Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into stackable_vol

6 files changed, 440 insertions, 11 deletions

diff --git a/tools/test/misc/CMakeTestsRepart.cmake b/tools/test/misc/CMakeTestsRepart.cmake
index 37da903..830de11 100644
--- a/tools/test/misc/CMakeTestsRepart.cmake
+++ b/tools/test/misc/CMakeTestsRepart.cmake
@@ -68,6 +68,7 @@
         scd_family00001.h5
         scd_family00002.h5
         scd_family00003.h5
+        family_to_single.h5
         family_to_sec2.h5
   )
   if (NOT "${last_test}" STREQUAL "")
@@ -84,6 +85,10 @@
   set_tests_properties (H5REPART-h5repart_5K PROPERTIES DEPENDS H5REPART-clearall-objects)
 
   # convert family file to sec2 file of 20,000 bytes
+  add_test (NAME H5REPART-h5repart_single COMMAND $<TARGET_FILE:h5repart> -m 20000 -family_to_single family_file%05d.h5 family_to_single.h5)
+  set_tests_properties (H5REPART-h5repart_single PROPERTIES DEPENDS H5REPART-clearall-objects)
+
+  # convert family file to sec2 file of 20,000 bytes (old argument)
   add_test (NAME H5REPART-h5repart_sec2 COMMAND $<TARGET_FILE:h5repart> -m 20000 -family_to_sec2 family_file%05d.h5 family_to_sec2.h5)
   set_tests_properties (H5REPART-h5repart_sec2 PROPERTIES DEPENDS H5REPART-clearall-objects)
 
diff --git a/tools/test/misc/repart_test.c b/tools/test/misc/repart_test.c
index 4016ee8..b8e0292 100644
--- a/tools/test/misc/repart_test.c
+++ b/tools/test/misc/repart_test.c
@@ -26,12 +26,13 @@
 const char *FILENAME[] = {
     "fst_family%05d.h5",
     "scd_family%05d.h5",
+    "family_to_single.h5",
     "family_to_sec2.h5",
     NULL
 };
 
 herr_t test_family_h5repart_opens(void);
-herr_t test_sec2_h5repart_opens(void);
+herr_t test_single_h5repart_opens(void);
 
 
 /*-------------------------------------------------------------------------
@@ -90,23 +91,28 @@ error:
 
 
 /*-------------------------------------------------------------------------
- * Function:    test_sec2_h5repart_opens
+ * Function:    test_single_h5repart_opens
  *
- * Purpose:     Tries to reopen a sec2 file.
+ * Purpose:     Tries to reopen a single file.
  *
  * Return:      SUCCEED/FAIL
  *
  *-------------------------------------------------------------------------
  */
 herr_t
-test_sec2_h5repart_opens(void)
+test_single_h5repart_opens(void)
 {
     hid_t       fid = -1;
 
-    /* open the sec2 file */
+    /* open the single file */
     if ((fid = H5Fopen(FILENAME[2], H5F_ACC_RDWR, H5P_DEFAULT)) < 0)
         goto error;
+    if (H5Fclose(fid) < 0)
+        goto error;
 
+    /* open the single file (created using the old argument) */
+    if ((fid = H5Fopen(FILENAME[3], H5F_ACC_RDWR, H5P_DEFAULT)) < 0)
+        goto error;
     if (H5Fclose(fid) < 0)
         goto error;
 
@@ -119,7 +125,7 @@ error:
 
     return FAIL;
 
-} /* end test_sec2_h5repart_opens() */
+} /* end test_single_h5repart_opens() */
 
 
 /*-------------------------------------------------------------------------
@@ -137,7 +143,7 @@ main(void)
     int     nerrors = 0;
 
     nerrors += test_family_h5repart_opens() < 0     ? 1 : 0;
-    nerrors += test_sec2_h5repart_opens() < 0       ? 1 : 0;
+    nerrors += test_single_h5repart_opens() < 0     ? 1 : 0;
 
     if (nerrors)
         goto error;
@@ -150,3 +156,4 @@ error:
             nerrors, 1 == nerrors ? "" : "S");
     HDexit(EXIT_FAILURE);
 } /* end main() */
+
diff --git a/tools/test/misc/testh5repart.sh.in b/tools/test/misc/testh5repart.sh.in
index 594d37e..143f607 100644
--- a/tools/test/misc/testh5repart.sh.in
+++ b/tools/test/misc/testh5repart.sh.in
@@ -171,7 +171,9 @@ COPY_TESTFILES_TO_TESTDIR
 TOOLTEST -m 20000 family_file%05d.h5 fst_family%05d.h5
 # repartition family member size to 5 KB.
 TOOLTEST -m 5k family_file%05d.h5 scd_family%05d.h5
-# convert family file to sec2 file of 20,000 bytes
+# convert family file to single file of 20,000 bytes
+TOOLTEST -m 20000 -family_to_single family_file%05d.h5 family_to_single.h5
+# convert family file to single file of 20,000 bytes (old argument)
 TOOLTEST -m 20000 -family_to_sec2 family_file%05d.h5 family_to_sec2.h5
 
