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-rw-r--r--examples/Makefile.in7
-rw-r--r--examples/ph5example.c1018
2 files changed, 1024 insertions, 1 deletions
diff --git a/examples/Makefile.in b/examples/Makefile.in
index fa5d93b..b36f86a 100644
--- a/examples/Makefile.in
+++ b/examples/Makefile.in
@@ -16,7 +16,8 @@ LIBHDF5=../src/libhdf5.la
## These are the programs that `make all' or `make tests' will build and which
## `make check' will run. List them in the order they should be run.
TEST_PROGS= h5_write h5_read h5_extend_write h5_chunk_read h5_compound \
- h5_group h5_select h5_attribute h5_mount h5_reference
+ h5_group h5_select h5_attribute h5_mount h5_reference \
+ ph5example
## These are the files that `make clean' (and derivatives) will remove from
## this directory.
@@ -62,4 +63,8 @@ h5_mount: h5_mount.lo
h5_reference: h5_reference.lo
@$(LT_LINK_EXE) $(CFLAGS) -o $@ h5_reference.lo $(LIBHDF5) $(LDFLAGS) $(LIBS)
+
+ph5example: ph5example.lo
+ @$(LT_LINK_EXE) $(CFLAGS) -o $@ $@.lo $(LIBHDF5) $(LDFLAGS) $(LIBS)
+
@CONCLUDE@
diff --git a/examples/ph5example.c b/examples/ph5example.c
new file mode 100644
index 0000000..2adffbc
--- /dev/null
+++ b/examples/ph5example.c
@@ -0,0 +1,1018 @@
+/*
+ * Example of using the parallel HDF5 library to access datasets.
+ * Last revised: March 22, 2001 for v1.4.0.
+ *
+ * This program contains two parts. In the first part, the mpi processes
+ * collectively create a new parallel HDF5 file and create two fixed
+ * dimension datasets in it. Then each process writes a hyperslab into
+ * each dataset in an independent mode. All processes collectively
+ * close the datasets and the file.
+ * In the second part, the processes collectively open the created file
+ * and the two datasets in it. Then each process reads a hyperslab from
+ * each dataset in an independent mode and prints them out.
+ * All processes collectively close the datasets and the file.
+ */
+
+#include <assert.h>
+#include <hdf5.h>
+
+#ifdef H5_HAVE_PARALLEL
+/* Temporary source code */
+#define FAIL -1
+/* temporary code end */
+
+/* Define some handy debugging shorthands, routines, ... */
+/* debugging tools */
+#define MESG(x)\
+ if (verbose) printf("%s\n", x);\
+
+#define MPI_BANNER(mesg)\
+ {printf("--------------------------------\n");\
+ printf("Proc %d: ", mpi_rank); \
+ printf("*** %s\n", mesg);\
+ printf("--------------------------------\n");}
+
+#define SYNC(comm)\
+ {MPI_BANNER("doing a SYNC"); MPI_Barrier(comm); MPI_BANNER("SYNC DONE");}
+/* 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 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 */
+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 */
+
+
+
+/*
+ * 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_fill(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset)
+{
+ DATATYPE *dataptr = dataset;
+ int i, j;
+
+ /* put some trivial data in the data_array */
+ for (i=0; i < count[0]; i++){
+ for (j=0; j < count[1]; j++){
+ *dataptr++ = (i*stride[0]+start[0])*100 + (j*stride[1]+start[1]+1);
+ }
+ }
+}
+
+
+/*
+ * Print the content of the 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: ", (int)(i*stride[0]+start[0]));
+ for (j=0; j < count[1]; j++){
+ printf("%03d ", *dataptr++);
+ }
+ printf("\n");
+ }
+}
+
+
+/*
+ * Print the content of the dataset.
+ */
+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++){
+ 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 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(char *filename)
+{
+ hid_t fid1, fid2; /* HDF5 file IDs */
+ hid_t acc_tpl1; /* File access templates */
+ 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 */
+ hsize_t dimslocal1[SPACE1_RANK] =
+ {SPACE1_DIM1,SPACE1_DIM2}; /* local 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 i, j;
+ int mpi_size, mpi_rank;
+ char *fname;
+ int mrc; /* mpi return code */
+
+ 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,&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 Parallel access with communicator */
+ ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
+ assert(ret != FAIL);
+ MESG("H5Pset_fapl_mpio 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 the slabs local to the MPI process.
