diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 339 | ||||
| -rw-r--r-- | src/H5Distore.c | 36 | ||||
| -rw-r--r-- | src/H5Dseq.c | 46 | ||||
| -rw-r--r-- | src/H5Farray.c | 53 | ||||
| -rw-r--r-- | src/H5Fistore.c | 36 | ||||
| -rw-r--r-- | src/H5Fpkg.h | 4 | ||||
| -rw-r--r-- | src/H5Fseq.c | 46 | ||||
| -rw-r--r-- | src/H5S.c | 8 | ||||
| -rw-r--r-- | src/H5Sall.c | 537 | ||||
| -rw-r--r-- | src/H5Shyper.c | 78 | ||||
| -rw-r--r-- | src/H5Spkg.h | 2 | ||||
| -rw-r--r-- | src/H5Spoint.c | 38 | ||||
| -rw-r--r-- | src/H5Sprivate.h | 1 | ||||
| -rw-r--r-- | src/H5Sselect.c | 53 | ||||
| -rw-r--r-- | test/tselect.c | 122 |
15 files changed, 740 insertions, 659 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index e0c78f9..90e2386 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -35,115 +35,118 @@ Bug Fixes since HDF5-1.4.2 Library ------- - * Fixed bug with contiguous hyperslabs not being detected, causing - slower I/O than necessary. - * Fixed bug where non-aligned hyperslab I/O on chunked datasets was - causing errors during I/O - * The RCSID string in H5public.h was causing the C++ compiling problem - because when it was included multiple times, C++ did not like multiple - definitions of the same static variable. All occurance of RCSID - definition are removed since we have not used it consistently before. - * Fixed bug with non-zero userblock sizes causing raw data to not write - correctly. - * Fixed build on Linux systems with --enable-static-exec flag. It now - works correctly. - * IMPORTANT: Fixed file metadata corruption bug which could cause metadata - data loss in certain situations. - * The allocation by alignment (H5Pset_alignment) feature code somehow - got dropped in some 1.3.x version. Re-implemented it with "new and - improved" algorithm. It keeps track of "wasted" file-fragment in - the free-list too. - * Removed limitation that the data transfer buffer size needed to be - set for datasets whose dimensions were too large for the 'all' selection - code to handle. Any size dimensioned datasets should be handled - correctly now. - * Changed behavior of H5Tget_member_type to correctly emulate HDF5 v1.2.x - when --enable-hdf5v1_2 configure flag is enabled. - * Tweaked a few API functions to use 'size_t' instead of 'unsigned' or - 'hsize_t', which may cause errors in some cases. - * Fixed a bug of H5pubconf.h causing repeated definitions if it is included - more than once. hdf5.h now includes H5public.h which includes - H5pubconf.h. Applications should #include hdf5.h which handles multiple - inclusion correctly. - * Fixed H5FDmpio.h to be C++ friendly by making Parallel HDF5 API's to be - external to C++. - * Fixed a bug in H5FD_mpio_flush() that might result in negative file seek - if both MPIO and Split-file drivers are used together. - * Added new parallel hdf5 tests in t_mpi. The new test checks if the - filesystem or the MPI-IO can really handle greater than 2GB files. - If it fails, it prints information message only without failing the - test. - * Fixed a bug when reading chunked datasets where the edge of the dataset - would be incorrectly detected and generate an assertion failure. - * Fixed a bug where reading an entire dataset wasn't being handled - optimally when the dataset had unlimited dimensions. Dataset is read - in a single low-level I/O now, instead of being broken into separate - pieces internally. - * Fixed a bug where reading or writing chunked data which needed datatype - conversion could result in data values getting corrupted. - * Fixed a bug where appending a point selection to the current selection - would not actually append the point when there were no points defined - currently. - * Fixed a bug where 'or'ing a hyperslab with a 'none' selection would - fail. Now adds that hyperslab as the first hyperlab in the selection. - * Fixed a bug in the 'big' test where quota limits weren't being detected - properly if they caused close() to fail. - * Fixed a bug in internal B-tree code where a B-tree was not being copied + * Fixed bug where selection offset was being ignored for certain hyperslab + selections when optimized I/O was being performed. QAK - 2002/04/02 + * Added serial multi-gigabyte file size test. "test/big -h" shows + the help page. AKC - 2002/03/29 + * Fixed bug where variable-length string type doesn't behave as + string. SLU - 2002/03/28 + * Fixed bug in H5Gget_objinfo() which was not setting the 'fileno' + of the H5G_stat_t struct. QAK - 2002/03/27 + * Fixed data corruption bug in hyperslab routines when contiguous + hyperslab that spans entire dimension and is larger than type + conversion buffer is attempted to be read. QAK - 2002/03/26 + * 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 - 2002/02/14 + * 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 - 2002/02/13 + * Fixed bug where raw data re-allocated from the free-list would sometimes + overlap with the metadata accumulator and get corrupted. QAK - 2002/01/23 + * Fixed bug where variable-length datatypes for attributes was not working correctly. + * Retired the DPSS virtual file driver (--with-gridstorage configure + option). + * Corrected behavior of H5Tinsert to not allow compound datatype fields to + be inserted past the end of the datatype. + * Fixed the internal macros used to encode & decode file metadata, to avoid + an unaligned access warning on IA64 machines. * Fixed an off-by-one error in H5Sselect_valid when hyperslab selections which would allow hyperslab selections which overlapped the edge of the selection by one element as valid. - * Fixed the internal macros used to encode & decode file metadata, to avoid - an unaligned access warning on IA64 machines. - * Corrected behavior of H5Tinsert to not allow compound datatype fields to - be inserted past the end of the datatype. - * Retired the DPSS virtual file driver (--with-gridstorage configure - option). - * Fixed bug where variable-length datatypes for attributes was not working + * Fixed a bug in internal B-tree code where a B-tree was not being copied correctly. - * Fixed bug where raw data re-allocated from the free-list would sometimes - overlap with the metadata accumulator and get corrupted. QAK - 1/23/02 - * 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 - * Fixed data corruption bug in hyperslab routines when contiguous - hyperslab that spans entire dimension and is larger than type - conversion buffer is attempted to be read. QAK - 3/26/02 - * Fixed bug in H5Gget_objinfo() which was not setting the 'fileno' - of the H5G_stat_t struct. QAK - 3/27/02 - * Fixed bug where variable-length string type doesn't behave as string. - * Added serial multi-gigabyte file size test. "test/big -h" shows - the help page. AKC - 2002/03/29 + * Fixed a bug in the 'big' test where quota limits weren't being detected + properly if they caused close() to fail. + * Fixed a bug where 'or'ing a hyperslab with a 'none' selection would + fail. Now adds that hyperslab as the first hyperlab in the selection. + * Fixed a bug where appending a point selection to the current selection + would not actually append the point when there were no points defined + currently. + * Fixed a bug where reading or writing chunked data which needed datatype + conversion could result in data values getting corrupted. + * Fixed a bug where reading an entire dataset wasn't being handled + optimally when the dataset had unlimited dimensions. Dataset is read + in a single low-level I/O now, instead of being broken into separate + pieces internally. + * Fixed a bug when reading chunked datasets where the edge of the dataset + would be incorrectly detected and generate an assertion failure. + * Added new parallel hdf5 tests in t_mpi. The new test checks if the + filesystem or the MPI-IO can really handle greater than 2GB files. + If it fails, it prints information message only without failing the + test. + * Fixed a bug in H5FD_mpio_flush() that might result in negative file seek + if both MPIO and Split-file drivers are used together. + * Fixed H5FDmpio.h to be C++ friendly by making Parallel HDF5 API's to be + external to C++. + * Fixed a bug of H5pubconf.h causing repeated definitions if it is included + more than once. hdf5.h now includes H5public.h which includes + H5pubconf.h. Applications should #include hdf5.h which handles multiple + inclusion correctly. + * Tweaked a few API functions to use 'size_t' instead of 'unsigned' or + 'hsize_t', which may cause errors in some cases. + * Changed behavior of H5Tget_member_type to correctly emulate HDF5 v1.2.x + when --enable-hdf5v1_2 configure flag is enabled. + * Removed limitation that the data transfer buffer size needed to be + set for datasets whose dimensions were too large for the 'all' selection + code to handle. Any size dimensioned datasets should be handled + correctly now. + * The allocation by alignment (H5Pset_alignment) feature code somehow + got dropped in some 1.3.x version. Re-implemented it with "new and + improved" algorithm. It keeps track of "wasted" file-fragment in + the free-list too. + * IMPORTANT: Fixed file metadata corruption bug which