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hdf5: fix build on SunOS
2022-03-26 22:52:36 +01:00
# $NetBSD: Makefile.common,v 1.23 2022/03/26 21:52:36 tnn Exp $
Changes 1.8.10: * The following new C function has been added: H5Pget_mpio_no_collective_cause * The following new Fortran subroutine has been added: h5pget_mpio_actual_io_mode_f * The syntax of the following high-level C function has changed: H5TBAget_fill This function’s return type has been changed to h5tri_t. A return value of 1 indicates that a fill value is present, 0 indicates that no fill value is present, and a negative value indicates an error. (The former return type was herr_t.) Note that H5TBAget_fill and a companion function H5TBAget_title, both in the HDF5 Table (H5TB) high-level API, are undocumented. These functions will be added to the HDF5 Reference Manual shortly after HDF5 Release 1.8.10. Changed Command-line Tool * h5import has been updated to accept an input file created by h5dump.
2012-12-09 01:07:38 +01:00
# used by devel/hdf5/Makefile
Update devel/hdf5 from 1.6.10nb1 to 1.8.7. A list of changes is available at http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html A list of new features of 1.8.x release is available at http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html This update removes "cxx" option from the package. New devel/hdf5-c++ should be used instead.
2011-10-07 12:38:50 +02:00
# used by devel/hdf5-c++/Makefile
hdf5: updated to 1.10.7 HDF5 version 1.10.7 released on 2020-09-11 ================================================================================ INTRODUCTION This document describes the differences between this release and the previous HDF5 release. It contains information on the platforms tested and known problems in this release. For more details check the HISTORY*.txt files in the HDF5 source. Note that documentation in the links below will be updated at the time of each final release. Links to HDF5 documentation can be found on The HDF5 web page: https://portal.hdfgroup.org/display/HDF5/HDF5 The official HDF5 releases can be obtained from: https://www.hdfgroup.org/downloads/hdf5/ HDF5 binaries provided are fully tested with ZLIB and the free Open Source SZIP successor Libaec (with BSD license). The official ZLIB and SZIP/Libaec pages are at: ZLIB: http://www.zlib.net/ http://www.zlib.net/zlib_license.html SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec https://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt Changes from Release to Release and New Features in the HDF5-1.10.x release series can be found at: https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS - New Features - Support for new platforms and languages - Bug Fixes since HDF5-1.10.6 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Disable memory sanity checks in the Autotools in release branches The library can be configured to use internal memory sanity checking, which replaces C API calls like malloc(3) and free(3) with our own calls which add things like heap canaries. These canaries can cause problems when external filter plugins reallocate canary-marked buffers. For this reason, the default will be to not use the memory allocation sanity check feature in release branches (e.g., hdf5_1_10_7). Debug builds in development branches (e.g., develop, hdf5_1_10) will still use them by default. This change only affects Autotools debug builds. Non-debug autotools builds and all CMake builds do not enable this feature by default. (DER - 2020/08/19) - Add file locking configure and CMake options HDF5 1.10.0 introduced a file locking scheme, primarily to help enforce SWMR setup. Formerly, the only user-level control of the scheme was via the HDF5_USE_FILE_LOCKING environment variable. This change introduces configure-time options that control whether or not file locking will be used and whether or not the library ignores errors when locking has been disabled on the file system (useful on some HPC Lustre installations). In both the Autotools and CMake, the settings have the effect of changing the default property list settings (see the H5Pset/get_file_locking() entry, below). The yes/no/best-effort file locking configure setting has also been added to the libhdf5.settings file. Autotools: An --enable-file-locking=(yes|no|best-effort) option has been added. yes: Use file locking. no: Do not use file locking. best-effort: Use file locking and ignore "disabled" errors. CMake: Two self-explanatory options have been added: HDF5_USE_FILE_LOCKING HDF5_IGNORE_DISABLED_FILE_LOCKS Setting both of these to ON is the equivalent to the Autotools' best-effort setting. NOTE: The precedence order of the various file locking control mechanisms is: 1) HDF5_USE_FILE_LOCKING environment variable (highest) 2) H5Pset_file_locking() 3) configure/CMake options (which set the property list defaults) 4) library defaults (currently best-effort) (DER - 2020/07/30, HDFFV-11092) - CMake option to link the generated Fortran MOD files into the include directory. The Fortran generation of MOD files by a Fortran compile can produce different binary files between SHARED and STATIC compiles with different compilers and/or different platforms. Note that it has been found that different versions of Fortran compilers will produce incompatible MOD files. Currently, CMake will locate these MOD files in subfolders of the include directory and add that path to the Fortran library target in the CMake config file, which can be used by the CMake find library process. For other build systems using the binary from a CMake install, a new CMake configuration can be used to copy the pre-chosen version of the Fortran MOD files into the install include directory. The default will depend on the configuration of BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: YES YES Default to SHARED YES NO Default to STATIC NO YES Default to SHARED NO NO Default to SHARED The defaults can be overriden by setting the config option HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC (ADB - 2020/07/09, HDFFV-11116) - CMake option to use AEC (open source SZip) library instead of SZip The open source AEC library is a replacement library for SZip. In order to use it for hdf5, the libaec CMake source was changed to add "-fPIC" and exclude test files. A new option USE_LIBAEC is required to compensate for the different files produced by AEC build. Autotools does not build the compression libraries within hdf5 builds, but will use an installed libaec when configured as before with the option --with-libsz=<path to libaec directory>. (ADB - 2020/04/22, OESS-65) - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER Some handcrafted tests in HDFTests.c have been removed and the CMake CHECK_STRUCT_HAS_MEMBER module has been used. (ADB - 2020/03/24, TRILAB-24) - Both build systems use same set of warnings flags GNU C, C++ and gfortran warnings flags were moved to files in a config sub-folder named gnu-warnings. Flags that only are available for a specific version of the compiler are in files named with that version. Clang C warnings flags were moved to files in a config sub-folder named clang-warnings. Intel C, Fortran warnings flags were moved to files in a config sub-folder named intel-warnings. There are flags in named "error-xxx" files with warnings that may be promoted to errors. Some source files may still need fixes. There are also pairs of files named "developer-xxx" and "no-developer-xxx" that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the configure option:--enable-developer-warnings. In addition, CMake no longer applies these warnings for examples. (ADB - 2020/03/24, TRILAB-192) - Update CMake minimum version to 3.12 Updated CMake minimum version to 3.12 and added version checks for Windows features. (ADB - 2020/02/05, TRILABS-142) - Fixed CMake include properties for Fortran libraries Corrected the library properties for Fortran to use the correct path for the Fortran module files. (ADB - 2020/02/04, HDFFV-11012) - Added common warnings files for gnu and intel Added warnings files to use one common set of flags during configure for both autotools and CMake build systems. The initial implementation only affects a general set of flags for gnu and intel compilers. (ADB - 2020/01/17) - Added new options to CMake for control of testing Added CMake options (default ON); HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL combined with: HDF5_TEST_TOOLS HDF5_TEST_EXAMPLES HDF5_TEST_SWMR HDF5_TEST_FORTRAN HDF5_TEST_CPP HDF5_TEST_JAVA (ADB - 2020/01/15, HDFFV-11001) - Added Clang sanitizers to CMake for analyzer support if compiler is clang. Added CMake code and files to execute the Clang sanitizers if HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option is set to one of the following: Address Memory MemoryWithOrigins Undefined Thread Leak 'Address;Undefined' (ADB - 2019/12/12, TRILAB-135) Library: -------- - Add metadata cache optimization to reduce skip list usage On file flush or close, the metadata cache attempts to write out all dirty entries in increasing address order. To do this, it needs an address sorted list of metadata entries. Further, since flushing one metadata cache entry can dirty another, this list must support efficient insertion and deletion. The metadata cache uses a skip list of all dirty entries for this purpose. Before this release, this skip list was maintained at all times. However, since profiling indicates that this imposes a significant cost, we now construct and maintain the skip list only when needed. Specifically, we enable the skip list and load it with a list of all dirty entries in the metadata cache just before a flush, and disable it after the flush. (JRM - 2020/08/17, HDFFV-11034) - Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that were previously accepted. This option turns on file locking but ignores locking errors when the library detects that file locking has been disabled on a file system (useful on some HPC Lustre installations). The capitalization of BEST_EFFORT is mandatory. See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Add H5Pset/get_file_locking() API calls This change adds new API calls which can be used to set or get the file locking parameters. The single API call sets both the "use file locking" flag and the "ignore disabled file locking" flag. When opening a file multiple times without closing, the file MUST be opened with the same file locking settings. Opening a file with different file locking settings will fail (this is similar to the behavior of H5Pset_fclose_degree()). See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Add Mirror VFD Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote machine. Must be used in conjunction with the Splitter VFD. (JOS - 2020/03/13, TBD) - Add Splitter VFD Maintain separate R/W and W/O channels for "concurrent" file writes to two files using a single HDF5 file handle. (JOS - 2020/03/13, TBD) - Fixed an assertion failure in the parallel library when collectively filling chunks. As it is required that chunks be written in monotonically non-decreasing order of offset in the file, this assertion was being triggered when the list of chunk file space allocations being passed to the collective chunk filling routine was not sorted according to this particular requirement. The addition of a sort of the out of order chunks trades a bit of performance for the elimination of this assertion and of any complaints from MPI implementations about the file offsets used being out of order. (JTH - 2019/10/07) Fortran Library: ---------------- - Add wrappers for H5Pset/get_file_locking() API calls h5pget_file_locking_f() h5pset_file_locking_f() See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Added new Fortran parameters: H5F_LIBVER_ERROR_F H5F_LIBVER_NBOUNDS_F H5F_LIBVER_V18_F H5F_LIBVER_V110_F - Added new Fortran API: h5pget_libver_bounds_f (MSB - 2020/02/11, HDFFV-11018) C++ Library: ------------ - Add wrappers for H5Pset/get_file_locking() API calls FileAccPropList::setFileLocking() FileAccPropList::getFileLocking() See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) Java Library: ---------------- - Add wrappers for H5Pset/get_file_locking() API calls H5Pset_file_locking() H5Pget_use_file_locking() H5Pget_ignore_disabled_file_locking() Unlike the C++ and Fortran wrappers, there are separate getters for the two file locking settings, each of which returns a boolean value. See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) Tools: ------ - h5repack added options to control how external links are handled. Currently h5repack preserves external links and cannot copy and merge data from the external files. Two options, merge and prune, were added to control how to merge data from an external link into the resulting file. --merge Follow external soft link recursively and merge data. --prune Do not follow external soft links and remove link. --merge --prune Follow external link, merge data and remove dangling link. (ADB - 2020/08/05, HDFFV-9984) High-Level APIs: --------------- - None C Packet Table API ------------------ - None Internal header file -------------------- - None Documentation ------------- - None Support for new platforms, languages and compilers. ======================================= - None Bug Fixes since HDF5-1.10.6 release ================================== Library ------- - Fix bug and simplify collective metadata write operation when some ranks have no entries to contribute. This fixes parallel regression test failures with IBM SpectrumScale MPI on the Summit system at ORNL. (QAK - 2020/09/02) - Avoid setting up complex MPI types with 0-length vectors, which some MPI implementations don't handle well. (In particular, IBM SpectrumScale MPI on the Summit system at ORNL) (QAK - 2020/08/21) - Fixed use-of-uninitialized-value error Appropriate initialization of local structs was added to remove the use-of-uninitialized-value errors reported by MemorySanitizer. (BMR - 2020/8/13, HDFFV-11101) - Creation of dataset with optional filter When the combination of type, space, etc doesn't work for filter and the filter is optional, it was supposed to be skipped but it was not skipped and the creation failed. A fix is applied to allow the creation of a dataset in such situation, as specified in the user documentation. (BMR - 2020/8/13, HDFFV-10933) - Explicitly declared dlopen to use RTLD_LOCAL dlopen documentation states that if neither RTLD_GLOBAL nor RTLD_LOCAL are specified, then the default behavior is unspecified. The default on linux is usually RTLD_LOCAL while macos will default to RTLD_GLOBAL. (ADB - 2020/08/12, HDFFV-11127) - Fixed issues CVE-2018-13870 and CVE-2018-13869 When a buffer overflow occurred because a name length was corrupted and became very large, h5dump crashed on memory access violation. A check for reading past the end of the buffer was added to multiple locations to prevent the crashes and h5dump now simply fails with an error message when this error condition occurs. (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121) - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which causes asserts/errors when passed to other dataspace API calls. H5S_NO_CLASS is an internal class value that should not have been exposed via a public API call. In debug builds of the library, this can cause asserts to trip. In non-debug builds, it will produce normal library errors. The new library behavior is for H5Sset_extent_none() to convert the dataspace into one of type H5S_NULL, which is better handled by the library and easier for developers to reason about. (DER - 2020/07/27, HDFFV-11027) - Fixed the segmentation fault when reading attributes with multiple threads It was reported that the reading of attributes with variable length string datatype will crash with segmentation fault particularly when the number of threads is high (>16 threads). The problem was due to the file pointer that was set in the variable length string datatype for the attribute. That file pointer was already closed when the attribute was accessed. The problem was fixed by setting the file pointer to the current opened file pointer when the attribute was accessed. Similar patch up was done before when reading dataset with variable length string datatype. (VC - 2020/07/13, HDFFV-11080) - Fixed issue CVE-2018-17438 A division by zero was discovered in H5D__select_io() of H5Dselect.c. https://security-tracker.debian.org/tracker/CVE-2018-17438 A check was added to protect against division by zero. When such situation occurs again, the normal HDF5 error handling will be invoked, instead of segmentation fault. (BMR, DER - 2020/07/09, HDFFV-10587) - Fixed CVE-2018-17435 The tool h52gif produced a segfault when the size of an attribute message was corrupted and caused a buffer overflow. The problem was fixed by verifying the attribute message's size against the buffer size before accessing the buffer. h52gif was also fixed to display the failure instead of silently exiting after the segfault was