
+ default:
+ /* unknown request */
+ fprintf(stderr, "Unknown IO type request (%d)\n", iot);
+ GOTOERROR(FAIL);
}
ndsets = param.num_dsets; /* number of datasets per file */
@@ -379,18 +362,18 @@ done:
/* close any opened files */
/* no remove(fname) because that should have happened normally. */
switch (iot) {
- case POSIXIO:
- if (fd.posixfd != -1)
- hrc = do_fclose(iot, &fd);
- break;
- case MPIO:
- if (fd.mpifd != MPI_FILE_NULL)
- hrc = do_fclose(iot, &fd);
- break;
- case PHDF5:
- if (fd.h5fd != -1)
- hrc = do_fclose(iot, &fd);
- break;
+ case POSIXIO:
+ if (fd.posixfd != -1)
+ hrc = do_fclose(iot, &fd);
+ break;
+ case MPIO:
+ if (fd.mpifd != MPI_FILE_NULL)
+ hrc = do_fclose(iot, &fd);
+ break;
+ case PHDF5:
+ if (fd.h5fd != -1)
+ hrc = do_fclose(iot, &fd);
+ break;
}
/* release generic resources */
@@ -423,15 +406,15 @@ pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t si
HDmemset(fullname, 0, size);
switch (iot) {
- case POSIXIO:
- suffix = ".posix";
- break;
- case MPIO:
- suffix = ".mpio";
- break;
- case PHDF5:
- suffix = ".h5";
- break;
+ case POSIXIO:
+ suffix = ".posix";
+ break;
+ case MPIO:
+ suffix = ".mpio";
+ break;
+ case PHDF5:
+ suffix = ".h5";
+ break;
}
/* First use the environment variable and then try the constant */
@@ -886,60 +869,59 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
switch (parms->io_type) {
case POSIXIO:
case MPIO:
- /* both posix and mpi io just need dataset offset in file*/
- dset_offset = (ndset - 1) * nbytes;
- break;
+ /* both posix and mpi io just need dataset offset in file*/
+ dset_offset = (ndset - 1) * nbytes;
+ break;
case PHDF5:
- h5dcpl = H5Pcreate(H5P_DATASET_CREATE);
- if (h5dcpl < 0) {
- fprintf(stderr, "HDF5 Property List Create failed\n");
- GOTOERROR(FAIL);
- }
- /* 1D dataspace */
- if (!parms->dim2d){
- /* Make the dataset chunked if asked */
- if(parms->h5_use_chunks) {
- /* Set the chunk size to be the same as the buffer size */
- h5dims[0] = blk_size;
- hrc = H5Pset_chunk(h5dcpl, 1, h5dims);
- if (hrc < 0) {
- fprintf(stderr, "HDF5 Property List Set failed\n");
- GOTOERROR(FAIL);
- } /* end if */
- } /* end if */
- }/* end if */
- else{
- /* 2D dataspace */
- if(parms->h5_use_chunks) {
- /* Set the chunk size to be the same as the block size */
- h5dims[0] = blk_size;
- h5dims[1] = blk_size;
- hrc = H5Pset_chunk(h5dcpl, 2, h5dims);
- if (hrc < 0) {
- fprintf(stderr, "HDF5 Property List Set failed\n");
+ h5dcpl = H5Pcreate(H5P_DATASET_CREATE);
+ if (h5dcpl < 0) {
+ fprintf(stderr, "HDF5 Property List Create failed\n");
GOTOERROR(FAIL);
- } /* end if */
- } /* end if */
- }/* end else */
-
- sprintf(dname, "Dataset_%ld", ndset);
- h5ds_id = H5DCREATE(fd->h5fd, dname, ELMT_H5_TYPE,
- h5dset_space_id, h5dcpl);
+ }
+ /* 1D dataspace */
+ if (!parms->dim2d){
+ /* Make the dataset chunked if asked */
+ if(parms->h5_use_chunks) {
+ /* Set the chunk size to be the same as the buffer size */
+ h5dims[0] = blk_size;
+ hrc = H5Pset_chunk(h5dcpl, 1, h5dims);
+ if (hrc < 0) {
+ fprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ } /* end if */
+ } /* end if */
+ }/* end if */
+ else{
+ /* 2D dataspace */
+ if(parms->h5_use_chunks) {
+ /* Set the chunk size to be the same as the block size */
+ h5dims[0] = blk_size;
+ h5dims[1] = blk_size;
+ hrc = H5Pset_chunk(h5dcpl, 2, h5dims);
+ if (hrc < 0) {
+ fprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ } /* end if */
+ } /* end if */
+ }/* end else */
- if (h5ds_id < 0) {
- fprintf(stderr, "HDF5 Dataset Create failed\n");
- GOTOERROR(FAIL);
- }
+ sprintf(dname, "Dataset_%ld", ndset);
+ h5ds_id = H5DCREATE(fd->h5fd, dname, ELMT_H5_TYPE,
+ h5dset_space_id, h5dcpl);
- hrc = H5Pclose(h5dcpl);
- /* verifying the close of the dcpl */
- if (hrc < 0) {
- fprintf(stderr, "HDF5 Property List Close failed\n");
- GOTOERROR(FAIL);
- }
+ if (h5ds_id < 0) {
+ fprintf(stderr, "HDF5 Dataset Create failed\n");
+ GOTOERROR(FAIL);
+ }
- break;
+ hrc = H5Pclose(h5dcpl);
+ /* verifying the close of the dcpl */
+ if (hrc < 0) {
+ fprintf(stderr, "HDF5 Property List Close failed\n");
+ GOTOERROR(FAIL);
+ }
+ break;
}
/* The task is to transfer bytes_count bytes, starting at
@@ -2462,119 +2444,96 @@ done:
do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags)
{
int ret_code = SUCCESS, mrc;
- herr_t hrc;
hid_t acc_tpl = -1; /* file access templates */
- hbool_t use_gpfs = FALSE; /* use GPFS hints */
switch (param->io_type) {
- case POSIXIO:
- if (flags & (PIO_CREATE | PIO_WRITE))
- fd->posixfd = POSIXCREATE(fname);
- else
- fd->posixfd = POSIXOPEN(fname, O_RDONLY);
-
- if (fd->posixfd < 0 ) {
- fprintf(stderr, "POSIX File Open failed(%s)\n", fname);
- GOTOERROR(FAIL);
- }
-
-
- /* The perils of POSIX I/O in a parallel environment. The problem is:
- *
- * - Process n opens a file with truncation and then starts
- * writing to the file.