+ * ------------------------- */
+ /* 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 succeed");
+
+
+
+ /* set up dimensions of the slab this process accesses */
+ start[0] = mpi_rank*SPACE1_DIM1/mpi_size;
+ start[1] = 0;
+ count[0] = SPACE1_DIM1/mpi_size;
+ count[1] = SPACE1_DIM2;
+ stride[0] = 1;
+ stride[1] =1;
+if (verbose)
+ printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\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");
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset1);
+ assert(file_dataspace != FAIL);
+ MESG("H5Dget_space succeed");
+ ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
+ count, NULL);
+ assert(ret != FAIL);
+ MESG("H5Sset_hyperslab succeed");
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
+ assert (mem_dataspace != FAIL);
+
+ /* write data independently */
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ assert(ret != FAIL);
+ MESG("H5Dwrite succeed");
+
+ /* write data independently */
+ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ assert(ret != FAIL);
+ MESG("H5Dwrite succeed");
+
+ /* release dataspace ID */
+ H5Sclose(file_dataspace);
+
+ /* close dataset 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 a dataset */
+void
+phdf5readInd(char *filename)
+{
+ hid_t fid1, fid2; /* HDF5 file IDs */
+ hid_t acc_tpl1; /* File access templates */
+ 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 i, j;
+ 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,&mpi_size);
+ MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+
+
+ /* setup file access template */
+ acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
+ assert(acc_tpl1 != FAIL);
+ /* set Parallel access with communicator */
+ ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
+ assert(ret != FAIL);
+
+
+ /* open the file collectively */
+ fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1);
+ assert(fid1 != FAIL);
+
+ /* Release file-access template */
+ ret=H5Pclose(acc_tpl1);
+ assert(ret != FAIL);
+
+ /* open the dataset1 collectively */
+ dataset1 = H5Dopen(fid1, DATASETNAME1);
+ assert(dataset1 != FAIL);
+
+ /* open another dataset collectively */
+ dataset2 = H5Dopen(fid1, DATASETNAME1);
+ assert(dataset2 != FAIL);
+
+
+ /* set up dimensions of the slab this process accesses */
+ start[0] = mpi_rank*SPACE1_DIM1/mpi_size;
+ start[1] = 0;
+ count[0] = SPACE1_DIM1/mpi_size;
+ count[1] = SPACE1_DIM2;
+ stride[0] = 1;
+ stride[1] =1;
+if (verbose)
+ printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\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);
+ ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
+ count, NULL);
+ assert(ret != FAIL);
+
+ /* 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]);
+
+ /* read data independently */
+ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ assert(ret != FAIL);
+
+ /* 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);
+
+ /* read data independently */
+ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ assert(ret != FAIL);
+
+ /* verify the read data with original expected data */
+ ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
+ assert(ret == 0);
+
+ /* close dataset collectively */
+ ret=H5Dclose(dataset1);
+ assert(ret != FAIL);
+ ret=H5Dclose(dataset2);
+ assert(ret != FAIL);
+
+ /* release all IDs created */
+ H5Sclose(file_dataspace);
+
+ /* close the file collectively */
+ H5Fclose(fid1);
+}
+
+
+/*
+ * 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 Parallel access with communicator */
+ ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
+ assert(ret != FAIL);
+ MESG("H5Pset_fapl_mpio 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[]=(%d,%d), total datapoints=%d\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=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
+ count, NULL);
+ 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_dxpl_mpio(xfer_plist, H5FD_MPIO_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[]=(%d,%d), total datapoints=%d\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=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
+ count, NULL);
+ 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_dxpl_mpio(xfer_plist, H5FD_MPIO_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 Parallel access with communicator */
+ ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
+ assert(ret != FAIL);
+ MESG("H5Pset_fapl_mpio 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[]=(%d,%d), total datapoints=%d\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=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
+ count, NULL);
+ 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_dxpl_mpio(xfer_plist, H5FD_MPIO_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[]=(%d,%d), total datapoints=%d\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=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
+ count, NULL);
+ 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_dxpl_mpio(xfer_plist, H5FD_MPIO_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
+ * processes of even ranks. The other (odd_comm) contains the original
+ * processes of odd ranks. Processes in even_comm creates a file, then
+ * cloose it, using even_comm. Processes in old_comm just do a barrier
+ * using odd_comm. Then they all do a barrier using COMM_WORLD.
