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[svn-r344] Added collective access tests to testphdf5.c.

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Changed the data file names to *.h5f to avoid potential mixup
with the split file convention.
This commit is contained in:
Albert Cheng
1998-04-12 23:35:49 -05:00
parent 33a49221fc
commit 851b448c9d
2 changed files with 605 additions and 139 deletions
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2
testpar/Makefile.irix64
View File

@@ -19,7 +19,7 @@ CPPFLAGS=-I. -I../src $(MPI_INC)
RM=rm -f
# temporary test files that can be cleaned away
MOSTLYCLEAN=ParaEg1.h5 Eg1.h5 shdf5.c go
MOSTLYCLEAN=ParaEg1.h5f ParaEg2.h5f Eg1.h5f Eg2.h5f shdf5.c go
# The default is to build the library and programs.
all: testphdf5

742
testpar/testphdf5.c
View File

@@ -27,91 +27,128 @@
#define MESG(x)\
if (verbose) printf("%s\n", x);\
#ifdef HAVE_PARALLEL
#define MPI_BANNER(mesg)\
{printf("--------------------------------\n");\
printf("Proc %d: ", mympirank); \
printf("Proc %d: ", mpi_rank); \
printf("*** %s\n", mesg);\
printf("--------------------------------\n");}
#else
#define MPI_BANNER(mesg)\
{printf("================================\n");\
printf("*** %s\n", mesg);\
printf("================================\n");}
#endif
#ifdef HAVE_PARALLEL
#define SYNC(comm)\
{MPI_BANNER("doing a SYNC"); MPI_Barrier(comm); MPI_BANNER("SYNC DONE");}
/* pause the process for a moment to allow debugger to attach if desired. */
/* Will pause more if greenlight file is not persent but will eventually */
/* continue. */
#include <sys/types.h>
#include <sys/stat.h>
void pause_proc(MPI_Comm comm, int mympirank, char* processor_name, int namelen,
int argc, char **argv)
{
int pid;
struct stat statbuf;
char greenlight[] = "go";
int maxloop = 10;
int time_int = 10;
/* check if an pause interval option is given */
if (--argc > 0 && isdigit(*++argv))
time_int = atoi(*argv);
pid = getpid();
printf("Proc %d (%*s): pid = %d\n",
mympirank, namelen, processor_name, pid);
if (mympirank == 0)
while ((stat(greenlight, &statbuf) == -1) && maxloop-- > 0){
printf("waiting(%ds) for file %s ...", time_int, greenlight);
fflush(stdout);
sleep(time_int);
}
MPI_Barrier(comm);
}
#endif /*HAVE_PARALLEL*/
/* End of Define some handy debugging shorthands, routines, ... */
/* Constants definitions */
/* 24 is a multiple of 2, 3, 4, 6, 8, 12. Neat for parallel tests. */
#define SPACE1_DIM1 8
#define SPACE1_DIM2 12
#define SPACE1_DIM1 24
#define SPACE1_DIM2 24
#define SPACE1_RANK 2
#define DATASETNAME1 "Data1"
#define DATASETNAME2 "Data2"
#define DATASETNAME3 "Data3"
/* hyperslab layout styles */
#define BYROW 1 /* divide into slabs of rows */
#define BYCOL 2 /* divide into blocks of columns */
/* dataset data type. Int's can be easily octo dumped. */
typedef int DATATYPE;
/* global variables */
char *filenames[]={
#ifdef HAVE_PARALLEL
"ParaEg1.h5f", "ParaEg2.h5f"
#else
"Eg1.h5f", "Eg2.h5f"
#endif
};
int nerrors = 0; /* errors count */
int mpi_size, mpi_rank; /* mpi variables */
/* option flags */
int verbose = 0; /* verbose, default as no. */
int doread=1; /* read test */
int dowrite=1; /* write test */
#ifdef USE_PAUSE
/* pause the process for a moment to allow debugger to attach if desired. */
/* Will pause more if greenlight file is not persent but will eventually */
/* continue. */
#include <sys/types.h>
#include <sys/stat.h>
void pause_proc(MPI_Comm comm, int mpi_rank, char* mpi_name, int mpi_namelen,
int argc, char **argv)
{
int pid;
struct stat statbuf;
char greenlight[] = "go";
int maxloop = 10;
int loops = 0;
int time_int = 10;
#ifdef DISABLED
/* check if an pause interval option is given */
if (--argc > 0 && isdigit(*++argv))
time_int = atoi(*argv);
#endif
pid = getpid();
if (mpi_rank == 0)
while ((stat(greenlight, &statbuf) == -1) && loops < maxloop){
if (!loops++){
printf("Proc %d (%*s, %d): You may attach %d for debugging.\n",
mpi_rank, mpi_namelen, mpi_name, pid, pid);
}
printf("waiting(%ds) for file %s ...\n", time_int, greenlight);
fflush(stdout);
sleep(time_int);
}
MPI_Barrier(comm);
}
#endif /* USE_PAUSE */
/*
* Setup the dimensions of the hyperslab.