- * - Process m also opens the file with truncation, but after
- * process n has already started to write to the file. Thus,
- * all of the stuff process n wrote is now lost.
- */
- MPI_Barrier(pio_comm_g);
-
- break;
-
- case MPIO:
- if (flags & (PIO_CREATE | PIO_WRITE)) {
- MPI_File_delete(fname, h5_io_info_g);
- mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_CREATE | MPI_MODE_RDWR,
- h5_io_info_g, &fd->mpifd);
+ case POSIXIO:
+ if (flags & (PIO_CREATE | PIO_WRITE))
+ fd->posixfd = POSIXCREATE(fname);
+ else
+ fd->posixfd = POSIXOPEN(fname, O_RDONLY);
- if (mrc != MPI_SUCCESS) {
- fprintf(stderr, "MPI File Open failed(%s)\n", fname);
- GOTOERROR(FAIL);
- }
+ if (fd->posixfd < 0 ) {
+ fprintf(stderr, "POSIX File Open failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
- /*since MPI_File_open with MPI_MODE_CREATE does not truncate */
- /*filesize , set size to 0 explicitedly. */
- mrc = MPI_File_set_size(fd->mpifd, (MPI_Offset)0);
- if (mrc != MPI_SUCCESS) {
- fprintf(stderr, "MPI_File_set_size failed\n");
- GOTOERROR(FAIL);
- }
- } else {
- mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_RDONLY,
- h5_io_info_g, &fd->mpifd);
+ /* The perils of POSIX I/O in a parallel environment. The problem is:
+ *
+ * - Process n opens a file with truncation and then starts
+ * writing to the file.
+ * - Process m also opens the file with truncation, but after
+ * process n has already started to write to the file. Thus,
+ * all of the stuff process n wrote is now lost.
+ */
+ MPI_Barrier(pio_comm_g);
- if (mrc != MPI_SUCCESS) {
- fprintf(stderr, "MPI File Open failed(%s)\n", fname);
- GOTOERROR(FAIL);
- }
- }
+ break;
- break;
+ case MPIO:
+ if (flags & (PIO_CREATE | PIO_WRITE)) {
+ MPI_File_delete(fname, h5_io_info_g);
+ mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_CREATE | MPI_MODE_RDWR,
+ h5_io_info_g, &fd->mpifd);
+
+ if (mrc != MPI_SUCCESS) {
+ fprintf(stderr, "MPI File Open failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
- case PHDF5:
- acc_tpl = H5Pcreate(H5P_FILE_ACCESS);
- if (acc_tpl < 0) {
- fprintf(stderr, "HDF5 Property List Create failed\n");
- GOTOERROR(FAIL);
- }
+ /*since MPI_File_open with MPI_MODE_CREATE does not truncate */
+ /*filesize , set size to 0 explicitedly. */
+ mrc = MPI_File_set_size(fd->mpifd, (MPI_Offset)0);
+ if (mrc != MPI_SUCCESS) {
+ fprintf(stderr, "MPI_File_set_size failed\n");
+ GOTOERROR(FAIL);
+ }
+ } else {
+ mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_RDONLY, h5_io_info_g, &fd->mpifd);
+ if (mrc != MPI_SUCCESS) {
+ fprintf(stderr, "MPI File Open failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
+ }
- /* Use the appropriate VFL driver */
- if(param->h5_use_mpi_posix) {
- /* Set the file driver to the MPI-posix driver */
- hrc = H5Pset_fapl_mpiposix(acc_tpl, pio_comm_g, use_gpfs);
- if (hrc < 0) {
- fprintf(stderr, "HDF5 Property List Set failed\n");
- GOTOERROR(FAIL);
- }
- } /* end if */
- else {
- /* Set the file driver to the MPI-I/O driver */
- hrc = H5Pset_fapl_mpio(acc_tpl, pio_comm_g, h5_io_info_g);
- if (hrc < 0) {
- fprintf(stderr, "HDF5 Property List Set failed\n");
- GOTOERROR(FAIL);
- }
- } /* end else */
+ break;
- /* Set the alignment of objects in HDF5 file */
- hrc = H5Pset_alignment(acc_tpl, param->h5_thresh, param->h5_align);
- if (hrc < 0) {
- fprintf(stderr, "HDF5 Property List Set failed\n");
- GOTOERROR(FAIL);
- }
+ case PHDF5:
+ if ((acc_tpl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+ fprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
- /* create the parallel file */
- if (flags & (PIO_CREATE | PIO_WRITE)) {
- fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
- } else {
- fd->h5fd = H5Fopen(fname, H5F_ACC_RDONLY, acc_tpl);
- }
+ /* Set the file driver to the MPI-IO driver */
+ if (H5Pset_fapl_mpio(acc_tpl, pio_comm_g, h5_io_info_g) < 0) {
+ fprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ }
- hrc = H5Pclose(acc_tpl);
+ /* Set the alignment of objects in HDF5 file */
+ if (H5Pset_alignment(acc_tpl, param->h5_thresh, param->h5_align) < 0) {
+ fprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ }
- if (fd->h5fd < 0) {
- fprintf(stderr, "HDF5 File Create failed(%s)\n", fname);
- GOTOERROR(FAIL);
- }
+ /* create the parallel file */
+ if (flags & (PIO_CREATE | PIO_WRITE))
+ fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
+ else
+ fd->h5fd = H5Fopen(fname, H5F_ACC_RDONLY, acc_tpl);
+ if (fd->h5fd < 0) {
+ fprintf(stderr, "HDF5 File Create failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
- /* verifying the close of the acc_tpl */
- if (hrc < 0) {
- fprintf(stderr, "HDF5 Property List Close failed\n");
- GOTOERROR(FAIL);
- }
+ /* verifying the close of the acc_tpl */
+ if (H5Pclose(acc_tpl) < 0) {
+ fprintf(stderr, "HDF5 Property List Close failed\n");
+ GOTOERROR(FAIL);
+ }
- break;
+ break;
}
done:
@@ -2665,449 +2624,6 @@ do_cleanupfile(iotype iot, char *fname)
}
}
-#ifdef H5_HAVE_GPFS
-
-/* Descriptions here come from the IBM GPFS Manual */
-
-/*
- * Function: gpfs_access_range
- * Purpose: Declares an access range within a file for an
- * application.