 # test the output files repartitioned above.
@@ -183,7 +185,7 @@ CLEAN_TESTFILES_AND_TESTDIR
 
 if test -z "$HDF5_NOCLEANUP"; then
     cd $actual_dir
-    rm -f fst_family*.h5 scd_family*.h5 family_to_sec2.h5
+    rm -f fst_family*.h5 scd_family*.h5 family_to_single.h5 family_to_sec2.h5
 fi
 
 if test $nerrors -eq 0 ; then
diff --git a/tools/test/perform/CMakeLists.txt b/tools/test/perform/CMakeLists.txt
index fa41608..14abdec 100644
--- a/tools/test/perform/CMakeLists.txt
+++ b/tools/test/perform/CMakeLists.txt
@@ -51,6 +51,16 @@ TARGET_C_PROPERTIES (iopipe STATIC)
 target_link_libraries (iopipe PRIVATE ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
 set_target_properties (iopipe PROPERTIES FOLDER perform)
 
+#-- Adding test for chunk_cache
+set (chunk_cache_SOURCES
+    ${HDF5_TOOLS_TEST_PERFORM_SOURCE_DIR}/chunk_cache.c
+)
+add_executable (chunk_cache ${chunk_cache_SOURCES})
+target_include_directories(chunk_cache PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+TARGET_C_PROPERTIES (chunk_cache STATIC)
+target_link_libraries (chunk_cache PRIVATE ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
+set_target_properties (chunk_cache PROPERTIES FOLDER perform)
+
 #-- Adding test for overhead
 set (overhead_SOURCES
     ${HDF5_TOOLS_TEST_PERFORM_SOURCE_DIR}/overhead.c
diff --git a/tools/test/perform/Makefile.am b/tools/test/perform/Makefile.am
index 5a89a66..39800d7 100644
--- a/tools/test/perform/Makefile.am
+++ b/tools/test/perform/Makefile.am
@@ -50,12 +50,12 @@ if BUILD_PARALLEL_CONDITIONAL
     TEST_PROG_PARA=h5perf perf
 endif
 # Serial test programs.
-TEST_PROG = iopipe chunk overhead zip_perf perf_meta h5perf_serial $(BUILD_ALL_PROGS)
+TEST_PROG = iopipe chunk chunk_cache overhead zip_perf perf_meta h5perf_serial $(BUILD_ALL_PROGS)
 
 # check_PROGRAMS will be built but not installed.  Do not any executable
 # that is in bin_PROGRAMS already. Otherwise, it will be removed twice in
 # "make clean" and some systems, e.g., AIX, do not like it.
-check_PROGRAMS= iopipe chunk overhead zip_perf perf_meta $(BUILD_ALL_PROGS) perf
+check_PROGRAMS= iopipe chunk chunk_cache overhead zip_perf perf_meta $(BUILD_ALL_PROGS) perf
 