could cause metadata + data loss in certain situations. + * Fixed build on Linux systems with --enable-static-exec flag. It now + works correctly. + * Fixed bug with non-zero userblock sizes causing raw data to not write + correctly. + * The RCSID string in H5public.h was causing the C++ compiling problem + because when it was included multiple times, C++ did not like multiple + definitions of the same static variable. All occurance of RCSID + definition are removed since we have not used it consistently before. + * Fixed bug where non-aligned hyperslab I/O on chunked datasets was + causing errors during I/O + * Fixed bug with contiguous hyperslabs not being detected, causing + slower I/O than necessary. Configuration ------------- - * Changed the default value of $NPROCS from 2 to 3 since 3 processes - have a much bigger chance catching parallel errors than just 2. - * Basic port to Compaq (nee DEC) Alpha OSF 5. - * Added --enable-linux-lfs flag to allow more control over whether to enable - or disable large file support on Linux. + * Can use just enable-threadsafe if the C compiler has builtin pthreads + support. * Require HDF (a.k.a. hdf4) software that consists of a newer version of zlib library which consists of the compress2() function. Versions HDF version 4.1r3 and newer meets this requirement. The compress2 uses a newer compression algorithm used by the HDF5 library. Also, 4.1r3 has an hdp tool that can handle "loops" in Vgroups. - * Can use just enable-threadsafe if the C compiler has builtin pthreads - support. + * Added --enable-linux-lfs flag to allow more control over whether to enable + or disable large file support on Linux. + * Basic port to Compaq (nee DEC) Alpha OSF 5. + * Changed the default value of $NPROCS from 2 to 3 since 3 processes + have a much bigger chance catching parallel errors than just 2. Tools ----- - * Fixed segfault when "-v" flag was used with the h5dumper. - * Fixed so that the "-i" flag works correctly with the h5dumper. * Fixed limitation in h5dumper with object names which reached over 1024 characters in length. We can now handle arbitrarily larger sizes for - object names. BW - 2/27/02 + object names. BW - 2002/02/27 + * Fixed so that the "-i" flag works correctly with the h5dumper. + * Fixed segfault when "-v" flag was used with the h5dumper. Documentation @@ -153,9 +156,85 @@ Documentation New Features ============ - * A helper script called ``h5cc'', which helps compilation of HDF5 - programs, is now distributed with HDF5. See the reference manual - for information on how to use this feature. + * Improved performance of single hyperslab I/O when datatype conversion is + unneccessary. QAK - 2002/04/02 + * Added new "H5Sget_select_type" API function to determine which type of + selection is defined for a dataspace ("all", "none", "hyperslab" or + "point"). QAK - 2002/02/7 + * Added support to read/write portions of chunks directly, if they are + uncompressed and too large to cache. This should speed up I/O on chunked + datasets for a few more cases. QAK - 2002/01/31 + * Parallel HDF5 is now supported on HP-UX 11.00 platforms. + * Added H5Rget_obj_type() API function, which performs the same functionality + as H5Rget_object_type(), but requires the reference type as a parameter + in order to correctly handle dataset region references. Moved + H5Rget_object_type() to be only compiled into the library when v1.4 + compatibility is enabled. + * Changed internal error handling macros to reduce code size of library by + about 10-20%. + * Added a new file access property, file close degree, to control file + close behavior. It has four values, H5F_CLOSE_WEAK, H5F_CLOSE_SEMI, + H5F_CLOSE_STRONG, and H5F_CLOSE_DEFAULT. Two correspont functions + H5Pset_fclose_degree and H5Pget_fclose_degree are also provided. Two + new functions H5Fget_obj_count and H5Fget_obj_ids are offerted to assist + this new feature. For full details, please refer to the reference + manual under the description of H5Fcreate, H5Fopen, H5Fclose and the + functions mentioned above. + * Removed H5P(get|set)_hyper_cache API function, since the property is no + longer used. + * Improved performance of non-contiguous hyperslabs (built up with + several hyperslab selection calls). + * Improved performance of single, contiguous hyperslabs when reading or + writing. + * As part of the transition to using generic properties everywhere, the + parameter of H5Pcreate changed from H5P_class_t to hid_t, as well + the return type of H5Pget_class changed from H5P_class_t to hid_t. + Further changes are still necessary and will be documented here as they + are made. + * Added a new test to verify the information provided by the configure + command. + * The H5Pset_fapl_split() accepts raw and meta file names similar to the + syntax of H5Pset_fapl_multi() in addition to what it used to accept. + * Added perform programs to test the HDF5 library performance. Programs + are installed in directory perform/. + * Added new checking in H5check_version() to verify the five HDF5 version + information macros (H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE, + H5_VERS_SUBRELEASE and H5_VERS_INFO) are consistent. + * Added a new public macro, H5_VERS_INFO, which is a string holding + the HDF5 library version information. This string is also compiled + into all HDF5 binary code which helps to identify the version + information of the binary code. One may use the Unix strings + command on the binary file and looks for the pattern "HDF5 library + version". + * Added a parallel HDF5 example examples/ph5example.c to illustrate + the basic way of using parallel HDF5. + * Added two simple parallel performance tests as mpi-perf.c (MPI + performance) and perf.c (PHDF5 performance) in testpar. + * Improved regular hyperslab I/O by about a factor of 6 or so. + * Modified the Pablo build procedure to permit building of the instrumented + library to link either with the Trace libraries as before or with the + Pablo Performance Caputure Facility. + * Verified correct operation of library on Solaris 2.8 in both 64-bit and + 32-bit compilation modes. See INSTALL document for instructions on + compiling the distribution with 64-bit support. + * Parallel HDF5 now runs on the HP V2500 and HP N4000 machines. + * H5 <-> GIF convertor has been added. This is available under + tools/gifconv. The convertor supports the ability to create animated + gifs as well. + * Added a global string variable H5_lib_vers_info_g which holds the + HDF5 library version information. This can be used to identify + an hdf5 library or hdf5 application binary. + Also added a verification of the consistency between H5_lib_vers_info_g + and other version information in the source code. + * File sizes greater than 2GB are now supported on Linux systems with + version 2.4.x or higher kernels. + * F90 APIs are available on HPUX 11.00 and IBM SP platforms. + * F90 static library is available on Windows platforms. See + INSTALL_Windows.txt for details. + * F90 API: + - Added aditional parameter "dims" to the h5dread/h5dwrite and + h5aread/h5awrite subroutines. This parameter is 1D array of size + 7 and contains the sizes of the data buffer dimensions. * C++ API: - Added two new member functions: Exception::getFuncName() and Exception::getCFuncName() to provide the name of the member @@ -165,83 +244,9 @@ New Features implementation. The new operator= functions invoke H5Tcopy, H5Scopy, and H5Pcopy to make a copy of a datatype, dataspace, and property list, respectively. - * F90 API: - - Added aditional parameter "dims" to the h5dread/h5dwrite and - h5aread/h5awrite subroutines. This parameter is 1D array of size - 7 and contains the sizes of the data buffer dimensions. - * F90 static library is available on Windows platforms. See - INSTALL_Windows.txt for details. - * F90 APIs are available on HPUX 11.00 and IBM SP platforms. - * File sizes greater than 2GB are now supported on Linux systems with - version 2.4.x or higher kernels. - * Added a global string variable H5_lib_vers_info_g which holds the - HDF5 library version information. This can be used to identify - an hdf5 library or hdf5 application binary. - Also added a verification of the consistency between H5_lib_vers_info_g - and other version information in the source code. - * H5 <-> GIF convertor has been added. This is available under - tools/gifconv. The convertor supports the ability to create animated - gifs as well. - * Parallel HDF5 now runs on the HP V2500 and HP N4000 machines. - * Verified correct operation of library on Solaris 2.8 in both 64-bit and - 32-bit compilation modes. See INSTALL document for instructions on - compiling the distribution with 64-bit support. - * Modified the Pablo build procedure to permit building of the instrumented - library to link either with the Trace libraries as before or with the - Pablo Performance Caputure Facility. - * Improved regular hyperslab I/O by about a factor of 6 or so. - * Added two simple parallel performance tests as mpi-perf.c (MPI - performance) and perf.c (PHDF5 performance) in testpar. - * Added a parallel HDF5 example