* Two modes--by rows or by columns.
* Assume dimension rank is 2.
*/
void
slab_set(hssize_t start[], hsize_t count[], hsize_t stride[], int mode)
{
switch (mode){
case BYROW:
/* Each process takes a slabs of rows. */
stride[0] = 1;
stride[1] = 1;
count[0] = SPACE1_DIM1/mpi_size;
count[1] = SPACE1_DIM2;
start[0] = mpi_rank*count[0];
start[1] = 0;
break;
case BYCOL:
/* Each process takes a block of columns. */
stride[0] = 1;
stride[1] = 1;
count[0] = SPACE1_DIM1;
count[1] = SPACE1_DIM2/mpi_size;
start[0] = 0;
start[1] = mpi_rank*count[1];
break;
default:
/* Unknown mode. Set it to cover the whole dataset. */
printf("unknown slab_set mode (%d)\n", mode);
stride[0] = 1;
stride[1] = 1;
count[0] = SPACE1_DIM1;
count[1] = SPACE1_DIM2;
start[0] = 0;
start[1] = 0;
break;
}
}
/*
* Fill the dataset with trivial data for testing.
* Assume dimension rank is 2 and data is stored contiguous.
*/
void
dataset_data(int start[], size_t count[], DATATYPE * dataset)
dataset_fill(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset)
{
DATATYPE *dataptr = dataset;
int i, j;
@@ -119,7 +156,7 @@ dataset_data(int start[], size_t count[], DATATYPE * dataset)
/* put some trivial data in the data_array */
for (i=0; i < count[0]; i++){
for (j=0; j < count[1]; j++){
*dataptr++ = (i+start[0])*100 + (j+1);
*dataptr++ = (i*stride[0]+start[0])*100 + (j*stride[1]+start[1]+1);
}
}
}
@@ -128,14 +165,14 @@ dataset_data(int start[], size_t count[], DATATYPE * dataset)
/*
* Print the content of the dataset.
*/
void dataset_print(int start[], size_t count[], DATATYPE * dataset)
void dataset_print(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset)
{
DATATYPE *dataptr = dataset;
int i, j;
/* print the slab read */
for (i=0; i < count[0]; i++){
printf("Row %d: ", i+start[0]);
printf("Row %ld: ", (long)i*stride[0]+start[0]);
for (j=0; j < count[1]; j++){
printf("%03d ", *dataptr++);
}
@@ -147,32 +184,50 @@ void dataset_print(int start[], size_t count[], DATATYPE * dataset)
/*
* Print the content of the dataset.
