First stage of moving H5DOread/write_chunk() to src/ and making

them H5D calls.
* Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*.
* Moved the hl/test/test_dset_opt test to test/ and renamed to
  direct_chunk.
* Moved the hl/test/dectris_hl_perf test to tools/test/perform
  and renamed to direct_write_perf.
* Updated autotools and CMake files.

1 files changed, 684 insertions, 0 deletions

diff --git a/tools/test/perform/direct_write_perf.c b/tools/test/perform/direct_write_perf.c
new file mode 100644
index 0000000..f13cd24
--- /dev/null
+++ b/tools/test/perform/direct_write_perf.c
@@ -0,0 +1,684 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * 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 COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * This tests the performance of the H5Dwrite_chunk() function.
+ *
+ */
+
+#include "hdf5.h"
+
+#ifdef H5_HAVE_FILTER_DEFLATE
+#include <zlib.h>
+
+#if !defined(WIN32) && !defined(__MINGW32__)
+
+#include <math.h>
+
+#ifdef H5_STDC_HEADERS
+#   include <errno.h>
+#   include <fcntl.h>
+#   include <stdio.h>
+#   include <stdlib.h>
+#endif
+
+#ifdef H5_HAVE_UNISTD_H
+#   include <sys/types.h>
+#   include <unistd.h>
+#endif
+
+#ifdef H5_HAVE_SYS_STAT_H
+#   include <sys/stat.h>
+#endif
+
+#if defined(H5_TIME_WITH_SYS_TIME)
+#   include <sys/time.h>
+#   include <time.h>
+#elif defined(H5_HAVE_SYS_TIME_H)
+#   include <sys/time.h>
+#else
+#   include <time.h>
+#endif
+
+const char *FILENAME[] = {
+    "direct_write",
+    "unix.raw",
+    NULL
+};
+
+/*
+ * Print the current location on the standard output stream.
+ */
+#define FUNC __func__
+#define AT()     printf ("   at %s:%d in %s()...\n",        \
+        __FILE__, __LINE__, FUNC);
+#define H5_FAILED()  {puts("*FAILED*");fflush(stdout);}
+#define TEST_ERROR      {H5_FAILED(); AT(); goto error;}
+#define TESTING(WHAT)  {printf("Testing %-62s",WHAT); fflush(stdout);}
+#define PASSED()  {puts(" PASSED");fflush(stdout);}
+
+#define DIRECT_UNCOMPRESSED_DSET        "direct_uncompressed_dset"
+#define DIRECT_COMPRESSED_DSET        "direct_compressed_dset"
+#define REG_COMPRESSED_DSET       "reg_compressed_dset"
+#define REG_NO_COMPRESS_DSET   "reg_no_compress_dset"
+#define RANK         3
+#define NX     100
+#define NY     1000
+#define NZ     250
+#define CHUNK_NX     1 
+#define CHUNK_NY     1000
+#define CHUNK_NZ     250
+
+#define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s))*1.001)+12)
+char        filename[1024];
+unsigned int *outbuf[NX];
+size_t         data_size[NX];
+double       total_size = 0.0;
+unsigned int *direct_buf[NX];
+double       MB = 1048576.0;
+
+/*--------------------------------------------------
+ * Function to report IO rate
+ *--------------------------------------------------
+ */
+void reportTime(struct timeval start, double mbytes)
+{
+    struct timeval timeval_stop,timeval_diff;
+
+    /*end timing*/
+    gettimeofday(&timeval_stop,NULL);
+
+    /* Calculate the elapsed gettimeofday time */
+    timeval_diff.tv_usec=timeval_stop.tv_usec-start.tv_usec;
+    timeval_diff.tv_sec=timeval_stop.tv_sec-start.tv_sec;
+
+    if(timeval_diff.tv_usec<0) {
+        timeval_diff.tv_usec+=1000000;
+        timeval_diff.tv_sec--;
+    } /* end if */
+
+/*printf("mbytes=%lf, sec=%lf, usec=%lf\n", mbytes, (double)timeval_diff.tv_sec, (double)timeval_diff.tv_usec);*/
+    printf("MBytes/second: %lf\n", (double)mbytes/((double)timeval_diff.tv_sec+((double)timeval_diff.tv_usec/(double)1000000.0)));        
+}
+
+/*--------------------------------------------------
+ *  Create file, datasets, and initialize data
+ *--------------------------------------------------
+ */
+int create_file(hid_t fapl_id)
+{
+    hid_t       file;                          /* handles */
+    hid_t       fapl;
+    hid_t       cparms;
+    hid_t       dataspace, dataset;
+    hsize_t     dims[RANK]  = {NX, NY, NZ};        
+    hsize_t     chunk_dims[RANK] ={CHUNK_NX, CHUNK_NY, CHUNK_NZ};
+    unsigned int         aggression = 9;     /* Compression aggression setting */
+    int         ret;
+    int         i, j, n;
+
+    int flag;
+    int unix_file;
+
+    unsigned int *p;
+    size_t      buf_size = CHUNK_NY*CHUNK_NZ*sizeof(unsigned int);
+
+    const Bytef *z_src;
+    Bytef	    *z_dst;		/*destination buffer		*/
+    uLongf	     z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
+    uLong	     z_src_nbytes = (uLong)buf_size;
+
+    TESTING("Create a file and dataset");
+
+    /*
+     * Create the data space with unlimited dimensions.