 h5perf_SOURCES=pio_perf.c pio_engine.c
 h5perf_serial_SOURCES=sio_perf.c sio_engine.c
diff --git a/tools/test/perform/chunk_cache.c b/tools/test/perform/chunk_cache.c
new file mode 100644
index 0000000..429f70a
--- /dev/null
+++ b/tools/test/perform/chunk_cache.c
@@ -0,0 +1,405 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ *  Purpose: check the performance of chunk cache in these two cases (HDFFV-10601):
+ *          1. partial chunks exist along any dimension.
+ *          2. number of slots in chunk cache is smaller than the number of chunks
+ *             in the fastest-growing dimension.
+ */
+#include "hdf5.h"
+#include "H5private.h"
+
+#define FILENAME    "chunk_cache_perf.h5"
+
+#define RANK        2
+
+#define DSET1_NAME  "partial_chunks"
+#define DSET1_DIM1   9 * 1000
+#define DSET1_DIM2   9
+#define CHUNK1_DIM1  2 * 1000
+#define CHUNK1_DIM2  2
+
+#define DSET2_NAME  "hash_value"
+#define DSET2_DIM1   300
+#define DSET2_DIM2   600
+#define CHUNK2_DIM1  100
+#define CHUNK2_DIM2  100
+
+#define RDCC_NSLOTS  5
+#define RDCC_NBYTES  1024 * 1024 * 10
+#define RDCC_W0      0.75F
+
+#define FILTER_COUNTER    306
+static size_t    nbytes_global;
+
+typedef struct test_time_t {
+    long tv_sec;
+    long tv_usec;
+} test_time_t;
+
+/* Local function prototypes for the dummy filter */
+static size_t
+counter (unsigned flags, size_t cd_nelmts,
+         const unsigned *cd_values, size_t nbytes,
+         size_t *buf_size, void **buf);
+
+/* This message derives from H5Z */
+const H5Z_class2_t H5Z_COUNTER[1] = {{
+    H5Z_CLASS_T_VERS,           /* H5Z_class_t version          */
+    FILTER_COUNTER,             /* Filter id number             */
+    1, 1,                       /* Encoding and decoding enabled */
+    "counter",                  /* Filter name for debugging    */
+    NULL,                       /* The "can apply" callback     */
+    NULL,                       /* The "set local" callback     */
+    counter,                    /* The actual filter function   */
+}};
+
+/*-------------------------------------------------------------------------
+ *      Count number of bytes but don't do anything else.  Keep
+ *      track of the data of chunks being read from file into memory.
+ */
+static size_t
+counter (unsigned flags, size_t cd_nelmts,
+         const unsigned *cd_values, size_t nbytes,
+         size_t *buf_size, void **buf)
+{
+    nbytes_global += nbytes;
+    return nbytes;
+}
+
+/*---------------------------------------------------------------------------*/
+double retrieve_time(void)
+{
+#ifdef H5_HAVE_GETTIMEOFDAY
+    struct timeval t;
+    HDgettimeofday(&t, NULL);
+    return ((double)t.tv_sec + (double)t.tv_usec / 1000000);
+#else
+    return 0.0;
+#endif
+}
+
+/*---------------------------------------------------------------------------*/
+static void
+cleanup (void)
+{
+    if (!getenv ("HDF5_NOCLEANUP")) {
+        remove (FILENAME);
+    }
+}
+
+/*-------------------------------------------------------------------------------
+ *      Create a chunked dataset with partial chunks along either dimensions:
+ *          dataset dimension:  9000 x 9
+ *          chunk dimension:    2000 x 2
+ */
+static int create_dset1(hid_t file)
+{
+    hid_t        dataspace, dataset;
+    hid_t        dcpl;
+    hsize_t      dims[RANK]  = {DSET1_DIM1, DSET1_DIM2};
+    hsize_t      chunk_dims[RANK] = {CHUNK1_DIM1, CHUNK1_DIM2};
+    int          data[DSET1_DIM1][DSET1_DIM2];    /* data for writing */
+    int          i, j;
+    
+    /* Create the data space. */
+    if((dataspace = H5Screate_simple (RANK, dims, NULL)) < 0)
+        goto error;
+    
+    /* Modify dataset creation properties, i.e. enable chunking  */
+    if((dcpl = H5Pcreate (H5P_DATASET_CREATE)) < 0)
+        goto error;
+    if(H5Pset_chunk (dcpl, RANK, chunk_dims) < 0)
+        goto error;
+    
+    /* Set the dummy filter simply for counting the number of bytes being read into the memory */
+    if(H5Zregister(H5Z_COUNTER) < 0)
+        goto error;
+    
+    if(H5Pset_filter(dcpl, FILTER_COUNTER, 0, 0, NULL) < 0)
+        goto error;
+    
+    /* Create a new dataset within the file using chunk creation properties.  */
+    if((dataset = H5Dcreate2 (file, DSET1_NAME, H5T_NATIVE_INT, dataspace,
