Merge pull request #1316 in HDFFV/hdf5 from ~SONGYULU/hdf5_ray:bugfix/HDFFV-10601-issues-with-chunk-cache-hash to develop

* commit 'cd13d24e5140578a880aebe4e2d8b899179d0870':
  HDFFV-10601: I added error checking to the HDF5 functions.
  HDFFV10601: Adding performance test to verify the improvement.
  HDFFV-10601: I changed to a better way to calculate the number of chunks in a dataset.
  HDFFV-10601 Issues with chunk cache hash value calcuation:

4 files changed, 479 insertions, 14 deletions

diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 22dc05a..cb6b925 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -949,7 +949,10 @@ H5D__chunk_init(H5F_t *f, const H5D_t *dset, hid_t dapl_id)
             /* Initial scaled dimension sizes */
             if(dset->shared->layout.u.chunk.dim[u] == 0)
                 HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u)
-            rdcc->scaled_dims[u] = dset->shared->curr_dims[u] / dset->shared->layout.u.chunk.dim[u];
+
+            /* Round up to the next integer # of chunks, to accommodate partial chunks */
+            rdcc->scaled_dims[u] = (dset->shared->curr_dims[u] + dset->shared->layout.u.chunk.dim[u] - 1) /
+                dset->shared->layout.u.chunk.dim[u];
 
             if( !(scaled_power2up = H5VM_power2up(rdcc->scaled_dims[u])) )
                 HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get the next power of 2")
@@ -2799,6 +2802,7 @@ H5D__chunk_hash_val(const H5D_shared_t *shared, const hsize_t *scaled)
     hsize_t val;        /* Intermediate value */
     unsigned ndims = shared->ndims;      /* Rank of dataset */
     unsigned ret = 0;   /* Value to return */
+    unsigned u;         /* Local index variable */
 
     FUNC_ENTER_STATIC_NOERR
 
@@ -2809,17 +2813,11 @@ H5D__chunk_hash_val(const H5D_shared_t *shared, const hsize_t *scaled)
     /* If the fastest changing dimension doesn't have enough entropy, use
      *  other dimensions too
      */
-    if(ndims > 1 && shared->cache.chunk.scaled_dims[ndims - 1] <= shared->cache.chunk.nslots) {
-        unsigned u;          /* Local index variable */
-
-        val = scaled[0];
-        for(u = 1; u < ndims; u++) {
-            val <<= shared->cache.chunk.scaled_encode_bits[u];
-            val ^= scaled[u];
-        } /* end for */
-    } /* end if */
-    else
-        val = scaled[ndims - 1];
+    val = scaled[0];
+    for(u = 1; u < ndims; u++) {
+        val <<= shared->cache.chunk.scaled_encode_bits[u];
+        val ^= scaled[u];
+    } /* end for */
 
     /* Modulo value against the number of array slots */
     ret = (unsigned)(val % shared->cache.chunk.nslots);
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..01571e2
--- /dev/null
+++ b/tools/test/perform/chunk_cache.c
@@ -0,0 +1,457 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 <stdio.h>
+#include <stdlib.h>
+#include <time.h>
+#include "hdf5.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;
+}
+
+/*---------------------------------------------------------------------------*/
+static int
+test_time_get_current(test_time_t *tv)
+{
+    struct timespec tp;
+    
+    if (!tv)
+        return -1;
+    if (clock_gettime(CLOCK_MONOTONIC, &tp))
+        return -1;
+    
+    tv->tv_sec = tp.tv_sec;
+    tv->tv_usec = tp.tv_nsec / 1000;
+    
+    return 0;
+}
+
+/*---------------------------------------------------------------------------*/
+static double
+test_time_to_double(test_time_t tv)
+{
+    return (double) tv.tv_sec + (double) (tv.tv_usec) * 0.000001;
+}
+
+/*---------------------------------------------------------------------------*/
+static test_time_t
+test_time_add(test_time_t in1, test_time_t in2)
+{
+    test_time_t out;
+    
+    out.tv_sec = in1.tv_sec + in2.tv_sec;
+    out.tv_usec = in1.tv_usec + in2.tv_usec;
+    if(out.tv_usec > 1000000) {
+        out.tv_usec -= 1000000;
+        out.tv_sec += 1;
+    }
+    
+    return out;
+}
+
+/*---------------------------------------------------------------------------*/
+static test_time_t
+test_time_subtract(test_time_t in1, test_time_t in2)
+{
+    test_time_t out;
+    
+    out.tv_sec = in1.tv_sec - in2.tv_sec;
+    out.tv_usec = in1.tv_usec - in2.tv_usec;
+    if(out.tv_usec < 0) {
+        out.tv_usec += 1000000;
+        out.tv_sec -= 1;
+    }
+    
+    return out;
+}
+/*-------------------------------------------------------------------------
+ * Function:  cleanup
+ *
+ * Purpose:  Removes test files
+ *
+ * Return:  void
+ *
+ * Programmer:  Robb Matzke
+ *              Thursday, June  4, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+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};
+    test_time_t t = {0, 0}, t1 = {0, 0}, t2 = {0, 0};
+    
+    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;
+    
+    test_time_get_current(&t1);
+    
+    /* 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;
+    }
+    
+    test_time_get_current(&t2);
+    t = test_time_add(t, test_time_subtract(t2, t1));
+    
+    printf("1. Partial chunks: total read time is %lf; number of bytes being read from file is %lu\n", test_time_to_double(t), nbytes_global);
+    
+    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};
+    test_time_t t = {0, 0}, t1 = {0, 0}, t2 = {0, 0};
+    
+    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;
+    
+    test_time_get_current(&t1);
+    
+    /* 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;
+    }
+    
+    test_time_get_current(&t2);
+    t = test_time_add(t, test_time_subtract(t2, t1));
+    
+    printf("2. Hash value: total read time is %lf; number of bytes being read from file is %lu\n", test_time_to_double(t), nbytes_global);
+    
+    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;
+}