[svn-r13537] These are old documents. Document were replaced by the

http://hdfgroup.org/HDF5/PHDF5 and examples is now in the examples/ directory.
author: Albert Cheng <acheng@hdfgroup.org> 2007-03-22 22:42:13 (GMT)
committer: Albert Cheng <acheng@hdfgroup.org> 2007-03-22 22:42:13 (GMT)
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diff --git a/doc/html/ph5design.html b/doc/html/ph5design.html
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-<HTML>
-<HEAD>
-<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=windows-1252">
-<META NAME="Generator" CONTENT="Microsoft Word 97">
-<TITLE>new</TITLE>
-<META NAME="Template" CONTENT="C:\PROGRAM FILES\MICROSOFT OFFICE\OFFICE\html.dot">
-</HEAD>
-<BODY LINK="#0000ff" VLINK="#800080">
-
-<B><FONT SIZE=6><P ALIGN="CENTER">Parallel HDF5 Design</P>
-</B></FONT><P ALIGN="CENTER">&nbsp;</P>
-<H1>1. Design Overview</H1>
-<P>In this section, I first describe the function requirements of the Parallel HDF5 (PHDF5) software and the assumed system requirements. Section 2 describes the programming model of the PHDF5 interface. Section 3 shows an example PHDF5 program. </P>
-<H2>1.1. Function requirements</H2>
-
-<UL>
-<LI>An API to support parallel file access for HDF5 files in a message passing environment. </LI>
-<LI>Fast parallel I/O to large datasets through standard parallel I/O interface.</LI>
-<LI>Processes are required to do collective API calls only when structural changes are needed for the HDF5 file. </LI>
-<LI>Each process may do independent I/O requests to different datasets in the same or different HDF5 files. </LI>
-<LI>Supports collective I/O requests for datasets (to be included in next version). </LI>
-<LI>Minimize diviation from HDF5 interface.</LI>
-</UL>
-
-<H2>1.2. System requirements</H2>
-
-<UL>
-<LI>C language interface is the initial requirement. Fortran77 interface will be added later. </LI>
-<LI>Use Message Passing Interface (MPI) for interprocess communication. </LI>
-<LI>Use MPI-IO calls for parallel file accesses. </LI>
-<LI>Initial platforms—IBM SP2, Intel TFLOPS and SGI Origin 2000. </LI></UL>
-
-<H1>2. Programming Model</H1>
-<P>HDF5 uses optional access template object to control the file access
-mechanism.  The general model in accessing an HDF5 file in parallel
-contains the following steps: </P>
-
-<UL>
-<LI>Setup access template</LI>
-<LI>File open </LI>
-<LI>Dataset open </LI>
-<LI>Dataset data access (zero or more) </LI>
-<LI>Dataset close </LI>
-<LI>File close </LI></UL>
-
-<H2>2.1. Setup access template</H2>
-<P>Each processes of the MPI communicator creates an access template and sets
-it up with MPI parallel access information (communicator, info object,
-access-mode).  </P>
-<H2>2.1. File open</H2>
-<P>All processes of the MPI communicator open an HDF5 file by a collective call
-(H5FCreate or H5Fopen) with the access template. </P>
-<H2>2.2. Dataset open</H2>
-<P>All processes of the MPI communicator open a dataset by a collective call (H5Dcreate or H5Dopen).&nbsp; This version supports only collective dataset open.&nbsp; Future version may support datasets open by a subset of the processes that have opened the file. </P>
-<H2>2.3. Dataset access</H2>
-<H3>2.3.1. Independent dataset access</H3>
-<P>Each process may do independent and arbitrary number of data I/O access by independent calls (H5Dread or H5Dwrite) to the dataset with the transfer template set for independent access.&nbsp; (The default transfer mode is independent transfer).&nbsp; If the dataset is an unlimited dimension one and if the H5Dwrite is writing data beyond the current dimension size of the dataset, all processes that have opened the dataset must make a collective call (H5Dallocate) to allocate more space for the dataset BEFORE the independent H5Dwrite call. </P>