- *
- * The application will access file offsets within the given
- * range, and will not access offsets outside the range.
- * Violating this hint may produce worse performance than if
- * no hint was specified.
- *
- * This hint is useful in situations where a file is
- * partitioned coarsely among several nodes. If the ranges
- * do not overlap, each node can specify which range of the
- * file it will access, with a performance improvement in
- * some cases, such as for sequential writing within a
- * range.
- *
- * Subsequent GPFS_ACCESS_RANGE hints will replace a hint
- * passed earlier.
- *
- * START - The start of the access range offset, in
- * bytes, from the beginning of the file
- * LENGTH - Length of the access range. 0 indicates to
- * the end of the file
- * IS_WRITE - 0 indicates READ access, 1 indicates WRITE access
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_access_range(int handle, off_t start, off_t length, int is_write)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsAccessRange_t access;
- } access_range;
-
- access_range.hdr.totalLength = sizeof(access_range);
- access_range.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- access_range.hdr.fcntlReserved = 0;
- access_range.access.structLen = sizeof(gpfsAccessRange_t);
- access_range.access.structType = GPFS_ACCESS_RANGE;
- access_range.access.start = start;
- access_range.access.length = length;
- access_range.access.isWrite = is_write;
-
- if (gpfs_fcntl(handle, &access_range) != 0) {
- fprintf(stderr,
- "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n",
- errno, access_range.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_free_range
- * Purpose: Undeclares an access range within a file for an
- * application.
- *
- * The application will no longer access file offsets within
- * the given range. GPFS flushes the data at the file
- * offsets and removes it from the cache.
- *
- * Multi-node applications that have finished one phase of
- * their computation may wish to use this hint before the
- * file is accessed in a conflicting mode from another node
- * in a later phase. The potential performance benefit is
- * that GPFS can avoid later synchronous cache consistency
- * operations.
- *
- * START - The start of the access range offset, in
- * bytes from the beginning of the file.
- * LENGTH - Length of the access range. 0 indicates to
- * the end of the file.
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_free_range(int handle, off_t start, off_t length)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsFreeRange_t range;
- } free_range;
-
- /* Issue the invalidate hint */
- free_range.hdr.totalLength = sizeof(free_range);
- free_range.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- free_range.hdr.fcntlReserved = 0;
- free_range.range.structLen = sizeof(gpfsFreeRange_t);
- free_range.range.structType = GPFS_FREE_RANGE;
- free_range.range.start = start;
- free_range.range.length = length;
-
- if (gpfs_fcntl(handle, &free_range) != 0) {
- fprintf(stderr,
- "gpfs_fcntl free range failed for range %d:%d. errno=%d errorOffset=%d\n",
- start, length, errno, free_range.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_clear_file_cache
- * Purpose: Indicates file access in the near future is not expected.
- *
- * The application does not expect to make any further
- * accesses to the file in the near future, so GPFS removes
- * any data or metadata pertaining to the file from its
- * cache.
- *
- * Multi-node applications that have finished one phase of
- * their computation may wish to use this hint before the
- * file is accessed in a conflicting mode from another node
- * in a later phase. The potential performance benefit is
- * that GPFS can avoid later synchronous cache consistency
- * operations.
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_clear_file_cache(int handle)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsClearFileCache_t clear;
- } clear_cache;
-
- clear_cache.hdr.totalLength = sizeof(clear_cache);
- clear_cache.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- clear_cache.hdr.fcntlReserved = 0;
- clear_cache.clear.structLen = sizeof(gpfsClearFileCache_t);
- clear_cache.clear.structType = GPFS_CLEAR_FILE_CACHE;
-
- if (gpfs_fcntl(handle, &clear_cache) != 0) {
- fprintf(stderr,
- "gpfs_fcntl clear file cache directive failed. errno=%d errorOffset=%d\n",
- errno, clear_cache.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_cancel_hints
- * Purpose: Indicates to remove any hints against the open file
- * handle.
- *
- * GPFS removes any hints that may have been issued against
- * this open file handle:
- *
- * - The hint status of the file is restored ot what it
- * would have been immediately after being opened, but
- * does not affect the contents of the GPFS file
- * cache. Cancelling an earlier hint that resulted in
- * data being removed from the GPFS file cache does
- * not bring that data back int othe cache; data
- * re-enters the cache only pon access by the
- * application or by user-driven or automatic
- * prefetching.
- * - Only the GPFS_MULTIPLE_ACCESS_RANGE hint has a
- * state that might be removed by the
- * GPFS_CANCEL_HINTS directive.
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_cancel_hints(int handle)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsCancelHints_t cancel;
- } cancel_hints;
-
- cancel_hints.hdr.totalLength = sizeof(cancel_hints);
- cancel_hints.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- cancel_hints.hdr.fcntlReserved = 0;
- cancel_hints.cancel.structLen = sizeof(gpfsCancelHints_t);
- cancel_hints.cancel.structType = GPFS_CANCEL_HINTS;
-
- if (gpfs_fcntl(handle, &cancel_hints) != 0) {
- fprintf(stderr,
- "gpfs_fcntl cancel hints directive failed. errno=%d errorOffset=%d\n",
- errno, cancel_hints.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_start_data_shipping
- * Purpose: Initiates data shipping mode.
- *
- * Once all participating threads have issued this directive
- * for a file, GPFS enters a mode where it logically
- * partitions the blocks of the file among a group of agent
- * nodes. The agents are those nodes on which one or more
- * threads have issued the GPFS_DATA_SHIP_START directive.
