[svn-r12381] This commit was manufactured by cvs2svn to create branch 'hdf5_1_6'.

1 files changed, 550 insertions, 0 deletions

diff --git a/testpar/t_chunk_alloc.c b/testpar/t_chunk_alloc.c
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+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
+ * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/* 
+ * This verifies if the storage space allocation methods are compatible between
+ * serial and parallel modes.
+ *
+ * Created by: Christian Chilan and Albert Cheng
+ * Date: 2006/05/25
+ */
+
+#include "testphdf5.h"
+static int	mpi_size, mpi_rank;
+
+#define DATASETNAME "ExtendibleArray" 
+#define CHUNKSIZE	1000		/* #elements per chunk */
+#define DSETCHUNKS		20000
+#define CLOSE           1
+#define NO_CLOSE        0
+
+static MPI_Offset
+get_filesize(const char *filename)
+{
+    int		mpierr;
+    MPI_File	fd;
+    MPI_Offset	filesize;
+
+    mpierr = MPI_File_open(MPI_COMM_SELF, (char*)filename, MPI_MODE_RDONLY,
+	MPI_INFO_NULL, &fd);
+    VRFY((mpierr == MPI_SUCCESS), "");
+
+    mpierr = MPI_File_get_size(fd, &filesize);
+    VRFY((mpierr == MPI_SUCCESS), "");
+
+    mpierr = MPI_File_close(&fd);
+    VRFY((mpierr == MPI_SUCCESS), "");
+
+    return(filesize);
+}
+
+typedef enum write_ {
+    none,
+    sec_last,
+    all
+} write_type;
+
+typedef enum access_ {
+    write_all,
+    open_only,
+    extend_only
+} access_type;
+
+
+/*
+ * This creates a dataset serially with 'nchunks' chunks, each of CHUNKSIZE
+ * elements. The allocation time is set to H5D_ALLOC_TIME_EARLY. Another
+ * routine will open this in parallel for extension test.
+ */
+void
+create_chunked_dataset(const char *filename, int nchunks, write_type write)
+{
+    hid_t       file_id, dataset;                          /* handles */
+    hid_t       dataspace,memspace;  
+    hid_t       cparms;
+    hsize_t      dims[1];
+    hsize_t      maxdims[1] = {H5S_UNLIMITED};
+    
+    hsize_t      chunk_dims[1] ={CHUNKSIZE};
+    hsize_t     count[1];
+    hsize_t     stride[1];
+    hsize_t     block[1];
+    hsize_t     offset[1];            /* Selection offset within dataspace */
+    /* Variables used in reading data back */
+    char         buffer[CHUNKSIZE];
+    int           i;
+
+    herr_t       hrc;                             
+
+    MPI_Offset  filesize,	    /* actual file size */
+		est_filesize;	    /* estimated file size */
+
+    /* set up MPI parameters */
+    MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
+    MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+
+    /* Only MAINPROCESS should create the file.  Others just wait. */
+    if (MAINPROCESS){
+
+	dims[0]=nchunks*CHUNKSIZE;
+	/* Create the data space with unlimited dimensions. */
+	dataspace = H5Screate_simple (1, dims, maxdims); 
+	VRFY((dataspace >= 0), "");
+
+	memspace = H5Screate_simple(1, chunk_dims, NULL);
+	VRFY((memspace >= 0), "");
+ 
+	/* Create a new file. If file exists its contents will be overwritten. */
+	file_id = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+	VRFY((file_id >= 0), "");
+
+	/* Modify dataset creation properties, i.e. enable chunking  */
+	cparms = H5Pcreate (H5P_DATASET_CREATE);
+	VRFY((cparms >= 0), "");
+
+	hrc = H5Pset_alloc_time(cparms, H5D_ALLOC_TIME_EARLY);
+	VRFY((hrc >= 0), "");
+
+	hrc = H5Pset_chunk ( cparms, 1, chunk_dims);
+	VRFY((hrc >= 0), "");
+
+	/* Create a new dataset within the file using cparms creation properties. */
+	dataset = H5Dcreate (file_id, DATASETNAME, H5T_NATIVE_UCHAR, dataspace, cparms);
+	VRFY((dataset >= 0), "");
+
+	switch (write) {
+
+	    /* writes only the second to last chunk */
+	    case sec_last:
+
+		memset(buffer, 100, CHUNKSIZE);
+
+		count[0] = 1;
+		stride[0] = 1;
+		block[0] = chunk_dims[0];
+		offset[0] = (nchunks-2)*chunk_dims[0];
+
+		hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block);
+		    VRFY((hrc >= 0), "");
+
+		/* Write sec_last chunk */
+		hrc = H5Dwrite(dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer);
+		VRFY((hrc >= 0), "H5Dwrite");
+
+		break;
+
+
+	    /* doesn't write anything */
+	    case none:
+
+		break;
+	}
+
+	/* Close resources */
+	hrc = H5Dclose (dataset);
+	VRFY((hrc >= 0), "");
+	dataset = -1;
+
+	hrc = H5Sclose (dataspace);
+	VRFY((hrc >= 0), "");
+
+	hrc = H5Sclose (memspace);
+	VRFY((hrc >= 0), "");
+
+	hrc = H5Pclose (cparms);
+	VRFY((hrc >= 0), "");
+
+	hrc = H5Fclose (file_id);
+	VRFY((hrc >= 0), "");
+	file_id = -1;
+
+	/* verify file size */
+	filesize = get_filesize(filename);
+	est_filesize = nchunks*CHUNKSIZE*sizeof(unsigned char);
+	VRFY((filesize >= est_filesize), "file size check");
+
+    }
+
+    /* Make sure all processes are done before exiting this routine.  Otherwise,
+     * other tests may start and change the test data file before some processes
+     * of this test are still accessing the file.