+     */
+    if((dataspace = H5Screate_simple(RANK, dims, NULL)) < 0)
+        TEST_ERROR;
+
+    /*
+     * Create a new file. If file exists its contents will be overwritten.
+     */
+    if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id)) < 0)
+        TEST_ERROR;
+
+    /*
+     * Modify dataset creation properties, i.e. enable chunking and compression
+     */
+    if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+        TEST_ERROR;
+
+    if(H5Pset_chunk( cparms, RANK, chunk_dims) < 0)
+        TEST_ERROR;
+
+    /*
+     * Create a new dataset within the file using cparms
+     * creation properties.
+     */
+    if((dataset = H5Dcreate2(file, DIRECT_UNCOMPRESSED_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+			cparms, H5P_DEFAULT)) < 0)
+        TEST_ERROR;
+
+    if(H5Dclose(dataset) < 0)
+        TEST_ERROR;
+
+    if((dataset = H5Dcreate2(file, REG_NO_COMPRESS_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+			cparms, H5P_DEFAULT)) < 0)
+        TEST_ERROR;
+
+    if(H5Dclose(dataset) < 0)
+        TEST_ERROR;
+
+    /* Set compression */
+    if(H5Pset_deflate( cparms, aggression) < 0)
+        TEST_ERROR;
+
+    if((dataset = H5Dcreate2(file, DIRECT_COMPRESSED_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+			cparms, H5P_DEFAULT)) < 0)
+        TEST_ERROR;
+
+    if(H5Dclose(dataset) < 0)
+        TEST_ERROR;
+
+
+    if((dataset = H5Dcreate2(file, REG_COMPRESSED_DSET, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
+			cparms, H5P_DEFAULT)) < 0)
+        TEST_ERROR;
+
+    if(H5Dclose(dataset) < 0)
+        TEST_ERROR;
+
+    if(H5Fclose(file) < 0) 
+        TEST_ERROR;
+
+    if(H5Sclose(dataspace) < 0)
+        TEST_ERROR;
+
+    if(H5Pclose(cparms) < 0)
+        TEST_ERROR;
+
+    /* create a unix file*/
+    flag = O_CREAT|O_TRUNC|O_WRONLY;
+
+    if ((unix_file=open(FILENAME[1],flag,S_IRWXU))== -1)
+        TEST_ERROR;
+
+    if (close(unix_file) < 0)
+    {
+        printf(" unable to close the file\n");
+        TEST_ERROR;
+    }
+
+
+    /* Initialize data for chunks */
+    for(i = 0; i < NX; i++) {
+	p = direct_buf[i] = (unsigned int*)malloc(CHUNK_NY*CHUNK_NZ*sizeof(unsigned int));
+        
+        for(j=0; j < CHUNK_NY*CHUNK_NZ; j++, p++)
+            *p = rand() % 65000;
+
+        z_src = (const Bytef*)direct_buf[i];
+
+        z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
+        /* Allocate output (compressed) buffer */
+        outbuf[i] = (unsigned int*)malloc((size_t)z_dst_nbytes);
+        z_dst = (Bytef *)outbuf[i];
+
+        /* Perform compression from the source to the destination buffer */
+        ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
+
+        data_size[i] = (size_t)z_dst_nbytes;
+        total_size += data_size[i];
+
+        /* Check for various zlib errors */
+        if(Z_BUF_ERROR == ret) {
+            fprintf(stderr, "overflow");
+            TEST_ERROR;
+        } else if(Z_MEM_ERROR == ret) {
+	    fprintf(stderr, "deflate memory error");
+            TEST_ERROR;
+        } else if(Z_OK != ret) {
+	    fprintf(stderr, "other deflate error");
+            TEST_ERROR;
+        }
+    }
+
+
+    PASSED();
+
+error:
+    H5E_BEGIN_TRY {
+        H5Dclose(dataset);
+        H5Sclose(dataspace);
+        H5Pclose(cparms);
+        H5Fclose(file);
+    } H5E_END_TRY;
+    return 1;
+}
+
+/*--------------------------------------------------
+ *  Benchmark the performance of the new function 
+ *  with precompressed data.
