From 0c4cec81b273ff0980c02d71ac271ab6fcd40537 Mon Sep 17 00:00:00 2001 From: Raymond Lu Date: Tue, 4 Dec 2012 14:47:35 -0500 Subject: [svn-r23075] I revised the code and test according to Quincey's review. I also added more test cases. Tested on koala. --- hl/src/H5DO.c | 90 +++-- hl/src/H5DOprivate.h | 2 +- hl/src/H5DOpublic.h | 2 +- hl/test/test_dset_opt.c | 893 +++++++++++++++++++++++++++++++++++++++++++++--- perform/dectris_perf.c | 8 +- src/H5Dchunk.c | 4 +- src/H5Dio.c | 25 +- src/H5Pdxpl.c | 8 +- 8 files changed, 935 insertions(+), 97 deletions(-) diff --git a/hl/src/H5DO.c b/hl/src/H5DO.c index 5b8041e..9cfd8c1 100644 --- a/hl/src/H5DO.c +++ b/hl/src/H5DO.c @@ -34,38 +34,53 @@ *------------------------------------------------------------------------- */ herr_t -H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, hsize_t *offset, +H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size, const void *buf) { - htri_t created_dxpl = FALSE; + hbool_t created_dxpl = FALSE; + herr_t ret_value = SUCCEED; /* Return value */ + + if(dset_id < 0) { + ret_value = FAIL; + goto done; + } - if(dset_id < 0) - goto error; + if(!buf) { + ret_value = FAIL; + goto done; + } - if(!buf) - goto error; - - if(!offset) - goto error; + if(!offset) { + ret_value = FAIL; + goto done; + } - if(!data_size) - goto error; + if(!data_size) { + ret_value = FAIL; + goto done; + } if(H5P_DEFAULT == dxpl_id) { - dxpl_id = H5Pcreate(H5P_DATASET_XFER); + if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0) { + ret_value = FAIL; + goto done; + } + created_dxpl = TRUE; } - if(H5DO_write_chunk(dset_id, dxpl_id, filters, offset, data_size, buf) < 0) - goto error; + if(H5DO_write_chunk(dset_id, dxpl_id, filters, offset, data_size, buf) < 0) { + ret_value = FAIL; + goto done; + } +done: if(created_dxpl) { if(H5Pclose(dxpl_id) < 0) - goto error; + ret_value = FAIL; } -error: - return FAIL; + return ret_value; } /*------------------------------------------------------------------------- @@ -82,30 +97,41 @@ error: *------------------------------------------------------------------------- */ herr_t -H5DO_write_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, hsize_t *offset, +H5DO_write_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size, const void *buf) { - htri_t do_direct_write = TRUE; + hbool_t do_direct_write = TRUE; + herr_t ret_value = SUCCEED; /* Return value */ - if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0) - goto error; + if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0) { + ret_value = FAIL; + goto done; + } - if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &filters) < 0) - goto error; + if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &filters) < 0) { + ret_value = FAIL; + goto done; + } - if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &offset) < 0) - goto error; + if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &offset) < 0) { + ret_value = FAIL; + goto done; + } - if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &data_size) < 0) - goto error; + if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &data_size) < 0) { + ret_value = FAIL; + goto done; + } - if(H5Dwrite(dset_id, 0, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0) - goto error; + if(H5Dwrite(dset_id, 0, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0) { + ret_value = FAIL; + goto done; + } +done: do_direct_write = FALSE; if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0) - goto error; + ret_value = FAIL; -error: - return FAIL; + return ret_value; } diff --git a/hl/src/H5DOprivate.h b/hl/src/H5DOprivate.h index 8617567..fcea585 100644 --- a/hl/src/H5DOprivate.h +++ b/hl/src/H5DOprivate.h @@ -30,7 +30,7 @@ H5_HLDLL herr_t H5DO_write_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, - hsize_t *offset, + const hsize_t *offset, size_t data_size, const void *buf); diff --git a/hl/src/H5DOpublic.h b/hl/src/H5DOpublic.h index b20de56..774709e 100644 --- a/hl/src/H5DOpublic.h +++ b/hl/src/H5DOpublic.h @@ -30,7 +30,7 @@ extern "C" { H5_HLDLL herr_t H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, - hsize_t *offset, + const hsize_t *offset, size_t data_size, const void *buf); diff --git a/hl/test/test_dset_opt.c b/hl/test/test_dset_opt.c index 35dc73c..ebe28cc 100644 --- a/hl/test/test_dset_opt.c +++ b/hl/test/test_dset_opt.c @@ -21,9 +21,14 @@ #include #include -#define FILE_NAME5 "test_dectris.h5" +#define FILE_NAME "test_dectris.h5" -#define DATASETNAME "Array" +#define DATASETNAME1 "direct_write" +#define DATASETNAME2 "skip_one_filter" +#define DATASETNAME3 "skip_two_filters" +#define DATASETNAME4 "data_conv" +#define DATASETNAME5 "contiguous_dset" +#define DATASETNAME6 "invalid_argue" #define RANK 2 #define NX 16 #define NY 16 @@ -32,22 +37,65 @@ #define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s))*1.001)+12) +/* Temporary filter IDs used for testing */ +#define H5Z_FILTER_BOGUS1 305 +#define H5Z_FILTER_BOGUS2 306 +#define ADD_ON 7 +#define FACTOR 3 + +/* Local prototypes for filter functions */ +static size_t filter_bogus1(unsigned int flags, size_t cd_nelmts, + const unsigned int *cd_values, size_t nbytes, size_t *buf_size, void **buf); +static size_t filter_bogus2(unsigned int flags, size_t cd_nelmts, + const unsigned int *cd_values, size_t nbytes, size_t *buf_size, void **buf); + +/* This message derives from H5Z */ +const H5Z_class2_t H5Z_BOGUS1[1] = {{ + H5Z_CLASS_T_VERS, /* H5Z_class_t version */ + H5Z_FILTER_BOGUS1, /* Filter id number */ + 1, 1, /* Encoding and decoding enabled */ + "bogus1", /* Filter name for debugging */ + NULL, /* The "can apply" callback */ + NULL, /* The "set local" callback */ + filter_bogus1, /* The actual filter function */ +}}; + +const H5Z_class2_t H5Z_BOGUS2[1] = {{ + H5Z_CLASS_T_VERS, /* H5Z_class_t version */ + H5Z_FILTER_BOGUS2, /* Filter id number */ + 1, 1, /* Encoding and decoding enabled */ + "bogus2", /* Filter name for debugging */ + NULL, /* The "can apply" callback */ + NULL, /* The "set local" callback */ + filter_bogus2, /* The actual filter function */ +}}; + +/*------------------------------------------------------------------------- + * Function: test_direct_chunk_write + * + * Purpose: Test the basic functionality of H5DOwrite_chunk + * + * Return: Success: 0 + * + * Failure: 1 + * + * Programmer: Raymond Lu + * 30 November 2012 + * + *------------------------------------------------------------------------- + */ static int -test_direct_chunk_write (void) +test_direct_chunk_write (hid_t file) { - char filename[1024]; - hid_t file; /* handles */ - hid_t fapl; - hid_t dataspace, dataset; - hid_t mem_space; - hid_t cparms, dxpl; + hid_t dataspace = -1, dataset = -1; + hid_t mem_space = -1; + hid_t cparms = -1, dxpl = -1; hsize_t dims[2] = {NX, NY}; hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED}; hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY}; herr_t status; int ret; int data[NX][NY]; - int check[NX][NY]; int i, j, n; unsigned filter_mask = 0; @@ -68,7 +116,7 @@ test_direct_chunk_write (void) hsize_t count[2]; /* Block count */ hsize_t block[2]; /* Block sizes */ - TESTING("H5DOwrite_chunk"); + TESTING("basic functionality of H5DOwrite_chunk"); /* * Create the data space with unlimited dimensions. @@ -80,12 +128,6 @@ test_direct_chunk_write (void) goto error; /* - * Create a new file. If file exists its contents will be overwritten. - */ - if((file = H5Fcreate(FILE_NAME5, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) - goto error; - - /* * Modify dataset creation properties, i.e. enable chunking and compression */ if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0) @@ -94,14 +136,14 @@ test_direct_chunk_write (void) if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0) goto error; - if((status = H5Pset_deflate( cparms, aggression)) < 0) + if((status = H5Pset_deflate( cparms, (unsigned) aggression)) < 0) goto error; /* * Create a new dataset within the file using cparms * creation properties. */ - if((dataset = H5Dcreate2(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, + if((dataset = H5Dcreate2(file, DATASETNAME1, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, cparms, H5P_DEFAULT)) < 0) goto error; @@ -159,17 +201,13 @@ test_direct_chunk_write (void) if(outbuf) free(outbuf); - if(H5Dclose(dataset) < 0) - goto error; - - if(H5Fclose(file) < 0) + if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0) goto error; - /* Reopen the file and dataset */ - if((file = H5Fopen(FILE_NAME5, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) + if(H5Dclose(dataset) < 0) goto error; - if((dataset = H5Dopen(file, DATASETNAME, H5P_DEFAULT)) < 0) + if((dataset = H5Dopen(file, DATASETNAME1, H5P_DEFAULT)) < 