diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 3 | ||||
| -rw-r--r-- | src/H5D.c | 13 | ||||
| -rw-r--r-- | src/H5Sall.c | 15 | ||||
| -rw-r--r-- | src/H5Smpio.c | 17 | ||||
| -rw-r--r-- | src/H5Spkg.h | 12 | ||||
| -rw-r--r-- | src/H5Sprivate.h | 28 | ||||
| -rw-r--r-- | test/tmisc.c | 81 |
7 files changed, 134 insertions, 35 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 6d5f50c..da49eb0 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -106,6 +106,9 @@ Library * Fixed bug where a preempted chunk in the chunk data could still be used by an internal pointer and cause an assertion failure or core dump. QAK - 2/13/02 + * Fixed bug where non-zero fill-value was not being read correctly from + certain chunked datasets when using an "all" or contiguous hyperslab + selection. QAK - 2/14/02 Configuration ------------- @@ -2238,11 +2238,13 @@ printf("%s: check 1.1, \n",FUNC); #endif if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get pipeline"); + if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill value"); if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get external file list"); status = (sconv->read)(dataset->ent.file, &(dataset->layout), &pline, - &efl, H5T_get_size(dataset->type), file_space, - mem_space, dxpl_id, buf/*out*/, &must_convert); + &fill, &efl, H5T_get_size(dataset->type), file_space, + mem_space, dxpl_id, buf/*out*/, &must_convert); /* Supports only no conversion, type or space, for now. */ if (status<0) @@ -2725,11 +2727,14 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #endif if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get pipeline"); + if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill value"); if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get external file list"); status = (sconv->write)(dataset->ent.file, &(dataset->layout), &pline, - &efl, H5T_get_size(dataset->type), file_space, - mem_space, dxpl_id, buf/*out*/, &must_convert); + &fill, &efl, H5T_get_size(dataset->type), file_space, + mem_space, dxpl_id, buf/*out*/, &must_convert); + /* Supports only no conversion, type or space, for now. */ if (status<0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed"); diff --git a/src/H5Sall.c b/src/H5Sall.c index fed5d18..76fe0d6 100644 --- a/src/H5Sall.c +++ b/src/H5Sall.c @@ -393,6 +393,7 @@ H5S_all_mscat (const void *tconv_buf, size_t elmt_size, */ herr_t H5S_all_read(H5F_t *f, const H5O_layout_t *layout, const H5O_pline_t *pline, + const struct H5O_fill_t *fill, const H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, void *_buf/*out*/, hbool_t *must_convert/*out*/) @@ -623,7 +624,7 @@ for (u=0; u<=mem_space->extent.u.simple.rank; u++) printf("file_offset[%u]=%lu\n",u,(unsigned long)file_offset[u]); #endif /* QAK */ /* Read data from the file */ - if (H5F_arr_read(f, dxpl_id, layout, pline, NULL, efl, size, + if (H5F_arr_read(f, dxpl_id, layout, pline, fill, efl, size, size, mem_offset, file_offset, buf/*out*/)<0) { HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read data from the file"); @@ -661,10 +662,12 @@ done: */ herr_t H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout, - const H5O_pline_t *pline, const H5O_efl_t *efl, - size_t elmt_size, const H5S_t *file_space, - const H5S_t *mem_space, hid_t dxpl_id, const void *_buf, - hbool_t *must_convert/*out*/) + const H5O_pline_t *pline, + const struct H5O_fill_t *fill, + const H5O_efl_t *efl, + size_t elmt_size, const H5S_t *file_space, + const H5S_t *mem_space, hid_t dxpl_id, const void *_buf, + hbool_t *must_convert/*out*/) { H5S_hyper_span_t *file_span=NULL,*mem_span=NULL; /* Hyperslab span node */ const char *buf=(const char*)_buf; /* Get pointer to buffer */ @@ -880,7 +883,7 @@ H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout, } /* end if */ /* Write data to the file */ - if (H5F_arr_write(f, dxpl_id, layout, pline, NULL, efl, size, + if (H5F_arr_write(f, dxpl_id, layout, pline, fill, efl, size, size, mem_offset, file_offset, buf)<0) { HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write data to the file"); diff --git a/src/H5Smpio.c b/src/H5Smpio.c index e6cc074..ab15ad6 100644 --- a/src/H5Smpio.c +++ b/src/H5Smpio.c @@ -551,6 +551,7 @@ H5S_mpio_space_type( const H5S_t *space, const size_t elmt_size, herr_t H5S_mpio_spaces_xfer(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t UNUSED *pline, + const struct H5O_fill_t UNUSED *fill, const struct H5O_efl_t UNUSED *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, void *buf /*out*/, @@ -720,6 +721,7 @@ done: herr_t H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, void *buf/*out*/, @@ -729,7 +731,7 @@ H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout, FUNC_ENTER (H5S_mpio_spaces_read, FAIL); - ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size, + ret_value = H5S_mpio_spaces_xfer(f, layout, pline, fill, efl, elmt_size, file_space, mem_space, dxpl_id, buf, must_convert/*out*/, 0/*read*/); @@ -755,17 +757,18 @@ H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout, */ herr_t H5S_mpio_spaces_write(H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_pline_t *pline, - const struct H5O_efl_t *efl, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - hid_t dxpl_id, const void *buf, - hbool_t *must_convert/*out*/) + const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, const H5S_t *mem_space, + hid_t dxpl_id, const void *buf, + hbool_t *must_convert/*out*/) { herr_t ret_value = FAIL; FUNC_ENTER (H5S_mpio_spaces_write, FAIL); - ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size, + ret_value = H5S_mpio_spaces_xfer(f, layout, pline, fill, efl, elmt_size, file_space, mem_space, dxpl_id, (void*)buf, must_convert/*out*/, 1/*write*/); diff --git a/src/H5Spkg.h b/src/H5Spkg.h index 9e44930..7e3da29 100644 --- a/src/H5Spkg.h +++ b/src/H5Spkg.h @@ -146,16 +146,18 @@ __DLL__ herr_t H5S_all_select_deserialize(H5S_t *space, const uint8_t *buf); __DLL__ herr_t H5S_all_bounds(H5S_t *space, hsize_t *start, hsize_t *end); __DLL__ herr_t H5S_all_read(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, void *buf/*out*/, hbool_t *must_convert/*out*/); __DLL__ herr_t H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_pline_t *pline, - const struct H5O_efl_t *efl, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - hid_t dxpl_id, const void *buf, - hbool_t *must_convert/*out*/); + const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, const H5S_t *mem_space, + hid_t dxpl_id, const void *buf, + hbool_t *must_convert/*out*/); __DLL__ herr_t H5S_all_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, void *operator_data); diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index 42986d7..e024502 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -142,6 +142,7 @@ typedef struct H5S_conv_t { /* Read from file to application w/o intermediate scratch buffer */ herr_t (*read)(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, void *buf/*out*/, @@ -150,11 +151,12 @@ typedef struct H5S_conv_t { /* Write directly from app buffer to file */ herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_pline_t *pline, - const struct H5O_efl_t *efl, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - hid_t dxpl_id, const void *buf, - hbool_t *must_convert/*out*/); + const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, const H5S_t *mem_space, + hid_t dxpl_id, const void *buf, + hbool_t *must_convert/*out*/); #ifdef H5S_DEBUG struct { @@ -227,6 +229,7 @@ __DLL__ herr_t H5S_sel_iter_release(const H5S_t *space, __DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, @@ -235,13 +238,14 @@ __DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f, /* MPI-IO function to write directly from app buffer to file rky980813 */ __DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f, - const struct H5O_layout_t *layout, - const struct H5O_pline_t *pline, - const struct H5O_efl_t *efl, - size_t elmt_size, const H5S_t *file_space, - const H5S_t *mem_space, hid_t dxpl_id, - const void *buf, - hbool_t *must_convert /*out*/ ); + const struct H5O_layout_t *layout, + const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, + const struct H5O_efl_t *efl, + size_t elmt_size, const H5S_t *file_space, + const H5S_t *mem_space, hid_t dxpl_id, + const void *buf, + hbool_t *must_convert /*out*/ ); #ifndef _H5S_IN_H5S_C /* Global var whose value comes from environment variable */ __DLLVAR__ hbool_t H5_mpi_opt_types_g; diff --git a/test/tmisc.c b/test/tmisc.c index b5682c5..6980fc3 100644 --- a/test/tmisc.c +++ b/test/tmisc.c @@ -41,6 +41,16 @@ typedef struct { char *string; } misc2_struct; +/* Definitions for misc. test #3 */ +#define MISC3_FILE "tmisc3.h5" +#define MISC3_RANK 2 +#define MISC3_DIM1 6 +#define MISC3_DIM2 6 +#define MISC3_CHUNK_DIM1 2 +#define MISC3_CHUNK_DIM2 2 +#define MISC3_FILL_VALUE 2 +#define MISC3_DSET_NAME "/chunked" + /**************************************************************** ** ** test_misc1(): test unlinking a dataset from a group and immediately @@ -252,7 +262,7 @@ static void test_misc2_read_attribute(const char *filename, const char *att_name free(data_check.string); ret = H5Aclose(att); - CHECK(ret, FAIL, "HAclose"); + CHECK(ret, FAIL, "H5Aclose"); ret = H5Tclose(type); CHECK(ret, FAIL, "H5Tclose"); @@ -285,6 +295,73 @@ test_misc2(void) /**************************************************************** ** +** test_misc3(): Test reading from chunked dataset with non-zero +** fill value +** +****************************************************************/ +static void +test_misc3(void) +{ + hid_t file, dataspace, dataset, dcpl; + int rank=MISC3_RANK; + hsize_t dims[MISC3_RANK]={MISC3_DIM1,MISC3_DIM2}; + hsize_t chunk_dims[MISC3_RANK]={MISC3_CHUNK_DIM1,MISC3_CHUNK_DIM2}; + int fill=MISC3_FILL_VALUE; + int read_buf[MISC3_DIM1][MISC3_DIM2]; + int i,j; + herr_t ret; + + /* Output message about test being performed */ + MESSAGE(5, ("Testing reading from chunked dataset with non-zero fill-value\n")); + + file = H5Fcreate(MISC3_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + CHECK(file, FAIL, "H5Fcreate"); + + /* Create a simple dataspace */ + dataspace = H5Screate_simple(rank,dims,NULL); + CHECK(dataspace, FAIL, "H5Screate_simple"); + + /* Create a dataset creation property list */ + dcpl = H5Pcreate(H5P_DATASET_CREATE); + CHECK(dcpl, FAIL, "H5Pcreate"); + + /* Set the chunk information */ + ret = H5Pset_chunk(dcpl,rank,chunk_dims); + CHECK(dcpl, FAIL, "H5Pset_chunk"); + + /* Set the fill-value information */ + ret = H5Pset_fill_value(dcpl,H5T_NATIVE_INT,&fill); + CHECK(dcpl, FAIL, "H5Pset_fill_value"); + + /* Create the dataset */ + dataset = H5Dcreate(file, MISC3_DSET_NAME, H5T_NATIVE_INT, dataspace, dcpl); + CHECK(dataset, FAIL, "H5Dcreate"); + + /* Read from the dataset (should be fill-values) */ + ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &read_buf); + CHECK(ret, FAIL, "H5Dread"); + + for(i=0; i<MISC3_DIM1; i++) + for(j=0; j<MISC3_DIM2; j++) + VERIFY(read_buf[i][j],fill,"H5Dread"); + + /* Release resources */ + ret = H5Pclose(dcpl); + CHECK(ret, FAIL, "H5Pclose"); + + ret = H5Sclose(dataspace); + CHECK(ret, FAIL, "H5Sclose"); + + ret = H5Dclose(dataset); + CHECK(ret, FAIL, "H5Dclose"); + + ret = H5Fclose(file); + CHECK(ret, FAIL, "H5Fclose"); +} /* end test_misc3() */ + + +/**************************************************************** +** ** test_misc(): Main misc. test routine. ** ****************************************************************/ @@ -296,6 +373,7 @@ test_misc(void) test_misc1(); /* Test unlinking a dataset & immediately re-using name */ test_misc2(); /* Test storing a VL-derived datatype in two different files */ + test_misc3(); /* Test reading from chunked dataset with non-zero fill value */ } /* test_misc() */ @@ -320,4 +398,5 @@ cleanup_misc(void) remove(MISC1_FILE); remove(MISC2_FILE_1); remove(MISC2_FILE_2); + remove(MISC3_FILE); } |