diff options
| -rw-r--r-- | MANIFEST | 1 | ||||
| -rw-r--r-- | Makefile.in | 2 | ||||
| -rw-r--r-- | README | 2 | ||||
| -rw-r--r-- | src/H5D.c | 254 | ||||
| -rw-r--r-- | src/H5Distore.c | 16 | ||||
| -rw-r--r-- | src/H5Fistore.c | 16 | ||||
| -rw-r--r-- | src/H5Fmpio.c | 13 | ||||
| -rw-r--r-- | test/Makefile.in | 10 | ||||
| -rw-r--r-- | test/fillval.c | 731 | ||||
| -rw-r--r-- | tools/Makefile.in | 3 |
10 files changed, 920 insertions, 128 deletions
@@ -289,6 +289,7 @@ ./test/dtypes.c ./test/extend.c ./test/external.c +./test/fillval.c ./test/gheap.c ./test/hyperslab.c ./test/iopipe.c diff --git a/Makefile.in b/Makefile.in index 17757e8..bb94c74 100644 --- a/Makefile.in +++ b/Makefile.in @@ -11,7 +11,7 @@ @COMMENCE@ # Subdirectories in build-order -SUBDIRS=src tools test +SUBDIRS=src test tools ############################################################################## # T A R G E T S @@ -1,4 +1,4 @@ -This is hdf5-1.1.10 released on Wed Sep 30 13:33:34 CDT 1998 +This is hdf5-1.1.10 released on Mon Oct 5 15:55:59 CDT 1998 Please refer to the INSTALL file for installation instructions. ------------------------------------------------------------------------------ @@ -28,7 +28,8 @@ static char RcsId[] = "@(#)$Revision$"; #include <H5Oprivate.h> /* Object headers */ #include <H5Pprivate.h> /* Property lists */ #include <H5Sprivate.h> /* Dataspace functions rky 980813 */ -#include <H5TBprivate.h> /* Temporary buffers */ +#include <H5TBprivate.h> /* Temporary buffers */ +#include <H5Vprivate.h> /* Vector and array functions */ #include <H5Zprivate.h> /* Data filters */ #ifdef QAK @@ -98,9 +99,7 @@ static hbool_t interface_initialize_g = FALSE; #define INTERFACE_INIT H5D_init_interface static herr_t H5D_init_interface(void); static void H5D_term_interface(void); -#ifdef HAVE_PARALLEL -static herr_t H5D_allocate (H5D_t *dataset, const H5D_xfer_t *xfer); -#endif +static herr_t H5D_init_storage(H5D_t *dataset, const H5S_t *space); /*-------------------------------------------------------------------------- @@ -932,7 +931,8 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, * Chunked storage allows any type of data space extension, so we * don't even bother checking. */ - if (new_dset->create_parms->chunk_ndims != H5S_get_simple_extent_ndims(space)) { + if (new_dset->create_parms->chunk_ndims != + H5S_get_simple_extent_ndims(space)) { HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space"); } @@ -1030,25 +1030,17 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, } } + /* Initialize the raw data */ + if (H5D_init_storage(new_dset, space)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, + "unable to initialize storage"); + } + /* Give the dataset a name */ if (H5G_insert(loc, name, &(new_dset->ent)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset"); } -#ifdef HAVE_PARALLEL - /* - * If the dataset uses chunk storage and is accessed via - * parallel I/O, allocate file space for all chunks now. - */ - if (new_dset->ent.file->shared->access_parms->driver == H5F_LOW_MPIO && - new_dset->layout.type == H5D_CHUNKED){ - if (H5D_allocate(new_dset, &H5D_xfer_dflt)<0) { - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, - "fail in file space allocation for chunks"); - } - } -#endif /* HAVE_PARALLEL */ - /* Success */ ret_value = new_dset; @@ -1193,22 +1185,18 @@ H5D_open(H5G_entry_t *loc, const char *name) "storage address is undefined an no external file list"); } -#ifdef HAVE_PARALLEL /* - * If the dataset uses chunk storage and is accessed via - * parallel I/O, and file is open writable, - * allocate file space for chunks that have not been - * allocated in its "previous access". + * Make sure all storage is properly initialized for chunked datasets. + * This is especially important for parallel I/O where the B-tree must + * be fully populated before I/O can happen. */ - if (dataset->ent.file->shared->access_parms->driver==H5F_LOW_MPIO && - dataset->layout.type == H5D_CHUNKED && - (dataset->ent.file->intent & H5F_ACC_RDWR)){ - if (H5D_allocate(dataset, &H5D_xfer_dflt)<0) { + if ((dataset->ent.file->intent & H5F_ACC_RDWR) && + H5D_CHUNKED==dataset->layout.type) { + if (H5D_init_storage(dataset, space)<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, - "fail in file space allocation dataset"); + "unable to initialize file storage"); } } -#endif /* HAVE_PARALLEL */ /* Success */ ret_value = dataset; @@ -1505,14 +1493,16 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, } if (NULL==(tconv_buf=xfer_parms->tconv_buf)) { /* Allocate temporary buffer */ - if (FAIL==(tconv_id = H5TB_get_buf (target_size,1,(void **)&tconv_buf))) { + if (FAIL==(tconv_id = H5TB_get_buf(target_size, 1, + (void **)&tconv_buf))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } } if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) { /* Allocate