eliminated. (BMR - 2020/6/19, HDFFV-10591) - Don't allocate an empty (0-dimensioned) chunked dataset's chunk index, until the dataset's dimensions are increased. (QAK - 2020/05/07) Configuration ------------- - Stopped addition of szip header and include directory path for incompatible libsz szlib.h is the same for both 32-bit and 64-bit szip, and the header file and its path were added to the HDF5 binary even though the configure check of a function in libsz later failed and szip compression was not enabled. The header file and include path are now added only when the libsz function passes the configure check. (LRK - 2020/08/17, HDFFV-10830) - Added -fsanitize=address autotools configure option for Clang compiler Clang sanitizer options were also added for Clang compilers with CMake. (LRK, 2020/08/05, HDFFV-10836) - Updated testh5cc.sh.in for functions versioned in HDF5 1.10. testh5cc.sh previously tested that the correct version of a function versioned in HDF5 1.6 or 1.8 was compiled when one of H5_NO_DEPRECATED_SYMBOLS or H5_USE_16_API_DEFAULT were defined. This test was extended for additional testing with H5_USE_18_API_DEFAULT. (LRK, 2020/06/22, HDFFV-11000) - Fixed CMake include properties for Fortran libraries Corrected the library properties for Fortran to use the correct path for the Fortran module files. (ADB - 2020/02/04, HDFFV-11012) Performance ------------- - None Java Library: ---------------- - None Fortran -------- - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. (MSB - 2020/2/18, HDFFV-11029) - Fixed configure issue when building HDF5 with NAG Fortran 7.0. HDF5 now accounts for the addition of half-precision floating-point in NAG 7.0 with a KIND=16. (MSB - 2020/02/28, HDFFV-11033) Tools ----- - The tools library was updated by standardizing the error stack process. General sequence is: h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); h5tools_init(); ... process the command-line (check for error-stack enable) ... h5tools_error_report(); ... (do work) ... h5diff_exit(ret); (ADB - 2020/07/20, HDFFV-11066) - h5diff fixed a command line parsing error. h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used. (ADB - 2020/07/20, HDFFV-10897) - h5diff added a command line option to ignore attributes. h5diff would ignore all objects with a supplied path if the exclude-path argument is used. Adding the exclude-attribute argument will only eclude attributes, with the supplied path, from comparision. (ADB - 2020/07/20, HDFFV-5935) - h5diff added another level to the verbose argument to print filenames. Added verbose level 3 that is level 2 plus the filenames. The levels are: 0 : Identical to '-v' or '--verbose' 1 : All level 0 information plus one-line attribute status summary 2 : All level 1 information plus extended attribute status report 3 : All level 2 information plus file names (ADB - 2020/07/20, HDFFV-10005) - h5repack was fixed to repack the reference attributes properly. The code line that checks if the update of reference inside a compound datatype is misplaced outside the code block loop that carries out the check. In consequence, the next attribute that is not the reference type was repacked again as the reference type and caused the failure of repacking. The fix is to move the corresponding code line to the correct code block. (KY -2020/02/10, HDFFV-11014) High-Level APIs: ------ - The H5DSis_scale function was updated to return "not a dimension scale" (0) instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are not written according to Dimension Scales Specification. (EIP - 2020/08/12, HDFFV-10436) Fortran High-Level APIs: ------ - None Documentation ------------- - None F90 APIs -------- - None C++ APIs -------- - None Testing ------- - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. (LRK, 2020/7/2, HDFFV-11063)
2021-06-07 13:52:48 +02:00
DISTNAME= hdf5-1.10.7
Update devel/hdf5 from 1.6.10nb1 to 1.8.7. A list of changes is available at http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html A list of new features of 1.8.x release is available at http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html This update removes "cxx" option from the package. New devel/hdf5-c++ should be used instead.
2011-10-07 12:38:50 +02:00
CATEGORIES= devel
hdf5: updated to 1.10.7 HDF5 version 1.10.7 released on 2020-09-11 ================================================================================ INTRODUCTION This document describes the differences between this release and the previous HDF5 release. It contains information on the platforms tested and known problems in this release. For more details check the HISTORY*.txt files in the HDF5 source. Note that documentation in the links below will be updated at the time of each final release. Links to HDF5 documentation can be found on The HDF5 web page: https://portal.hdfgroup.org/display/HDF5/HDF5 The official HDF5 releases can be obtained from: https://www.hdfgroup.org/downloads/hdf5/ HDF5 binaries provided are fully tested with ZLIB and the free Open Source SZIP successor Libaec (with BSD license). The official ZLIB and SZIP/Libaec pages are at: ZLIB: http://www.zlib.net/ http://www.zlib.net/zlib_license.html SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec https://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt Changes from Release to Release and New Features in the HDF5-1.10.x release series can be found at: https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS - New Features - Support for new platforms and languages - Bug Fixes since HDF5-1.10.6 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Disable memory sanity checks in the Autotools in release branches The library can be configured to use internal memory sanity checking, which replaces C API calls like malloc(3) and free(3) with our own calls which add things like heap canaries. These canaries can cause problems when external filter plugins reallocate canary-marked buffers. For this reason, the default will be to not use the memory allocation sanity check feature in release branches (e.g., hdf5_1_10_7). Debug builds in development branches (e.g., develop, hdf5_1_10) will still use them by default. This change only affects Autotools debug builds. Non-debug autotools builds and all CMake builds do not enable this feature by default. (DER - 2020/08/19) - Add file locking configure and CMake options HDF5 1.10.0 introduced a file locking scheme, primarily to help enforce SWMR setup. Formerly, the only user-level control of the scheme was via the HDF5_USE_FILE_LOCKING environment variable. This change introduces configure-time options that control whether or not file locking will be used and whether or not the library ignores errors when locking has been disabled on the file system (useful on some HPC Lustre installations). In both the Autotools and CMake, the settings have the effect of changing the default property list settings (see the H5Pset/get_file_locking() entry, below). The yes/no/best-effort file locking configure setting has also been added to the libhdf5.settings file. Autotools: An --enable-file-locking=(yes|no|best-effort) option has been added. yes: Use file locking. no: Do not use file locking. best-effort: Use file locking and ignore "disabled" errors. CMake: Two self-explanatory options have been added: HDF5_USE_FILE_LOCKING HDF5_IGNORE_DISABLED_FILE_LOCKS Setting both of these to ON is the equivalent to the Autotools' best-effort setting. NOTE: The precedence order of the various file locking control mechanisms is: 1) HDF5_USE_FILE_LOCKING environment variable (highest) 2) H5Pset_file_locking() 3) configure/CMake options (which set the property list defaults) 4) library defaults (currently best-effort) (DER - 2020/07/30, HDFFV-11092) - CMake option to link the generated Fortran MOD files into the include directory. The Fortran generation of MOD files by a Fortran compile can produce different binary files between SHARED and STATIC compiles with different compilers and/or different platforms. Note that it has been found that different versions of Fortran compilers will produce incompatible MOD files. Currently, CMake will locate these MOD files in subfolders of the include directory and add that path to the Fortran library target in the CMake config file, which can be used by the CMake find library process. For other build systems using the binary from a CMake install, a new CMake configuration can be used to copy the pre-chosen version of the Fortran MOD files into the install include directory. The