examples/ph5example.c to illustrate - the basic way of using parallel HDF5. - * Added a new public macro, H5_VERS_INFO, which is a string holding - the HDF5 library version information. This string is also compiled - into all HDF5 binary code which helps to identify the version - information of the binary code. One may use the Unix strings - command on the binary file and looks for the pattern "HDF5 library - version". - * Added new checking in H5check_version() to verify the five HDF5 version - information macros (H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE, - H5_VERS_SUBRELEASE and H5_VERS_INFO) are consistent. - * Added perform programs to test the HDF5 library performance. Programs - are installed in directory perform/. - * The H5Pset_fapl_split() accepts raw and meta file names similar to the - syntax of H5Pset_fapl_multi() in addition to what it used to accept. - * Added a new test to verify the information provided by the configure - command. - * As part of the transition to using generic properties everywhere, the - parameter of H5Pcreate changed from H5P_class_t to hid_t, as well - the return type of H5Pget_class changed from H5P_class_t to hid_t. - Further changes are still necessary and will be documented here as they - are made. - * Improved performance of single, contiguous hyperslabs when reading or - writing. - * Improved performance of non-contiguous hyperslabs (built up with - several hyperslab selection calls). - * Removed H5P(get|set)_hyper_cache API function, since the property is no - longer used. - * Added a new file access property, file close degree, to control file - close behavior. It has four values, H5F_CLOSE_WEAK, H5F_CLOSE_SEMI, - H5F_CLOSE_STRONG, and H5F_CLOSE_DEFAULT. Two correspont functions - H5Pset_fclose_degree and H5Pget_fclose_degree are also provided. Two - new functions H5Fget_obj_count and H5Fget_obj_ids are offerted to assist - this new feature. For full details, please refer to the reference - manual under the description of H5Fcreate, H5Fopen, H5Fclose and the - functions mentioned above. - * Changed internal error handling macros to reduce code size of library by - about 10-20%. - * Added H5Rget_obj_type() API function, which performs the same functionality - as H5Rget_object_type(), but requires the reference type as a parameter - in order to correctly handle dataset region references. Moved - H5Rget_object_type() to be only compiled into the library when v1.4 - compatibility is enabled. - * Parallel HDF5 is now supported on HP-UX 11.00 platforms. - * Added support to read/write portions of chunks directly, if they are - uncompressed and too large to cache. This should speed up I/O on chunked - datasets for a few more cases. -QAK, 1/31/02 - * Added new "H5Sget_select_type" API function to determine which type of - selection is defined for a dataspace ("all", "none", "hyperslab" or - "point"). -QAK, 2/7/02 + * A helper script called ``h5cc'', which helps compilation of HDF5 + programs, is now distributed with HDF5. See the reference manual + for information on how to use this feature. Platforms Tested diff --git a/src/H5Distore.c b/src/H5Distore.c index 1a9a3d6..c12a98e 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -1695,15 +1695,17 @@ H5F_istore_unlock(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Robb Matzke, 1999-08-02 * The data transfer property list is passed as an object ID * since that's how the virtual file layer wants it. + * + * Quincey Koziol, 2002-04-02 + * Enable hyperslab I/O into memory buffer *------------------------------------------------------------------------- */ herr_t H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, const H5O_pline_t *pline, const H5O_fill_t *fill, + const hsize_t size_m[], const hssize_t offset_m[], const hssize_t offset_f[], const hsize_t size[], void *buf) { - hssize_t offset_m[H5O_LAYOUT_NDIMS]; - hsize_t size_m[H5O_LAYOUT_NDIMS]; hsize_t idx_cur[H5O_LAYOUT_NDIMS]; hsize_t idx_min[H5O_LAYOUT_NDIMS]; hsize_t idx_max[H5O_LAYOUT_NDIMS]; @@ -1726,19 +1728,15 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, assert(layout && H5D_CHUNKED==layout->type); assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(layout->addr)); + assert(size_m); + assert(offset_m); assert(offset_f); assert(size); assert(buf); - /* - * For now, a hyperslab of the file must be read into an array in - * memory.We do not yet support reading into a hyperslab of memory. - */ - for (u=0, chunk_size=1; u<layout->ndims; u++) { - offset_m[u] = 0; - size_m[u] = size[u]; + /* Compute chunk size */ + for (u=0, chunk_size=1; u<layout->ndims; u++) chunk_size *= layout->dim[u]; - } /* end for */ #ifndef NDEBUG for (u=0; u<layout->ndims; u++) { @@ -1874,16 +1872,18 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Robb Matzke, 1999-08-02 * The data transfer property list is passed as an object ID * since that's how the virtual file layer wants it. + * + * Quincey Koziol, 2002-04-02 + * Enable hyperslab I/O into memory buffer *------------------------------------------------------------------------- */ herr_t H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, const H5O_pline_t *pline, const H5O_fill_t *fill, + const hsize_t size_m[], const hssize_t offset_m[], const hssize_t offset_f[], const hsize_t size[], const void *buf) { - hssize_t offset_m[H5O_LAYOUT_NDIMS]; - hsize_t size_m[H5O_LAYOUT_NDIMS]; int i, carry; unsigned u; hsize_t idx_cur[H5O_LAYOUT_NDIMS]; @@ -1905,19 +1905,15 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, assert(layout && H5D_CHUNKED==layout->type); assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(layout->addr)); + assert(size_m); + assert(offset_m); assert(offset_f); assert(size); assert(buf); - /* - * For now the source must not be a hyperslab. It must be an entire - * memory buffer. - */ - for (u=0, chunk_size=1; u<layout->ndims; u++) { - offset_m[u] = 0; - size_m[u] = size[u]; + /* Compute chunk size */ + for (u=0, chunk_size=1; u<layout->ndims; u++) chunk_size *= layout->dim[u]; - } /* end for */ #ifndef NDEBUG for (u=0; u<layout->ndims; u++) { diff --git a/src/H5Dseq.c b/src/H5Dseq.c index 0fec03d..20c71a7 100644 --- a/src/H5Dseq.c +++ b/src/H5Dseq.c @@ -152,6 +152,7 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hsize_t file_offset; /* Offset in dataset */ hsize_t seq_len; /* Number of bytes to read */ hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */ + hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in memory buffer */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */ hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/ hsize_t down_size[H5O_LAYOUT_NDIMS]; /* Cumulative yperslab sizes (in elements) */ @@ -283,10 +284,13 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions"); /* Build the array of cumulative hyperslab sizes */ + /* (And set the memory offset to zero) */ for(acc=1, i=(ndims-1); i>=0; i--) { + mem_offset[i]=0; down_size[i]=acc; acc*=dset_dims[i]; } /* end for */ + mem_offset[ndims]=0; /* Brute-force, stupid way to implement the vectors, but too complex to do other ways... */ for(v=0; v<nseq; v++) { @@ -336,8 +340,9 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read in the partial hyperslab */ - if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_read(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, + buf)<0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } @@ -396,8 +401,8 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read the full hyperslab in */ - if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_read(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, buf)<0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } @@ -443,8 +448,9 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read in the partial hyperslab */ - if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_read(f, dxpl_id, layout, pline, + fill, hslab_size, mem_offset, coords, + hslab_size, buf)<0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } @@ -478,8 +484,9 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read in the partial hyperslab */ - if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_read(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, + buf)<0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } @@ -538,6 +545,7 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hsize_t file_offset; /* Offset in dataset */ hsize_t seq_len; /* Number of bytes to read */ hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */ + hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in memory buffer */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */ hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/ hsize_t down_size[H5O_LAYOUT_NDIMS]; /* Cumulative hyperslab sizes (in elements) */ @@ -671,10 +679,13 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions"); /* Build the array of cumulative hyperslab sizes */ + /* (And set the memory offset to zero) */ for(acc=1, i=(ndims-1); i>=0; i--) { + mem_offset[i]=0; down_size[i]=acc; acc*=dset_dims[i]; } /* end for */ + mem_offset[ndims]=0; /* Brute-force, stupid way to implement the vectors, but too complex to do other ways... */ for(v=0; v<nseq; v++) { @@ -724,8 +735,9 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write out the partial hyperslab */ - if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_write(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset,coords, hslab_size, + buf)<0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); } @@ -784,8 +796,8 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write the full hyperslab in */ - if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_write(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, buf)<0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); } @@ -831,8 +843,9 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write out the partial hyperslab */ - if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_write(f, dxpl_id, layout, pline, + fill, hslab_size, mem_offset, coords, + hslab_size, buf)<0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); } @@ -866,8 +879,9 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write out the final partial hyperslab */ - if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_write(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, + buf)<0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); } diff --git a/src/H5Farray.c b/src/H5Farray.c index 6b4155c..58d8558 100644 --- a/src/H5Farray.c +++ b/src/H5Farray.c @@ -352,29 +352,20 @@ H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, case H5D_CHUNKED: /* - * This method is unable to access external raw data files or to copy - * into a proper hyperslab. + * This method is unable to access external raw data files */ - if (efl && efl->nused>0) { - HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, - "chunking and external files are mutually exclusive"); - } - for (u=0; u<layout->ndims; u++) { - if (0!=mem_offset[u] || hslab_size[u]!=mem_size[u]) { - HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, - "unable to copy into a proper hyperslab"); - } - } - if (H5F_istore_read(f, dxpl_id, layout, pline, fill, file_offset, - hslab_size, buf)<0) { + if (efl && efl->nused>0) + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "chunking and external files are mutually exclusive"); + + /* Go get the data from the chunks */ + if (H5F_istore_read(f, dxpl_id, layout, pline, fill, mem_size, + mem_offset, file_offset, hslab_size, buf)<0) HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); - } break; default: assert("not implemented yet" && 0); - HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, - "unsupported storage layout"); + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout"); } FUNC_LEAVE(SUCCEED); @@ -628,30 +619,20 @@ H5F_arr_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, case H5D_CHUNKED: /* - * This method is unable to access external raw data files or to copy - * from a proper hyperslab. + * This method is unable to access external raw data files */ - if (efl && efl->nused>0) { - HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, - "chunking and external files are mutually exclusive"); - } - for (u=0; u<layout->ndims; u++) { - if (0!=mem_offset[u] || hslab_size[u]!=mem_size[u]) { - HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, - "unable to copy from a proper hyperslab"); - } - } - if (H5F_istore_write(f, dxpl_id, layout, pline, fill, file_offset, - hslab_size, buf)<0) { - HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, - "chunked write failed"); - } + if (efl && efl->nused>0) + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "chunking and external files are mutually exclusive"); + + /* Write the read to the chunks */ + if (H5F_istore_write(f, dxpl_id, layout, pline, fill, mem_size, + mem_offset, file_offset, hslab_size, buf)<0) + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); break; default: assert("not implemented yet" && 0); - HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, - "unsupported storage layout"); + HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout"); } FUNC_LEAVE (SUCCEED); diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 1a9a3d6..c12a98e 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -1695,15 +1695,17 @@ H5F_istore_unlock(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Robb Matzke, 1999-08-02 * The data transfer property list is passed as an object ID * since that's how the virtual file layer wants it. + * + * Quincey Koziol, 2002-04-02 + * Enable hyperslab I/O into memory buffer *------------------------------------------------------------------------- */ herr_t H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, const H5O_pline_t *pline, const H5O_fill_t *fill, + const hsize_t size_m[], const hssize_t offset_m[], const hssize_t offset_f[], const hsize_t size[], void *buf) { - hssize_t offset_m[H5O_LAYOUT_NDIMS]; - hsize_t size_m[H5O_LAYOUT_NDIMS]; hsize_t idx_cur[H5O_LAYOUT_NDIMS]; hsize_t idx_min[H5O_LAYOUT_NDIMS]; hsize_t idx_max[H5O_LAYOUT_NDIMS]; @@ -1726,19 +1728,15 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, assert(layout && H5D_CHUNKED==layout->type); assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(layout->addr)); + assert(size_m); + assert(offset_m); assert(offset_f); assert(size); assert(buf); - /* - * For now, a hyperslab of the file must be read into an array in - * memory.We do not yet support reading into a hyperslab of memory. - */ - for (u=0, chunk_size=1; u<layout->ndims; u++) { - offset_m[u] = 0; - size_m[u] = size[u]; + /* Compute chunk size */ + for (u=0, chunk_size=1; u<layout->ndims; u++) chunk_size *= layout->dim[u]; - } /* end for */ #ifndef NDEBUG for (u=0; u<layout->ndims; u++) { @@ -1874,16 +1872,18 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Robb Matzke, 1999-08-02 * The data transfer property list is passed as an object ID * since that's how the virtual file layer wants it. + * + * Quincey Koziol, 2002-04-02 + * Enable hyperslab I/O into memory buffer *------------------------------------------------------------------------- */ herr_t H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, const H5O_pline_t *pline, const H5O_fill_t *fill, + const hsize_t size_m[], const hssize_t offset_m[], const hssize_t offset_f[], const hsize_t size[], const void *buf) { - hssize_t offset_m[H5O_LAYOUT_NDIMS]; - hsize_t size_m[H5O_LAYOUT_NDIMS]; int i, carry; unsigned u; hsize_t idx_cur[H5O_LAYOUT_NDIMS]; @@ -1905,19 +1905,15 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, assert(layout && H5D_CHUNKED==layout->type); assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(layout->addr)); + assert(size_m); + assert(offset_m); assert(offset_f); assert(size); assert(buf); - /* - * For now the source must not be a hyperslab. It must be an entire - * memory buffer. - */ - for (u=0, chunk_size=1; u<layout->ndims; u++) { - offset_m[u] = 0; - size_m[u] = size[u]; + /* Compute chunk size */ + for (u=0, chunk_size=1; u<layout->ndims; u++) chunk_size *= layout->dim[u]; - } /* end for */ #ifndef NDEBUG for (u=0; u<layout->ndims; u++) { diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h index 822896d..5c81dfc 100644 --- a/src/H5Fpkg.h +++ b/src/H5Fpkg.h @@ -186,12 +186,14 @@ __DLL__ herr_t H5F_istore_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, const struct H5O_fill_t *fill, - const hssize_t offset[], const hsize_t size[], + const hsize_t size_m[], const hssize_t offset_m[], + const hssize_t offset_f[], const hsize_t size[], void *buf/*out*/); __DLL__ herr_t H5F_istore_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, const struct H5O_fill_t *fill, + const hsize_t size_m[], const hssize_t offset_m[], const hssize_t offset[], const hsize_t size[], const void *buf); __DLL__ herr_t H5F_istore_allocate (H5F_t *f, hid_t dxpl_id, diff --git a/src/H5Fseq.c b/src/H5Fseq.c index 0fec03d..20c71a7 100644 --- a/src/H5Fseq.c +++ b/src/H5Fseq.c @@ -152,6 +152,7 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hsize_t file_offset; /* Offset in dataset */ hsize_t seq_len; /* Number of bytes to read */ hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */ + hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in memory buffer */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */ hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/ hsize_t down_size[H5O_LAYOUT_NDIMS]; /* Cumulative yperslab sizes (in elements) */ @@ -283,10 +284,13 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions"); /* Build the array of cumulative hyperslab sizes */ + /* (And set the memory offset to zero) */ for(acc=1, i=(ndims-1); i>=0; i--) { + mem_offset[i]=0; down_size[i]=acc; acc*=dset_dims[i]; } /* end for */ + mem_offset[ndims]=0; /* Brute-force, stupid way to implement the vectors, but too complex to do other ways... */ for(v=0; v<nseq; v++) { @@ -336,8 +340,9 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read in the partial hyperslab */ - if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_read(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, + buf)<0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } @@ -396,8 +401,8 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read the full hyperslab in */ - if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_read(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, buf)<0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } @@ -443,8 +448,9 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read in the partial hyperslab */ - if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_read(f, dxpl_id, layout, pline, + fill, hslab_size, mem_offset, coords, + hslab_size, buf)<0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } @@ -478,8 +484,9 @@ H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read in the partial hyperslab */ - if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_read(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, + buf)<0) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } @@ -538,6 +545,7 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hsize_t file_offset; /* Offset in dataset */ hsize_t seq_len; /* Number of bytes to read */ hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */ + hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in memory buffer */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */ hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/ hsize_t down_size[H5O_LAYOUT_NDIMS]; /* Cumulative hyperslab sizes (in elements) */ @@ -671,10 +679,13 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions"); /* Build the array of cumulative hyperslab sizes */ + /* (And set the memory offset to zero) */ for(acc=1, i=(ndims-1); i>=0; i--) { + mem_offset[i]=0; down_size[i]=acc; acc*=dset_dims[i]; } /* end for */ + mem_offset[ndims]=0; /* Brute-force, stupid way to implement the vectors, but too complex to do other ways... */ for(v=0; v<nseq; v++) { @@ -724,8 +735,9 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write out the partial hyperslab */ - if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_write(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset,coords, hslab_size, + buf)<0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); } @@ -784,8 +796,8 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write the full hyperslab in */ - if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_write(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, buf)<0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); } @@ -831,8 +843,9 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write out the partial hyperslab */ - if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_write(f, dxpl_id, layout, pline, + fill, hslab_size, mem_offset, coords, + hslab_size, buf)<0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); } @@ -866,8 +879,9 @@ H5F_seq_writev(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write out the final partial hyperslab */ - if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords, - hslab_size, buf)<0) { + if (H5F_istore_write(f, dxpl_id, layout, pline, fill, + hslab_size, mem_offset, coords, hslab_size, + buf)<0) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); } @@ -1525,8 +1525,8 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space) /* * Initialize direct read/write functions */ - c1=H5S_select_contiguous(file_space); - c2=H5S_select_contiguous(mem_space); + c1=H5S_select_single(file_space); + c2=H5S_select_single(mem_space); if(c1==FAIL || c2==FAIL) HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, NULL, "invalid check for contiguous dataspace "); @@ -1563,8 +1563,8 @@ H5S_find (const H5S_t *mem_space, const H5S_t *file_space) /* * Initialize direct read/write functions */ - c1=H5S_select_contiguous(file_space); - c2=H5S_select_contiguous(mem_space); + c1=H5S_select_single(file_space); + c2=H5S_select_single(mem_space); if(c1==FAIL || c2==FAIL) HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, NULL, "invalid check for contiguous dataspace "); diff --git a/src/H5Sall.c b/src/H5Sall.c index 3c111f7..1692ff7 100644 --- a/src/H5Sall.c +++ b/src/H5Sall.c @@ -400,18 +400,13 @@ H5S_all_read(H5F_t *f, const H5O_layout_t *layout, const H5O_pline_t *pline, { H5S_hyper_span_t *file_span=NULL,*mem_span=NULL; /* Hyperslab span node */ char *buf=(char*)_buf; /* Get pointer to buffer */ - hsize_t mem_size,file_size; - hssize_t file_off,mem_off; - hssize_t count; /* Regular hyperslab count */ - hsize_t size[H5O_LAYOUT_NDIMS]; - hssize_t file_offset[H5O_LAYOUT_NDIMS]; - hssize_t mem_offset[H5O_LAYOUT_NDIMS]; - unsigned u; - unsigned small_contiguous=0, /* Flags for indicating contiguous hyperslabs */ - large_contiguous=0; - int i; - size_t down_size[H5O_LAYOUT_NDIMS]; - hsize_t acc; + hsize_t mem_elmts,file_elmts; /* Number of elements in each dimension of selection */ + hssize_t file_off,mem_off; /* Offset (in elements) of selection */ + hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Size of memory buffer */ + hsize_t size[H5O_LAYOUT_NDIMS]; /* Size of selection */ + hssize_t file_offset[H5O_LAYOUT_NDIMS]; /* Offset of selection in file */ + hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* Offset of selection in memory */ + unsigned u; /* Index variable */ herr_t ret_value=SUCCEED; FUNC_ENTER(H5S_all_read, FAIL); @@ -428,204 +423,95 @@ printf("%s: check 1.0\n",FUNC); if (mem_space->extent.u.simple.rank!=file_space->extent.u.simple.rank) HGOTO_DONE(SUCCEED); - /* Check for a single hyperslab block defined in memory dataspace */ - if (mem_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "regular" hyperslab selection */ - if(mem_space->select.sel_info.hslab.diminfo != NULL) { - /* Check each dimension */ - for(count=1,u=0; u<mem_space->extent.u.simple.rank; u++) - count*=mem_space->select.sel_info.hslab.diminfo[u].count; - /* If the regular hyperslab definition creates more than one hyperslab, fall through */ - if(count>1) - HGOTO_DONE(SUCCEED); - } /* end if */ - else { - /* Get the pointer to the hyperslab spans to check */ - mem_span=mem_space->select.sel_info.hslab.span_lst->head; - - /* Spin through the spans, checking for more than one span in each dimension */ - while(mem_span!=NULL) { - /* If there are more than one span in the dimension, we can't use this routine */ - if(mem_span->next!=NULL) - HGOTO_DONE(SUCCEED); - - /* Advance to the next span, if it's available */ - if(mem_span->down==NULL) - break; - else - mem_span=mem_span->down->head; - } /* end while */ - - /* Get the pointer to the hyperslab spans to use */ - mem_span=mem_space->select.sel_info.hslab.span_lst->head; - } /* end else */ - } /* end if */ - else - if(mem_space->select.type!=H5S_SEL_ALL) - HGOTO_DONE(SUCCEED); - - /* Check for a single hyperslab block defined in file dataspace */ - if (file_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "regular" hyperslab selection */ - if(file_space->select.sel_info.hslab.diminfo != NULL) { - /* Check each dimension */ - for(count=1,u=0; u<file_space->extent.u.simple.rank; u++) - count*=file_space->select.sel_info.hslab.diminfo[u].count; - /* If the regular hyperslab definition creates more than one hyperslab, fall through */ - if(count>1) - HGOTO_DONE(SUCCEED); - } /* end if */ - else { - /* Get the pointer to the hyperslab spans to check */ - file_span=file_space->select.sel_info.hslab.span_lst->head; - - /* Spin through the spans, checking for more than one span in each dimension */ - while(file_span!=NULL) { - /* If there are more than one span in the dimension, we can't use this routine */ - if(file_span->next!=NULL) - HGOTO_DONE(SUCCEED); - - /* Advance to the next span, if it's available */ - if(file_span->down==NULL) - break; - else - file_span=file_span->down->head; - } /* end while */ - - /* Get the pointer to the hyperslab spans to use */ - file_span=file_space->select.sel_info.hslab.span_lst->head; - } /* end else */ - } /* end if */ - else - if(file_space->select.type!=H5S_SEL_ALL) - HGOTO_DONE(SUCCEED); - /* Get information about memory and file */ for (u=0; u<mem_space->extent.u.simple.rank; u++) { - if(mem_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "regular" hyperslab selection */ - if(mem_space->select.sel_info.hslab.diminfo != NULL) { - mem_size=mem_space->select.sel_info.hslab.diminfo[u].block; - mem_off=mem_space->select.sel_info.hslab.diminfo[u].start; - } /* end if */ - else { - mem_size=(mem_span->high-mem_span->low)+1; - mem_off=mem_span->low; - mem_span=mem_span->down->head; - } /* end else */ - } /* end if */ - else { - mem_size=mem_space->extent.u.simple.size[u]; - mem_off=0; - } /* end else */ - - if(file_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "regular" hyperslab selection */ - if(file_space->select.sel_info.hslab.diminfo != NULL) { - file_size=file_space->select.sel_info.hslab.diminfo[u].block; - file_off=file_space->select.sel_info.hslab.diminfo[u].start; - } /* end if */ - else { - file_size=(file_span->high-file_span->low)+1; - file_off=file_span->low; - file_span=file_span->down->head; - } /* end else */ - } /* end if */ - else { - file_size=file_space->extent.u.simple.size[u]; - file_off=0; - } /* end else */ - - if (mem_size!