temporary buffer */ - if (FAIL==(bkg_id = H5TB_get_buf (request_nelmts*dst_type_size,1,(void **)&bkg_buf))) { + if (FAIL==(bkg_id = H5TB_get_buf(request_nelmts*dst_type_size, 1, + (void **)&bkg_buf))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } @@ -1873,14 +1863,16 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, } if (NULL==(tconv_buf=xfer_parms->tconv_buf)) { /* Allocate temporary buffer */ - if (FAIL==(tconv_id = H5TB_get_buf (target_size,1,(void **)&tconv_buf))) { + if (FAIL==(tconv_id = H5TB_get_buf(target_size, 1, + (void **)&tconv_buf))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } } if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) { /* Allocate temporary buffer */ - if (FAIL==(bkg_id = H5TB_get_buf (request_nelmts*dst_type_size,1,(void **)&bkg_buf))) { + if (FAIL==(bkg_id = H5TB_get_buf(request_nelmts*dst_type_size, 1, + (void **)&bkg_buf))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } @@ -2069,7 +2061,6 @@ H5D_extend (H5D_t *dataset, const hsize_t *size) * able to muck things up. */ - /* Increase the size of the data space */ if (NULL==(space=H5S_read (&(dataset->ent)))) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, @@ -2080,26 +2071,37 @@ H5D_extend (H5D_t *dataset, const hsize_t *size) "unable to increase size of data space"); } - /* Save the new dataspace in the file if necessary */ if (changed>0){ + /* Save the new dataspace in the file if necessary */ if (H5S_modify (&(dataset->ent), space)<0) { HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); } -#ifdef HAVE_PARALLEL + + /* Initialize the new parts of the dataset */ +#ifdef LATER + if (H5S_select_all(space)<0 || + H5S_select_hyperslab(space, H5S_SELECT_DIFF, zero, NULL, + old_dims, NULL)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to select new extents for fill value"); + } +#else /* - * If the dataset uses chunk storage and is accessed via - * parallel I/O, need to allocate file space for all extended - * chunks now. + * We don't have the H5S_SELECT_DIFF operator yet. We really only + * need it for contiguous datasets because the chunked datasets will + * either fill on demand during I/O or attempt a fill of all chunks. */ - if (dataset->ent.file->shared->access_parms->driver==H5F_LOW_MPIO && - dataset->layout.type==H5D_CHUNKED){ - if (H5D_allocate(dataset, &H5D_xfer_dflt)<0) { - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "fail in file space allocation for chunks"); - } + if (H5D_CONTIGUOUS==dataset->layout.type && + dataset->create_parms->fill.buf) { + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, + "unable to select fill value region"); + } +#endif + if (H5D_init_storage(dataset, space)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to initialize dataset with fill value"); } -#endif /* HAVE_PARALLEL */ } @@ -2161,86 +2163,134 @@ H5D_typeof (H5D_t *dset) } -#ifdef HAVE_PARALLEL /*------------------------------------------------------------------------- - * Function: H5D_allocate + * Function: H5D_init_storage * - * Purpose: Allocate file space for the data storage of the dataset. - * Return SUCCEED if all needed allocation succeed, otherwise - * FAIL. + * Purpose: Initialize the data for a new dataset. If a selection is + * defined for SPACE then initialize only that part of the + * dataset. * * Return: Success: SUCCEED * * Failure: FAIL * - * Note: Current implementation allocates chunked dataset only. - * - * Programmer: Albert Cheng - * July 9, 1998 + * Programmer: Robb Matzke + * Monday, October 5, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t -H5D_allocate (H5D_t *dataset, const H5D_xfer_t *xfer) +H5D_init_storage(H5D_t *dset, const H5S_t *space) { - H5S_t *space = NULL; + intn ndims; + hsize_t dim[H5O_LAYOUT_NDIMS]; + hsize_t npoints, ptsperbuf; + size_t i, size, bufsize=8*1024; + hbool_t all_zero; + hid_t buf_id = -1; + haddr_t addr; herr_t ret_value = FAIL; - hsize_t space_dim[H5O_LAYOUT_NDIMS]; - intn space_ndims; - H5O_layout_t *layout; + void *buf = NULL; - FUNC_ENTER(H5D_allocate, FAIL); -#ifdef AKC - printf("Enter %s:\n", FUNC); -#endif - - /* Check args */ - assert(dataset); - assert(&(dataset->layout)); - layout = &(dataset->layout); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(&(layout->addr))); - + FUNC_ENTER(H5D_init_storage, FAIL); + assert(dset); + assert(space); - switch (layout->type) { + switch (dset->layout.type) { case H5D_CONTIGUOUS: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet"); - - case H5D_CHUNKED: - if (NULL==(space=H5S_read (&(dataset->ent)))) { - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to read data space info from dataset header"); + /* + * If the fill value is non-zero then write the fill value to the + * specified selection. + */ + for (i=0, all_zero=TRUE; i<dset->create_parms->fill.size; i++) { + if (((uint8*)(dset->create_parms->fill.buf))[i]) { + all_zero = FALSE; + break; + } } - /* get current dims of dataset */ - if ((space_ndims=H5S_get_simple_extent_dims(space, space_dim, - NULL)) <= 0 || - space_ndims+1 != layout->ndims){ - HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, - "unable to allocate chunk storage"); + npoints = H5S_get_simple_extent_npoints(space); + + if (!all_zero && npoints==H5S_get_select_npoints(space)) { + /* + * Fill the entire current extent with the fill value. We can do + * this quite efficiently by making sure we copy the fill value + * in relatively large pieces. + */ + ptsperbuf = MAX(1, bufsize/dset->create_parms->fill.size); + bufsize = ptsperbuf * dset->create_parms->fill.size; + if ((buf_id=H5TB_get_buf(bufsize, TRUE, &buf))<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to get buffer for fill value"); + } + H5V_array_fill(buf, dset->create_parms->fill.buf, + dset->create_parms->fill.size, ptsperbuf); + if (dset->create_parms->efl.nused) { + H5F_addr_reset(&addr); + } else { + addr = dset->layout.addr; + } + + while (npoints>0) { + size = MIN(ptsperbuf, npoints) * dset->create_parms->fill.size; + if (dset->create_parms->efl.nused) { + if (H5O_efl_write(dset->ent.file, + &(dset->create_parms->efl), + &addr, size, buf)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to write fill value to dataset"); + } + } else { + if (H5F_block_write(dset->ent.file, &addr, size, + H5D_XFER_DFLT, buf)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to write fill value to dataset"); + } + } + npoints -= MIN(ptsperbuf, npoints); + H5F_addr_inc(&addr, size); + } + } else if (!all_zero) { + /* + * Fill the specified selection with the fill value. + */ + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, + "unable to initialize dataset with fill value"); } - /* copy the element size over */ - space_dim[space_ndims] = layout->dim[space_ndims]; + break; - if (H5F_istore_allocate(dataset->ent.file, - (layout), space_dim, xfer->split_ratios, - &(dataset->create_parms->pline), - &(dataset->create_parms->fill))<0) { - HRETURN(FAIL); + case H5D_CHUNKED: + /* + * If the dataset is accessed via parallel I/O, allocate file space + * for all chunks now and initialize each chunk with the fill value. + */ + if (H5F_LOW_MPIO==dset->ent.file->shared->access_parms->driver) { + /* We only handle simple data spaces so far */ + if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to get simple data space info"); + } + dim[ndims] = dset->layout.dim[ndims]; + ndims++; + + if (H5F_istore_allocate(dset->ent.file, &(dset->layout), + dim, H5D_xfer_dflt.split_ratios, + &(dset->create_parms->pline), + &(dset->create_parms->fill))<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to allocate all chunks of dataset"); + } } break; - - default: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet"); } - ret_value = SUCCEED; - done: - if (space) - H5S_close(space); - + done: + if (buf_id>=0 && H5TB_release_buf(buf_id)<0) { + HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to release fill value temporary buffer"); + } FUNC_LEAVE(ret_value); } -#endif + diff --git a/src/H5Distore.c b/src/H5Distore.c index 8c9dd1b..ed0659e 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -2001,7 +2001,6 @@ H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent, } -#ifdef HAVE_PARALLEL /*------------------------------------------------------------------------- * Function: H5F_istore_get_addr * @@ -2172,20 +2171,21 @@ H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, if (carry) break; } +#ifdef HAVE_PARALLEL /* * rky 980923 - * The following barrier is a temporary fix to prevent overwriting - * real data caused by a race between one proc's call of H5F_istore_allocate - * (from H5D_allocate, ultimately from H5Dcreate and H5Dextend) - * and another proc's call of H5Dwrite. - * Eventually, this barrier should be removed, - * when H5D_allocate is changed to call H5MF_alloc directly + * + * The following barrier is a temporary fix to prevent overwriting real + * data caused by a race between one proc's call of H5F_istore_allocate + * (from H5D_init_storage, ultimately from H5Dcreate and H5Dextend) and + * another proc's call of H5Dwrite. Eventually, this barrier should be + * removed, when H5D_init_storage is changed to call H5MF_alloc directly * to allocate space, instead of calling H5F_istore_unlock. */ if (MPI_Barrier( f->shared->access_parms->u.mpio.comm )) { HRETURN_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "MPI_Barrier failed"); } +#endif FUNC_LEAVE(SUCCEED); } -#endif diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 8c9dd1b..ed0659e 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -2001,7 +2001,6 @@ H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent, } -#ifdef