-<H3>2.3.2. Collective dataset access</H3>
-<P>All processes that have opened the dataset may do collective data I/O access by collective calls (H5Dread or H5Dwrite) to the dataset with the transfer template set for collective access.&nbsp; Pre-allocation (H5Dallocate) is not needed for unlimited dimension datasets since the H5Dallocate call, if needed, is done internally by the collective data access call. </P>
-<H3>2.3.3. Dataset attributes access</H3>
-<P>Changes to attributes can only occur at the <I>"main process" </I>(process 0).&nbsp; Read only access to attributes can occur independent in each process that has opened the dataset.&nbsp; (API to be defined later.) <BR>
-&nbsp; </P>
-<H2>2.4. Dataset close</H2>
-<P>All processes that have opened the dataset must close the dataset by a collective call (H5Dclose). </P>
-<H2>2.5. File close</H2>
-<P>All processes that have opened the file must close the file by a collective call (H5Fclose). <BR>
-&nbsp; </P>
-<H1>3. Parallel HDF5 Example</H1>
-<PRE>
-<CODE>
-</CODE><A HREF="ph5example.c">Example code</A>
-</PRE>
-<P><HR></P>
-<P>Send comments to <BR>
-<A HREF="mailto:hdfparallel@ncsa.uiuc.edu">hdfparallel@ncsa.uiuc.edu</A> </P>
-<H6>Last Modified: Feb 16, 1998</H6></BODY>
-</HTML>
diff --git a/doc/html/ph5example.c b/doc/html/ph5example.c
deleted file mode 100644
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--- a/doc/html/ph5example.c
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@@ -1,1018 +0,0 @@
-/*
- * Example of using the parallel HDF5 library to access datasets.
- * Last revised: April 24, 2001.
- *
- * 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(hsize_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(hsize_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(hsize_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(hsize_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 */
-
-    hsize_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 */
-
-    hsize_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 */
-
-    hsize_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 */
-
-    hsize_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 */
diff --git a/doc/html/ph5implement.txt b/doc/html/ph5implement.txt
deleted file mode 100644
index 2fcbb3d..0000000
--- a/doc/html/ph5implement.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-Release information for parallel HDF5
--------------------------------------
-
-+) Current release supports independent access to fixed dimension datasets
-   only.
-
-+) The comm and info arguments of H5Pset_mpi are not used.  All parallel
-   I/O are done via MPI_COMM_WORLD.  Access_mode for H5Pset_mpi can be
-   H5ACC_INDEPENDENT only.
-
-+) This release of parallel HDF5 has been tested on IBM SP2 and SGI
-   Origin 2000 systems.  It uses the ROMIO version of MPIO interface
-   for parallel I/O supports.
-
-+) Useful URL's.
-   Parallel HDF webpage: "http://hdf.ncsa.uiuc.edu/Parallel_HDF/"
-   ROMIO webpage: "http://www.mcs.anl.gov/home/thakur/romio/"
-
-+) Some to-do items for future releases
-      support for Intel Teraflop platform.
-      support for unlimited dimension datasets.
-      support for file access via a communicator besides MPI_COMM_WORLD.
-      support for collective access to datasets.
-      support for independent create/open of datasets.
-
-----
-Last updated: Feb 16, 1998.
author	Albert Cheng <acheng@hdfgroup.org>	2007-03-22 22:42:13 (GMT)
committer	Albert Cheng <acheng@hdfgroup.org>	2007-03-22 22:42:13 (GMT)
commit	e9d75fa7e219c022ccd055490c94af7ab51e0742 (patch)
tree	c34e128d76d8ee1dc62ad428fef08acc85db7f02 /doc
parent	20d8084fba23bfc53ff0c6e3321885747c07a383 (diff)
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