+                          H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
+        goto error;
+    
+    for (i = 0; i < DSET1_DIM1; i++)
+        for (j = 0; j < DSET1_DIM2; j++)
+            data[i][j] = i+j;
+    
+    /* Write data to dataset */
+    if(H5Dwrite (dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+                       H5P_DEFAULT, data) < 0)
+        goto error;
+    
+    /* Close resources */
+    H5Dclose (dataset);
+    H5Pclose (dcpl);
+    H5Sclose (dataspace);
+    return 0;
+    
+error:
+    H5E_BEGIN_TRY {
+        H5Dclose (dataset);
+        H5Pclose (dcpl);
+        H5Sclose (dataspace);
+    } H5E_END_TRY;
+    
+    return 1;
+}
+
+/*---------------------------------------------------------------------------
+ *      Create a chunked dataset for testing hash values:
+ *          dataset dimensions: 300 x 600
+ *          chunk dimensions:   100 x 100
+ */
+static int create_dset2(hid_t file)
+{
+    hid_t        dataspace, dataset;
+    hid_t        dcpl;
+    hsize_t      dims[RANK]  = {DSET2_DIM1, DSET2_DIM2};
+    hsize_t      chunk_dims[RANK] = {CHUNK2_DIM1, CHUNK2_DIM2};
+    int          data[DSET2_DIM1][DSET2_DIM2];    /* data for writing */
+    int          i, j;
+    
+    /* Create the data space. */
+    if((dataspace = H5Screate_simple (RANK, dims, NULL)) < 0)
+        goto error;
+    
+    /* Modify dataset creation properties, i.e. enable chunking  */
+    if((dcpl = H5Pcreate (H5P_DATASET_CREATE)) < 0)
+        goto error;
+    if(H5Pset_chunk (dcpl, RANK, chunk_dims) < 0)
+        goto error;
+    
+    /* Set the dummy filter simply for counting the number of bytes being read into the memory */
+    if(H5Zregister(H5Z_COUNTER) < 0)
+        goto error;
+    if(H5Pset_filter(dcpl, FILTER_COUNTER, 0, 0, NULL) < 0)
+        goto error;
+    
+    /* Create a new dataset within the file using chunk creation properties.  */
+    if((dataset = H5Dcreate2 (file, DSET2_NAME, H5T_NATIVE_INT, dataspace,
+                          H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
+        goto error;
+    
+    for (i = 0; i < DSET2_DIM1; i++)
+        for (j = 0; j < DSET2_DIM2; j++)
+            data[i][j] = i+j;
+    
+    /* Write data to dataset */
+    if(H5Dwrite (dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+                       H5P_DEFAULT, data) < 0)
+        goto error;
+    
+    /* Close resources */
+    H5Dclose (dataset);
+    H5Pclose (dcpl);
+    H5Sclose (dataspace);
+    
+    return 0;
+    
+error:
+    H5E_BEGIN_TRY {
+        H5Dclose (dataset);
+        H5Pclose (dcpl);
+        H5Sclose (dataspace);
+    } H5E_END_TRY;
+    
+    return 1;
+}
+/*---------------------------------------------------------------------------
+ *      Check the performance of the chunk cache when partial chunks exist
+ *      along the dataset dimensions.
+ */
+static int check_partial_chunks_perf(hid_t file)
+{
+    hid_t        dataset;
+    hid_t        filespace;
+    hid_t        memspace;
+    hid_t        dapl;
+    
+    int          rdata[DSET1_DIM2];   /* data for reading */
+    int          i;
+    
+    hsize_t      row_rank = 1;
+    hsize_t      row_dim[1] = {DSET1_DIM2};
+    hsize_t      start[RANK] = {0, 0};
+    hsize_t      count[RANK] = {1, DSET1_DIM2};
+    double       start_t, end_t;
+    
+    if((dapl = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
+        goto error;
+    if(H5Pset_chunk_cache (dapl, RDCC_NSLOTS, RDCC_NBYTES, RDCC_W0) < 0)
+        goto error;
+
+    dataset = H5Dopen2 (file, DSET1_NAME, dapl);
+    
+    memspace = H5Screate_simple(row_rank, row_dim, NULL);
+    filespace = H5Dget_space(dataset);
+    
+    nbytes_global = 0;
+    
+    start_t = retrieve_time();
+    
+    /* Read the data row by row */
+    for(i = 0; i < DSET1_DIM1; i++) {
+        start[0] = i;
+        if(H5Sselect_hyperslab(filespace, H5S_SELECT_SET,
+                                     start, NULL, count, NULL) < 0)
+            goto error;
+        
+        if(H5Dread (dataset, H5T_NATIVE_INT, memspace, filespace,
+                          H5P_DEFAULT, rdata) < 0)
+            goto error;
+    }
+    
+    end_t = retrieve_time();
+    
+#ifdef H5_HAVE_GETTIMEOFDAY