HAVE_PARALLEL /*------------------------------------------------------------------------- * Function: H5F_istore_get_addr * @@ -2172,20 +2171,21 @@ H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, if (carry) break; } +#ifdef HAVE_PARALLEL /* * rky 980923 - * The following barrier is a temporary fix to prevent overwriting - * real data caused by a race between one proc's call of H5F_istore_allocate - * (from H5D_allocate, ultimately from H5Dcreate and H5Dextend) - * and another proc's call of H5Dwrite. - * Eventually, this barrier should be removed, - * when H5D_allocate is changed to call H5MF_alloc directly + * + * The following barrier is a temporary fix to prevent overwriting real + * data caused by a race between one proc's call of H5F_istore_allocate + * (from H5D_init_storage, ultimately from H5Dcreate and H5Dextend) and + * another proc's call of H5Dwrite. Eventually, this barrier should be + * removed, when H5D_init_storage is changed to call H5MF_alloc directly * to allocate space, instead of calling H5F_istore_unlock. */ if (MPI_Barrier( f->shared->access_parms->u.mpio.comm )) { HRETURN_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "MPI_Barrier failed"); } +#endif FUNC_LEAVE(SUCCEED); } -#endif diff --git a/src/H5Fmpio.c b/src/H5Fmpio.c index 8ca50d8..2ebe5c8 100644 --- a/src/H5Fmpio.c +++ b/src/H5Fmpio.c @@ -335,7 +335,8 @@ H5F_mpio_open(const char *name, const H5F_access_t *access_parms, uintn flags, } #endif - mpierr = MPI_File_open(access_parms->u.mpio.comm, (char*)name, mpi_amode, access_parms->u.mpio.info, &fh); + mpierr = MPI_File_open(access_parms->u.mpio.comm, (char*)name, mpi_amode, + access_parms->u.mpio.info, &fh); if (MPI_SUCCESS != mpierr) { MPI_Error_string( mpierr, mpierrmsg, &msglen ); HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL, mpierrmsg ); @@ -511,7 +512,7 @@ H5F_mpio_read(H5F_low_t *lf, H5F_access_t *access_parms, "couldn't convert addr to MPIOffset" ); } size_i = (int)size; - if (size_i != size) { /* check type conversion */ + if ((size_t)size_i != size) { /* check type conversion */ HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "couldn't convert size to int" ); } @@ -764,7 +765,7 @@ H5F_mpio_write(H5F_low_t *lf, H5F_access_t *access_parms, "couldn't convert addr to MPIOffset" ); } size_i = (int)size; - if (size_i != size) { /* check type conversion */ + if ((size_t)size_i != size) { /* check type conversion */ HRETURN_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "couldn't convert size to int" ); } @@ -975,9 +976,11 @@ H5F_MPIOff_to_haddr( MPI_Offset mpi_off, haddr_t *addr ) * Problems and limitations: * * Return: Success: return value is SUCCEED - * and the MPIOffset contains the converted value + * and the MPIOffset contains the converted + * value. * - * Failure: return value is FAIL, the MPIOffset is undefined + * Failure: return value is FAIL, the MPIOffset is + * undefined. * * Programmer: * January 30, 1998 diff --git a/test/Makefile.in b/test/Makefile.in index fc671a4..10923c0 100644 --- a/test/Makefile.in +++ b/test/Makefile.in @@ -12,7 +12,7 @@ CPPFLAGS=-I. -I../src @CPPFLAGS@ # These are our main targets. They should be listed in the order to be # executed, generally most specific tests to least specific tests. TESTS=testhdf5 gheap hyperslab istore bittests dtypes dsets cmpd_dset extend \ - external shtype links unlink big mtime + external shtype links unlink big mtime fillval TIMINGS=iopipe chunk ragged overhead # Temporary files @@ -24,7 +24,8 @@ MOSTLYCLEAN=cmpd_dset.h5 dataset.h5 extend.h5 istore.h5 tfile1.h5 tfile2.h5 \ gheap1.h5 gheap2.h5 gheap3.h5 gheap4.h5 shtype0.h5 shtype1.h5 \ shtype2a.h5 shtype2b.h5 shtype3.h5 links.h5 chunk.h5 big.data \ big[0-9][0-9][0-9][0-9][0-9].h5 dtypes1.h5 dtypes2.h5 tattr.h5 \ - tselect.h5 mtime.h5 ragged.h5 grptime.h5 unlink.h5 overhead.h5 + tselect.h5 mtime.h5 ragged.h5 grptime.h5 unlink.h5 overhead.h5 \ + fillval_[0-9].h5 CLEAN=$(TIMINGS) # Source and object files for programs... The TEST_SRC list contains all the @@ -34,7 +35,7 @@ CLEAN=$(TIMINGS) TEST_SRC=testhdf5.c tattr.c tfile.c theap.c tmeta.c tohdr.c tselect.c tstab.c \ th5s.c dtypes.c hyperslab.c istore.c dsets.c cmpd_dset.c extend.c \ external.c iopipe.c gheap.c shtype.c big.c links.c chunk.c bittests.c \ - mtime.c ragged.c unlink.c overhead.c + mtime.c ragged.c unlink.c overhead.c fillval.c TEST_OBJ=$(TEST_SRC:.c=.o) # Private header files (not to be installed)... @@ -112,4 +113,7 @@ unlink: unlink.o ../src/libhdf5.a overhead: overhead.o ../src/libhdf5.a $(CC) $(CFLAGS) -o $@ overhead.o ../src/libhdf5.a $(LIBS) +fillval: fillval.o ../src/libhdf5.a + $(CC) $(CFLAGS) -o $@ fillval.o ../src/libhdf5.a $(LIBS) + @CONCLUDE@ diff --git a/test/fillval.c b/test/fillval.c new file mode 100644 index 0000000..3880e23 --- /dev/null +++ b/test/fillval.c @@ -0,0 +1,731 @@ +/* + * Copyright (C) 1998 NCSA + * All rights reserved. + * + * Programmer: Robb Matzke <robb@arborea.spizella.com> + * Thursday, October 1, 1998 + * + * Purpose: Tests dataset fill values. + */ +#include <fcntl.h> +#include <hdf5.h> +#include <stdlib.h> +#include <unistd.h> + +/* + * Define NO_FILLING if you want to compare how this test works when there is + * no fill value (that is, when the fill value is zero). + */ +/* #define NO_FILLING */ + + +#define FILE_NAME_1 "fillval_1.h5" +#define FILE_NAME_2 "fillval_2.h5" +#define FILE_NAME_3 "fillval_3.h5" +#define FILE_NAME_4 "fillval_4.h5" +#define FILE_NAME_5 "fillval_5.h5" +#define FILE_NAME_6 "fillval_6.h5" +#define FILE_NAME_RAW "fillval.raw" + +#include <H5config.h> +#ifndef HAVE_ATTRIBUTE +# undef __attribute__ +# define __attribute__(X) /*void*/ +# define __unused__ /*void*/ +#else +# define __unused__ __attribute__((unused)) +#endif + + +/*------------------------------------------------------------------------- + * 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(FILE_NAME_1); + remove(FILE_NAME_2); + remove(FILE_NAME_3); + remove(FILE_NAME_4); + remove(FILE_NAME_5); + remove(FILE_NAME_6); + remove(FILE_NAME_RAW); + } +} + + +/*------------------------------------------------------------------------- + * Function: display_error_cb + * + * Purpose: Displays the error stack after printing "*FAILED*". + * + * Return: Success: 0 + * + * Failure: -1 + * + * Programmer: Robb Matzke + * Wednesday, March 4, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +display_error_cb(void __unused__ *client_data) +{ + puts("*FAILED*"); + H5Eprint(stdout); + return 0; +} + + +/*------------------------------------------------------------------------- + * Function: test_getset + * + * Purpose: Tests the H5Pget_fill_value() and H5Pset_fill_value() + * functions. + * + * Return: Success: 0 + * + * Failure: number of errors + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static int +test_getset(void) +{ + herr_t status; + hid_t dcpl; + int fill_i; + hid_t type_ss, type_si; + struct fill_si { + int v1, v2; + } fill_si; + struct fill_ss { + short v1, v2; + } fill_ss, fill_ss_rd; + + printf("%-70s", "Testing property lists"); + fflush(stdout); + + /* + * Create the dataset creation property list and the data types that will + * be used during this test. + */ + if ((dcpl=H5Pcreate(H5P_DATASET_CREATE))<0) goto error; + if ((type_ss=H5Tcreate(H5T_COMPOUND, sizeof fill_ss))<0 || + H5Tinsert(type_ss, "v1", HOFFSET(struct fill_ss, v1), + H5T_NATIVE_SHORT)<0 || + H5Tinsert(type_ss, "v2", HOFFSET(struct fill_ss, v2), + H5T_NATIVE_SHORT)<0) { + goto error; + } + if ((type_si=H5Tcreate(H5T_COMPOUND, sizeof fill_si))<0 || + H5Tinsert(type_si, "v1", HOFFSET(struct fill_si, v1), + H5T_NATIVE_INT)<0 || + H5Tinsert(type_si, "v2", HOFFSET(struct fill_si, v2), + H5T_NATIVE_INT)<0) { + goto error; + } + + /* + * Reading the fill value from a dataset creation property list that has + * no fill value should result in a failure. + */ + H5E_BEGIN_TRY { + status = H5Pget_fill_value(dcpl, H5T_NATIVE_INT, &fill_i); + } H5E_END_TRY; + if (status>=0) { + puts("*FAILED*"); + puts(" H5Pget_fill_value() should have been negative"); + goto error; + } + + /* + * Set the fill value using a struct as the data type. + */ + fill_ss.v1 = 1111; + fill_ss.v2 = 2222; + if (H5Pset_fill_value(dcpl, type_ss, &fill_ss)<0) goto error; + + /* + * Get the fill value using the same data type that was used to set it. + */ + if (H5Pget_fill_value(dcpl, type_ss, &fill_ss_rd)<0) goto error; + if (fill_ss.v1!=fill_ss_rd.v1 || fill_ss.v2!=fill_ss_rd.v2) { + puts("*FAILED*"); + puts(" Failed to get fill value using same data type that was used"); + puts(" to set the fill value."); + goto error; + } + + /* + * Get the fill value using some other data type. + */ + if (H5Pget_fill_value(dcpl, type_si, &fill_si)<0) goto error; + if (fill_ss.v1!=fill_si.v1 || fill_ss.v2!=fill_si.v2) { + puts("*FAILED*"); + puts(" Failed to get fill value using a data type other than what"); + puts(" was used to set the fill value."); + goto error; + } + + /* + * Reset the fill value + */ + if (H5Pset_fill_value(dcpl, type_si, &fill_si)<0) goto error; + if (H5Pget_fill_value(dcpl, type_ss, &fill_ss)<0) goto error; + if (fill_si.v1!=fill_ss.v1 || fill_si.v2!