0) goto error; /* @@ -237,17 +275,13 @@ test_direct_chunk_write (void) if(outbuf) free(outbuf); - if(H5Dclose(dataset) < 0) + if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0) goto error; - if(H5Fclose(file) < 0) - goto error; - - /* Reopen the file and dataset */ - if((file = H5Fopen(FILE_NAME5, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) + if(H5Dclose(dataset) < 0) goto error; - if((dataset = H5Dopen(file, DATASETNAME, H5P_DEFAULT)) < 0) + if((dataset = H5Dopen(file, DATASETNAME1, H5P_DEFAULT)) < 0) goto error; /* Read the chunk back */ @@ -274,9 +308,7 @@ test_direct_chunk_write (void) H5Sclose(dataspace); H5Pclose(cparms); H5Pclose(dxpl); - H5Fclose(file); - /* h5_cleanup(FILE_NAME5, fapl); */ PASSED(); return 0; @@ -287,7 +319,6 @@ error: H5Sclose(dataspace); H5Pclose(cparms); H5Pclose(dxpl); - H5Fclose(file); } H5E_END_TRY; if(outbuf) @@ -297,15 +328,795 @@ error: } /*------------------------------------------------------------------------- -* the main program -*------------------------------------------------------------------------- -*/ + * Function: test_skip_compress_write1 + * + * Purpose: Test skipping compression filter when it is the only filter + * for the dataset + * + * Return: Success: 0 + * + * Failure: 1 + * + * Programmer: Raymond Lu + * 30 November 2012 + * + *------------------------------------------------------------------------- + */ +static int +test_skip_compress_write1(hid_t file) +{ + hid_t dataspace = -1, dataset = -1; + hid_t mem_space = -1; + hid_t cparms = -1, dxpl = -1; + hsize_t dims[2] = {NX, NY}; + hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED}; + hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY}; + herr_t status; + int i, j, n; + + unsigned filter_mask = 0; + int direct_buf[CHUNK_NX][CHUNK_NY]; + int check_chunk[CHUNK_NX][CHUNK_NY]; + hsize_t offset[2] = {0, 0}; + size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int); + int aggression = 9; /* Compression aggression setting */ + + hsize_t start[2]; /* Start of hyperslab */ + hsize_t stride[2]; /* Stride of hyperslab */ + hsize_t count[2]; /* Block count */ + hsize_t block[2]; /* Block sizes */ + + TESTING("skipping compression filter for H5DOwrite_chunk"); + + /* + * Create the data space with unlimited dimensions. + */ + if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0) + goto error; + + if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0) + goto error; + + /* + * Modify dataset creation properties, i.e. enable chunking and compression + */ + if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0) + goto error; + + if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0) + goto error; + + if((status = H5Pset_deflate( cparms, (unsigned ) aggression)) < 0) + goto error; + + /* + * Create a new dataset within the file using cparms + * creation properties. + */ + if((dataset = H5Dcreate2(file, DATASETNAME2, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, + cparms, H5P_DEFAULT)) < 0) + goto error; + + if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0) + goto error; + + /* Initialize data for one chunk */ + for(i = n = 0; i < CHUNK_NX; i++) + for(j = 0; j < CHUNK_NY; j++) { + direct_buf[i][j] = n++; + } + + /* write the uncompressed chunk data repeatedly to dataset, using the direct writing function. + * Indicate skipping the compression filter. */ + offset[0] = CHUNK_NX; + offset[1] = CHUNK_NY; + + filter_mask = 0x00000001; + + if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) < 0) + goto error; + + if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0) + goto error; + + if(H5Dclose(dataset) < 0) + goto error; + + if((dataset = H5Dopen(file, DATASETNAME2, H5P_DEFAULT)) < 0) + goto error; + + /* + * Select hyperslab for the chunk just written in the file + */ + start[0] = CHUNK_NX; start[1] = CHUNK_NY; + stride[0] = 1; stride[1] = 1; + count[0] = 1; count[1] = 1; + block[0] = CHUNK_NX; block[1] = CHUNK_NY; + if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0) + goto error; + + /* Read the chunk back */ + if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0) + goto error; + + /* Check that the values read are the same as the values written */ + for(i = 0; i < CHUNK_NX; i++) { + for(j = 0; j < CHUNK_NY; j++) { + if(direct_buf[i][j] != check_chunk[i][j]) { + printf(" 1. Read