*/
int dataset_vrfy(int start[], size_t count[], DATATYPE *dataset, DATATYPE *original)
int dataset_vrfy(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original)
{
#define MAX_ERR_REPORT 10 /* Maximum number of errors reported */
DATATYPE *dataptr = dataset;
DATATYPE *originptr = original;
int i, j, nerrors;
/* print it if verbose */
if (verbose)
dataset_print(start, count, stride, dataset);
nerrors = 0;
for (i=0; i < count[0]; i++){
for (j=0; j < count[1]; j++){
if (*dataset++ != *original++){
printf("Dataset Verify failed at [%d][%d]: expect %d, got %d\n",
i, j, *(dataset-1), *(original-1));
nerrors++;
nerrors++;
if (nerrors <= MAX_ERR_REPORT){
printf("Dataset Verify failed at [%d][%d](row %d, col %d): expect %d, got %d\n",
i, j,
(int) i*stride[0]+start[0], (int) j*stride[1]+start[1],
*(dataset-1), *(original-1));
}
}
}
}
if (nerrors > MAX_ERR_REPORT)
printf("[more errors ...]\n");
if (nerrors)
printf("%d errors found in dataset_vrfy\n", nerrors);
return(nerrors);
}
/* Example of using the parallel HDF5 library to create a dataset */
/*
* Example of using the parallel HDF5 library to create two datasets
* in one HDF5 files with parallel MPIO access support.
* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
* Each process controls only a slab of size DIM1 x DIM2 within each
* dataset.
*/
void
phdf5writeInd()
phdf5writeInd(char *filename)
{
hid_t fid1, fid2; /* HDF5 file IDs */
hid_t acc_tpl1; /* File access templates */
@@ -181,52 +236,45 @@ phdf5writeInd()
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
int rank = SPACE1_RANK; /* Logical rank of dataspace */
size_t dims1[SPACE1_RANK] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
hsize_t dims1[SPACE1_RANK] =
{SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
hsize_t dimslocal1[SPACE1_RANK] =
{SPACE1_DIM1,SPACE1_DIM2}; /* local dataspace dim sizes */
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
int start[SPACE1_RANK]; /* for hyperslab setting */
size_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
hssize_t start[SPACE1_RANK]; /* for hyperslab setting */
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int i, j;
int numprocs, mympirank;
int mpi_size, mpi_rank;
char *fname;
int color = 0; /* used for MPI_Comm_split */
int mrc; /* mpi return code */
#ifdef HAVE_PARALLEL
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Independent write test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
MPI_Comm_rank(MPI_COMM_WORLD,&mympirank);
#else
numprocs = 1;
mympirank = 0;
#endif
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
#ifdef NO
/* split into two new communicators, one contains the originally */
/* odd rank processes, the other the even ones. */
color = mympirank%2;
mrc = MPI_Comm_split (MPI_COMM_WORLD, color, mympirank, &comm);
assert(mrc==MPI_SUCCESS);
#endif
/* setup file access template */
/* -------------------
* START AN HDF5 FILE
* -------------------*/
/* setup file access template with parallel IO access. */
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
assert(acc_tpl1 != FAIL);
MESG("H5Pcreate access succeed");
#ifdef HAVE_PARALLEL
/* set Independent Parallel access with communicator */
ret = H5Pset_mpi(acc_tpl1, comm, info, H5ACC_INDEPENDENT);
assert(ret != FAIL);
MESG("H5Pset_mpi succeed");
#endif
/* create the file collectively */
fid1=H5Fcreate(filenames[color],H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1);
fid1=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1);
assert(fid1 != FAIL);
MESG("H5Fcreate succeed");
@@ -235,6 +283,10 @@ phdf5writeInd()
assert(ret != FAIL);
/* --------------------------
* Define the dimensions of the overall datasets
* and the slabs local to the MPI process.