=fill_ss.v2) { + puts("*FAILED*"); + puts(" Resetting the fill value was unsuccessful."); + goto error; + } + + /* Success */ + if (H5Pclose(dcpl)<0) goto error; + puts(" PASSED"); + return 0; + + error: + H5Pclose(dcpl); + return 1; +} + + +/*------------------------------------------------------------------------- + * Function: test_create + * + * Purpose: Tests creating datasets that have fill values. + * + * Return: Success: 0 + * + * Failure: number of errors + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static int +test_create(const char *filename, H5D_layout_t layout) +{ + hid_t file, space, dcpl, dset; + hsize_t cur_size[5] = {32, 16, 8, 4, 2}; + hsize_t ch_size[5] = {1, 1, 1, 4, 2}; + int fillval = 0x4c70f1cd, fillval_rd=0; + char test[256]; + + if (H5D_CHUNKED==layout) { + strcpy(test, "Testing chunked dataset creation"); + } else { + strcpy(test, "Testing contiguous dataset creation"); + } + printf("%-70s", test); + fflush(stdout); + + /* Create a file and dataset */ + if ((file=H5Fcreate(filename, H5F_ACC_TRUNC, + H5P_DEFAULT, H5P_DEFAULT))<0) goto error; + if ((space=H5Screate_simple(5, cur_size, cur_size))<0) goto error; + if ((dcpl=H5Pcreate(H5P_DATASET_CREATE))<0) goto error; + if (H5D_CHUNKED==layout) { + if (H5Pset_chunk(dcpl, 5, ch_size)<0) goto error; + } +#ifndef NO_FILLING + if (H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fillval)<0) goto error; +#endif + if ((dset=H5Dcreate(file, "dset", H5T_NATIVE_INT, space, dcpl))<0) + goto error; + if (H5Dclose(dset)<0) goto error; + if (H5Sclose(space)<0) goto error; + if (H5Pclose(dcpl)<0) goto error; + if (H5Fclose(file)<0) goto error; + + /* Open the file and get the dataset fill value */ + if ((file=H5Fopen(FILE_NAME_1, H5F_ACC_RDONLY, H5P_DEFAULT))<0) + goto error; + if ((dset=H5Dopen(file, "dset"))<0) goto error; + if ((dcpl=H5Dget_create_plist(dset))<0) goto error; +#ifndef NO_FILLING + if (H5Pget_fill_value(dcpl, H5T_NATIVE_INT, &fillval_rd)<0) goto error; + if (fillval_rd!=fillval) { + puts("*FAILED*"); + puts(" Got a different fill value than what was set."); + goto error; + } +#endif + if (H5Pclose(dcpl)<0) goto error; + if (H5Dclose(dset)<0) goto error; + if (H5Fclose(file)<0) goto error; + + puts(" PASSED"); + return 0; + + error: + H5E_BEGIN_TRY { + H5Pclose(dcpl); + H5Sclose(space); + H5Dclose(dset); + H5Fclose(file); + } H5E_END_TRY; + return 1; +} + + +/*------------------------------------------------------------------------- + * Function: test_rdwr + * + * Purpose: Tests fill values for chunked datasets. + * + * Return: Success: 0 + * + * Failure: number of errors + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static int +test_rdwr(const char *filename, H5D_layout_t layout) +{ + hid_t file, fspace, mspace, dcpl, dset; + hsize_t cur_size[5] = {32, 16, 8, 4, 2}; + hsize_t ch_size[5] = {1, 16, 8, 4, 2}; + hsize_t one[5] = {1, 1, 1, 1, 1}; + hssize_t hs_size[5], hs_offset[5], hs_stride[5], nelmts; +#ifdef NO_FILLING + int fillval = 0; +#else + int fillval = 0x4c70f1cd; +#endif + int val_rd, should_be; + int i, j, *buf=NULL, odd; + char test[256]; + + if (H5D_CHUNKED==layout) { + strcpy(test, "Testing chunked dataset I/O"); + } else { + strcpy(test, "Testing contiguous dataset I/O"); + } + printf("%-70s", test); + fflush(stdout); + + /* Create a file and dataset */ + if ((file=H5Fcreate(filename, H5F_ACC_TRUNC, + H5P_DEFAULT, H5P_DEFAULT))<0) goto error; + if ((fspace=H5Screate_simple(5, cur_size, cur_size))<0) goto error; + if ((dcpl=H5Pcreate(H5P_DATASET_CREATE))<0) goto error; + if (H5D_CHUNKED==layout) { + if (H5Pset_chunk(dcpl, 5, ch_size)<0) goto error; + } +#ifndef NO_FILLING + if (H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fillval)<0) goto error; +#endif + if ((dset=H5Dcreate(file, "dset", H5T_NATIVE_INT, fspace, dcpl))<0) + goto error; + + /* Read some data and make sure it's the fill value */ + if ((mspace=H5Screate_simple(5, one, NULL))<0) goto error; + for (i=0; i<1000; i++) { + for (j=0; j<5; j++) { + hs_offset[j] = rand() % cur_size[j]; + } + if (H5Sselect_hyperslab(fspace, H5S_SELECT_SET, hs_offset, NULL, + one, NULL)<0) goto error; + if (H5Dread(dset, H5T_NATIVE_INT, mspace, fspace, H5P_DEFAULT, + &val_rd)<0) goto error; + if (val_rd!=fillval) { + puts("*FAILED*"); + puts(" Value read was not a fill value."); + printf(" Elmt={%ld,%ld,%ld,%ld,%ld}, read: %u, " + "Fill value: %u\n", + (long)hs_offset[0], (long)hs_offset[1], + (long)hs_offset[2], (long)hs_offset[3], + (long)hs_offset[4], val_rd, fillval); + goto error; + } + } + if (H5Sclose(mspace)<0) goto error; + + /* Write to all odd data locations */ + for (i=0, nelmts=1; i<5; i++) { + hs_size[i] = cur_size[i]/2; + hs_offset[i] = 0; + hs_stride[i] = 2; + nelmts *= hs_size[i]; + } + if ((mspace=H5Screate_simple(5, hs_size, hs_size))<0) goto error; + buf = malloc(nelmts*sizeof(int)); + for (i=0; i<nelmts; i++) buf[i] = 9999; + if (H5Sselect_hyperslab(fspace, H5S_SELECT_SET, hs_offset, hs_stride, + hs_size, NULL)<0) goto error; + if (H5Dwrite(dset, H5T_NATIVE_INT, mspace, fspace, H5P_DEFAULT, + buf)<0) goto error; + free(buf); + buf = NULL; + H5Sclose(mspace); + + /* Read some data and make sure it's the right value */ + if ((mspace=H5Screate_simple(5, one, NULL))<0) goto error; + for (i=0; i<1000; i++) { + for (j=0, odd=0; j<5; j++) { + hs_offset[j] = rand() % cur_size[j]; + odd += hs_offset[j]%2; + } + should_be = odd ? fillval : 9999; + if (H5Sselect_hyperslab(fspace, H5S_SELECT_SET, hs_offset, NULL, + one, NULL)<0) goto error; + if (H5Dread(dset, H5T_NATIVE_INT, mspace, fspace, H5P_DEFAULT, + &val_rd)<0) goto error; + + if (val_rd!