different values than written."); + printf(" At index %d,%d\n", i, j); + printf(" direct_buf=%d, check_chunk=%d\n", direct_buf[i][j], check_chunk[i][j]); + goto error; + } + } + } + + /* + * Close/release resources. + */ + H5Dclose(dataset); + H5Sclose(mem_space); + H5Sclose(dataspace); + H5Pclose(cparms); + H5Pclose(dxpl); + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY { + H5Dclose(dataset); + H5Sclose(mem_space); + H5Sclose(dataspace); + H5Pclose(cparms); + H5Pclose(dxpl); + } H5E_END_TRY; + + return 1; +} + +/*------------------------------------------------------------------------- + * Function: filter_bogus1 + * + * Purpose: A bogus filte that adds ADD_ON to the original value + * + * Return: Success: Data chunk size + * + * Programmer: Raymond Lu + * 30 November 2012 + * + *------------------------------------------------------------------------- + */ +static size_t +filter_bogus1(unsigned int flags, size_t UNUSED cd_nelmts, + const unsigned int UNUSED *cd_values, size_t nbytes, + size_t *buf_size, void **buf) +{ + int *int_ptr=(int *)*buf; /* Pointer to the data values */ + size_t buf_left=*buf_size; /* Amount of data buffer left to process */ + + if(flags & H5Z_FLAG_REVERSE) { /* read */ + /* Substract the "add on" value to all the data values */ + while(buf_left>0) { + *int_ptr++ -= (int)ADD_ON; + buf_left -= sizeof(int); + } /* end while */ + } /* end if */ + else { /* write */ + /* Add the "add on" value to all the data values */ + while(buf_left>0) { + *int_ptr++ += (int)ADD_ON; + buf_left -= sizeof(int); + } /* end while */ + } /* end else */ + + return nbytes; +} + +/*------------------------------------------------------------------------- + * Function: filter_bogus2 + * + * Purpose: A bogus filter that multiplies the original value by FACTOR. + * + * Return: Success: Data chunk size + * + * Programmer: Raymond Lu + * 30 November 2012 + *------------------------------------------------------------------------- + */ +static size_t +filter_bogus2(unsigned int flags, size_t UNUSED cd_nelmts, + const unsigned int UNUSED *cd_values, size_t nbytes, + size_t *buf_size, void **buf) +{ + int *int_ptr=(int *)*buf; /* Pointer to the data values */ + size_t buf_left=*buf_size; /* Amount of data buffer left to process */ + + if(flags & H5Z_FLAG_REVERSE) { /* read */ + /* Substract the "add on" value to all the data values */ + while(buf_left>0) { + *int_ptr++ /= (int)FACTOR; + buf_left -= sizeof(int); + } /* end while */ + } /* end if */ + else { /* write */ + /* Add the "add on" value to all the data values */ + while(buf_left>0) { + *int_ptr++ *= (int)FACTOR; + buf_left -= sizeof(int); + } /* end while */ + } /* end else */ + + return nbytes; +} + +/*------------------------------------------------------------------------- + * Function: test_skip_compress_write2 + * + * Purpose: Test skipping compression filter when there are three filters + * for the dataset + * + * Return: Success: 0 + * + * Failure: 1 + * + * Programmer: Raymond Lu + * 30 November 2012 + * + *------------------------------------------------------------------------- + */ +static int +test_skip_compress_write2(hid_t file) +{ + hid_t dataspace = -1, dataset = -1; + hid_t mem_space = -1; + hid_t cparms = -1, dxpl = -1; + hsize_t dims[2] = {NX, NY}; + hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED}; + hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY}; + herr_t status; + int i, j, n; + + unsigned filter_mask = 0; + int origin_direct_buf[CHUNK_NX][CHUNK_NY]; + int direct_buf[CHUNK_NX][CHUNK_NY]; + int check_chunk[CHUNK_NX][CHUNK_NY]; + hsize_t offset[2] = {0, 0}; + size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int); + int aggression = 9; /* Compression aggression setting */ + + hsize_t start[2]; /* Start of hyperslab */ + hsize_t stride[2]; /* Stride of hyperslab */ + hsize_t count[2]; /* Block count */ + hsize_t block[2]; /* Block sizes */ + + TESTING("skipping compression filters but keep two other filters"); + + /* + * Create the data space with unlimited dimensions. + */ + if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0) + goto error; + + if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0) + goto error; + + /* + * Modify dataset creation properties, i.e. enable chunking and compression. + * The order of filters is bogus 1 + deflate + bogus 2. + */ + if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0) + goto error; + + if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0) + goto error; + + /* Register and enable first bogus filter */ + if(H5Zregister (H5Z_BOGUS1) < 0) + goto error; + + if(H5Pset_filter(cparms, H5Z_FILTER_BOGUS1, 0, (size_t)0, NULL) < 0) + goto error; + + /* Enable compression filter */ + if((status = H5Pset_deflate( cparms, (unsigned) aggression)) < 0) + goto error; + + /* Register and enable second bogus filter */ + if(H5Zregister (H5Z_BOGUS2) < 0) + goto error; + + if(H5Pset_filter(cparms, H5Z_FILTER_BOGUS2, 0, (size_t)0, NULL) < 0) + goto error; + + /* + * Create a new dataset within the file using cparms + * creation properties. + */ + if((dataset = H5Dcreate2(file, DATASETNAME3, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, + cparms, H5P_DEFAULT)) < 0) + goto error; + + if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0) + goto error; + + /* Initialize data for one chunk. Apply operations of two bogus filters to the chunk */ + for(i = n = 0; i < CHUNK_NX; i++) + for(j = 0; j < CHUNK_NY; j++) { + origin_direct_buf[i][j] = n++; + direct_buf[i][j] = (origin_direct_buf[i][j] + ADD_ON) * FACTOR; + } + + /* write the uncompressed chunk data repeatedly to dataset, using the direct writing function. + * Indicate skipping the compression filter but keep the other two bogus filters */ + offset[0] = CHUNK_NX; + offset[1] = CHUNK_NY; + + /* compression filter is the middle one to be skipped */ + filter_mask = 0x00000002; + + if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) < 0) + goto error; + + if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0) + goto error; + + if(H5Dclose(dataset) < 0) + goto error; + + if((dataset = H5Dopen(file, DATASETNAME3, H5P_DEFAULT)) < 0) + goto error; + + /* + * Select hyperslab for one chunk in the file + */ + start[0] = CHUNK_NX; start[1] = CHUNK_NY; + stride[0] = 1; stride[1] = 1; + count[0] = 1; count[1] = 1; + block[0] = CHUNK_NX; block[1] = CHUNK_NY; + if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0) + goto error; + + /* Read the chunk back */ + if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0) + goto error; + + /* Check that the values read are the same as the values written */ + for(i = 0; i < CHUNK_NX; i++) { + for(j = 0; j < CHUNK_NY; j++) { + if(origin_direct_buf[i][j] != check_chunk[i][j]) { + printf(" 1. Read different values than written."); + printf(" At index %d,%d\n", i, j); + printf(" origin_direct_buf=%d, check_chunk=%d\n", origin_direct_buf[i][j], check_chunk[i][j]); + goto error; + } + } + } + + /* + * Close/release resources. + */ + H5Dclose(dataset); + H5Sclose(mem_space); + H5Sclose(dataspace); + H5Pclose(cparms); + H5Pclose(dxpl); + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY { + H5Dclose(dataset); + H5Sclose(mem_space); + H5Sclose(dataspace); + H5Pclose(cparms); + H5Pclose(dxpl); + } H5E_END_TRY; + + return 1; +} + +/*------------------------------------------------------------------------- + * Function: test_data_conv + * + * Purpose: Test data conversion + * + * Return: Success: 0 + * + * Failure: 1 + * + * Programmer: Raymond Lu + * 30 November 2012 + * + *------------------------------------------------------------------------- + */ +static int +test_data_conv(hid_t file) +{ + typedef struct { + int a, b, c[4], d, e; + } src_type_t; + typedef struct { + int a, c[4], e; + } dst_type_t; + + hid_t dataspace = -1, dataset = -1; + hid_t mem_space = -1; + hid_t cparms = -1, dxpl = -1; + hsize_t dims[2] = {NX, NY}; + hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED}; + hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY}; + herr_t status; + int i, j, n; + const hsize_t four = 4; + hid_t st=-1, dt=-1; + hid_t array_dt; + + unsigned filter_mask = 0; + src_type_t direct_buf[CHUNK_NX][CHUNK_NY]; + dst_type_t check_chunk[CHUNK_NX][CHUNK_NY]; + hsize_t offset[2] = {0, 0}; + size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(src_type_t); + + hsize_t start[2]; /* Start of hyperslab */ + hsize_t stride[2]; /* Stride of hyperslab */ + hsize_t count[2]; /* Block count */ + hsize_t block[2]; /* Block sizes */ + + TESTING("data conversion for H5DOwrite_chunk"); + + /* + * Create the data space with unlimited dimensions. + */ + if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0) + goto