default will depend on the configuration of BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: YES YES Default to SHARED YES NO Default to STATIC NO YES Default to SHARED NO NO Default to SHARED The defaults can be overriden by setting the config option HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC (ADB - 2020/07/09, HDFFV-11116) - CMake option to use AEC (open source SZip) library instead of SZip The open source AEC library is a replacement library for SZip. In order to use it for hdf5, the libaec CMake source was changed to add "-fPIC" and exclude test files. A new option USE_LIBAEC is required to compensate for the different files produced by AEC build. Autotools does not build the compression libraries within hdf5 builds, but will use an installed libaec when configured as before with the option --with-libsz=<path to libaec directory>. (ADB - 2020/04/22, OESS-65) - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER Some handcrafted tests in HDFTests.c have been removed and the CMake CHECK_STRUCT_HAS_MEMBER module has been used. (ADB - 2020/03/24, TRILAB-24) - Both build systems use same set of warnings flags GNU C, C++ and gfortran warnings flags were moved to files in a config sub-folder named gnu-warnings. Flags that only are available for a specific version of the compiler are in files named with that version. Clang C warnings flags were moved to files in a config sub-folder named clang-warnings. Intel C, Fortran warnings flags were moved to files in a config sub-folder named intel-warnings. There are flags in named "error-xxx" files with warnings that may be promoted to errors. Some source files may still need fixes. There are also pairs of files named "developer-xxx" and "no-developer-xxx" that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the configure option:--enable-developer-warnings. In addition, CMake no longer applies these warnings for examples. (ADB - 2020/03/24, TRILAB-192) - Update CMake minimum version to 3.12 Updated CMake minimum version to 3.12 and added version checks for Windows features. (ADB - 2020/02/05, TRILABS-142) - Fixed CMake include properties for Fortran libraries Corrected the library properties for Fortran to use the correct path for the Fortran module files. (ADB - 2020/02/04, HDFFV-11012) - Added common warnings files for gnu and intel Added warnings files to use one common set of flags during configure for both autotools and CMake build systems. The initial implementation only affects a general set of flags for gnu and intel compilers. (ADB - 2020/01/17) - Added new options to CMake for control of testing Added CMake options (default ON); HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL combined with: HDF5_TEST_TOOLS HDF5_TEST_EXAMPLES HDF5_TEST_SWMR HDF5_TEST_FORTRAN HDF5_TEST_CPP HDF5_TEST_JAVA (ADB - 2020/01/15, HDFFV-11001) - Added Clang sanitizers to CMake for analyzer support if compiler is clang. Added CMake code and files to execute the Clang sanitizers if HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option is set to one of the following: Address Memory MemoryWithOrigins Undefined Thread Leak 'Address;Undefined' (ADB - 2019/12/12, TRILAB-135) Library: -------- - Add metadata cache optimization to reduce skip list usage On file flush or close, the metadata cache attempts to write out all dirty entries in increasing address order. To do this, it needs an address sorted list of metadata entries. Further, since flushing one metadata cache entry can dirty another, this list must support efficient insertion and deletion. The metadata cache uses a skip list of all dirty entries for this purpose. Before this release, this skip list was maintained at all times. However, since profiling indicates that this imposes a significant cost, we now construct and maintain the skip list only when needed. Specifically, we enable the skip list and load it with a list of all dirty entries in the metadata cache just before a flush, and disable it after the flush. (JRM - 2020/08/17, HDFFV-11034) - Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that were previously accepted. This option turns on file locking but ignores locking errors when the library detects that file locking has been disabled on a file system (useful on some HPC Lustre installations). The capitalization of BEST_EFFORT is mandatory. See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Add H5Pset/get_file_locking() API calls This change adds new API calls which can be used to set or get the file locking parameters. The single API call sets both the "use file locking" flag and the "ignore disabled file locking" flag. When opening a file multiple times without closing, the file MUST be opened with the same file locking settings. Opening a file with different file locking settings will fail (this is similar to the behavior of H5Pset_fclose_degree()). See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Add Mirror VFD Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote machine. Must be used in conjunction with the Splitter VFD. (JOS - 2020/03/13, TBD) - Add Splitter VFD Maintain separate R/W and W/O channels for "concurrent" file writes to two files using a single HDF5 file handle. (JOS - 2020/03/13, TBD) - Fixed an assertion failure in the parallel library when collectively filling chunks. As it is required that chunks be written in monotonically non-decreasing order of offset in the file, this assertion was being triggered when the list of chunk file space allocations being passed to the collective chunk filling routine was not sorted according to this particular requirement. The addition of a sort of the out of order chunks trades a bit of performance for the elimination of this assertion and of any complaints from MPI implementations about the file offsets used being out of order. (JTH - 2019/10/07) Fortran Library: ---------------- - Add wrappers for H5Pset/get_file_locking() API calls h5pget_file_locking_f() h5pset_file_locking_f() See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Added new Fortran parameters: H5F_LIBVER_ERROR_F H5F_LIBVER_NBOUNDS_F H5F_LIBVER_V18_F H5F_LIBVER_V110_F - Added new Fortran API: h5pget_libver_bounds_f (MSB - 2020/02/11, HDFFV-11018) C++ Library: ------------ - Add wrappers for H5Pset/get_file_locking() API calls FileAccPropList::setFileLocking() FileAccPropList::getFileLocking() See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) Java Library: ---------------- - Add wrappers for H5Pset/get_file_locking() API calls H5Pset_file_locking() H5Pget_use_file_locking() H5Pget_ignore_disabled_file_locking() Unlike the C++ and Fortran wrappers, there are separate getters for the two file locking settings, each of which returns a boolean value. See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) Tools: ------ - h5repack added options to control how external links are handled. Currently h5repack preserves external links and cannot copy and merge data from the external files. Two options, merge and prune, were added to control how to merge data from an external link into the resulting file. --merge Follow external soft link recursively and merge data. --prune Do not follow external soft links and remove link. --merge --prune Follow external link, merge data and remove dangling link. (ADB - 2020/08/05, HDFFV-9984) High-Level APIs: --------------- - None C Packet Table API ------------------ - None Internal header file -------------------- - None Documentation ------------- - None Support for new platforms, languages and compilers. ======================================= - None Bug Fixes since HDF5-1.10.6 release ================================== Library ------- - Fix bug and simplify collective metadata write operation when some ranks have no entries to contribute. This fixes parallel regression test failures with IBM SpectrumScale MPI on the Summit system at ORNL. (QAK - 2020/09/02) - Avoid setting up complex MPI types with 0-length vectors, which some MPI implementations don't handle well. (In particular, IBM SpectrumScale MPI on the Summit system at ORNL) (QAK - 2020/08/21) - Fixed use-of-uninitialized-value error Appropriate initialization of local structs was added to remove the use-of-uninitialized-value errors reported by MemorySanitizer. (BMR - 2020/8/13, HDFFV-11101) - Creation of dataset with optional filter When the combination of type, space, etc doesn't work for filter and the filter is optional, it was supposed to be skipped but it was not skipped and the creation failed. A fix is applied