- * Each thread that has issued a GPFS_DATA_SHIP_START
- * directive and the associated agent nodes are referred to
- * as the data shipping collective.
- *
- * The second parameter is the total number of open
- * instances on all nodes that will be operating on the
- * file. Must be called for every such instance with the
- * same value of NUM_INSTS.
- *
- * NUM_INSTS - The number of open file instances, on all
- * nodes, collaborating to operate on the file
- * Return: Nothing
- * Programmer: Bill Wendling, 28. May 2002
- * Modifications:
- */
- static void
-gpfs_start_data_shipping(int handle, int num_insts)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsDataShipStart_t start;
- } ds_start;
-
- ds_start.hdr.totalLength = sizeof(ds_start);
- ds_start.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- ds_start.hdr.fcntlReserved = 0;
- ds_start.start.structLen = sizeof(gpfsDataShipStart_t);
- ds_start.start.structType = GPFS_DATA_SHIP_START;
- ds_start.start.numInstances = num_insts;
- ds_start.start.reserved = 0;
-
- if (gpfs_fcntl(handle, &ds_start) != 0) {
- fprintf(stderr,
- "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n",
- errno, ds_start.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_start_data_ship_map
- * Purpose: Indicates which agent nodes are to be used for data
- * shipping. GPFS recognizes which agent nodes to use for
- * data shipping.
- *
- * PARTITION_SIZE - The number of contiguous bytes per
- * server. This value must be a
- * multiple of the number of bytes in a
- * single file system block
- * AGENT_COUNT - The number of entries in the
- * agentNodeNumber array
- * AGENT_NODE_NUM - The data ship agent node numbers as
- * listed in the SDT or the global ODM
- *
- * Return: Nothing
- * Programmer: Bill Wendling, 10. Jul 2002
- * Modifications:
- */
- static void
-gpfs_start_data_ship_map(int handle, int partition_size, int agent_count,
- int *agent_node_num)
-{
- int i;
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsDataShipMap_t map;
- } ds_map;
-
- ds_map.hdr.totalLength = sizeof(ds_map);
- ds_map.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- ds_map.hdr.fcntlReserved = 0;
- ds_map.map.structLen = sizeof(gpfsDataShipMap_t);
- ds_map.map.structType = GPFS_DATA_SHIP_MAP;
- ds_map.map.partitionSize = partition_size;
- ds_map.map.agentCount = agent_count;
-
- for (i = 0; i < agent_count; ++i)
- ds_map.map.agentNodeNumber[i] = agent_node_num[i];
-
- if (gpfs_fcntl(handle, &ds_map) != 0) {
- fprintf(stderr,
- "gpfs_fcntl DS map directive failed. errno=%d errorOffset=%d\n",
- errno, ds_map.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_stop_data_shipping
- * Purpose: Takes a file out of the data shipping mode.
- *
- * - GPFS waits for all threads that issued the
- * GPFS_DATA_SHIP_START directive to issue this directive,
- * then flushes the dirty file data to disk.
- *
- * - While a gpfs_cntl() call is blocked for other threads,
- * the call can be interrupted by any signal. If a signal
- * is delivered to any of the waiting calls, all waiting
- * calls on every node will be interrupted and will return
- * EINTR. GPFS will not cancel data shipping mode if such
- * a signal occurs. It is the responsibility of the
- * application to mask off any signals that might normally
- * occur while waiting for another node in the data
- * shipping collective. Several libraries use SIGALRM; the
- * thread that makes the gpfs_fcntl() call should use
- * sigthreadmask to mask off delivery of this signal while
- * inside the call.
- * Return: Nothing
- * Programmer: Bill Wendling, 28. May 2002
- * Modifications:
- */
- static void
-gpfs_stop_data_shipping(int handle)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsDataShipStop_t stop;
- } ds_stop;
-
- ds_stop.hdr.totalLength = sizeof(ds_stop);
- ds_stop.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- ds_stop.hdr.fcntlReserved = 0;
- ds_stop.stop.structLen = sizeof(ds_stop.stop);
- ds_stop.stop.structType = GPFS_DATA_SHIP_STOP;
-
- if (gpfs_fcntl(handle, &ds_stop) != 0)
- fprintf(stderr,
- "gpfs_fcntl DS stop directive failed. errno=%d errorOffset=%d\n",
- errno, ds_stop.hdr.errorOffset);
-}
-
-/*
- * Function: gpfs_invalidate_file_cache
- * Purpose: Invalidate all cached data held on behalf of a file on
- * this node.
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_invalidate_file_cache(const char *filename)
-{
- int handle;
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsClearFileCache_t inv;
- } inv_cache_hint;
-
- /* Open the file. If the open fails, the file cannot be cached. */
- handle = open(filename, O_RDONLY, 0);
-
- if (handle == -1)
- return;
-
- /* Issue the invalidate hint */
- inv_cache_hint.hdr.totalLength = sizeof(inv_cache_hint);
- inv_cache_hint.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- inv_cache_hint.hdr.fcntlReserved = 0;
- inv_cache_hint.inv.structLen = sizeof(gpfsClearFileCache_t);
- inv_cache_hint.inv.structType = GPFS_CLEAR_FILE_CACHE;
-
- if (gpfs_fcntl(handle, &inv_cache_hint) != 0) {
- fprintf(stderr,
- "gpfs_fcntl clear cache hint failed for file '%s'.",
- filename);
- fprintf(stderr, " errno=%d errorOffset=%d\n",
- errno, inv_cache_hint.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-
- /* Close the file */
- if (close(handle) == -1) {
- fprintf(stderr,
- "could not close file '%s' after flushing file cache, ",
- filename);
- fprintf(stderr, "errno=%d\n", errno);
- exit(EXIT_FAILURE);
- }
-}
-
-#else
-
-/* turn the stubs off since some compilers are warning they are not used */
-#if 0
-/* H5_HAVE_GPFS isn't defined...stub functions */
-
- static void
-gpfs_access_range(int UNUSED handle, off_t UNUSED start, off_t UNUSED length,
- int UNUSED is_write)
-{
- return;
-}
-
- static void
-gpfs_free_range(int UNUSED handle, off_t UNUSED start, off_t UNUSED length)
-{
- return;
-}
-
- static void
-gpfs_clear_file_cache(int UNUSED handle)
-{
- return;
-}
-
- static void
-gpfs_cancel_hints(int UNUSED handle)
-{
- return;
-}
-
- static void
-gpfs_start_data_shipping(int UNUSED handle, int UNUSED num_insts)
-{
- return;
-}
-
- static void
-gpfs_stop_data_shipping(int UNUSED handle)
-{
- return;
-}
-
- static void
-gpfs_start_data_ship_map(int UNUSED handle, int UNUSED partition_size,
- int UNUSED agent_count, int UNUSED *agent_node_num)
-{
- return;
-}
-
- static void
-gpfs_invalidate_file_cache(const char UNUSED *filename)
-{
- return;
-}
-
-#endif /* 0 */
-
-#endif /* H5_HAVE_GPFS */
-
#ifdef TIME_MPI
/* instrument the MPI_File_wrirte_xxx and read_xxx calls to measure
* pure time spent in MPI_File code.