+ *--------------------------------------------------
+ */
+int
+test_direct_write_uncompressed_data(hid_t fapl_id)
+{
+    hid_t       file;                          /* handles */
+    hid_t       dataspace, dataset;
+    hid_t       dxpl;
+    herr_t      status;
+    int         i;
+
+    unsigned    filter_mask = 0;
+    hsize_t     offset[RANK] = {0, 0, 0};
+
+    struct timeval timeval_start;    
+    
+    TESTING("H5Dwrite_chunk for uncompressed data");
+
+    if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+        TEST_ERROR;
+
+    /* Start the timer */
+    gettimeofday(&timeval_start,NULL);
+
+    /* Reopen the file and dataset */
+    if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
+        TEST_ERROR;
+
+    if((dataset = H5Dopen2(file, DIRECT_UNCOMPRESSED_DSET, H5P_DEFAULT)) < 0)
+        TEST_ERROR;
+
+
+    /* Write the compressed chunk data repeatedly to cover all the chunks in the 
+     * dataset, using the direct writing function.     */ 
+    for(i=0; i<NX; i++) {
+        status = H5Dwrite_chunk(dataset, dxpl, filter_mask, offset, CHUNK_NY*CHUNK_NZ*sizeof(unsigned int), direct_buf[i]);
+        (offset[0])++;
+    }
+
+    /*
+     * Close/release resources.
+     */
+    H5Dclose(dataset);
+    H5Pclose(dxpl);
+    H5Fclose(file);
+
+    /* Report the performance */ 
+    reportTime(timeval_start, (double)(NX*NY*NZ*sizeof(unsigned int)/MB));    
+
+    PASSED();
+    return 0;
+
+error:
+    H5E_BEGIN_TRY {
+        H5Dclose(dataset);
+        H5Pclose(dxpl);
+        H5Fclose(file);
+    } H5E_END_TRY;
+    return 1;
+}
+
+
+/*--------------------------------------------------
+ *  Benchmark the performance of the new function 
+ *  with precompressed data.
+ *--------------------------------------------------
+ */
+int
+test_direct_write_compressed_data(hid_t fapl_id)
+{
+    hid_t       file;                          /* handles */
+    hid_t       dataspace, dataset;
+    hid_t       dxpl;
+    herr_t      status;
+    int         i;
+
+    unsigned    filter_mask = 0;
+    hsize_t     offset[RANK] = {0, 0, 0};
+
+    struct timeval timeval_start;    
+    
+    TESTING("H5DOwrite_chunk for pre-compressed data");
+
+    if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+        TEST_ERROR;
+
+    /* Start the timer */
+    gettimeofday(&timeval_start,NULL);
+
+    /* Reopen the file and dataset */
+    if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
+        TEST_ERROR;
+
+    if((dataset = H5Dopen2(file, DIRECT_COMPRESSED_DSET, H5P_DEFAULT)) < 0)
+        TEST_ERROR;
+
+
+    /* Write the compressed chunk data repeatedly to cover all the chunks in the 
+     * dataset, using the direct writing function.     */ 
+    for(i=0; i<NX; i++) {
+        status = H5Dwrite_chunk(dataset, dxpl, filter_mask, offset, data_size[i], outbuf[i]);
+        (offset[0])++;
+    }
+
+    /*
+     * Close/release resources.
+     */
+    H5Dclose(dataset);
+    H5Pclose(dxpl);
+    H5Fclose(file);
+  
+    /* Report the performance */ 
+    reportTime(timeval_start, (double)(total_size/MB));    
+
+    PASSED();
+    return 0;
+
+error:
+    H5E_BEGIN_TRY {
+        H5Dclose(dataset);
+        H5Pclose(dxpl);
+        H5Fclose(file);
+    } H5E_END_TRY;
+    return 1;
+}
+
+/*--------------------------------------------------
+ *  Benchmark the performance of the regular H5Dwrite
+ *  with compression filter enabled.