to allow the creation of a dataset in such situation, as specified in the user documentation. (BMR - 2020/8/13, HDFFV-10933) - Explicitly declared dlopen to use RTLD_LOCAL dlopen documentation states that if neither RTLD_GLOBAL nor RTLD_LOCAL are specified, then the default behavior is unspecified. The default on linux is usually RTLD_LOCAL while macos will default to RTLD_GLOBAL. (ADB - 2020/08/12, HDFFV-11127) - Fixed issues CVE-2018-13870 and CVE-2018-13869 When a buffer overflow occurred because a name length was corrupted and became very large, h5dump crashed on memory access violation. A check for reading past the end of the buffer was added to multiple locations to prevent the crashes and h5dump now simply fails with an error message when this error condition occurs. (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121) - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which causes asserts/errors when passed to other dataspace API calls. H5S_NO_CLASS is an internal class value that should not have been exposed via a public API call. In debug builds of the library, this can cause asserts to trip. In non-debug builds, it will produce normal library errors. The new library behavior is for H5Sset_extent_none() to convert the dataspace into one of type H5S_NULL, which is better handled by the library and easier for developers to reason about. (DER - 2020/07/27, HDFFV-11027) - Fixed the segmentation fault when reading attributes with multiple threads It was reported that the reading of attributes with variable length string datatype will crash with segmentation fault particularly when the number of threads is high (>16 threads). The problem was due to the file pointer that was set in the variable length string datatype for the attribute. That file pointer was already closed when the attribute was accessed. The problem was fixed by setting the file pointer to the current opened file pointer when the attribute was accessed. Similar patch up was done before when reading dataset with variable length string datatype. (VC - 2020/07/13, HDFFV-11080) - Fixed issue CVE-2018-17438 A division by zero was discovered in H5D__select_io() of H5Dselect.c. https://security-tracker.debian.org/tracker/CVE-2018-17438 A check was added to protect against division by zero. When such situation occurs again, the normal HDF5 error handling will be invoked, instead of segmentation fault. (BMR, DER - 2020/07/09, HDFFV-10587) - Fixed CVE-2018-17435 The tool h52gif produced a segfault when the size of an attribute message was corrupted and caused a buffer overflow. The problem was fixed by verifying the attribute message's size against the buffer size before accessing the buffer. h52gif was also fixed to display the failure instead of silently exiting after the segfault was eliminated. (BMR - 2020/6/19, HDFFV-10591) - Don't allocate an empty (0-dimensioned) chunked dataset's chunk index, until the dataset's dimensions are increased. (QAK - 2020/05/07) Configuration ------------- - Stopped addition of szip header and include directory path for incompatible libsz szlib.h is the same for both 32-bit and 64-bit szip, and the header file and its path were added to the HDF5 binary even though the configure check of a function in libsz later failed and szip compression was not enabled. The header file and include path are now added only when the libsz function passes the configure check. (LRK - 2020/08/17, HDFFV-10830) - Added -fsanitize=address autotools configure option for Clang compiler Clang sanitizer options were also added for Clang compilers with CMake. (LRK, 2020/08/05, HDFFV-10836) - Updated testh5cc.sh.in for functions versioned in HDF5 1.10. testh5cc.sh previously tested that the correct version of a function versioned in HDF5 1.6 or 1.8 was compiled when one of H5_NO_DEPRECATED_SYMBOLS or H5_USE_16_API_DEFAULT were defined. This test was extended for additional testing with H5_USE_18_API_DEFAULT. (LRK, 2020/06/22, HDFFV-11000) - Fixed CMake include properties for Fortran libraries Corrected the library properties for Fortran to use the correct path for the Fortran module files. (ADB - 2020/02/04, HDFFV-11012) Performance ------------- - None Java Library: ---------------- - None Fortran -------- - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. (MSB - 2020/2/18, HDFFV-11029) - Fixed configure issue when building HDF5 with NAG Fortran 7.0. HDF5 now accounts for the addition of half-precision floating-point in NAG 7.0 with a KIND=16. (MSB - 2020/02/28, HDFFV-11033) Tools ----- - The tools library was updated by standardizing the error stack process. General sequence is: h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); h5tools_init(); ... process the command-line (check for error-stack enable) ... h5tools_error_report(); ... (do work) ... h5diff_exit(ret); (ADB - 2020/07/20, HDFFV-11066) - h5diff fixed a command line parsing error. h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used. (ADB - 2020/07/20, HDFFV-10897) - h5diff added a command line option to ignore attributes. h5diff would ignore all objects with a supplied path if the exclude-path argument is used. Adding the exclude-attribute argument will only eclude attributes, with the supplied path, from comparision. (ADB - 2020/07/20, HDFFV-5935) - h5diff added another level to the verbose argument to print filenames. Added verbose level 3 that is level 2 plus the filenames. The levels are: 0 : Identical to '-v' or '--verbose' 1 : All level 0 information plus one-line attribute status summary 2 : All level 1 information plus extended attribute status report 3 : All level 2 information plus file names (ADB - 2020/07/20, HDFFV-10005) - h5repack was fixed to repack the reference attributes properly. The code line that checks if the update of reference inside a compound datatype is misplaced outside the code block loop that carries out the check. In consequence, the next attribute that is not the reference type was repacked again as the reference type and caused the failure of repacking. The fix is to move the corresponding code line to the correct code block. (KY -2020/02/10, HDFFV-11014) High-Level APIs: ------ - The H5DSis_scale function was updated to return "not a dimension scale" (0) instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are not written according to Dimension Scales Specification. (EIP - 2020/08/12, HDFFV-10436) Fortran High-Level APIs: ------ - None Documentation ------------- - None F90 APIs -------- - None C++ APIs -------- - None Testing ------- - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. (LRK, 2020/7/2, HDFFV-11063)
2021-06-07 13:52:48 +02:00
MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${PKGVERSION_NOREV:R}/hdf5-${PKGVERSION_NOREV}/src/
Changes 1.8.10: * The following new C function has been added: H5Pget_mpio_no_collective_cause * The following new Fortran subroutine has been added: h5pget_mpio_actual_io_mode_f * The syntax of the following high-level C function has changed: H5TBAget_fill This function’s return type has been changed to h5tri_t. A return value of 1 indicates that a fill value is present, 0 indicates that no fill value is present, and a negative value indicates an error. (The former return type was herr_t.) Note that H5TBAget_fill and a companion function H5TBAget_title, both in the HDF5 Table (H5TB) high-level API, are undocumented. These functions will be added to the HDF5 Reference Manual shortly after HDF5 Release 1.8.10. Changed Command-line Tool * h5import has been updated to accept an input file created by h5dump.
2012-12-09 01:07:38 +01:00
EXTRACT_SUFX= .tar.bz2
Update devel/hdf5 from 1.6.10nb1 to 1.8.7. A list of changes is available at http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html A list of new features of 1.8.x release is available at http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html This update removes "cxx" option from the package. New devel/hdf5-c++ should be used instead.
2011-10-07 12:38:50 +02:00
Drop maintainership.
2015-08-23 01:03:39 +02:00
MAINTAINER= pkgsrc-users@NetBSD.org
Follow some http redirects.
2017-08-16 22:21:03 +02:00
HOMEPAGE= https://www.hdfgroup.org/HDF5/
Update devel/hdf5 from 1.6.10nb1 to 1.8.7. A list of changes is available at http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html A list of new features of 1.8.x release is available at http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html This update removes "cxx" option from the package. New devel/hdf5-c++ should be used instead.