diff --git a/perform/pio_perf.c b/perform/pio_perf.c
index a47754b..cf41cbe 100644
--- a/perform/pio_perf.c
+++ b/perform/pio_perf.c
@@ -216,14 +216,6 @@ static struct long_options l_opts[] = {
{ "min-xfe", require_arg, 'x' },
{ "min-xf", require_arg, 'x' },
{ "min-x", require_arg, 'x' },
- { "mpi-posix", no_arg, 'm' },
- { "mpi-posi", no_arg, 'm' },
- { "mpi-pos", no_arg, 'm' },
- { "mpi-po", no_arg, 'm' },
- { "mpi-p", no_arg, 'm' },
- { "mpi-", no_arg, 'm' },
- { "mpi", no_arg, 'm' },
- { "mp", no_arg, 'm' },
{ "num-bytes", require_arg, 'e' },
{ "num-byte", require_arg, 'e' },
{ "num-byt", require_arg, 'e' },
@@ -294,7 +286,6 @@ struct options {
off_t h5_threshold; /* threshold for alignment in HDF5 file */
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
- unsigned h5_use_mpi_posix; /* Use MPI-posix VFD for HDF5 I/O (instead of MPI-I/O VFD) */
int verify; /* Verify data correctness */
};
@@ -444,7 +435,6 @@ run_test_loop(struct options *opts)
parms.h5_thresh = opts->h5_threshold;
parms.h5_use_chunks = opts->h5_use_chunks;
parms.h5_write_only = opts->h5_write_only;
- parms.h5_use_mpi_posix = opts->h5_use_mpi_posix;
parms.verify = opts->verify;
/* start with max_num_procs and decrement it by half for each loop. */
@@ -562,18 +552,15 @@ run_test(iotype iot, parameters parms, struct options *opts)
output_report("IO API = ");
switch (iot) {
- case POSIXIO:
- output_report("POSIX\n");
- break;
- case MPIO:
- output_report("MPIO\n");
- break;
- case PHDF5:
- if(parms.h5_use_mpi_posix)
- output_report("PHDF5 (w/MPI-posix driver)\n");
- else
- output_report("PHDF5 (w/MPI-I/O driver)\n");
- break;
+ case POSIXIO:
+ output_report("POSIX\n");
+ break;
+ case MPIO:
+ output_report("MPIO\n");
+ break;
+ case PHDF5:
+ output_report("PHDF5 (w/MPI-IO driver)\n");
+ break;
}
MPI_Comm_size(pio_comm_g, &comm_size);
@@ -1232,11 +1219,7 @@ report_parameters(struct options *opts)
else
HDfprintf(output, "1D\n");
- HDfprintf(output, "rank %d: VFL used for HDF5 I/O=", rank);
- if(opts->h5_use_mpi_posix)
- HDfprintf(output, "MPI-posix driver\n");
- else
- HDfprintf(output, "MPI-I/O driver\n");
+ HDfprintf(output, "rank %d: VFL used for HDF5 I/O=%s\n", rank, "MPI-IO driver");
HDfprintf(output, "rank %d: Data storage method in HDF5=", rank);
if(opts->h5_use_chunks)
@@ -1295,7 +1278,6 @@ parse_command_line(int argc, char *argv[])
cl_opts->h5_threshold = 1; /* No threshold for aligning HDF5 objects by default */
cl_opts->h5_use_chunks = FALSE; /* Don't chunk the HDF5 dataset by default */
cl_opts->h5_write_only = FALSE; /* Do both read and write by default */
- cl_opts->h5_use_mpi_posix = FALSE; /* Don't use MPI-posix VFD for HDF5 I/O by default */
cl_opts->verify = FALSE; /* No Verify data correctness by default */
while ((opt = get_option(argc, (const char **)argv, s_opts, l_opts)) != EOF) {
@@ -1428,10 +1410,6 @@ parse_command_line(int argc, char *argv[])
case 'I':
cl_opts->interleaved = 1;
break;
- case 'm':
- /* Turn on MPI-posix VFL driver for HDF5 I/O */
- cl_opts->h5_use_mpi_posix = TRUE;
- break;
case 'o':
cl_opts->output_file = opt_arg;
break;
@@ -1604,8 +1582,6 @@ usage(const char *prog)
printf(" -I, --interleaved Interleaved access pattern\n");
printf(" (see below for example)\n");
printf(" [default: Contiguous access pattern]\n");
- printf(" -m, --mpi-posix Use MPI-posix driver for HDF5 I/O\n");
- printf(" [default: use MPI-I/O driver]\n");
printf(" -o F, --output=F Output raw data into file F [default: none]\n");
printf(" -p N, --min-num-processes=N Minimum number of processes to use [default: 1]\n");
printf(" -P N, --max-num-processes=N Maximum number of processes to use\n");
diff --git a/perform/pio_perf.h b/perform/pio_perf.h
index 094b31d..3295e2b 100644
--- a/perform/pio_perf.h
+++ b/perform/pio_perf.h
@@ -54,7 +54,6 @@ typedef struct parameters_ {
hsize_t h5_thresh; /* HDF5 object alignment threshold */
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
- unsigned h5_use_mpi_posix; /* Use MPI-posix VFD for HDF5 I/O (instead of MPI-I/O VFD) */
int verify; /* Verify data correctness */
} parameters;
diff --git a/perform/sio_engine.c b/perform/sio_engine.c
index 0ab5c3e..dec2f98 100644
--- a/perform/sio_engine.c
+++ b/perform/sio_engine.c
@@ -28,10 +28,6 @@
#include "hdf5.h"
-#ifdef H5_HAVE_GPFS
-# include <gpfs_fcntl.h>
-#endif /* H5_HAVE_GPFS */
-
#include "sio_perf.h"
#include "sio_timer.h"
@@ -94,19 +90,6 @@ hid_t set_vfd(parameters *param);
static herr_t do_fclose(iotype iot, file_descr *fd);
static void do_cleanupfile(iotype iot, char *fname);
-/* GPFS-specific functions */
-#ifdef H5_HAVE_GPFS
-static void gpfs_access_range(int handle, off_t start, off_t length, int is_write);
-static void gpfs_free_range(int handle, off_t start, off_t length);
-static void gpfs_clear_file_cache(int handle);
-static void gpfs_cancel_hints(int handle);
-static void gpfs_start_data_shipping(int handle, int num_insts);
-static void gpfs_start_data_ship_map(int handle, int partition_size,
- int agent_count, int *agent_node_num);
-static void gpfs_stop_data_shipping(int handle);