* ------------------------- */
/* setup dimensionality object */
sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL);
assert (sid1 != FAIL);
@@ -256,9 +308,9 @@ phdf5writeInd()
/* set up dimensions of the slab this process accesses */
start[0] = mympirank*SPACE1_DIM1/numprocs;
start[0] = mpi_rank*SPACE1_DIM1/mpi_size;
start[1] = 0;
count[0] = SPACE1_DIM1/numprocs;
count[0] = SPACE1_DIM1/mpi_size;
count[1] = SPACE1_DIM2;
stride[0] = 1;
stride[1] =1;
@@ -267,7 +319,7 @@ if (verbose)
start[0], start[1], count[0], count[1], count[0]*count[1]);
/* put some trivial data in the data_array */
dataset_data(start, count, &data_array1[0][0]);
dataset_fill(start, count, stride, &data_array1[0][0]);
MESG("data_array initialized");
/* create a file dataspace independently */
@@ -314,7 +366,7 @@ if (verbose)
/* Example of using the parallel HDF5 library to read a dataset */
void
phdf5readInd()
phdf5readInd(char *filename)
{
hid_t fid1, fid2; /* HDF5 file IDs */
hid_t acc_tpl1; /* File access templates */
@@ -323,41 +375,38 @@ phdf5readInd()
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
int rank = SPACE1_RANK; /* Logical rank of dataspace */
size_t dims1[] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
hsize_t dims1[] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */
int start[SPACE1_RANK]; /* for hyperslab setting */
size_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
hssize_t start[SPACE1_RANK]; /* for hyperslab setting */
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int i, j;
int numprocs, mympirank;
#ifdef HAVE_PARALLEL
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Independent read test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
MPI_Comm_rank(MPI_COMM_WORLD,&mympirank);
#else
numprocs = 1;
mympirank = 0;
#endif
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* setup file access template */
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
assert(acc_tpl1 != FAIL);
#ifdef HAVE_PARALLEL
/* set Independent Parallel access with communicator */
ret = H5Pset_mpi(acc_tpl1, comm, info, H5ACC_INDEPENDENT);
assert(ret != FAIL);
#endif
/* open the file collectively */
fid1=H5Fopen(filenames[0],H5F_ACC_RDWR,acc_tpl1);
fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1);
assert(fid1 != FAIL);
/* Release file-access template */
@@ -374,9 +423,9 @@ phdf5readInd()
/* set up dimensions of the slab this process accesses */
start[0] = mympirank*SPACE1_DIM1/numprocs;
start[0] = mpi_rank*SPACE1_DIM1/mpi_size;
start[1] = 0;
count[0] = SPACE1_DIM1/numprocs;
count[0] = SPACE1_DIM1/mpi_size;
count[1] = SPACE1_DIM2;
stride[0] = 1;
stride[1] =1;
@@ -395,7 +444,7 @@ if (verbose)
assert (mem_dataspace != FAIL);
/* fill dataset with test data */
dataset_data(start, count, &data_origin1[0][0]);
dataset_fill(start, count, stride, &data_origin1[0][0]);
/* read data independently */
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
@@ -403,7 +452,7 @@ if (verbose)
assert(ret != FAIL);
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, &data_array1[0][0], &data_origin1[0][0]);
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
assert(ret != FAIL);
/* read data independently */
@@ -412,7 +461,7 @@ if (verbose)
assert(ret != FAIL);
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, &data_array1[0][0], &data_origin1[0][0]);
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
assert(ret == 0);
/* close dataset collectively */
@@ -428,7 +477,401 @@ if (verbose)
H5Fclose(fid1);
}
#ifdef HAVE_PARALLEL
/*
* Example of using the parallel HDF5 library to create two datasets
* in one HDF5 file with collective parallel access support.
* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
* Each process controls only a slab of size DIM1 x DIM2 within each
* dataset. [Note: not so yet. Datasets are of sizes DIM1xDIM2 and
* each process controls a hyperslab within.]