2011-10-07 12:38:50 +02:00
LICENSE= original-bsd
USE_LIBTOOL= yes
USE_TOOLS+= pax tr
GNU_CONFIGURE= yes
hdf5: updated to 1.10.7 HDF5 version 1.10.7 released on 2020-09-11 ================================================================================ INTRODUCTION This document describes the differences between this release and the previous HDF5 release. It contains information on the platforms tested and known problems in this release. For more details check the HISTORY*.txt files in the HDF5 source. Note that documentation in the links below will be updated at the time of each final release. Links to HDF5 documentation can be found on The HDF5 web page: https://portal.hdfgroup.org/display/HDF5/HDF5 The official HDF5 releases can be obtained from: https://www.hdfgroup.org/downloads/hdf5/ HDF5 binaries provided are fully tested with ZLIB and the free Open Source SZIP successor Libaec (with BSD license). The official ZLIB and SZIP/Libaec pages are at: ZLIB: http://www.zlib.net/ http://www.zlib.net/zlib_license.html SZIP/Libaec: https://gitlab.dkrz.de/k202009/libaec https://gitlab.dkrz.de/k202009/libaec/-/blob/master/Copyright.txt Changes from Release to Release and New Features in the HDF5-1.10.x release series can be found at: https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide If you have any questions or comments, please send them to the HDF Help Desk: help@hdfgroup.org CONTENTS - New Features - Support for new platforms and languages - Bug Fixes since HDF5-1.10.6 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms - Known Problems - CMake vs. Autotools installations New Features ============ Configuration: ------------- - Disable memory sanity checks in the Autotools in release branches The library can be configured to use internal memory sanity checking, which replaces C API calls like malloc(3) and free(3) with our own calls which add things like heap canaries. These canaries can cause problems when external filter plugins reallocate canary-marked buffers. For this reason, the default will be to not use the memory allocation sanity check feature in release branches (e.g., hdf5_1_10_7). Debug builds in development branches (e.g., develop, hdf5_1_10) will still use them by default. This change only affects Autotools debug builds. Non-debug autotools builds and all CMake builds do not enable this feature by default. (DER - 2020/08/19) - Add file locking configure and CMake options HDF5 1.10.0 introduced a file locking scheme, primarily to help enforce SWMR setup. Formerly, the only user-level control of the scheme was via the HDF5_USE_FILE_LOCKING environment variable. This change introduces configure-time options that control whether or not file locking will be used and whether or not the library ignores errors when locking has been disabled on the file system (useful on some HPC Lustre installations). In both the Autotools and CMake, the settings have the effect of changing the default property list settings (see the H5Pset/get_file_locking() entry, below). The yes/no/best-effort file locking configure setting has also been added to the libhdf5.settings file. Autotools: An --enable-file-locking=(yes|no|best-effort) option has been added. yes: Use file locking. no: Do not use file locking. best-effort: Use file locking and ignore "disabled" errors. CMake: Two self-explanatory options have been added: HDF5_USE_FILE_LOCKING HDF5_IGNORE_DISABLED_FILE_LOCKS Setting both of these to ON is the equivalent to the Autotools' best-effort setting. NOTE: The precedence order of the various file locking control mechanisms is: 1) HDF5_USE_FILE_LOCKING environment variable (highest) 2) H5Pset_file_locking() 3) configure/CMake options (which set the property list defaults) 4) library defaults (currently best-effort) (DER - 2020/07/30, HDFFV-11092) - CMake option to link the generated Fortran MOD files into the include directory. The Fortran generation of MOD files by a Fortran compile can produce different binary files between SHARED and STATIC compiles with different compilers and/or different platforms. Note that it has been found that different versions of Fortran compilers will produce incompatible MOD files. Currently, CMake will locate these MOD files in subfolders of the include directory and add that path to the Fortran library target in the CMake config file, which can be used by the CMake find library process. For other build systems using the binary from a CMake install, a new CMake configuration can be used to copy the pre-chosen version of the Fortran MOD files into the install include directory. The default will depend on the configuration of BUILD_STATIC_LIBS and BUILD_SHARED_LIBS: YES YES Default to SHARED YES NO Default to STATIC NO YES Default to SHARED NO NO Default to SHARED The defaults can be overriden by setting the config option HDF5_INSTALL_MOD_FORTRAN to one of NO, SHARED, or STATIC (ADB - 2020/07/09, HDFFV-11116) - CMake option to use AEC (open source SZip) library instead of SZip The open source AEC library is a replacement library for SZip. In order to use it for hdf5, the libaec CMake source was changed to add "-fPIC" and exclude test files. A new option USE_LIBAEC is required to compensate for the different files produced by AEC build. Autotools does not build the compression libraries within hdf5 builds, but will use an installed libaec when configured as before with the option --with-libsz=<path to libaec directory>. (ADB - 2020/04/22, OESS-65) - CMake ConfigureChecks.cmake file now uses CHECK_STRUCT_HAS_MEMBER Some handcrafted tests in HDFTests.c have been removed and the CMake CHECK_STRUCT_HAS_MEMBER module has been used. (ADB - 2020/03/24, TRILAB-24) - Both build systems use same set of warnings flags GNU C, C++ and gfortran warnings flags were moved to files in a config sub-folder named gnu-warnings. Flags that only are available for a specific version of the compiler are in files named with that version. Clang C warnings flags were moved to files in a config sub-folder named clang-warnings. Intel C, Fortran warnings flags were moved to files in a config sub-folder named intel-warnings. There are flags in named "error-xxx" files with warnings that may be promoted to errors. Some source files may still need fixes. There are also pairs of files named "developer-xxx" and "no-developer-xxx" that are chosen by the CMake option:HDF5_ENABLE_DEV_WARNINGS or the configure option:--enable-developer-warnings. In addition, CMake no longer applies these warnings for examples. (ADB - 2020/03/24, TRILAB-192) - Update CMake minimum version to 3.12 Updated CMake minimum version to 3.12 and added version checks for Windows features. (ADB - 2020/02/05, TRILABS-142) - Fixed CMake include properties for Fortran libraries Corrected the library properties for Fortran to use the correct path for the Fortran module files. (ADB - 2020/02/04, HDFFV-11012) - Added common warnings files for gnu and intel Added warnings files to use one common set of flags during configure for both autotools and CMake build systems. The initial implementation only affects a general set of flags for gnu and intel compilers. (ADB - 2020/01/17) - Added new options to CMake for control of testing Added CMake options (default ON); HDF5_TEST_SERIAL AND/OR HDF5_TEST_PARALLEL combined with: HDF5_TEST_TOOLS HDF5_TEST_EXAMPLES HDF5_TEST_SWMR HDF5_TEST_FORTRAN HDF5_TEST_CPP HDF5_TEST_JAVA (ADB - 2020/01/15, HDFFV-11001) - Added Clang sanitizers to CMake for analyzer support if compiler is clang. Added CMake code and files to execute the Clang sanitizers if HDF5_ENABLE_SANITIZERS is enabled and the USE_SANITIZER option is set to one of the following: Address Memory MemoryWithOrigins Undefined Thread Leak 'Address;Undefined' (ADB - 2019/12/12, TRILAB-135) Library: -------- - Add metadata cache optimization to reduce skip list usage On file flush or close, the metadata cache attempts to write out all dirty entries in increasing address order. To do this, it needs an address sorted list of metadata entries. Further, since flushing one metadata cache entry can dirty another, this list must support efficient insertion and deletion. The metadata cache uses a skip list of all dirty entries for this purpose. Before this release, this skip list was maintained at all times. However, since profiling indicates that this imposes a significant cost, we now construct and maintain the skip list only when