-static void gpfs_invalidate_file_cache(const char *filename);
-#endif /* H5_HAVE_GPFS */
-
/* global variables */
static off_t offset[MAX_DIMS]; /* dataset size in bytes */
static size_t buf_offset[MAX_DIMS]; /* dataset size in bytes */
@@ -1325,447 +1308,3 @@ do_cleanupfile(iotype iot, char *filename)
}
}
-#ifdef H5_HAVE_GPFS
-
-/* Descriptions here come from the IBM GPFS Manual */
-
-/*
- * Function: gpfs_access_range
- * Purpose: Declares an access range within a file for an
- * application.
- *
- * The application will access file offsets within the given
- * range, and will not access offsets outside the range.
- * Violating this hint may produce worse performance than if
- * no hint was specified.
- *
- * This hint is useful in situations where a file is
- * partitioned coarsely among several nodes. If the ranges
- * do not overlap, each node can specify which range of the
- * file it will access, with a performance improvement in
- * some cases, such as for sequential writing within a
- * range.
- *
- * Subsequent GPFS_ACCESS_RANGE hints will replace a hint
- * passed earlier.
- *
- * START - The start of the access range offset, in
- * bytes, from the beginning of the file
- * LENGTH - Length of the access range. 0 indicates to
- * the end of the file
- * IS_WRITE - 0 indicates READ access, 1 indicates WRITE access
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_access_range(int handle, off_t start, off_t length, int is_write)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsAccessRange_t access;
- } access_range;
-
- access_range.hdr.totalLength = sizeof(access_range);
- access_range.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- access_range.hdr.fcntlReserved = 0;
- access_range.access.structLen = sizeof(gpfsAccessRange_t);
- access_range.access.structType = GPFS_ACCESS_RANGE;
- access_range.access.start = start;
- access_range.access.length = length;
- access_range.access.isWrite = is_write;
-
- if (gpfs_fcntl(handle, &access_range) != 0) {
- fprintf(stderr,
- "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n",
- errno, access_range.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_free_range
- * Purpose: Undeclares an access range within a file for an
- * application.
- *
- * The application will no longer access file offsets within
- * the given range. GPFS flushes the data at the file
- * offsets and removes it from the cache.
- *
- * Multi-node applications that have finished one phase of
- * their computation may wish to use this hint before the
- * file is accessed in a conflicting mode from another node
- * in a later phase. The potential performance benefit is
- * that GPFS can avoid later synchronous cache consistency
- * operations.
- *
- * START - The start of the access range offset, in
- * bytes from the beginning of the file.
- * LENGTH - Length of the access range. 0 indicates to
- * the end of the file.
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_free_range(int handle, off_t start, off_t length)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsFreeRange_t range;
- } free_range;
-
- /* Issue the invalidate hint */
- free_range.hdr.totalLength = sizeof(free_range);
- free_range.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- free_range.hdr.fcntlReserved = 0;
- free_range.range.structLen = sizeof(gpfsFreeRange_t);
- free_range.range.structType = GPFS_FREE_RANGE;
- free_range.range.start = start;
- free_range.range.length = length;
-
- if (gpfs_fcntl(handle, &free_range) != 0) {
- fprintf(stderr,
- "gpfs_fcntl free range failed for range %d:%d. errno=%d errorOffset=%d\n",
- start, length, errno, free_range.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_clear_file_cache
- * Purpose: Indicates file access in the near future is not expected.
- *
- * The application does not expect to make any further
- * accesses to the file in the near future, so GPFS removes
- * any data or metadata pertaining to the file from its
- * cache.
- *
- * Multi-node applications that have finished one phase of
- * their computation may wish to use this hint before the
- * file is accessed in a conflicting mode from another node
- * in a later phase. The potential performance benefit is
- * that GPFS can avoid later synchronous cache consistency
- * operations.
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_clear_file_cache(int handle)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsClearFileCache_t clear;
- } clear_cache;
-
- clear_cache.hdr.totalLength = sizeof(clear_cache);
- clear_cache.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- clear_cache.hdr.fcntlReserved = 0;
- clear_cache.clear.structLen = sizeof(gpfsClearFileCache_t);
- clear_cache.clear.structType = GPFS_CLEAR_FILE_CACHE;
-
- if (gpfs_fcntl(handle, &clear_cache) != 0) {
- fprintf(stderr,
- "gpfs_fcntl clear file cache directive failed. errno=%d errorOffset=%d\n",
- errno, clear_cache.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_cancel_hints
- * Purpose: Indicates to remove any hints against the open file
- * handle.