*/
void
phdf5writeAll(char *filename)
{
hid_t fid1, fid2; /* HDF5 file IDs */
hid_t acc_tpl1; /* File access templates */
hid_t xfer_plist; /* Dataset transfer properties list */
hid_t sid1,sid2; /* Dataspace ID */
hid_t file_dataspace; /* File dataspace ID */
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
int rank = SPACE1_RANK; /* Logical rank of dataspace */
hsize_t dims1[SPACE1_RANK] =
{SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
hssize_t start[SPACE1_RANK]; /* for hyperslab setting */
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Collective write test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* -------------------
* START AN HDF5 FILE
* -------------------*/
/* setup file access template with parallel IO access. */
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
assert(acc_tpl1 != FAIL);
MESG("H5Pcreate access succeed");
/* set Independent Parallel access with communicator */
ret = H5Pset_mpi(acc_tpl1, comm, info, H5ACC_INDEPENDENT);
assert(ret != FAIL);
MESG("H5Pset_mpi succeed");
/* create the file collectively */
fid1=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1);
assert(fid1 != FAIL);
MESG("H5Fcreate succeed");
/* Release file-access template */
ret=H5Pclose(acc_tpl1);
assert(ret != FAIL);
/* --------------------------
* Define the dimensions of the overall datasets
* and create the dataset
* ------------------------- */
/* setup dimensionality object */
sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL);
assert (sid1 != FAIL);
MESG("H5Screate_simple succeed");
/* create a dataset collectively */
dataset1 = H5Dcreate(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, H5P_DEFAULT);
assert(dataset1 != FAIL);
MESG("H5Dcreate succeed");
/* create another dataset collectively */
dataset2 = H5Dcreate(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, H5P_DEFAULT);
assert(dataset2 != FAIL);
MESG("H5Dcreate 2 succeed");
/*
* Set up dimensions of the slab this process accesses.
*/
/* Dataset1: each process takes a block of rows. */
slab_set(start, count, stride, BYROW);
if (verbose)
printf("start[]=(%d,%d), count[]=(%lu,%lu), total datapoints=%lu\n",
start[0], start[1], count[0], count[1], count[0]*count[1]);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
assert(file_dataspace != FAIL);
MESG("H5Dget_space succeed");
ret=H5Sset_hyperslab(file_dataspace, start, count, stride);
assert(ret != FAIL);
MESG("H5Sset_hyperslab succeed");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
assert (mem_dataspace != FAIL);
/* fill the local slab with some trivial data */
dataset_fill(start, count, stride, &data_array1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
assert(xfer_plist != FAIL);
ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE);
assert(ret != FAIL);
MESG("H5Pcreate xfer succeed");
/* write data collectively */
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
assert(ret != FAIL);
MESG("H5Dwrite succeed");
/* release all temporary handles. */
/* Could have used them for dataset2 but it is cleaner */
/* to create them again.*/
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/* Dataset2: each process takes a block of columns. */
slab_set(start, count, stride, BYCOL);
if (verbose)
printf("start[]=(%d,%d), count[]=(%lu,%lu), total datapoints=%lu\n",
start[0], start[1], count[0], count[1], count[0]*count[1]);
/* put some trivial data in the data_array */
dataset_fill(start, count, stride, &data_array1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
assert(file_dataspace != FAIL);
MESG("H5Dget_space succeed");
ret=H5Sset_hyperslab(file_dataspace, start, count, stride);
assert(ret != FAIL);
MESG("H5Sset_hyperslab succeed");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
assert (mem_dataspace != FAIL);
/* fill the local slab with some trivial data */
dataset_fill(start, count, stride, &data_array1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
assert(xfer_plist != FAIL);
ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE);
assert(ret != FAIL);
MESG("H5Pcreate xfer succeed");
/* write data independently */
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
assert(ret != FAIL);
MESG("H5Dwrite succeed");
/* release all temporary handles. */
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/*
* All writes completed. Close datasets collectively
*/
ret=H5Dclose(dataset1);
assert(ret != FAIL);
MESG("H5Dclose1 succeed");
ret=H5Dclose(dataset2);
assert(ret != FAIL);
MESG("H5Dclose2 succeed");
/* release all IDs created */
H5Sclose(sid1);
/* close the file collectively */
H5Fclose(fid1);
}
/*
* Example of using the parallel HDF5 library to read two datasets
* in one HDF5 file with collective parallel access support.
* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
* Each process controls only a slab of size DIM1 x DIM2 within each
* dataset. [Note: not so yet. Datasets are of sizes DIM1xDIM2 and
* each process controls a hyperslab within.]