needed. Specifically, we enable the skip list and load it with a list of all dirty entries in the metadata cache just before a flush, and disable it after the flush. (JRM - 2020/08/17, HDFFV-11034) - Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable This change adds a BEST_EFFORT to the TRUE/FALSE, 1/0 settings that were previously accepted. This option turns on file locking but ignores locking errors when the library detects that file locking has been disabled on a file system (useful on some HPC Lustre installations). The capitalization of BEST_EFFORT is mandatory. See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Add H5Pset/get_file_locking() API calls This change adds new API calls which can be used to set or get the file locking parameters. The single API call sets both the "use file locking" flag and the "ignore disabled file locking" flag. When opening a file multiple times without closing, the file MUST be opened with the same file locking settings. Opening a file with different file locking settings will fail (this is similar to the behavior of H5Pset_fclose_degree()). See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Add Mirror VFD Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote machine. Must be used in conjunction with the Splitter VFD. (JOS - 2020/03/13, TBD) - Add Splitter VFD Maintain separate R/W and W/O channels for "concurrent" file writes to two files using a single HDF5 file handle. (JOS - 2020/03/13, TBD) - Fixed an assertion failure in the parallel library when collectively filling chunks. As it is required that chunks be written in monotonically non-decreasing order of offset in the file, this assertion was being triggered when the list of chunk file space allocations being passed to the collective chunk filling routine was not sorted according to this particular requirement. The addition of a sort of the out of order chunks trades a bit of performance for the elimination of this assertion and of any complaints from MPI implementations about the file offsets used being out of order. (JTH - 2019/10/07) Fortran Library: ---------------- - Add wrappers for H5Pset/get_file_locking() API calls h5pget_file_locking_f() h5pset_file_locking_f() See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) - Added new Fortran parameters: H5F_LIBVER_ERROR_F H5F_LIBVER_NBOUNDS_F H5F_LIBVER_V18_F H5F_LIBVER_V110_F - Added new Fortran API: h5pget_libver_bounds_f (MSB - 2020/02/11, HDFFV-11018) C++ Library: ------------ - Add wrappers for H5Pset/get_file_locking() API calls FileAccPropList::setFileLocking() FileAccPropList::getFileLocking() See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) Java Library: ---------------- - Add wrappers for H5Pset/get_file_locking() API calls H5Pset_file_locking() H5Pget_use_file_locking() H5Pget_ignore_disabled_file_locking() Unlike the C++ and Fortran wrappers, there are separate getters for the two file locking settings, each of which returns a boolean value. See the configure option discussion for HDFFV-11092 (above) for more information on the file locking feature and how it's controlled. (DER - 2020/07/30, HDFFV-11092) Tools: ------ - h5repack added options to control how external links are handled. Currently h5repack preserves external links and cannot copy and merge data from the external files. Two options, merge and prune, were added to control how to merge data from an external link into the resulting file. --merge Follow external soft link recursively and merge data. --prune Do not follow external soft links and remove link. --merge --prune Follow external link, merge data and remove dangling link. (ADB - 2020/08/05, HDFFV-9984) High-Level APIs: --------------- - None C Packet Table API ------------------ - None Internal header file -------------------- - None Documentation ------------- - None Support for new platforms, languages and compilers. ======================================= - None Bug Fixes since HDF5-1.10.6 release ================================== Library ------- - Fix bug and simplify collective metadata write operation when some ranks have no entries to contribute. This fixes parallel regression test failures with IBM SpectrumScale MPI on the Summit system at ORNL. (QAK - 2020/09/02) - Avoid setting up complex MPI types with 0-length vectors, which some MPI implementations don't handle well. (In particular, IBM SpectrumScale MPI on the Summit system at ORNL) (QAK - 2020/08/21) - Fixed use-of-uninitialized-value error Appropriate initialization of local structs was added to remove the use-of-uninitialized-value errors reported by MemorySanitizer. (BMR - 2020/8/13, HDFFV-11101) - Creation of dataset with optional filter When the combination of type, space, etc doesn't work for filter and the filter is optional, it was supposed to be skipped but it was not skipped and the creation failed. A fix is applied to allow the creation of a dataset in such situation, as specified in the user documentation. (BMR - 2020/8/13, HDFFV-10933) - Explicitly declared dlopen to use RTLD_LOCAL dlopen documentation states that if neither RTLD_GLOBAL nor RTLD_LOCAL are specified, then the default behavior is unspecified. The default on linux is usually RTLD_LOCAL while macos will default to RTLD_GLOBAL. (ADB - 2020/08/12, HDFFV-11127) - Fixed issues CVE-2018-13870 and CVE-2018-13869 When a buffer overflow occurred because a name length was corrupted and became very large, h5dump crashed on memory access violation. A check for reading past the end of the buffer was added to multiple locations to prevent the crashes and h5dump now simply fails with an error message when this error condition occurs. (BMR - 2020/7/31, HDFFV-11120 and HDFFV-11121) - H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which causes asserts/errors when passed to other dataspace API calls. H5S_NO_CLASS is an internal class value that should not have been exposed via a public API call. In debug builds of the library, this can cause asserts to trip. In non-debug builds, it will produce normal library errors. The new library behavior is for H5Sset_extent_none() to convert the dataspace into one of type H5S_NULL, which is better handled by the library and easier for developers to reason about. (DER - 2020/07/27, HDFFV-11027) - Fixed the segmentation fault when reading attributes with multiple threads It was reported that the reading of attributes with variable length string datatype will crash with segmentation fault particularly when the number of threads is high (>16 threads). The problem was due to the file pointer that was set in the variable length string datatype for the attribute. That file pointer was already closed when the attribute was accessed. The problem was fixed by setting the file pointer to the current opened file pointer when the attribute was accessed. Similar patch up was done before when reading dataset with variable length string datatype. (VC - 2020/07/13, HDFFV-11080) - Fixed issue CVE-2018-17438 A division by zero was discovered in H5D__select_io() of H5Dselect.c. https://security-tracker.debian.org/tracker/CVE-2018-17438 A check was added to protect against division by zero. When such situation occurs again, the normal HDF5 error handling will be invoked, instead of segmentation fault. (BMR, DER - 2020/07/09, HDFFV-10587) - Fixed CVE-2018-17435 The tool h52gif produced a segfault when the size of an attribute message was corrupted and caused a buffer overflow. The problem was fixed by verifying the attribute message's size against the buffer size before accessing the buffer. h52gif was also fixed to display the failure instead of silently exiting after the segfault was eliminated. (BMR - 2020/6/19, HDFFV-10591) - Don't allocate an empty (0-dimensioned) chunked dataset's chunk index, until the dataset's dimensions are increased. (QAK - 2020/05/07) Configuration ------------- - Stopped addition of szip header and include directory path for incompatible libsz szlib.h is the same for both 32-bit and 64-bit szip, and the header file and its path were added to the HDF5 binary even though the configure check of a function in libsz later failed and szip compression was not enabled. The header file and include path are now added only when the libsz function passes the configure check. (LRK - 2020/08/17, HDFFV-10830) - Added -fsanitize=address autotools configure option for Clang compiler Clang sanitizer options were