- *
- * GPFS removes any hints that may have been issued against
- * this open file handle:
- *
- * - The hint status of the file is restored ot what it
- * would have been immediately after being opened, but
- * does not affect the contents of the GPFS file
- * cache. Cancelling an earlier hint that resulted in
- * data being removed from the GPFS file cache does
- * not bring that data back int othe cache; data
- * re-enters the cache only pon access by the
- * application or by user-driven or automatic
- * prefetching.
- * - Only the GPFS_MULTIPLE_ACCESS_RANGE hint has a
- * state that might be removed by the
- * GPFS_CANCEL_HINTS directive.
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_cancel_hints(int handle)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsCancelHints_t cancel;
- } cancel_hints;
-
- cancel_hints.hdr.totalLength = sizeof(cancel_hints);
- cancel_hints.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- cancel_hints.hdr.fcntlReserved = 0;
- cancel_hints.cancel.structLen = sizeof(gpfsCancelHints_t);
- cancel_hints.cancel.structType = GPFS_CANCEL_HINTS;
-
- if (gpfs_fcntl(handle, &cancel_hints) != 0) {
- fprintf(stderr,
- "gpfs_fcntl cancel hints directive failed. errno=%d errorOffset=%d\n",
- errno, cancel_hints.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_start_data_shipping
- * Purpose: Initiates data shipping mode.
- *
- * Once all participating threads have issued this directive
- * for a file, GPFS enters a mode where it logically
- * partitions the blocks of the file among a group of agent
- * nodes. The agents are those nodes on which one or more
- * threads have issued the GPFS_DATA_SHIP_START directive.
- * Each thread that has issued a GPFS_DATA_SHIP_START
- * directive and the associated agent nodes are referred to
- * as the data shipping collective.
- *
- * The second parameter is the total number of open
- * instances on all nodes that will be operating on the
- * file. Must be called for every such instance with the
- * same value of NUM_INSTS.
- *
- * NUM_INSTS - The number of open file instances, on all
- * nodes, collaborating to operate on the file
- * Return: Nothing
- * Programmer: Bill Wendling, 28. May 2002
- * Modifications:
- */
- static void
-gpfs_start_data_shipping(int handle, int num_insts)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsDataShipStart_t start;
- } ds_start;
-
- ds_start.hdr.totalLength = sizeof(ds_start);
- ds_start.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- ds_start.hdr.fcntlReserved = 0;
- ds_start.start.structLen = sizeof(gpfsDataShipStart_t);
- ds_start.start.structType = GPFS_DATA_SHIP_START;
- ds_start.start.numInstances = num_insts;
- ds_start.start.reserved = 0;
-
- if (gpfs_fcntl(handle, &ds_start) != 0) {
- fprintf(stderr,
- "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n",
- errno, ds_start.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_start_data_ship_map
- * Purpose: Indicates which agent nodes are to be used for data
- * shipping. GPFS recognizes which agent nodes to use for
- * data shipping.
- *
- * PARTITION_SIZE - The number of contiguous bytes per
- * server. This value must be a
- * multiple of the number of bytes in a
- * single file system block
- * AGENT_COUNT - The number of entries in the
- * agentNodeNumber array
- * AGENT_NODE_NUM - The data ship agent node numbers as
- * listed in the SDT or the global ODM
- *
- * Return: Nothing
- * Programmer: Bill Wendling, 10. Jul 2002
- * Modifications:
- */
- static void
-gpfs_start_data_ship_map(int handle, int partition_size, int agent_count,
- int *agent_node_num)
-{
- int i;
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsDataShipMap_t map;
- } ds_map;
-
- ds_map.hdr.totalLength = sizeof(ds_map);
- ds_map.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- ds_map.hdr.fcntlReserved = 0;
- ds_map.map.structLen = sizeof(gpfsDataShipMap_t);
- ds_map.map.structType = GPFS_DATA_SHIP_MAP;
- ds_map.map.partitionSize = partition_size;
- ds_map.map.agentCount = agent_count;
-
- for (i = 0; i < agent_count; ++i)
- ds_map.map.agentNodeNumber[i] = agent_node_num[i];
-
- if (gpfs_fcntl(handle, &ds_map) != 0) {
- fprintf(stderr,
- "gpfs_fcntl DS map directive failed. errno=%d errorOffset=%d\n",
- errno, ds_map.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-}
-
-/*
- * Function: gpfs_stop_data_shipping
- * Purpose: Takes a file out of the data shipping mode.
- *
- * - GPFS waits for all threads that issued the
- * GPFS_DATA_SHIP_START directive to issue this directive,
- * then flushes the dirty file data to disk.
- *
- * - While a gpfs_cntl() call is blocked for other threads,
- * the call can be interrupted by any signal. If a signal
- * is delivered to any of the waiting calls, all waiting
- * calls on every node will be interrupted and will return
- * EINTR. GPFS will not cancel data shipping mode if such
- * a signal occurs. It is the responsibility of the
- * application to mask off any signals that might normally
- * occur while waiting for another node in the data
- * shipping collective. Several libraries use SIGALRM; the
- * thread that makes the gpfs_fcntl() call should use
- * sigthreadmask to mask off delivery of this signal while
- * inside the call.
- * Return: Nothing
- * Programmer: Bill Wendling, 28. May 2002
- * Modifications:
- */
- static void
-gpfs_stop_data_shipping(int handle)
-{
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsDataShipStop_t stop;
- } ds_stop;
-
- ds_stop.hdr.totalLength = sizeof(ds_stop);
- ds_stop.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- ds_stop.hdr.fcntlReserved = 0;
- ds_stop.stop.structLen = sizeof(ds_stop.stop);
- ds_stop.stop.structType = GPFS_DATA_SHIP_STOP;
-
- if (gpfs_fcntl(handle, &ds_stop) != 0)
- fprintf(stderr,
- "gpfs_fcntl DS stop directive failed. errno=%d errorOffset=%d\n",
- errno, ds_stop.hdr.errorOffset);
-}
-
-/*
- * Function: gpfs_invalidate_file_cache
- * Purpose: Invalidate all cached data held on behalf of a file on
- * this node.