+ * If the file creation and cloose does not do correct collective action
+ * according to the communicator argument, the processes will freeze up
+ * sooner or later due to barrier mixed up.
+ */
+void
+test_split_comm_access(char *filenames[])
+{
+ int mpi_size, myrank;
+ MPI_Comm comm;
+ MPI_Info info = MPI_INFO_NULL;
+ int color, mrc;
+ int newrank, newprocs;
+ hid_t fid; /* file IDs */
+ 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,&mpi_size);
+ MPI_Comm_rank(MPI_COMM_WORLD,&myrank);
+ color = myrank%2;
+ mrc = MPI_Comm_split (MPI_COMM_WORLD, color, myrank, &comm);
+ assert(mrc==MPI_SUCCESS);
+ MPI_Comm_size(comm,&newprocs);
+ MPI_Comm_rank(comm,&newrank);
+
+ if (color){
+ /* odd-rank processes */
+ mrc = MPI_Barrier(comm);
+ assert(mrc==MPI_SUCCESS);
+ }else{
+ /* even-rank processes */
+ /* setup file access template */
+ acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
+ assert(acc_tpl != FAIL);
+
+ /* set Parallel access with communicator */
+ ret = H5Pset_fapl_mpio(acc_tpl, comm, info);
+ assert(ret != FAIL);
+
+ /* create the file collectively */
+ fid=H5Fcreate(filenames[color],H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
+ assert(fid != FAIL);
+ MESG("H5Fcreate succeed");
+
+ /* Release file-access template */
+ ret=H5Pclose(acc_tpl);
+ assert(ret != FAIL);
+
+ ret=H5Fclose(fid);
+ assert(ret != FAIL);
+ }
+ if (myrank == 0){
+ mrc = MPI_File_delete(filenames[color], info);
+ assert(mrc==MPI_SUCCESS);
+ }
+}
+
+/*
+ * Show command usage
+ */
+void
+usage()
+{
+ printf("Usage: testphdf5 [-r] [-w] [-v]\n");
+ printf("\t-r\tno read\n");
+ printf("\t-w\tno write\n");
+ printf("\t-v\tverbose on\n");
+ printf("\tdefault do write then read\n");
+ printf("\n");
+}
+
+
+/*
+ * parse the command line options
+ */
+int
+parse_options(int argc, char **argv){
+ while (--argc){
+ if (**(++argv) != '-'){
+ break;
+ }else{
+ switch(*(*argv+1)){
+ case 'r': doread = 0;
+ break;
+ case 'w': dowrite = 0;
+ break;
+ case 'v': verbose = 1;
+ break;
+ default: usage();
+ nerrors++;
+ return(1);
+ }
+ }
+ }
+ return(0);
+}
+
+
+int
+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;
+ }
+
+ if (parse_options(argc, argv) != 0)
+ goto finish;
+
+ if (dowrite){
+ MPI_BANNER("testing PHDF5 dataset using split communicators...");
+ test_split_comm_access(filenames);
+ MPI_BANNER("testing PHDF5 dataset independent write...");
+ phdf5writeInd(filenames[0]);
+ MPI_BANNER("testing PHDF5 dataset collective write...");
+ phdf5writeAll(filenames[1]);
+ }
+ if (doread){
+ MPI_BANNER("testing PHDF5 dataset independent read...");
+ phdf5readInd(filenames[0]);
+ MPI_BANNER("testing PHDF5 dataset collective read...");
+ phdf5readAll(filenames[1]);
+ }
+
+ if (!(dowrite || doread)){
+ usage();
+ nerrors++;
+ }
+
+finish:
+ if (mpi_rank == 0){ /* only process 0 reports */
+ if (nerrors)
+ printf("***PHDF5 tests detected %d errors***\n", nerrors);
+ else{
+ printf("===================================\n");
+ printf("PHDF5 tests finished with no errors\n");
+ printf("===================================\n");
+ }
+ }
+ MPI_Finalize();
+
+ return(nerrors);
+}
+
+#else /* H5_HAVE_PARALLEL */
+/* dummy program since H5_HAVE_PARALLE is not configured in */
+int
+main()
+{
+printf("No PHDF5 example because parallel is not configured in\n");
+return(0);
+}
+#endif /* H5_HAVE_PARALLEL */