=file_size) + switch(mem_space->select.type) { + case H5S_SEL_HYPERSLABS: + /* Check for a "regular" hyperslab selection */ + if(mem_space->select.sel_info.hslab.diminfo != NULL) { + mem_elmts=mem_space->select.sel_info.hslab.diminfo[u].block; + mem_off=mem_space->select.sel_info.hslab.diminfo[u].start; + } /* end if */ + else { + mem_elmts=(mem_span->high-mem_span->low)+1; + mem_off=mem_span->low; + mem_span=mem_span->down->head; + } /* end else */ + mem_off+=mem_space->select.offset[u]; + break; + + case H5S_SEL_ALL: + mem_elmts=mem_space->extent.u.simple.size[u]; + mem_off=0; + break; + + case H5S_SEL_POINTS: + mem_elmts=1; + mem_off=mem_space->select.sel_info.pnt_lst->head->pnt[u] + +mem_space->select.offset[u]; + break; + + default: + assert(0 && "Invalid selection type!"); + } /* end switch */ + + switch(file_space->select.type) { + case H5S_SEL_HYPERSLABS: + /* Check for a "regular" hyperslab selection */ + if(file_space->select.sel_info.hslab.diminfo != NULL) { + file_elmts=file_space->select.sel_info.hslab.diminfo[u].block; + file_off=file_space->select.sel_info.hslab.diminfo[u].start; + } /* end if */ + else { + file_elmts=(file_span->high-file_span->low)+1; + file_off=file_span->low; + file_span=file_span->down->head; + } /* end else */ + file_off+=file_space->select.offset[u]; + break; + + case H5S_SEL_ALL: + file_elmts=file_space->extent.u.simple.size[u]; + file_off=0; + break; + + case H5S_SEL_POINTS: + file_elmts=1; + file_off=file_space->select.sel_info.pnt_lst->head->pnt[u] + +file_space->select.offset[u]; + break; + + default: + assert(0 && "Invalid selection type!"); + } /* end switch */ + + if (mem_elmts!=file_elmts) HGOTO_DONE(SUCCEED); - size[u] = file_size; + mem_size[u]=mem_space->extent.u.simple.size[u]; + size[u] = file_elmts; file_offset[u] = file_off; mem_offset[u] = mem_off; } + mem_size[u]=elmt_size; size[u] = elmt_size; file_offset[u] = 0; mem_offset[u] = 0; - /* Disallow reading a memory hyperslab in the "middle" of a dataset which */ - /* spans multiple rows in "interior" dimensions, but allow reading a */ - /* hyperslab which is in the "middle" of the fastest or slowest changing */ - /* dimension because a hyperslab which "fills" the interior dimensions is */ - /* contiguous in memory. i.e. these are allowed: */ - /* --------------------- --------------------- */ - /* | | | | */ - /* |*******************| | ********* | */ - /* |*******************| | | */ - /* | | | | */ - /* | | | | */ - /* --------------------- --------------------- */ - /* ("large" contiguous block) ("small" contiguous block) */ - /* But this is not: */ - /* --------------------- */ - /* | | */ - /* | ********* | */ - /* | ********* | */ - /* | | */ - /* | | */ - /* --------------------- */ - /* (not contiguous in memory) */ - if(mem_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "small" contiguous block */ - if(size[0]==1) { - small_contiguous=1; - /* size of block in all dimensions except the fastest must be '1' */ - for (u=0; u<(mem_space->extent.u.simple.rank-1); u++) { - if(size[u]>1) { - small_contiguous=0; - break; - } /* end if */ - } /* end for */ - } /* end if */ - /* Check for a "large" contiguous block */ - else { - large_contiguous=1; - /* size of block in all dimensions except the slowest must be the */ - /* full size of the dimension */ - for (u=1; u<mem_space->extent.u.simple.rank; u++) { - if(size[u]!=mem_space->extent.u.simple.size[u]) { - large_contiguous=0; - break; - } /* end if */ - } /* end for */ - } /* end else */ - - /* Check for contiguous block */ - if(small_contiguous || large_contiguous) { - /* Compute the "down sizes" for each dimension */ - for (acc=elmt_size, i=(mem_space->extent.u.simple.rank-1); i>=0; i--) { - H5_ASSIGN_OVERFLOW(down_size[i],acc,hsize_t,size_t); - acc*=mem_space->extent.u.simple.size[i]; - } /* end for */ - - /* Adjust the buffer offset and memory offsets by the proper amount */ - for (u=0; u<mem_space->extent.u.simple.rank; u++) { - buf+=mem_offset[u]*down_size[u]; - mem_offset[u]=0; - } /* end for */ - } /* end if */ - else { - /* Non-contiguous hyperslab block */ - HGOTO_DONE(SUCCEED); - } /* end else */ - } /* end if */ - #ifdef QAK printf("%s: check 2.0\n",FUNC); for (u=0; u<mem_space->extent.u.simple.rank; u++) printf("size[%u]=%lu\n",u,(unsigned long)size[u]); for (u=0; u<=mem_space->extent.u.simple.rank; u++) + printf("mem_size[%u]=%lu\n",u,(unsigned long)mem_size[u]); +for (u=0; u<=mem_space->extent.u.simple.rank; u++) printf("mem_offset[%u]=%lu\n",u,(unsigned long)mem_offset[u]); 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, fill, efl, size, - size, mem_offset, file_offset, buf/*out*/)<0) { + mem_size, mem_offset, file_offset, buf/*out*/)<0) { HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read data from the file"); } @@ -671,23 +557,21 @@ H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout, { H5S_hyper_span_t *file_span=NULL,*mem_span=NULL; /* Hyperslab span node */ const char *buf=(const char*)_buf; /* Get pointer to buffer */ - hsize_t mem_size,file_size; - hssize_t file_off,mem_off; - hssize_t count; /* Regular hyperslab count */ - hsize_t size[H5O_LAYOUT_NDIMS]; - hssize_t file_offset[H5O_LAYOUT_NDIMS]; - hssize_t mem_offset[H5O_LAYOUT_NDIMS]; - unsigned u; - unsigned small_contiguous=0, /* Flags for indicating contiguous hyperslabs */ - large_contiguous=0; - int i; - size_t down_size[H5O_LAYOUT_NDIMS]; - hsize_t acc; + hsize_t mem_elmts,file_elmts; /* Number of elements in each dimension of selection */ + hssize_t file_off,mem_off; /* Offset (in elements) of selection */ + hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Size of memory buffer */ + hsize_t size[H5O_LAYOUT_NDIMS]; /* Size of selection */ + hssize_t file_offset[H5O_LAYOUT_NDIMS]; /* Offset of selection in file */ + hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* Offset of selection in memory */ + unsigned u; /* Index variable */ herr_t ret_value=SUCCEED; FUNC_ENTER(H5S_all_write, FAIL); *must_convert = TRUE; +#ifdef QAK +printf("%s: check 1.0\n",FUNC); +#endif /* QAK */ /* Check whether we can handle this */ if (H5S_SIMPLE!=mem_space->extent.type) HGOTO_DONE(SUCCEED); @@ -696,201 +580,100 @@ H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout, if (mem_space->extent.u.simple.rank!=file_space->extent.u.simple.rank) HGOTO_DONE(SUCCEED); - /* Check for a single hyperslab block defined in memory dataspace */ - if (mem_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "regular" hyperslab selection */ - if(mem_space->select.sel_info.hslab.diminfo != NULL) { - /* Check each dimension */ - for(count=1,u=0; u<mem_space->extent.u.simple.rank; u++) - count*=mem_space->select.sel_info.hslab.diminfo[u].count; - /* If the regular hyperslab definition creates more than one hyperslab, fall through */ - if(count>1) - HGOTO_DONE(SUCCEED); - } /* end if */ - else { - /* Get the pointer to the hyperslab spans to check */ - mem_span=mem_space->select.sel_info.hslab.span_lst->head; - - /* Spin through the spans, checking for more than one span in each dimension */ - while(mem_span!=NULL) { - /* If there are more than one span in the dimension, we can't use this routine */ - if(mem_span->next!=NULL) - HGOTO_DONE(SUCCEED); - - /* Advance to the next span, if it's available */ - if(mem_span->down==NULL) - break; - else - mem_span=mem_span->down->head; - } /* end while */ - - /* Get the pointer to the hyperslab spans to use */ - mem_span=mem_space->select.sel_info.hslab.span_lst->head; - } /* end else */ - } /* end if */ - else - if(mem_space->select.type!=H5S_SEL_ALL) - HGOTO_DONE(SUCCEED); - - /* Check for a single hyperslab block defined in file dataspace */ - if (file_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "regular" hyperslab selection */ - if(file_space->select.sel_info.hslab.diminfo != NULL) { - /* Check each dimension */ - for(count=1,u=0; u<file_space->extent.u.simple.rank; u++) - count*=file_space->select.sel_info.hslab.diminfo[u].count; - /* If the regular hyperslab definition creates more than one hyperslab, fall through */ - if(count>1) - HGOTO_DONE(SUCCEED); - } /* end if */ - else { - /* Get the pointer to the hyperslab spans to check */ - file_span=file_space->select.sel_info.hslab.span_lst->head; - - /* Spin through the spans, checking for more than one span in each dimension */ - while(file_span!=NULL) { - /* If there are more than one span in the dimension, we can't use this routine */ - if(file_span->next!=NULL) - HGOTO_DONE(SUCCEED); - - /* Advance to the next span, if it's available */ - if(file_span->down==NULL) - break; - else - file_span=file_span->down->head; - } /* end while */ - - /* Get the pointer to the hyperslab spans to use */ - file_span=file_space->select.sel_info.hslab.span_lst->head; - } /* end else */ - } /* end if */ - else - if(file_space->select.type!