+ *--------------------------------------------------
+ */
+int
+test_compressed_write(hid_t fapl_id)
+{
+    hid_t       file;                          /* handles */
+    hid_t       dataspace, dataset;
+    hid_t       mem_space;
+    hsize_t     chunk_dims[RANK] ={CHUNK_NX, CHUNK_NY, CHUNK_NZ};
+    hid_t       dxpl;
+    herr_t      status;
+    int         i;
+
+    hsize_t start[RANK];  /* Start of hyperslab */
+    hsize_t stride[RANK]; /* Stride of hyperslab */
+    hsize_t count[RANK];  /* Block count */
+    hsize_t block[RANK];  /* Block sizes */
+
+    struct timeval timeval_start;    
+
+    TESTING("H5Dwrite with compression enabled");
+
+    if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+        TEST_ERROR;
+
+    if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
+        TEST_ERROR;
+
+    /* Start the timer */
+    gettimeofday(&timeval_start,NULL);
+
+    /* Reopen the file and dataset */
+    if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
+        TEST_ERROR;
+
+    if((dataset = H5Dopen2(file, REG_COMPRESSED_DSET, H5P_DEFAULT)) < 0)
+        TEST_ERROR;
+
+    if((dataspace = H5Dget_space(dataset)) < 0)
+        TEST_ERROR;
+
+    start[0]  = start[1]  = start[2] = 0;
+    stride[0] = stride[1] = stride[2] = 1;
+    count[0]  = count[1]  = count[2] = 1;
+    block[0]  = CHUNK_NX; block[1]  = CHUNK_NY; block[2] = CHUNK_NZ;
+    
+    for(i=0; i<NX; i++) {
+        /*
+         * Select hyperslab for one chunk in the file
+         */
+        if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
+            TEST_ERROR;
+        (start[0])++;        
+
+        if((status = H5Dwrite(dataset, H5T_NATIVE_INT, mem_space, dataspace,
+    		      H5P_DEFAULT, direct_buf[i])) < 0)
+            TEST_ERROR;
+    }
+
+    /*
+     * Close/release resources.
+     */
+    H5Dclose(dataset);
+    H5Sclose(dataspace);
+    H5Sclose(mem_space);
+    H5Pclose(dxpl);
+    H5Fclose(file);
+ 
+    /* Report the performance */ 
+    reportTime(timeval_start, (double)(NX*NY*NZ*sizeof(unsigned int)/MB));    
+   
+    PASSED();
+    return 0;
+
+error:
+    H5E_BEGIN_TRY {
+        H5Dclose(dataset);
+        H5Sclose(dataspace);
+        H5Sclose(mem_space);
+        H5Pclose(dxpl);
+        H5Fclose(file);
+    } H5E_END_TRY;
+    return 1;
+}
+
+/*--------------------------------------------------
+ *  Benchmark the performance of the regular H5Dwrite
+ *  with compression
+ *--------------------------------------------------
+ */
+int
+test_no_compress_write(hid_t fapl_id)
+{
+    hid_t       file;                          /* handles */
+    hid_t       dataspace, dataset;
+    hid_t       mem_space;
+    hsize_t     chunk_dims[RANK] ={CHUNK_NX, CHUNK_NY, CHUNK_NZ};
+    hid_t       dxpl;
+    herr_t      status;
+    int         i;
+
+    hsize_t start[RANK];  /* Start of hyperslab */
+    hsize_t stride[RANK]; /* Stride of hyperslab */
+    hsize_t count[RANK];  /* Block count */
+    hsize_t block[RANK];  /* Block sizes */
+
+    struct timeval timeval_start;    
+
+    TESTING("H5Dwrite without compression");
+
+    if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
+        TEST_ERROR;
+
+    if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0)
+        TEST_ERROR;
+
+    /* Start the timer */
+    gettimeofday(&timeval_start,NULL);
+
+    /* Reopen the file and dataset */
+    if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id)) < 0)
+        TEST_ERROR;
+
+    if((dataset = H5Dopen2(file, REG_NO_COMPRESS_DSET, H5P_DEFAULT)) < 0)
+        TEST_ERROR;
+
+    if((dataspace = H5Dget_space(dataset)) < 0)
+        TEST_ERROR;
+
+    start[0]  = start[1]  = start[2] = 0;
+    stride[0] = stride[1] = stride[2] = 1;
+    count[0]  = count[1]  = count[2] = 1;
+    block[0]  = CHUNK_NX; block[1]  = CHUNK_NY; block[2] = CHUNK_NZ;
+    
+    for(i=0; i<NX; i++) {
+        /*
+         * Select hyperslab for one chunk in the file
+         */
+        if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
+            TEST_ERROR;
+        (start[0])++;        
+
+        if((status = H5Dwrite(dataset, H5T_NATIVE_INT, mem_space, dataspace,
+    		      H5P_DEFAULT, direct_buf[i])) < 0)
+            TEST_ERROR;
+    }
+
+    /*
+     * Close/release resources.