*/
void
phdf5readAll(char *filename)
{
hid_t fid1, fid2; /* HDF5 file IDs */
hid_t acc_tpl1; /* File access templates */
hid_t xfer_plist; /* Dataset transfer properties list */
hid_t sid1,sid2; /* Dataspace ID */
hid_t file_dataspace; /* File dataspace ID */
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
int rank = SPACE1_RANK; /* Logical rank of dataspace */
hsize_t dims1[] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */
hssize_t start[SPACE1_RANK]; /* for hyperslab setting */
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Collective read test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* -------------------
* OPEN AN HDF5 FILE
* -------------------*/
/* setup file access template with parallel IO access. */
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
assert(acc_tpl1 != FAIL);
MESG("H5Pcreate access succeed");
/* set Independent Parallel access with communicator */
ret = H5Pset_mpi(acc_tpl1, comm, info, H5ACC_INDEPENDENT);
assert(ret != FAIL);
MESG("H5Pset_mpi succeed");
/* open the file collectively */
fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1);
assert(fid1 != FAIL);
MESG("H5Fopen succeed");
/* Release file-access template */
ret=H5Pclose(acc_tpl1);
assert(ret != FAIL);
/* --------------------------
* Open the datasets in it
* ------------------------- */
/* open the dataset1 collectively */
dataset1 = H5Dopen(fid1, DATASETNAME1);
assert(dataset1 != FAIL);
MESG("H5Dopen succeed");
/* open another dataset collectively */
dataset2 = H5Dopen(fid1, DATASETNAME1);
assert(dataset2 != FAIL);
MESG("H5Dopen 2 succeed");
/*
* Set up dimensions of the slab this process accesses.
*/
/* Dataset1: each process takes a block of columns. */
slab_set(start, count, stride, BYCOL);
if (verbose)
printf("start[]=(%d,%d), count[]=(%lu,%lu), total datapoints=%lu\n",
start[0], start[1], count[0], count[1], count[0]*count[1]);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
assert(file_dataspace != FAIL);
MESG("H5Dget_space succeed");
ret=H5Sset_hyperslab(file_dataspace, start, count, stride);
assert(ret != FAIL);
MESG("H5Sset_hyperslab succeed");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
assert (mem_dataspace != FAIL);
/* fill dataset with test data */
dataset_fill(start, count, stride, &data_origin1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
assert(xfer_plist != FAIL);
ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE);
assert(ret != FAIL);
MESG("H5Pcreate xfer succeed");
/* read data collectively */
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
assert(ret != FAIL);
MESG("H5Dread succeed");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
assert(ret != FAIL);
/* release all temporary handles. */
/* Could have used them for dataset2 but it is cleaner */
/* to create them again.*/
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/* Dataset2: each process takes a block of rows. */
slab_set(start, count, stride, BYROW);
if (verbose)
printf("start[]=(%d,%d), count[]=(%lu,%lu), total datapoints=%lu\n",
start[0], start[1], count[0], count[1], count[0]*count[1]);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
assert(file_dataspace != FAIL);
MESG("H5Dget_space succeed");
ret=H5Sset_hyperslab(file_dataspace, start, count, stride);
assert(ret != FAIL);
MESG("H5Sset_hyperslab succeed");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
assert (mem_dataspace != FAIL);
/* fill dataset with test data */
dataset_fill(start, count, stride, &data_origin1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
assert(xfer_plist != FAIL);
ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE);
assert(ret != FAIL);
MESG("H5Pcreate xfer succeed");
/* read data independently */
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
assert(ret != FAIL);
MESG("H5Dread succeed");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
assert(ret != FAIL);
/* release all temporary handles. */
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/*
* All reads completed. Close datasets collectively
*/
ret=H5Dclose(dataset1);
assert(ret != FAIL);
MESG("H5Dclose1 succeed");
ret=H5Dclose(dataset2);
assert(ret != FAIL);
MESG("H5Dclose2 succeed");
/* close the file collectively */
H5Fclose(fid1);
}
/*
* test file access by communicator besides COMM_WORLD.