=should_be) { + puts("*FAILED*"); + puts(" Value read was not correct."); + printf(" Elmt={%ld,%ld,%ld,%ld,%ld}, read: %u, " + "should be: %u\n", + (long)hs_offset[0], (long)hs_offset[1], + (long)hs_offset[2], (long)hs_offset[3], + (long)hs_offset[4], val_rd, should_be); + goto error; + } + } + if (H5Sclose(mspace)<0) goto error; + + + + if (H5Dclose(dset)<0) goto error; + if (H5Sclose(fspace)<0) goto error; + if (H5Pclose(dcpl)<0) goto error; + if (H5Fclose(file)<0) goto error; + puts(" PASSED"); + return 0; + + error: + H5E_BEGIN_TRY { + H5Dclose(dset); + H5Sclose(fspace); + H5Sclose(mspace); + H5Pclose(dcpl); + H5Fclose(file); + } H5E_END_TRY; + return 1; +} + + +/*------------------------------------------------------------------------- + * Function: test_extend + * + * Purpose: Test that filling works okay when a dataset is extended. + * + * Return: Success: 0 + * + * Failure: number of errors + * + * Programmer: Robb Matzke + * Monday, October 5, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static int +test_extend(const char *filename, H5D_layout_t layout) +{ + hid_t file, fspace, mspace, dcpl, dset; + hsize_t cur_size[5] = {32, 16, 8, 4, 2}; + hsize_t max_size[5] = {128, 64, 32, 16, 8}; + hsize_t ch_size[5] = {1, 16, 8, 4, 2}; + hsize_t one[5] = {1, 1, 1, 1, 1}; + hssize_t hs_size[5], hs_offset[5], hs_stride[5], nelmts; +#ifdef NO_FILLING + int fillval = 0; +#else + int fillval = 0x4c70f1cd; +#endif + int val_rd, should_be; + int i, j, *buf=NULL, odd, fd; + char test[256]; + + if (H5D_CHUNKED==layout) { + strcpy(test, "Testing chunked dataset extend"); + } else { + strcpy(test, "Testing contiguous dataset extend"); + } + printf("%-70s", test); + fflush(stdout); + + if ((dcpl=H5Pcreate(H5P_DATASET_CREATE))<0) goto error; + if (H5D_CHUNKED==layout) { + if (H5Pset_chunk(dcpl, 5, ch_size)<0) goto error; + } +#ifndef NO_FILLING + if (H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fillval)<0) goto error; +#endif + +#if 1 + /* + * Remove this once contiguous datasets can support extensions in other + * than the slowest varying dimension. The purpose of this block is to + * make only the slowest varying dimension extendible and yet have the + * same total number of elements as originally. + * + * If this is removed prematurely then you will get an error `only the + * first dimension can be extendible' as long as the test isn't skipped + * below. + */ + if (H5D_CONTIGUOUS==layout) { + max_size[0] = (max_size[0]*max_size[1]*max_size[2]* + max_size[3]*max_size[4]) / + (cur_size[1]*cur_size[2]*cur_size[3]*cur_size[4]); + max_size[1] = cur_size[1]; + max_size[2] = cur_size[2]; + max_size[3] = cur_size[3]; + max_size[4] = cur_size[4]; + } +#endif + +#if 1 + /* + * Remove this once internal contiguous datasets can support + * extending. If it's removed prematurely you will get an error + * `extendible contiguous non-external dataset' as long as the test isn't + * skipped below. + */ + if (H5D_CONTIGUOUS==layout) { + nelmts = max_size[0]*max_size[1]*max_size[2]*max_size[3]*max_size[4]; + if ((fd=open(FILE_NAME_RAW, O_RDWR|O_CREAT|O_TRUNC, 0666))<0 || + close(fd)<0) goto error; + if (H5Pset_external(dcpl, FILE_NAME_RAW, 0, nelmts*sizeof(int))<0) + goto error; + } +#endif + +#if 1 + /* + * Remove this when contiguous datasets can be exended to some + * predetermined fininte size, even if it's just in the slowest varying + * dimension. If it's removed prematurely then you'll get one of the + * errors described above or `unable to select fill value region'. + */ + if (H5D_CONTIGUOUS==layout) { + puts(" SKIP"); + puts(" Not implemented yet -- needs H5S_SELECT_DIFF operator"); + return 0; + } +#endif + + /* Create a file and dataset */ + if ((file=H5Fcreate(filename, H5F_ACC_TRUNC, + H5P_DEFAULT, H5P_DEFAULT))<0) goto error; + if ((fspace=H5Screate_simple(5, cur_size, max_size))<0) goto error; + if ((dset=H5Dcreate(file, "dset", H5T_NATIVE_INT, fspace, dcpl))<0) + goto error; + + /* Read some data and make sure it's the fill value */ + if ((mspace=H5Screate_simple(5, one, NULL))<0) goto error; + for (i=0; i<1000; i++) { + for (j=0; j<5; j++) { + hs_offset[j] = rand() % cur_size[j]; + } + if (H5Sselect_hyperslab(fspace, H5S_SELECT_SET, hs_offset, NULL, + one, NULL)<0) goto error; + if (H5Dread(dset, H5T_NATIVE_INT, mspace, fspace, H5P_DEFAULT, + &val_rd)<0) goto error; + if (val_rd!