also added for Clang compilers with CMake. (LRK, 2020/08/05, HDFFV-10836) - Updated testh5cc.sh.in for functions versioned in HDF5 1.10. testh5cc.sh previously tested that the correct version of a function versioned in HDF5 1.6 or 1.8 was compiled when one of H5_NO_DEPRECATED_SYMBOLS or H5_USE_16_API_DEFAULT were defined. This test was extended for additional testing with H5_USE_18_API_DEFAULT. (LRK, 2020/06/22, HDFFV-11000) - Fixed CMake include properties for Fortran libraries Corrected the library properties for Fortran to use the correct path for the Fortran module files. (ADB - 2020/02/04, HDFFV-11012) Performance ------------- - None Java Library: ---------------- - None Fortran -------- - Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. (MSB - 2020/2/18, HDFFV-11029) - Fixed configure issue when building HDF5 with NAG Fortran 7.0. HDF5 now accounts for the addition of half-precision floating-point in NAG 7.0 with a KIND=16. (MSB - 2020/02/28, HDFFV-11033) Tools ----- - The tools library was updated by standardizing the error stack process. General sequence is: h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); h5tools_init(); ... process the command-line (check for error-stack enable) ... h5tools_error_report(); ... (do work) ... h5diff_exit(ret); (ADB - 2020/07/20, HDFFV-11066) - h5diff fixed a command line parsing error. h5diff would ignore the argument to -d (delta) if it is smaller than DBL_EPSILON. The macro H5_DBL_ABS_EQUAL was removed and a direct value comparision was used. (ADB - 2020/07/20, HDFFV-10897) - h5diff added a command line option to ignore attributes. h5diff would ignore all objects with a supplied path if the exclude-path argument is used. Adding the exclude-attribute argument will only eclude attributes, with the supplied path, from comparision. (ADB - 2020/07/20, HDFFV-5935) - h5diff added another level to the verbose argument to print filenames. Added verbose level 3 that is level 2 plus the filenames. The levels are: 0 : Identical to '-v' or '--verbose' 1 : All level 0 information plus one-line attribute status summary 2 : All level 1 information plus extended attribute status report 3 : All level 2 information plus file names (ADB - 2020/07/20, HDFFV-10005) - h5repack was fixed to repack the reference attributes properly. The code line that checks if the update of reference inside a compound datatype is misplaced outside the code block loop that carries out the check. In consequence, the next attribute that is not the reference type was repacked again as the reference type and caused the failure of repacking. The fix is to move the corresponding code line to the correct code block. (KY -2020/02/10, HDFFV-11014) High-Level APIs: ------ - The H5DSis_scale function was updated to return "not a dimension scale" (0) instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are not written according to Dimension Scales Specification. (EIP - 2020/08/12, HDFFV-10436) Fortran High-Level APIs: ------ - None Documentation ------------- - None F90 APIs -------- - None C++ APIs -------- - None Testing ------- - Stopped java/test/junit.sh.in installing libs for testing under ${prefix} Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. (LRK, 2020/7/2, HDFFV-11063)
2021-06-07 13:52:48 +02:00
CONFIGURE_ARGS+= --with-examplesdir=${PREFIX}/share/examples/hdf5
Update devel/hdf5 from 1.6.10nb1 to 1.8.7. A list of changes is available at http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html A list of new features of 1.8.x release is available at http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html This update removes "cxx" option from the package. New devel/hdf5-c++ should be used instead.
2011-10-07 12:38:50 +02:00
TEST_TARGET= check
Fix build on SunOS.
2012-02-16 19:45:59 +01:00
CFLAGS.SunOS+= -std=c99 -D_XOPEN_SOURCE=600 -D__EXTENSIONS__
hdf5: fix build on SunOS
2022-03-26 22:52:36 +01:00
CONFIGURE_ENV.SunOS+= ac_cv_func_gettimeofday=yes
Fix build on SunOS.
2012-02-16 19:45:59 +01:00
Update to HDF5 1.8.9 This doesn't pass self-tests, but it isn't regression, previous package didn't pass them as well. (While here, make both packages share the same distinfo.) Changes in HDF5 1.8.9 HDF5 1.8.9 is a minor release, but contains several important new features and bug fixes. Changes in this release include the following: * Committed datatypes can now be merged when copying objects, using the new flag H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG. Several new API routines have been included in support of this feature. * A file in memory can now be accessed in the same way as a file on disk. New APIs were added to support this feature. * Many changes to the tools have been made, including the following: + The h5repack performance has been improved dramatically for large chunked datasets. + The -S (or --summary) option was added to h5stat to display a summary of the file space usage for a file. + A wildcard can now be used with h5dump to specify multiple files. * H5LTpath_valid was added to determine if a path is correct and a link resolves to a valid object. * The Fortran counterpart to H5Ocopy, h5ocopy_f, was added. This release contains many other changes and bug fixes not listed here. Please be sure to read the Release Notes for a comprehensive list of new features and bug fixes. Changes in HDF5 1.8.8 HDF5 1.8.8 is a minor release, but contains a few important new features and bug fixes. Changes in this release include the following: * Changes to the Fortran interface: + Fortran wrappers for the Dimension Scales APIs were added. For the new subroutine signatures, see: http://www.hdfgroup.org/HDF5/doc/HL/RM_H5DS.html + The Fortran interface now uses the Fortran 2003 standard, enabling a wider set of Fortran and HDF5 datatypes to be supported, including: o Any kind of INTEGER or REAL o Fortran derived types o Fortran and HDF5 enumeration o HDF5 variable-length datatypes o HDF5 compound datatypes of any complexity It also contains new subroutines corresponding to those C APIs which have callback functions as parameters. For a general overview and information on how to enable these new Fortran features, please see the following paper: http://www.hdfgroup.org/HDF5/doc/fortran/NewFeatures_F2003.pdf HDF5 examples that use Fortran 2003 (with the suffix "F03") can be found here: http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/api18-fortran.html The --enable-fortran2003 configure flag was added to enable Fortran 2003 support in the HDF5 Fortran library. This flag should be used along with the --enable-fortran flag and takes affect only when a Fortran compiler is Fortran 2003 compliant. * H5Tcreate now supports a string type (fixed-length and variable-length). * New APIs, H5Pget_mpio_actual_chunk_opt_mode and H5Pget_mpio_actual_io_mode, were added for querying whether/how a collective I/O operation completed. * Numerous changes were made to the tools (h5diff, h5repack, h5jam, h5dump).
2012-10-27 10:54:48 +02:00
DISTINFO_FILE= ${.CURDIR}/../../devel/hdf5/distinfo
Update devel/hdf5 from 1.6.10nb1 to 1.8.7. A list of changes is available at http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html A list of new features of 1.8.x release is available at http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html This update removes "cxx" option from the package. New devel/hdf5-c++ should be used instead.
2011-10-07 12:38:50 +02:00
PATCHDIR= ${.CURDIR}/../../devel/hdf5/patches
devel/hdf5: skip some files for the portability check
2020-03-17 23:29:34 +01:00
# These 2 files are not used in the build. They use [[ ... ]].
CHECK_PORTABILITY_SKIP= bin/snapshot hl/tools/h5watch/testh5watch.sh.in
Update devel/hdf5 from 1.6.10nb1 to 1.8.7. A list of changes is available at http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html A list of new features of 1.8.x release is available at http://www.hdfgroup.uiuc.edu/HDF5/doc_1.8pre/WhatsNew180.html This update removes "cxx" option from the package. New devel/hdf5-c++ should be used instead.
2011-10-07 12:38:50 +02:00
# it appears that this file is informative only and is not actually
# used by any installed tools
CHECK_WRKREF_SKIP= ${PREFIX}/lib/libhdf5.settings
INSTALL_ENV+= INSTALL_SCRIPT=${INSTALL_SCRIPT:Q}
post-extract:
${CP} ${WRKSRC}/config/freebsd ${WRKSRC}/config/netbsd
${CP} ${WRKSRC}/config/freebsd ${WRKSRC}/config/netbsdelf
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