* Split COMM_WORLD into two, one (even_comm) contains the original
@@ -441,9 +884,9 @@ if (verbose)
* sooner or later due to barrier mixed up.
*/
void
test_split_comm_access()
test_split_comm_access(char *filenames[])
{
int numprocs, myrank;
int mpi_size, myrank;
MPI_Comm comm;
MPI_Info info = MPI_INFO_NULL;
int color, mrc;
@@ -452,8 +895,12 @@ test_split_comm_access()
hid_t acc_tpl; /* File access properties */
herr_t ret; /* generic return value */
if (verbose)
printf("Independent write test on file %s %s\n",
filenames[0], filenames[1]);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&myrank);
color = myrank%2;
mrc = MPI_Comm_split (MPI_COMM_WORLD, color, myrank, &comm);
@@ -492,8 +939,10 @@ test_split_comm_access()
assert(mrc==MPI_SUCCESS);
}
}
#endif
/*
* Show command usage
*/
void
usage()
{
@@ -506,22 +955,11 @@ usage()
}
main(int argc, char **argv)
{
int numprocs, mympirank, namelen;
char processor_name[MPI_MAX_PROCESSOR_NAME];
#ifdef HAVE_PARALLEL
MPI_Init(&argc,&argv);
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
MPI_Comm_rank(MPI_COMM_WORLD,&mympirank);
MPI_Get_processor_name(processor_name,&namelen);
#ifdef USE_PAUSE
pause_proc(MPI_COMM_WORLD, mympirank, processor_name, namelen, argc, argv);
#endif
#endif
/* parse option */
/*
* parse the command line options
*/
int
parse_options(int argc, char **argv){
while (--argc){
if (**(++argv) != '-'){
break;
@@ -535,23 +973,53 @@ main(int argc, char **argv)
break;
default: usage();
nerrors++;
goto finish;
return(1);
}
}
}
return(0);
}
main(int argc, char **argv)
{
char *filenames[]={ "ParaEg1.h5f", "ParaEg2.h5f" };
int mpi_namelen;
char mpi_name[MPI_MAX_PROCESSOR_NAME];
MPI_Init(&argc,&argv);
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
MPI_Get_processor_name(mpi_name,&mpi_namelen);
/* Make sure datasets can be divided into equal chunks by the processes */
if ((SPACE1_DIM1 % mpi_size) || (SPACE1_DIM2 % mpi_size)){
printf("DIM1(%d) and DIM2(%d) must be multiples of processes (%d)\n",
SPACE1_DIM1, SPACE1_DIM2, mpi_size);
nerrors++;
goto finish;
}
#ifdef USE_PAUSE
pause_proc(MPI_COMM_WORLD, mpi_rank, mpi_name, mpi_namelen, argc, argv);
#endif
if (parse_options(argc, argv) != 0)
goto finish;
if (dowrite){
#ifdef HAVE_PARALLEL
MPI_BANNER("testing PHDF5 dataset using split communicators...");
test_split_comm_access();
#endif
test_split_comm_access(filenames);
MPI_BANNER("testing PHDF5 dataset independent write...");
phdf5writeInd();
phdf5writeInd(filenames[0]);
MPI_BANNER("testing PHDF5 dataset collective write...");
phdf5writeAll(filenames[1]);
}
if (doread){
MPI_BANNER("testing PHDF5 dataset independent read...");
phdf5readInd();
phdf5readInd(filenames[0]);
MPI_BANNER("testing PHDF5 dataset collective read...");
phdf5readAll(filenames[1]);
}
if (!(dowrite || doread)){
@@ -560,7 +1028,7 @@ main(int argc, char **argv)
}
finish:
if (mympirank == 0){ /* only process 0 reports */
if (mpi_rank == 0){ /* only process 0 reports */
if (nerrors)
printf("***PHDF5 tests detected %d errors***\n", nerrors);
else{
@@ -569,9 +1037,7 @@ finish:
printf("===================================\n");
}
}
#ifdef HAVE_PARALLEL
MPI_Finalize();
#endif
return(nerrors);
}