+     */
+    H5Dclose(dataset);
+    H5Sclose(dataspace);
+    H5Sclose(mem_space);
+    H5Pclose(dxpl);
+    H5Fclose(file);
+ 
+    /* Report the performance */ 
+    reportTime(timeval_start, (double)(NX*NY*NZ*sizeof(unsigned int)/MB));    
+   
+    PASSED();
+    return 0;
+
+error:
+    H5E_BEGIN_TRY {
+        H5Dclose(dataset);
+        H5Sclose(dataspace);
+        H5Sclose(mem_space);
+        H5Pclose(dxpl);
+        H5Fclose(file);
+    } H5E_END_TRY;
+    return 1;
+}
+
+/*--------------------------------------------------
+ *  Benchmark the performance for writing compressed
+ *  data to a Unix file
+ *--------------------------------------------------
+ */
+int 
+test_unix_write(void)
+{
+    int file, flag;
+    ssize_t op_size;    
+    int i;
+    struct timeval timeval_start;    
+
+    TESTING("Write compressed data to a Unix file");
+
+    /* create file*/
+    flag = O_WRONLY;
+
+    /* Start the timer */
+    gettimeofday(&timeval_start,NULL);
+
+    if ((file=open(FILENAME[1],flag))== -1)
+        TEST_ERROR;
+
+    /* Write the compressed chunk data repeatedly to cover all the chunks in the 
+     * dataset, using the direct writing function.     */ 
+    for(i=0; i<NX; i++) {
+        op_size = write(file, outbuf[i],data_size[i]);
+        if (op_size < 0)
+        {
+            printf(" Error in writing data to file because %s \n", strerror(errno));
+            TEST_ERROR;
+        }
+        else if (op_size == 0)
+        {
+            printf(" unable to write sufficent data to file because %s \n", strerror(errno));
+            TEST_ERROR;
+        }
+    }
+
+    if (close(file) < 0)
+    {
+        printf(" unable to close the file\n");
+        TEST_ERROR;
+    }
+
+    /* Report the performance */ 
+    reportTime(timeval_start, (double)(total_size/MB));    
+
+    PASSED();
+    return 0;
+
+error:
+    return 1; 
+}
+
+/*--------------------------------------------------
+ *  Main function
+ *--------------------------------------------------
+ */
+int
+main (void)
+{
+    hid_t       fapl = H5P_DEFAULT;
+    int         i;
+
+    sprintf(filename, "%s.h5", FILENAME[0]);
+
+    create_file(fapl);
+    test_direct_write_uncompressed_data(fapl);
+    test_direct_write_compressed_data(fapl);
+    test_no_compress_write(fapl);
+    test_compressed_write(fapl);
+    test_unix_write();
+
+    for(i=0; i<NX; i++) {
+        free(outbuf[i]);
+        free(direct_buf[i]);
+    }
+ 
+    return 0;
+}
+
+#else /* WIN32 / MINGW32 */
+
+int
+main(void)
+{
+    printf("Non-POSIX platform. Exiting.\n");
+    return EXIT_FAILURE;
+} /* end main() */
+
+#endif /* WIN32 / MINGW32 */
+
+#else  /* !H5_HAVE_FILTER_DEFLATE */
+
+/*
+ * Function:    main
+ * Purpose:     Dummy main() function for if HDF5 was configured without
+ *              zlib stuff.
+ * Return:      EXIT_SUCCESS
+ */
+int
+main(void)
+{
+    HDfprintf(stdout, "No compression IO performance because zlib was not configured\n");
+    return EXIT_SUCCESS;
+}
+
+#endif  /* !H5_HAVE_FILTER_DEFLATE */
+