+     */
+
+    MPI_Barrier(MPI_COMM_WORLD);
+}     
+
+
+/*
+ * This program performs three different types of parallel access. It writes on
+ * the entire dataset, it extends the dataset to nchunks*CHUNKSIZE, and it only
+ * opens the dataset. At the end, it verifies the size of the dataset to be
+ * consistent with argument 'nchunks'.
+ */
+void
+parallel_access_dataset(const char *filename, int nchunks, access_type action, hid_t *file_id, hid_t *dataset)
+{
+    /* HDF5 gubbins */
+    hid_t    memspace, dataspace;     /* HDF5 file identifier */
+    hid_t    access_plist;         /* HDF5 ID for file access property list */
+    herr_t   hrc;                  /* HDF5 return code */
+    hsize_t  size[1];
+    hsize_t  dim_size;
+
+    hsize_t     chunk_dims[1] ={CHUNKSIZE};
+    hsize_t     count[1];
+    hsize_t     stride[1];
+    hsize_t     block[1];
+    hsize_t     offset[1];            /* Selection offset within dataspace */
+    /* Variables used in reading data back */
+    char         buffer[CHUNKSIZE];
+    int         i;
+
+    /* MPI Gubbins */
+    MPI_Offset  filesize,	    /* actual file size */
+		est_filesize;	    /* estimated file size */
+    int         mpierr;
+
+    /* Initialize MPI */
+    MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
+    MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+
+    /* Set up MPIO file access property lists */
+    access_plist  = H5Pcreate(H5P_FILE_ACCESS);
+    VRFY((access_plist >= 0), "");
+
+    hrc = H5Pset_fapl_mpio(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL);
+    VRFY((hrc >= 0), "");
+
+    /* Open the file */
+    if (*file_id<0){
+        *file_id = H5Fopen(filename, H5F_ACC_RDWR, access_plist);
+        VRFY((*file_id >= 0), "");
+    }
+
+    /* Open dataset*/
+    if (*dataset<0){
+        *dataset = H5Dopen(*file_id, DATASETNAME);
+        VRFY((*dataset >= 0), "");
+    }
+
+    memspace = H5Screate_simple(1, chunk_dims, NULL);
+    VRFY((memspace >= 0), "");
+
+    dataspace = H5Dget_space(*dataset);            
+    VRFY((dataspace >= 0), "");
+
+    size[0] = nchunks*CHUNKSIZE;
+
+    switch (action) {
+
+        /* all chunks are written by all the processes in an interleaved way*/
+        case write_all:
+
+            for (i=0; i<nchunks/mpi_size; i++){ 
+
+                memset(buffer, mpi_rank+1, CHUNKSIZE);
+
+                offset[0] = (i*mpi_size+mpi_rank)*chunk_dims[0];
+                count[0] = 1;
+                stride[0] = 1;
+                block[0] = chunk_dims[0];
+
+                hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block);
+                VRFY((hrc >= 0), "");
+
+                /* Write the buffer out */
+                hrc = H5Dwrite(*dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer);
+                VRFY((hrc >= 0), "H5Dwrite");
+
+            }
+
+            /* remainder writing */
+            if (mpi_rank < nchunks%mpi_size){
+
+                memset(buffer, mpi_rank+1, CHUNKSIZE);
+
+                offset[0] = ((nchunks/mpi_size)*mpi_size+mpi_rank)*chunk_dims[0];
+                count[0] = 1;
+                stride[0] = 1;
+                block[0] = chunk_dims[0];
+
+                hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block);
+                VRFY((hrc >= 0), "");
+
+                /* Write the buffer out */
+                hrc = H5Dwrite(*dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer);
+                VRFY((hrc >= 0), "H5Dwrite");
+            }
+
+            break;
+
+        /* only extends the dataset */
+        case extend_only:
+            /* Extend dataset*/
+            hrc = H5Dextend(*dataset, size);
+            VRFY((hrc >= 0), "");
+
+            break;
+
+        /* only opens the dataset */
+        case open_only:
+
+            break;
+    }
+
+    /* Close up */
+    hrc = H5Dclose(*dataset);
+    VRFY((hrc >= 0), "");
+    *dataset = -1;
+
+    hrc = H5Sclose (dataspace);
+	VRFY((hrc >= 0), "");
+
+	hrc = H5Sclose (memspace);
+	VRFY((hrc >= 0), "");
+
+    hrc = H5Fclose(*file_id);
+    VRFY((hrc >= 0), "");
+    *file_id = -1;
+
+    /* verify file size */
+    filesize = get_filesize(filename);
+    est_filesize = nchunks*CHUNKSIZE*sizeof(unsigned char);
+    VRFY((filesize >= est_filesize), "file size check");
+
+    /* Can close some plists */
+    hrc = H5Pclose(access_plist);
+    VRFY((hrc >= 0), "");
+
+    /* Make sure all processes are done before exiting this routine.  Otherwise,
+     * other tests may start and change the test data file before some processes
+     * of this test are still accessing the file.