error; + + if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0) + goto error; + + /* + * Modify dataset creation properties, i.e. enable chunking + */ + if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0) + goto error; + + if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0) + goto error; + + /* Build hdf5 datatypes */ + array_dt = H5Tarray_create2(H5T_NATIVE_INT, 1, &four); + if((st = H5Tcreate(H5T_COMPOUND, sizeof(src_type_t))) < 0 || + H5Tinsert(st, "a", HOFFSET(src_type_t, a), H5T_NATIVE_INT) < 0 || + H5Tinsert(st, "b", HOFFSET(src_type_t, b), H5T_NATIVE_INT) < 0 || + H5Tinsert(st, "c", HOFFSET(src_type_t, c), array_dt) < 0 || + H5Tinsert(st, "d", HOFFSET(src_type_t, d), H5T_NATIVE_INT) < 0 || + H5Tinsert(st, "e", HOFFSET(src_type_t, e), H5T_NATIVE_INT) < 0) + goto error; + + if(H5Tclose(array_dt) < 0) + goto error; + + array_dt = H5Tarray_create2(H5T_NATIVE_INT, 1, &four); + if((dt = H5Tcreate(H5T_COMPOUND, sizeof(dst_type_t))) < 0 || + H5Tinsert(dt, "a", HOFFSET(dst_type_t, a), H5T_NATIVE_INT) < 0 || + H5Tinsert(dt, "c", HOFFSET(dst_type_t, c), array_dt) < 0 || + H5Tinsert(dt, "e", HOFFSET(dst_type_t, e), H5T_NATIVE_INT) < 0) + goto error; + + if(H5Tclose(array_dt) < 0) + goto error; + + /* + * Create a new dataset within the file using cparms + * creation properties. + */ + if((dataset = H5Dcreate2(file, DATASETNAME4, st, dataspace, H5P_DEFAULT, + cparms, H5P_DEFAULT)) < 0) + goto error; + + if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0) + goto error; + + /* Initialize data for one chunk */ + for(i = n = 0; i < CHUNK_NX; i++) { + for(j = 0; j < CHUNK_NY; j++) { + (direct_buf[i][j]).a = i*j+0; + (direct_buf[i][j]).b = i*j+1; + (direct_buf[i][j]).c[0] = i*j+2; + (direct_buf[i][j]).c[1] = i*j+3; + (direct_buf[i][j]).c[2] = i*j+4; + (direct_buf[i][j]).c[3] = i*j+5; + (direct_buf[i][j]).d = i*j+6; + (direct_buf[i][j]).e = i*j+7; + } + } + + /* write the chunk data to dataset, using the direct writing function. + * There should be no data conversion involved. */ + offset[0] = CHUNK_NX; + offset[1] = CHUNK_NY; + + if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) < 0) + goto error; + + if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0) + goto error; + + if(H5Dclose(dataset) < 0) + goto error; + + if((dataset = H5Dopen(file, DATASETNAME4, H5P_DEFAULT)) < 0) + goto error; + + /* + * Select hyperslab for the chunk just written in the file + */ + start[0] = CHUNK_NX; start[1] = CHUNK_NY; + stride[0] = 1; stride[1] = 1; + count[0] = 1; count[1] = 1; + block[0] = CHUNK_NX; block[1] = CHUNK_NY; + if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0) + goto error; + + /* Read the chunk back. Data should be converted */ + if((status = H5Dread(dataset, dt, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0) + goto error; + + /* Check that the values read are the same as the values written */ + for(i = 0; i < CHUNK_NX; i++) { + for(j = 0; j < CHUNK_NY; j++) { + if ((direct_buf[i][j]).a != (check_chunk[i][j]).a || + (direct_buf[i][j]).c[0] != (check_chunk[i][j]).c[0] || + (direct_buf[i][j]).c[1] != (check_chunk[i][j]).c[1] || + (direct_buf[i][j]).c[2] != (check_chunk[i][j]).c[2] || + (direct_buf[i][j]).c[3] != (check_chunk[i][j]).c[3] || + (direct_buf[i][j]).e != (check_chunk[i][j]).e) { + printf(" 1. Read different values than written."); + printf(" At index %d,%d\n", i, j); + printf(" src={a=%d, b=%d, c=[%d,%d,%d,%d], d=%d, e=%d\n", + (direct_buf[i][j]).a, (direct_buf[i][j]).b, (direct_buf[i][j]).c[0], (direct_buf[i][j]).c[1], + (direct_buf[i][j]).c[2], (direct_buf[i][j]).c[3], (direct_buf[i][j]).d, (direct_buf[i][j]).e); + printf(" dst={a=%d, c=[%d,%d,%d,%d], e=%d\n", + (check_chunk[i][j]).a, (check_chunk[i][j]).c[0], (check_chunk[i][j]).c[1], (check_chunk[i][j]).c[2], + (check_chunk[i][j]).c[3], (check_chunk[i][j]).e); + + goto error; + } + } + } + + /* + * Close/release resources. + */ + H5Dclose(dataset); + H5Sclose(mem_space); + H5Sclose(dataspace); + H5Pclose(cparms); + H5Pclose(dxpl); + H5Tclose(st); + H5Tclose(dt); + + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY { + H5Dclose(dataset); + H5Sclose(mem_space); + H5Sclose(dataspace); + H5Pclose(cparms); + H5Pclose(dxpl); + H5Tclose(st); + H5Tclose(dt); + } H5E_END_TRY; + + return 1; +} + +/*------------------------------------------------------------------------- + * Function: test_invalid_parameters + * + * Purpose: Test invalid parameters for H5DOwrite_chunk + * + * Return: Success: 0 + * + * Failure: 1 + * + * Programmer: Raymond Lu + * 30 November 2012 + * + *------------------------------------------------------------------------- + */ +static int +test_invalid_parameters(hid_t file) +{ + hid_t dataspace = -1, dataset = -1; + hid_t mem_space = -1; + hid_t cparms = -1, dxpl = -1; + hsize_t dims[2] = {NX, NY}; + hsize_t chunk_dims[2] ={CHUNK_NX, CHUNK_NY}; + herr_t status; + int i, j, n; + + unsigned filter_mask = 0; + int direct_buf[CHUNK_NX][CHUNK_NY]; + int check_chunk[CHUNK_NX][CHUNK_NY]; + hsize_t offset[2] = {0, 0}; + size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int); + int aggression = 9; /* Compression aggression setting */ + + TESTING("invalid parameters for H5DOwrite_chunk"); + + /* + * Create the data space with unlimited dimensions. + */ + if((dataspace = H5Screate_simple(RANK, dims, NULL)) < 0) + goto error; + + if((mem_space = H5Screate_simple(RANK, chunk_dims, NULL)) < 0) + goto error; + + /* + * Modify dataset creation properties + */ + if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0) + goto error; + + /* + * Create a new contiguous dataset to verify H5DOwrite_chunk doesn't work + */ + if((dataset = H5Dcreate2(file, DATASETNAME5, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, + cparms, H5P_DEFAULT)) < 0) + goto error; + + if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0) + goto error; + + /* Initialize data for one chunk */ + for(i = n = 0; i < CHUNK_NX; i++) + for(j = 0; j < CHUNK_NY; j++) { + direct_buf[i][j] = n++; + } + + /* Try to write the chunk data to contiguous dataset. It should fail */ + offset[0] = CHUNK_NX; + offset[1] = CHUNK_NY; + + H5E_BEGIN_TRY { + if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL) + goto error; + } H5E_END_TRY; + + if(H5Dclose(dataset) < 0) + goto error; + + /* Create a chunked dataset with compression filter */ + if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0) + goto error; + + if((status = H5Pset_deflate( cparms, (unsigned ) aggression)) < 0) + goto error; + + /* + * Create a new dataset within the file using cparms + * creation properties. + */ + if((dataset = H5Dcreate2(file, DATASETNAME6, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, + cparms, H5P_DEFAULT)) < 0) + goto error; + + /* Check invalid dataset ID */ + H5E_BEGIN_TRY { + if((status = H5DOwrite_chunk(-1, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL) + goto error; + } H5E_END_TRY; + + /* Check invalid DXPL ID */ + H5E_BEGIN_TRY { + if((status = H5DOwrite_chunk(dataset, -1, filter_mask, offset, buf_size, direct_buf)) != FAIL) + goto error; + } H5E_END_TRY; + + /* Check invalid OFFSET */ + H5E_BEGIN_TRY { + if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, NULL, buf_size, direct_buf)) != FAIL) + goto error; + } H5E_END_TRY; + + /* Check when OFFSET is out of dataset range */ + offset[0] = NX + 1; + offset[1] = NY; + H5E_BEGIN_TRY { + if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL) + goto error; + } H5E_END_TRY; + + /* Check when OFFSET is not on chunk boundary */ + offset[0] = CHUNK_NX; + offset[1] = CHUNK_NY + 1; + H5E_BEGIN_TRY { + if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL) + goto error; + } H5E_END_TRY; + + /* Check invalid buffer size */ + offset[0] = CHUNK_NX; + offset[1] = CHUNK_NY; + buf_size = 0; + H5E_BEGIN_TRY { + if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL) + goto error; + } H5E_END_TRY; + + /* Check invalid data buffer */ + buf_size = CHUNK_NX*CHUNK_NY*sizeof(int); + H5E_BEGIN_TRY { + if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, NULL)) != FAIL) + goto error; + } H5E_END_TRY; + + if(H5Dclose(dataset) < 0) + goto error; + + /* + * Close/release resources. + */ + H5Sclose(mem_space); + H5Sclose(dataspace); + H5Pclose(cparms); + H5Pclose(dxpl); + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY { + H5Dclose(dataset); + H5Sclose(mem_space); + H5Sclose(dataspace); + H5Pclose(cparms); + H5Pclose(dxpl); + } H5E_END_TRY; + + return 1; +} + +/*------------------------------------------------------------------------- + * Function: Main function + * + * Purpose: Test direct chunk write function H5DOwrite_chunk + * + * Return: Success: 0 + * + * Failure: 1 + * + * Programmer: Raymond Lu + * 30 November 2012 + * + *------------------------------------------------------------------------- + */ int main( void ) { - int nerrors=0; + hid_t file_id; + int nerrors=0; + + /* + * Create a new file. If file exists its contents will be overwritten. + */ + if((file_id = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto error; /* Test direct chunk write */ - nerrors += test_direct_chunk_write(); + nerrors += test_direct_chunk_write(file_id); + nerrors += test_skip_compress_write1(file_id); + nerrors += test_skip_compress_write2(file_id); + nerrors += test_data_conv(file_id); + nerrors += test_invalid_parameters(file_id); + + if(H5Fclose(file_id) < 0) + goto error; /* check for errors */ if (nerrors) diff --git a/perform/dectris_perf.c b/perform/dectris_perf.c index abaa92f..4d2284d 100644 --- a/perform/dectris_perf.c +++ b/perform/dectris_perf.c @@ -53,11 +53,11 @@ const char *FILENAME[] = { #define REG_NO_COMPRESS_DSET "reg_no_compress_dset" #define RANK 3 #define NX 100 -#define NY 1000 -#define NZ 250 +#define NY 2000 +#define NZ 3000 #define CHUNK_NX 1 -#define CHUNK_NY 1000 -#define CHUNK_NZ 250 +#define CHUNK_NY 2000 +#define CHUNK_NZ 3000 #define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s))*1.001)+12) char filename[1024]; diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 3b96fa0..c307b8c 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -283,7 +283,7 @@ H5FL_BLK_DEFINE_STATIC(chunk); /*------------------------------------------------------------------------- - * Function: H5D__direct_write + * Function: H5D__chunk_direct_write * * Purpose: Internal routine for H5PSIdirect_write to write a chunk * directly into the file. @@ -310,7 +310,6 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, hsiz H5FD_t *lf; herr_t ret_value = SUCCEED; /* Return value */ - /*FUNC_ENTER_PACKAGE*/ FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL) /* Allocate data space and initialize it if it hasn't been. */ @@ -382,7 +381,6 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, hsiz done: - /*FUNC_LEAVE_NOAPI(ret_value)*/ FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL) } diff --git a/src/H5Dio.c b/src/H5Dio.c index e5a9ccc..095c8a5 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -140,6 +140,10 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") if(NULL == dset->oloc.file) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + + if(mem_space_id < 0 || file_space_id < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space") + if(H5S_ALL != mem_space_id) { if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space") @@ -252,10 +256,10 @@ H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, { H5D_t *dset = NULL; H5P_genplist_t *plist; /* Property list pointer */ - htri_t direct_write = FALSE; + hbool_t direct_write = FALSE; herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI(FAIL) + FUNC_ENTER_STATIC /* check arguments */ if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) @@ -283,14 +287,13 @@ H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hsize_t *direct_offset; size_t direct_datasize = 0; int ndims = 0; - hsize_t *dims = NULL; - hsize_t *internal_offset = NULL; + hsize_t dims[H5O_LAYOUT_NDIMS]; + hsize_t internal_offset[H5O_LAYOUT_NDIMS]; int i; if(H5D_CHUNKED != dset->shared->layout.type) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset") - if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &direct_filters) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting filter info for direct chunk write") @@ -302,14 +305,7 @@ H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, /* The library's chunking code requires the offset terminates with a zero. So transfer the * offset array to an internal offset array */ - ndims = (int)H5S_GET_EXTENT_NDIMS(dset->shared->space); - if(NULL == (dims = (hsize_t *)H5MM_malloc(ndims*sizeof(hsize_t)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for dimensions") - - if(NULL == (internal_offset = (hsize_t *)H5MM_malloc((ndims+1)*sizeof(hsize_t)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for offset") - - if(H5S_get_simple_extent_dims(dset->shared->space, dims, NULL) < 0) + if((ndims = H5S_get_simple_extent_dims(dset->shared->space, dims, NULL)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve dataspace extent dims") for(i=0; i