- * Return: Nothing
- * Programmer: Bill Wendling, 03. June 2002
- * Modifications:
- */
- static void
-gpfs_invalidate_file_cache(const char *filename)
-{
- int handle;
- struct {
- gpfsFcntlHeader_t hdr;
- gpfsClearFileCache_t inv;
- } inv_cache_hint;
-
- /* Open the file. If the open fails, the file cannot be cached. */
- handle = open(filename, O_RDONLY, 0);
-
- if (handle == -1)
- return;
-
- /* Issue the invalidate hint */
- inv_cache_hint.hdr.totalLength = sizeof(inv_cache_hint);
- inv_cache_hint.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
- inv_cache_hint.hdr.fcntlReserved = 0;
- inv_cache_hint.inv.structLen = sizeof(gpfsClearFileCache_t);
- inv_cache_hint.inv.structType = GPFS_CLEAR_FILE_CACHE;
-
- if (gpfs_fcntl(handle, &inv_cache_hint) != 0) {
- fprintf(stderr,
- "gpfs_fcntl clear cache hint failed for file '%s'.",
- filename);
- fprintf(stderr, " errno=%d errorOffset=%d\n",
- errno, inv_cache_hint.hdr.errorOffset);
- exit(EXIT_FAILURE);
- }
-
- /* Close the file */
- if (close(handle) == -1) {
- fprintf(stderr,
- "could not close file '%s' after flushing file cache, ",
- filename);
- fprintf(stderr, "errno=%d\n", errno);
- exit(EXIT_FAILURE);
- }
-}
-
-#else
-
-/* turn the stubs off since some compilers are warning they are not used */
-#if 0
-/* H5_HAVE_GPFS isn't defined...stub functions */
-
- static void
-gpfs_access_range(int UNUSED handle, off_t UNUSED start, off_t UNUSED length,
- int UNUSED is_write)
-{
- return;
-}
-
- static void
-gpfs_free_range(int UNUSED handle, off_t UNUSED start, off_t UNUSED length)
-{
- return;
-}
-
- static void
-gpfs_clear_file_cache(int UNUSED handle)
-{
- return;
-}
-
- static void
-gpfs_cancel_hints(int UNUSED handle)
-{
- return;
-}
-
- static void
-gpfs_start_data_shipping(int UNUSED handle, int UNUSED num_insts)
-{
- return;
-}
-
- static void
-gpfs_stop_data_shipping(int UNUSED handle)
-{
- return;
-}
-
- static void
-gpfs_start_data_ship_map(int UNUSED handle, int UNUSED partition_size,
- int UNUSED agent_count, int UNUSED *agent_node_num)
-{
- return;
-}
-
- static void
-gpfs_invalidate_file_cache(const char UNUSED *filename)
-{
- return;
-}
-
-#endif /* 0 */
-
-#endif /* H5_HAVE_GPFS */
-
-
diff --git a/perform/sio_perf.c b/perform/sio_perf.c
index 7df9337..26cec6d 100644
--- a/perform/sio_perf.c
+++ b/perform/sio_perf.c
@@ -210,14 +210,6 @@ static struct long_options l_opts[] = {
{ "min-xfe", require_arg, 'x' },
{ "min-xf", require_arg, 'x' },
{ "min-x", require_arg, 'x' },
- { "mpi-posix", no_arg, 'm' },
- { "mpi-posi", no_arg, 'm' },
- { "mpi-pos", no_arg, 'm' },
- { "mpi-po", no_arg, 'm' },
- { "mpi-p", no_arg, 'm' },
- { "mpi-", no_arg, 'm' },
- { "mpi", no_arg, 'm' },
- { "mp", no_arg, 'm' },
{ "num-bytes", require_arg, 'e' },
{ "num-byte", require_arg, 'e' },
{ "num-byt", require_arg, 'e' },
@@ -302,7 +294,6 @@ struct options {
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
int h5_extendable; /* Perform the write tests only */
- unsigned h5_use_mpi_posix; /* Use MPI-posix VFD for HDF5 I/O (instead of MPI-I/O VFD) */
int verify; /* Verify data correctness */
vfdtype vfd; /* File driver */
@@ -411,7 +402,6 @@ run_test_loop(struct options *opts)
parms.h5_use_chunks = opts->h5_use_chunks;
parms.h5_extendable = opts->h5_extendable;
parms.h5_write_only = opts->h5_write_only;
- parms.h5_use_mpi_posix = opts->h5_use_mpi_posix;
parms.verify = opts->verify;
parms.vfd = opts->vfd;
@@ -982,7 +972,6 @@ parse_command_line(int argc, char *argv[])
cl_opts->h5_use_chunks = FALSE; /* Don't chunk the HDF5 dataset by default */
cl_opts->h5_write_only = FALSE; /* Do both read and write by default */
cl_opts->h5_extendable = FALSE; /* Use extendable dataset */
- cl_opts->h5_use_mpi_posix = FALSE; /* Don't use MPI-posix VFD for HDF5 I/O by default */
cl_opts->verify = FALSE; /* No Verify data correctness by default */
while ((opt = get_option(argc, (const char **)argv, s_opts, l_opts)) != EOF) {
@@ -1144,10 +1133,6 @@ parse_command_line(int argc, char *argv[])
case 'i':
cl_opts->num_iters = atoi(opt_arg);
break;
- case 'm':
- /* Turn on MPI-posix VFL driver for HDF5 I/O */
- cl_opts->h5_use_mpi_posix = TRUE;
- break;
case 'o':
cl_opts->output_file = opt_arg;
break;
diff --git a/perform/sio_perf.h b/perform/sio_perf.h
index 3e4456a..b40fed3 100644
--- a/perform/sio_perf.h
+++ b/perform/sio_perf.h
@@ -66,7 +66,6 @@ typedef struct parameters_ {
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_extendable; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
- unsigned h5_use_mpi_posix; /* VFD for HDF5 I/O */
int verify; /* Verify data correctness */
} parameters;