+    printf("1. Partial chunks: total read time is %lf; number of bytes being read from file is %lu\n", (end_t -start_t), nbytes_global);
+#else
+    printf("1. Partial chunks: no total read time because gettimeofday() is not available; number of bytes being read from file is %lu\n", nbytes_global);
+#endif
+    
+    H5Dclose (dataset);
+    H5Sclose (filespace);
+    H5Sclose (memspace);
+    H5Pclose (dapl);
+    
+    return 0;
+error:
+    H5E_BEGIN_TRY {
+        H5Dclose (dataset);
+        H5Sclose (filespace);
+        H5Sclose (memspace);
+        H5Pclose (dapl);
+    } H5E_END_TRY;
+    return 1;
+}
+
+/*---------------------------------------------------------------------------
+ *      Check the performance of chunk cache when the number of cache slots
+ *      is smaller than the number of chunks along the fastest-growing
+ *      dimension of the dataset.
+ */
+static int check_hash_value_perf(hid_t file)
+{
+    hid_t        dataset;
+    hid_t        filespace;
+    hid_t        memspace;
+    hid_t        dapl;
+    
+    int          rdata[DSET2_DIM1];   /* data for reading */
+    int          i;
+    
+    hsize_t      column_rank = 1;
+    hsize_t      column_dim[1] = {DSET2_DIM1};
+    hsize_t      start[RANK] = {0, 0};
+    hsize_t      count[RANK] = {DSET2_DIM1, 1};
+    double       start_t, end_t;
+    
+    if((dapl = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
+        goto error;
+    if(H5Pset_chunk_cache (dapl, RDCC_NSLOTS, RDCC_NBYTES, RDCC_W0) < 0)
+        goto error;
+    
+    if((dataset = H5Dopen2 (file, DSET2_NAME, dapl)) < 0)
+        goto error;
+    if((memspace = H5Screate_simple(column_rank, column_dim, NULL)) < 0)
+        goto error;
+    if((filespace = H5Dget_space(dataset)) < 0)
+        goto error;
+    
+    nbytes_global = 0;
+    
+    start_t = retrieve_time();
+    
+    /* Read the data column by column */
+    for(i = 0; i < DSET2_DIM2; i++) {
+        start[1] = i;
+        if(H5Sselect_hyperslab(filespace, H5S_SELECT_SET,
+                                     start, NULL, count, NULL) < 0)
+            goto error;
+        
+        if(H5Dread (dataset, H5T_NATIVE_INT, memspace, filespace,
+                          H5P_DEFAULT, rdata) < 0)
+            goto error;
+    }
+    
+    end_t = retrieve_time();
+    
+#ifdef H5_HAVE_GETTIMEOFDAY
+    printf("2. Hash value: total read time is %lf; number of bytes being read from file is %lu\n", (end_t -start_t), nbytes_global);
+#else
+    printf("2. Hash value: no total read time because gettimeofday() is not available; number of bytes being read from file is %lu\n", nbytes_global);
+#endif
+    
+    H5Dclose (dataset);
+    H5Sclose (filespace);
+    H5Sclose (memspace);
+    H5Pclose (dapl);
+    return 0;
+    
+error:
+    H5E_BEGIN_TRY {
+        H5Dclose (dataset);
+        H5Sclose (filespace);
+        H5Sclose (memspace);
+        H5Pclose (dapl);
+    } H5E_END_TRY;
+    return 1;
+}
+
+/*-------------------------------------------------------------------------------------
+ *  Purpose: check the performance of chunk cache in these two cases (HDFFV-10601):
+ *          1. partial chunks exist along any dimension.
+ *          2. number of slots in chunk cache is smaller than the number of chunks
+ *             in the fastest-growing dimension.
+ *-------------------------------------------------------------------------------------*/
+int
+main (void)
+{
+    hid_t        file;                          /* handles */
+    int          nerrors = 0;
+    
+    /* Create a new file. If file exists its contents will be overwritten. */
+    if((file = H5Fcreate (FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+        goto error;
+
+    nerrors += create_dset1(file);
+    nerrors += create_dset2(file);
+    
+    if(H5Fclose (file) < 0)
+        goto error;
+
+    /* Re-open the file for testing performance. */
+    if((file = H5Fopen (FILENAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
+        goto error;
+
+    nerrors += check_partial_chunks_perf(file);
+    nerrors += check_hash_value_perf(file);
+    
+    if(H5Fclose (file) < 0)
+        goto error;
+    
+    if (nerrors>0) goto error;
+    cleanup();
+    return 0;
+    
+error:
+    fprintf(stderr, "*** ERRORS DETECTED ***\n");
+    return 1;
+}