+     */
+    MPI_Barrier(MPI_COMM_WORLD);
+}
+
+/*
+ * This routine verifies the data written in the dataset. It does one of the
+ * three cases according to the value of parameter `write'.
+ * 1. it returns correct fill values though the dataset has not been written;
+ * 2. it still returns correct fill values though only a small part is written;
+ * 3. it returns correct values when the whole dataset has been written in an
+ *    interleaved pattern.
+ */
+void verify_data(const char *filename, int nchunks, write_type write, int close, hid_t *file_id, hid_t *dataset)
+{
+    /* HDF5 gubbins */
+    hid_t    dataspace, memspace;     /* HDF5 file identifier */
+    hid_t    access_plist;         /* HDF5 ID for file access property list */
+    herr_t   hrc;                  /* HDF5 return code */
+
+    hsize_t     chunk_dims[1] ={CHUNKSIZE};
+    hsize_t     count[1];
+    hsize_t     stride[1];
+    hsize_t     block[1];
+    hsize_t     offset[1];            /* Selection offset within dataspace */
+    /* Variables used in reading data back */
+    char         buffer[CHUNKSIZE];
+    int         value, i;
+    int         index, current;
+
+    /* MPI Gubbins */
+    MPI_Offset  filesize,	    /* actual file size */
+		est_filesize;	    /* estimated file size */
+    int         mpierr;
+
+    /* Initialize MPI */
+    MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
+    MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+
+    /* Set up MPIO file access property lists */
+    access_plist  = H5Pcreate(H5P_FILE_ACCESS);
+    VRFY((access_plist >= 0), "");
+
+    hrc = H5Pset_fapl_mpio(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL);
+    VRFY((hrc >= 0), "");
+
+    /* Open the file */
+    if (*file_id<0){
+        *file_id = H5Fopen(filename, H5F_ACC_RDWR, access_plist);
+        VRFY((*file_id >= 0), "");
+    }
+
+    /* Open dataset*/
+    if (*dataset<0){
+        *dataset = H5Dopen(*file_id, DATASETNAME);
+        VRFY((*dataset >= 0), "");
+    }
+
+    memspace = H5Screate_simple(1, chunk_dims, NULL);
+    VRFY((memspace >= 0), "");
+
+    dataspace = H5Dget_space(*dataset);            
+    VRFY((dataspace >= 0), "");
+
+    /* expected value in the dataset */
+    if (write == all)
+        value = mpi_rank + 1;
+    else
+        value =0;
+
+    /* checks main portion of the dataset */
+    for (i=0; i<nchunks/mpi_size; i++){ 
+
+        memset(buffer, -1, CHUNKSIZE);
+
+        offset[0] = (i*mpi_size+mpi_rank)*chunk_dims[0];
+        count[0] = 1;
+        stride[0] = 1;
+        block[0] = chunk_dims[0];
+
+        hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block);
+        VRFY((hrc >= 0), "");
+
+        /* Read the chunk */
+        hrc = H5Dread(*dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer);
+        VRFY((hrc >= 0), "H5Dread");
+
+        /* adjust expected value for sec_last chunk */
+        if (i == nchunks/mpi_size-1 && !(nchunks%mpi_size) && write==sec_last){
+            if (mpi_rank == mpi_size-2)
+                value = 100;
+            else
+                value = 0;
+        }
+
+        /* verify content of the chunk */
+        for (index = 0; index < CHUNKSIZE; index++)
+            VRFY((buffer[index] == value), "data verification");
+        
+    }
+
+    /* remainder checking */
+    if (mpi_rank < nchunks%mpi_size){
+
+        memset(buffer, -1, CHUNKSIZE);
+
+        offset[0] = ((nchunks/mpi_size)*mpi_size+mpi_rank)*chunk_dims[0];
+        count[0] = 1;
+        stride[0] = 1;
+        block[0] = chunk_dims[0];
+
+        hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block);
+        VRFY((hrc >= 0), "");
+
+        /* read the buffer out */
+        hrc = H5Dread(*dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer);