=H5S_SEL_ALL) - HGOTO_DONE(SUCCEED); - /* Get information about memory and file */ for (u=0; u<mem_space->extent.u.simple.rank; u++) { - if(mem_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "regular" hyperslab selection */ - if(mem_space->select.sel_info.hslab.diminfo != NULL) { - mem_size=mem_space->select.sel_info.hslab.diminfo[u].block; - mem_off=mem_space->select.sel_info.hslab.diminfo[u].start; - } /* end if */ - else { - mem_size=(mem_span->high-mem_span->low)+1; - mem_off=mem_span->low; - mem_span=mem_span->down->head; - } /* end else */ - } /* end if */ - else { - mem_size=mem_space->extent.u.simple.size[u]; - mem_off=0; - } /* end else */ - - if(file_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "regular" hyperslab selection */ - if(file_space->select.sel_info.hslab.diminfo != NULL) { - file_size=file_space->select.sel_info.hslab.diminfo[u].block; - file_off=file_space->select.sel_info.hslab.diminfo[u].start; - } /* end if */ - else { - file_size=(file_span->high-file_span->low)+1; - file_off=file_span->low; - file_span=file_span->down->head; - } /* end else */ - } /* end if */ - else { - file_size=file_space->extent.u.simple.size[u]; - file_off=0; - } /* end else */ - - if (mem_size!=file_size) + switch(mem_space->select.type) { + case H5S_SEL_HYPERSLABS: + /* Check for a "regular" hyperslab selection */ + if(mem_space->select.sel_info.hslab.diminfo != NULL) { + mem_elmts=mem_space->select.sel_info.hslab.diminfo[u].block; + mem_off=mem_space->select.sel_info.hslab.diminfo[u].start; + } /* end if */ + else { + mem_elmts=(mem_span->high-mem_span->low)+1; + mem_off=mem_span->low; + mem_span=mem_span->down->head; + } /* end else */ + mem_off+=mem_space->select.offset[u]; + break; + + case H5S_SEL_ALL: + mem_elmts=mem_space->extent.u.simple.size[u]; + mem_off=0; + break; + + case H5S_SEL_POINTS: + mem_elmts=1; + mem_off=mem_space->select.sel_info.pnt_lst->head->pnt[u] + +mem_space->select.offset[u]; + break; + + default: + assert(0 && "Invalid selection type!"); + } /* end switch */ + + switch(file_space->select.type) { + case H5S_SEL_HYPERSLABS: + /* Check for a "regular" hyperslab selection */ + if(file_space->select.sel_info.hslab.diminfo != NULL) { + file_elmts=file_space->select.sel_info.hslab.diminfo[u].block; + file_off=file_space->select.sel_info.hslab.diminfo[u].start; + } /* end if */ + else { + file_elmts=(file_span->high-file_span->low)+1; + file_off=file_span->low; + file_span=file_span->down->head; + } /* end else */ + file_off+=file_space->select.offset[u]; + break; + + case H5S_SEL_ALL: + file_elmts=file_space->extent.u.simple.size[u]; + file_off=0; + break; + + case H5S_SEL_POINTS: + file_elmts=1; + file_off=file_space->select.sel_info.pnt_lst->head->pnt[u] + +file_space->select.offset[u]; + break; + + default: + assert(0 && "Invalid selection type!"); + } /* end switch */ + + if (mem_elmts!=file_elmts) HGOTO_DONE(SUCCEED); - size[u] = file_size; + mem_size[u]=mem_space->extent.u.simple.size[u]; + size[u] = file_elmts; file_offset[u] = file_off; mem_offset[u] = mem_off; } + mem_size[u]=elmt_size; size[u] = elmt_size; file_offset[u] = 0; mem_offset[u] = 0; - /* Disallow reading a memory hyperslab in the "middle" of a dataset which */ - /* spans multiple rows in "interior" dimensions, but allow reading a */ - /* hyperslab which is in the "middle" of the fastest or slowest changing */ - /* dimension because a hyperslab which "fills" the interior dimensions is */ - /* contiguous in memory. i.e. these are allowed: */ - /* --------------------- --------------------- */ - /* | | | | */ - /* |*******************| | ********* | */ - /* |*******************| | | */ - /* | | | | */ - /* | | | | */ - /* --------------------- --------------------- */ - /* ("large" contiguous block) ("small" contiguous block) */ - /* But this is not: */ - /* --------------------- */ - /* | | */ - /* | ********* | */ - /* | ********* | */ - /* | | */ - /* | | */ - /* --------------------- */ - /* (not contiguous in memory) */ - if(mem_space->select.type==H5S_SEL_HYPERSLABS) { - /* Check for a "small" contiguous block */ - if(size[0]==1) { - small_contiguous=1; - /* size of block in all dimensions except the fastest must be '1' */ - for (u=0; u<(mem_space->extent.u.simple.rank-1); u++) { - if(size[u]>1) { - small_contiguous=0; - break; - } /* end if */ - } /* end for */ - } /* end if */ - /* Check for a "large" contiguous block */ - else { - large_contiguous=1; - /* size of block in all dimensions except the slowest must be the */ - /* full size of the dimension */ - for (u=1; u<mem_space->extent.u.simple.rank; u++) { - if(size[u]!=mem_space->extent.u.simple.size[u]) { - large_contiguous=0; - break; - } /* end if */ - } /* end for */ - } /* end else */ - - /* Check for contiguous block */ - if(small_contiguous || large_contiguous) { - /* Compute the "down sizes" for each dimension */ - for (acc=elmt_size, i=(mem_space->extent.u.simple.rank-1); i>=0; i--) { - H5_ASSIGN_OVERFLOW(down_size[i],acc,hsize_t,size_t); - acc*=mem_space->extent.u.simple.size[i]; - } /* end for */ - - /* Adjust the buffer offset and memory offsets by the proper amount */ - for (u=0; u<mem_space->extent.u.simple.rank; u++) { - buf+=mem_offset[u]*down_size[u]; - mem_offset[u]=0; - } /* end for */ - } /* end if */ - else { - /* Non-contiguous hyperslab block */ - HGOTO_DONE(SUCCEED); - } /* end else */ - } /* end if */ - +#ifdef QAK +printf("%s: check 2.0\n",FUNC); +for (u=0; u<mem_space->extent.u.simple.rank; u++) + printf("size[%u]=%lu\n",u,(unsigned long)size[u]); +for (u=0; u<=mem_space->extent.u.simple.rank; u++) + printf("mem_size[%u]=%lu\n",u,(unsigned long)mem_size[u]); +for (u=0; u<=mem_space->extent.u.simple.rank; u++) + printf("mem_offset[%u]=%lu\n",u,(unsigned long)mem_offset[u]); +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 */ /* Write data to the file */ if (H5F_arr_write(f, dxpl_id, layout, pline, fill, efl, size, - size, mem_offset, file_offset, buf)<0) { + mem_size, mem_offset, file_offset, buf)<0) { HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write data to the file"); } *must_convert = FALSE; - done: FUNC_LEAVE(ret_value); } diff --git a/src/H5Shyper.c b/src/H5Shyper.c index c6639d7..487de1b 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -5935,6 +5935,84 @@ H5S_hyper_select_contiguous(const H5S_t *space) /*-------------------------------------------------------------------------- NAME + H5S_hyper_select_single + PURPOSE + Check if a hyperslab selection is a single block within the dataspace extent. + USAGE + htri_t H5S_select_single(space) + H5S_t *space; IN: Dataspace pointer to check + RETURNS + TRUE/FALSE/FAIL + DESCRIPTION + Checks to see if the current selection in the dataspace is a single block. + This is primarily used for reading the entire selection in one swoop. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +htri_t +H5S_hyper_select_single(const H5S_t *space) +{ + H5S_hyper_span_info_t *spans; /* Hyperslab span info node */ + H5S_hyper_span_t *span; /* Hyperslab span node */ + unsigned u; /* index variable */ + htri_t ret_value=FALSE; /* return value */ + + FUNC_ENTER (H5S_hyper_select_single, FAIL); + + assert(space); + + /* Check for a "regular" hyperslab selection */ + if(space->select.sel_info.hslab.diminfo != NULL) { + /* + * For a regular hyperslab to be single, it must have only one + * block (i.e. count==1 in all dimensions) + */ + + /* Initialize flags */ + ret_value=TRUE; /* assume true and reset if the dimensions don't match */ + + /* Check for a single block */ + for(u=0; u<space->extent.u.simple.rank; u++) { + if(space->select.sel_info.hslab.diminfo[u].count>1) { + ret_value=FALSE; + break; + } /* end if */ + } /* end for */ + } /* end if */ + else { + /* + * For a region to be single, it must have only one block + */ + /* Initialize flags */ + ret_value=TRUE; /* assume true and reset if the dimensions don't match */ + + /* Get information for slowest changing information */ + spans=space->select.sel_info.hslab.span_lst; + + /* Cycle down the spans until we run out of down spans or find a non-contiguous span */ + while(spans!=NULL) { + span=spans->head; + + /* Check that this is the only span and it spans the entire dimension */ + if(span->next!=NULL) { + ret_value=FALSE; + break; + } /* end if */ + else { + /* Walk down to the next span */ + spans=span->down; + } /* end else */ + } /* end while */ + } /* end else */ + + FUNC_LEAVE (ret_value); +} /* H5S_hyper_select_single() */ + + +/*-------------------------------------------------------------------------- + NAME H5S_hyper_select_iterate_helper PURPOSE Internal routine to iterate over the elements of a span tree hyperslab selection diff --git a/src/H5Spkg.h b/src/H5Spkg.h index 7e3da29..0e6a0c5 100644 --- a/src/H5Spkg.h +++ b/src/H5Spkg.h @@ -132,6 +132,7 @@ __DLL__ herr_t H5S_point_select_serialize(const H5S_t *space, uint8_t *buf); __DLL__ herr_t H5S_point_select_deserialize(H5S_t *space, const uint8_t *buf); __DLL__ herr_t H5S_point_bounds(H5S_t *space, hsize_t *start, hsize_t *end); __DLL__ htri_t H5S_point_select_contiguous(const H5S_t *space); +__DLL__ htri_t H5S_point_select_single(const H5S_t *space); __DLL__ herr_t H5S_select_elements (H5S_t *space, H5S_seloper_t op, size_t num_elem, const hssize_t **coord); __DLL__ herr_t H5S_point_select_iterate(void *buf, hid_t type_id, H5S_t *space, @@ -174,6 +175,7 @@ __DLL__ hssize_t H5S_hyper_span_nblocks(H5S_hyper_span_info_t *spans); __DLL__ herr_t H5S_hyper_span_blocklist(H5S_hyper_span_info_t *spans, hssize_t start[], hssize_t end[], hsize_t rank, hsize_t *startblock, hsize_t *numblocks, hsize_t **buf); __DLL__ herr_t H5S_hyper_bounds(H5S_t *space, hsize_t *start, hsize_t *end); __DLL__ htri_t H5S_hyper_select_contiguous(const H5S_t *space); +__DLL__ htri_t H5S_hyper_select_single(const H5S_t *space); __DLL__ herr_t H5S_hyper_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, void *operator_data); diff --git a/src/H5Spoint.c b/src/H5Spoint.c index 06f198d..5cb9079 100644 --- a/src/H5Spoint.c +++ b/src/H5Spoint.c @@ -1086,6 +1086,7 @@ H5S_point_bounds(H5S_t *space, hsize_t *start, hsize_t *end) FUNC_LEAVE (ret_value); } /* H5Sget_point_bounds() */ + /*-------------------------------------------------------------------------- NAME @@ -1129,6 +1130,43 @@ H5S_point_select_contiguous(const H5S_t *space) /*-------------------------------------------------------------------------- NAME + H5S_point_select_single + PURPOSE + Check if a point selection is single within the dataspace extent. + USAGE + htri_t H5S_point_select_contiguous(space) + H5S_t *space; IN: Dataspace pointer to check + RETURNS + TRUE/FALSE/FAIL + DESCRIPTION + Checks to see if the current selection in the dataspace is a single block. + This is primarily used for reading the entire selection in one swoop. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +htri_t +H5S_point_select_single(const H5S_t *space) +{ + htri_t ret_value=FAIL; /* return value */ + + FUNC_ENTER (H5S_point_select_single, FAIL); + + assert(space); + + /* One point is definitely contiguous */ + if(space->select.num_elem==1) + ret_value=TRUE; + else + ret_value=FALSE; + + FUNC_LEAVE (ret_value); +} /* H5S_point_select_single() */ + + +/*-------------------------------------------------------------------------- + NAME H5S_select_elements PURPOSE Specify a series of elements in the dataspace to select diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index e024502..86a46bc 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -219,6 +219,7 @@ __DLL__ hssize_t H5S_select_serial_size(const H5S_t *space); __DLL__ herr_t H5S_select_serialize(const H5S_t *space, uint8_t *buf); __DLL__ herr_t H5S_select_deserialize(H5S_t *space, const uint8_t *buf); __DLL__ htri_t H5S_select_contiguous(const H5S_t *space); +__DLL__ htri_t H5S_select_single(const H5S_t *space); __DLL__ herr_t H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, void *operator_data); __DLL__ herr_t H5S_sel_iter_release(const H5S_t *space, diff --git a/src/H5Sselect.c b/src/H5Sselect.c index 9fc4149..b592e9f 100644 --- a/src/H5Sselect.c +++ b/src/H5Sselect.c @@ -1316,3 +1316,56 @@ H5Sget_select_type(hid_t space_id) FUNC_LEAVE(space->select.type); } /* end H5Sget_select_type() */ + +/*-------------------------------------------------------------------------- + NAME + H5S_select_single + PURPOSE + Check if the selection is a single block within the dataspace extent. + USAGE + htri_t H5S_select_single(space) + H5S_t *space; IN: Dataspace pointer to check + RETURNS + TRUE/FALSE/FAIL + DESCRIPTION + Checks to see if the current selection in the dataspace is a single block. + This is primarily used for reading the entire selection in one swoop. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +htri_t +H5S_select_single(const H5S_t *space) +{ + htri_t ret_value=FAIL; /* return value */ + + FUNC_ENTER (H5S_select_single, FAIL); + + assert(space); + + switch(space->select.type) { + case H5S_SEL_POINTS: /* Sequence of points selected */ + ret_value=H5S_point_select_single(space); + break; + + case H5S_SEL_HYPERSLABS: /* Hyperslab selection defined */ + ret_value=H5S_hyper_select_single(space); + break; + + case H5S_SEL_ALL: /* Entire extent selected */ + ret_value=TRUE; + break; + + case H5S_SEL_NONE: /* Nothing selected */ + ret_value=FALSE; + break; + + case H5S_SEL_ERROR: + case H5S_SEL_N: + break; + } + + FUNC_LEAVE (ret_value); +} /* H5S_select_single() */ + diff --git a/test/tselect.c b/test/tselect.c index 2a32a78..d0454d6 100644 --- a/test/tselect.c +++ b/test/tselect.c @@ -1227,9 +1227,7 @@ test_select_hyper_contig2(hid_t dset_type, hid_t xfer_plist) hid_t sid1,sid2; /* Dataspace ID */ hsize_t dims2[] = {SPACE8_DIM4, SPACE8_DIM3, SPACE8_DIM2, SPACE8_DIM1}; hssize_t start[SPACE8_RANK]; /* Starting location of hyperslab */ - hsize_t stride[SPACE8_RANK]; /* Stride of hyperslab */ hsize_t count[SPACE8_RANK]; /* Element count of hyperslab */ - hsize_t block[SPACE8_RANK]; /* Block size of hyperslab */ uint16_t *wbuf, /* buffer to write to disk */ *rbuf, /* buffer read from disk */ *tbuf; /* temporary buffer pointer */ @@ -1830,6 +1828,125 @@ test_select_hyper_offset(void) /**************************************************************** ** +** test_select_hyper_offset2(): Test basic H5S (dataspace) selection code. +** Tests optimized hyperslab I/O with selection offsets. +** +****************************************************************/ +static void +test_select_hyper_offset2(void) +{ + hid_t fid1; /* HDF5 File IDs */ + hid_t dataset; /* Dataset ID */ + hid_t sid1,sid2; /* Dataspace ID */ + hsize_t dims1[] = {SPACE7_DIM1, SPACE7_DIM2}; + hsize_t dims2[] = {SPACE7_DIM1, SPACE7_DIM2}; + hssize_t start[SPACE7_RANK]; /* Starting location of hyperslab */ + hsize_t count[SPACE7_RANK]; /* Element count of hyperslab */ + hssize_t offset[SPACE7_RANK]; /* Offset of selection */ + uint8_t *wbuf, /* buffer to write to disk */ + *rbuf, /* buffer read from disk */ + *tbuf, /* temporary buffer pointer */ + *tbuf2; /* temporary buffer pointer */ + int i,j; /* Counters */ + herr_t ret; /* Generic return value */ + htri_t valid; /* Generic boolean return value */ + + /* Output message about test being performed */ + MESSAGE(5, ("Testing More Hyperslab Selection Functions with Offsets\n")); + + /* Allocate write & read buffers */ + wbuf=malloc(sizeof(uint8_t)*SPACE7_DIM1*SPACE7_DIM2); + rbuf=calloc(sizeof(uint8_t),SPACE7_DIM1*SPACE7_DIM2); + + /* Initialize write buffer */ + for(i=0, tbuf=wbuf; i<SPACE7_DIM1; i++) + for(j=0; j<SPACE7_DIM2; j++) + *tbuf++=(uint8_t)((i*SPACE7_DIM2)+j); + + /* Create file */ + fid1 = H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + CHECK(fid1, FAIL, "H5Fcreate"); + + /* Create dataspace for dataset */ + sid1 = H5Screate_simple(SPACE7_RANK, dims1, NULL); + CHECK(sid1, FAIL, "H5Screate_simple"); + + /* Create dataspace for writing buffer */ + sid2 = H5Screate_simple(SPACE7_RANK, dims2, NULL); + CHECK(sid2, FAIL, "H5Screate_simple"); + + /* Select 4x10 hyperslab for disk dataset */ + start[0]=1; start[1]=0; + count[0]=4; count[1]=10; + ret = H5Sselect_hyperslab(sid1,H5S_SELECT_SET,start,NULL,count,NULL); + CHECK(ret, FAIL, "H5Sselect_hyperslab"); + + /* Set offset */ + offset[0]=1; offset[1]=0; + ret = H5Soffset_simple(sid1,offset); + CHECK(ret, FAIL, "H5Soffset_simple"); + valid = H5Sselect_valid(sid1); + VERIFY(valid, TRUE, "H5Sselect_valid"); + + /* Select 4x10 hyperslab for memory dataset */ + start[0]=1; start[1]=0; + count[0]=4; count[1]=10; + ret = H5Sselect_hyperslab(sid2,H5S_SELECT_SET,start,NULL,count,NULL); + CHECK(ret, FAIL, "H5Sselect_hyperslab"); + + /* Choose a valid offset for the memory dataspace */ + offset[0]=2; offset[1]=0; + ret = H5Soffset_simple(sid2,offset); + CHECK(ret, FAIL, "H5Soffset_simple"); + valid = H5Sselect_valid(sid2); + VERIFY(valid, TRUE, "H5Sselect_valid"); + + /* Create a dataset */ + dataset=H5Dcreate(fid1,"Dataset1",H5T_NATIVE_UCHAR,sid1,H5P_DEFAULT); + + /* Write selection to disk */ + ret=H5Dwrite(dataset,H5T_NATIVE_UCHAR,sid2,sid1,H5P_DEFAULT,wbuf); + CHECK(ret, FAIL, "H5Dwrite"); + + /* Read selection from disk */ + ret=H5Dread(dataset,H5T_NATIVE_UCHAR,sid2,sid1,H5P_DEFAULT,rbuf); + CHECK(ret, FAIL, "H5Dread"); + + /* Compare data read with data written out */ + for(i=0; i<4; i++) { + tbuf=wbuf+((i+3)*SPACE7_DIM2); + tbuf2=rbuf+((i+3)*SPACE7_DIM2); + for(j=0; j<SPACE7_DIM2; j++, tbuf++, tbuf2++) { + if(*tbuf!=*tbuf2) { + printf("%d: hyperslab values don't match!, i=%d, j=%d, *tbuf=%u, *tbuf2=%u\n",__LINE__,i,j,(unsigned)*tbuf,(unsigned)*tbuf2); + num_errs++; + } /* end if */ + } /* end for */ + } /* end for */ + + /* Close memory dataspace */ + ret = H5Sclose(sid2); + CHECK(ret, FAIL, "H5Sclose"); + + /* Close disk dataspace */ + ret = H5Sclose(sid1); + CHECK(ret, FAIL, "H5Sclose"); + + /* Close Dataset */ + ret = H5Dclose(dataset); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close file */ + ret = H5Fclose(fid1); + CHECK(ret, FAIL, "H5Fclose"); + + /* Free memory buffers */ + free(wbuf); + free(rbuf); +} /* test_select_hyper_offset2() */ + +/**************************************************************** +** ** test_select_point_offset(): Test basic H5S (dataspace) selection code. ** Tests element selections between dataspaces of various sizes ** and dimensionalities with selection offsets. @@ -4345,6 +4462,7 @@ test_select(void) test_select_hyper_copy(); /* Test hyperslab selection copying code */ test_select_point_copy(); /* Test point selection copying code */ test_select_hyper_offset(); /* Test selection offset code with hyperslabs */ + test_select_hyper_offset2();/* Test more selection offset code with hyperslabs */ test_select_point_offset(); /* Test selection offset code with elements */ test_select_hyper_union(); /* Test hyperslab union code */ #ifdef NEW_HYPERSLAB_API |