=fillval) { + puts("*FAILED*"); + puts(" Value read was not a fill value."); + printf(" Elmt={%ld,%ld,%ld,%ld,%ld}, read: %u, " + "Fill value: %u\n", + (long)hs_offset[0], (long)hs_offset[1], + (long)hs_offset[2], (long)hs_offset[3], + (long)hs_offset[4], val_rd, fillval); + goto error; + } + } + if (H5Sclose(mspace)<0) goto error; + + /* Write to all odd data locations */ + for (i=0, nelmts=1; i<5; i++) { + hs_size[i] = cur_size[i]/2; + hs_offset[i] = 0; + hs_stride[i] = 2; + nelmts *= hs_size[i]; + } + if ((mspace=H5Screate_simple(5, hs_size, hs_size))<0) goto error; + buf = malloc(nelmts*sizeof(int)); + for (i=0; i<nelmts; i++) buf[i] = 9999; + if (H5Sselect_hyperslab(fspace, H5S_SELECT_SET, hs_offset, hs_stride, + hs_size, NULL)<0) goto error; + if (H5Dwrite(dset, H5T_NATIVE_INT, mspace, fspace, H5P_DEFAULT, + buf)<0) goto error; + free(buf); + buf = NULL; + H5Sclose(mspace); + + /* Read some data and make sure it's the right value */ + if ((mspace=H5Screate_simple(5, one, NULL))<0) goto error; + for (i=0; i<1000; i++) { + for (j=0, odd=0; j<5; j++) { + hs_offset[j] = rand() % cur_size[j]; + odd += hs_offset[j]%2; + } + should_be = odd ? fillval : 9999; + if (H5Sselect_hyperslab(fspace, H5S_SELECT_SET, hs_offset, NULL, + one, NULL)<0) goto error; + if (H5Dread(dset, H5T_NATIVE_INT, mspace, fspace, H5P_DEFAULT, + &val_rd)<0) goto error; + + if (val_rd!=should_be) { + puts("*FAILED*"); + puts(" Value read was not correct."); + printf(" Elmt={%ld,%ld,%ld,%ld,%ld}, read: %u, " + "should be: %u\n", + (long)hs_offset[0], (long)hs_offset[1], + (long)hs_offset[2], (long)hs_offset[3], + (long)hs_offset[4], val_rd, should_be); + goto error; + } + } + if (H5Sclose(mspace)<0) goto error; + + /* Extend the dataset */ + if (H5Dextend(dset, max_size)<0) goto error; + if (H5Sclose(fspace)<0) goto error; + if ((fspace=H5Dget_space(dset))<0) goto error; + + /* Read some data and make sure it's the right value */ + if ((mspace=H5Screate_simple(5, one, NULL))<0) goto error; + for (i=0; i<1000; i++) { + for (j=0, odd=0; j<5; j++) { + hs_offset[j] = rand() % max_size[j]; + if ((hsize_t)hs_offset[j]>=cur_size[j]) { + odd = 1; + } else { + odd += hs_offset[j]%2; + } + } + + should_be = odd ? fillval : 9999; + if (H5Sselect_hyperslab(fspace, H5S_SELECT_SET, hs_offset, NULL, + one, NULL)<0) goto error; + if (H5Dread(dset, H5T_NATIVE_INT, mspace, fspace, H5P_DEFAULT, + &val_rd)<0) goto error; + + if (val_rd!=should_be) { + puts("*FAILED*"); + puts(" Value read was not correct."); + printf(" Elmt={%ld,%ld,%ld,%ld,%ld}, read: %u, " + "should be: %u\n", + (long)hs_offset[0], (long)hs_offset[1], + (long)hs_offset[2], (long)hs_offset[3], + (long)hs_offset[4], val_rd, should_be); + goto error; + } + } + if (H5Sclose(mspace)<0) goto error; + + if (H5Dclose(dset)<0) goto error; + if (H5Sclose(fspace)<0) goto error; + if (H5Pclose(dcpl)<0) goto error; + if (H5Fclose(file)<0) goto error; + puts(" PASSED"); + return 0; + + error: + H5E_BEGIN_TRY { + H5Dclose(dset); + H5Sclose(fspace); + H5Sclose(mspace); + H5Pclose(dcpl); + H5Fclose(file); + } H5E_END_TRY; + return 1; +} + + + +/*------------------------------------------------------------------------- + * Function: main + * + * Purpose: Tests fill values + * + * Return: Success: + * + * Failure: + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +int +main(int argc, char *argv[]) +{ + int nerrors=0, argno, test_contig=1, test_chunk=1; + + if (argc>=2) { + test_contig = test_chunk = 0; + for (argno=1; argno<argc; argno++) { + if (!strcmp(argv[argno], "contiguous")) { + test_contig = 1; + } else if (!strcmp(argv[argno], "chunked")) { + test_chunk = 1; + } else { + fprintf(stderr, "usage: %s [contiguous] [chunked]\n", argv[0]); + exit(1); + } + } + } + + H5Eset_auto(display_error_cb, NULL); + + + nerrors += test_getset(); + + /* Chunked storage layout tests */ + if (test_chunk) { + nerrors += test_create(FILE_NAME_1, H5D_CHUNKED); + nerrors += test_rdwr(FILE_NAME_3, H5D_CHUNKED); + nerrors += test_extend(FILE_NAME_5, H5D_CHUNKED); + } + + /* Contiguous storage layout tests */ + if (test_contig) { + nerrors += test_create(FILE_NAME_2, H5D_CONTIGUOUS); + nerrors += test_rdwr(FILE_NAME_4, H5D_CONTIGUOUS); + nerrors += test_extend(FILE_NAME_6, H5D_CONTIGUOUS); + } + + if (nerrors) goto error; + puts("All fill value tests passed."); + cleanup(); + return 0; + + error: + puts("***** FILL VALUE TESTS FAILED *****"); + return 1; +} diff --git a/tools/Makefile.in b/tools/Makefile.in index 96a757f..d6ea8c9 100644 --- a/tools/Makefile.in +++ b/tools/Makefile.in @@ -26,6 +26,9 @@ PROG_SRC=h5debug.c h5import.c h5ls.c h5repart.c h5dump.c h5dumputil.c PROG_OBJ=$(PROG_SRC:.c=.o) PRIVATE_HDR=h5tools.h +# Programs have to be built before they can be tested! +test: $(PROGS) + # How to build the programs... h5debug: h5debug.o $(LIB) ../src/libhdf5.a $(CC) $(CFLAGS) -o $@ h5debug.o $(LIBS) |