+        VRFY((hrc >= 0), "H5Dread");
+
+        /* adjust expected value for sec_last chunk */
+        if (write == sec_last){
+            if (mpi_rank == nchunks%mpi_size-2)
+                value = 100;
+            else
+                value = 0;
+        }
+
+        /* verify content of the chunk */
+        for (index = 0; index < CHUNKSIZE; index++)
+            VRFY((buffer[index] == value), "data verification");
+    
+    }
+
+    hrc = H5Sclose (dataspace);
+	VRFY((hrc >= 0), "");
+
+	hrc = H5Sclose (memspace);
+	VRFY((hrc >= 0), "");
+
+    /* Can close some plists */
+    hrc = H5Pclose(access_plist);
+    VRFY((hrc >= 0), "");
+
+    /* Close up */
+    if (close){
+        hrc = H5Dclose(*dataset);
+        VRFY((hrc >= 0), "");
+        *dataset = -1;
+
+        hrc = H5Fclose(*file_id);
+        VRFY((hrc >= 0), "");
+        *file_id = -1;
+    }
+
+    /* Make sure all processes are done before exiting this routine.  Otherwise,
+     * other tests may start and change the test data file before some processes
+     * of this test are still accessing the file.
+     */
+    MPI_Barrier(MPI_COMM_WORLD);
+}
+
+
+
+/*
+ * Test following possible scenarios,
+ * Case 1:
+ * Sequential create a file and dataset with H5D_ALLOC_TIME_EARLY and large
+ * size, no write, close, reopen in parallel, read to verify all return
+ * the fill value.
+ * Case 2:
+ * Sequential create a file and dataset with H5D_ALLOC_TIME_EARLY but small
+ * size, no write, close, reopen in parallel, extend to large size, then close,
+ * then reopen in parallel and read to verify all return the fill value.
+ * Case 3:
+ * Sequential create a file and dataset with H5D_ALLOC_TIME_EARLY and large
+ * size, write just a small part of the dataset (second to the last), close,
+ * then reopen in parallel, read to verify all return the fill value except
+ * those small portion that has been written.  Without closing it, writes
+ * all parts of the dataset in a interleave pattern, close it, and reopen
+ * it, read to verify all data are as written.
+ */
+void
+test_chunk_alloc(void)
+{
+    const char *filename;
+    hid_t file_id, dataset;
+
+    file_id = dataset = -1;
+  
+    filename = GetTestParameters();
+    if (VERBOSE_MED)
+	printf("Extend Chunked allocation test on file %s\n", filename);
+
+    /* Case 1 */
+    /* Create chunked dataset without writing anything.*/
+    create_chunked_dataset(filename, DSETCHUNKS, none);
+    /* reopen dataset in parallel and check for file size */
+    parallel_access_dataset(filename, DSETCHUNKS, open_only, &file_id, &dataset);
+    /* reopen dataset in parallel, read and verify the data */
+    verify_data(filename, DSETCHUNKS, none, CLOSE, &file_id, &dataset); 
+
+    /* Case 2 */
+    /* Create chunked dataset without writing anything */
+    create_chunked_dataset(filename, 20, none);
+    /* reopen dataset in parallel and only extend it */
+    parallel_access_dataset(filename, DSETCHUNKS, extend_only, &file_id, &dataset);
+    /* reopen dataset in parallel, read and verify the data */
+    verify_data(filename, DSETCHUNKS, none, CLOSE, &file_id, &dataset);
+
+    /* Case 3 */
+    /* Create chunked dataset and write in the second to last chunk */
+    create_chunked_dataset(filename, DSETCHUNKS, sec_last);
+    /* Reopen dataset in parallel, read and verify the data. The file and dataset are not closed*/
+    verify_data(filename, DSETCHUNKS, sec_last, NO_CLOSE, &file_id, &dataset); 
+    /* All processes write in all the chunks in a interleaved way */
+    parallel_access_dataset(filename, DSETCHUNKS, write_all, &file_id, &dataset);
+    /* reopen dataset in parallel, read and verify the data */
+    verify_data(filename, DSETCHUNKS, all, CLOSE, &file_id, &dataset); 
+
+}