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* Fixes minor issues in various virtual file driversDana Robinson2020-10-291-2/+0
| | | | | | | | | | | | - HDFS VFD files now ignored in the Autotools when the HDFS VFD is not being built. - All VFD init code uses idiomatic H5I_INVALID_HID instead of -1 or FAIL. - The HDFS VFD now includes H5FDdrvr_module.h in the right place. - The HDFS tests in test/hdfs.c no longer pass NULL to VERIFY macros, which raised warnings. - Minor tweaks to fix const, unused variables, etc. warnings in several VFDs.
* HD prefix updates in src/ and test/Dana Robinson2020-10-241-6/+6
| | | | | | | Adds missing HD prefixes to API calls in src and test. Adds some extra processing to bin/checkposix to keep the noise levels down when running the script (not comprehensive).
* Clang-format of source filesAllen Byrne2020-09-301-851/+835
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* File changes to affect formattingAllen Byrne2020-09-041-6/+6
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* Fixes the splitter VFD test on Windows.Dana Robinson2020-08-121-1/+1
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* Removes staff email addresses from the repositoryDana Robinson2020-08-071-1/+1
| | | | Removes redundant C library headers from hl library
* Fixes warnings in the splitter VFD and testsDana Robinson2020-08-061-109/+148
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* Minor normalizations with hdf5_1_10Dana Robinson2020-07-311-4/+3
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* * Fix intermittent error with Splitter VFD.Jacob Smith2020-06-251-34/+46
| | | | | | | | Mismatch in time of test file creation was creating false negatives. Add file-duplication routine: `h5_duplicate_file_by_bytes()`. * Change library calls in `h5test.c:h5_compare_file_bytes()` to their HD-prefixed equivalents.
* Patch a few holes in the Splitter VFD implementation.Jacob Smith2020-05-291-1/+2
| | | | | * Missing logfile close on driver-open failure. * Initialize empty string in test/vfd (logfile path in W/O compat check).
* Add Splitter VFD to library.Jacob Smith2020-03-131-5/+1092
| | | | | | | | | | | | | | | * "Simultaneous and equivalent" Read-Write and Write-Only channels for file I/O. * Only supports drivers with the H5FD_FEAT_DEFAULT_VFD_COMPATIBLE flag for now, preventing issues with multi-file drivers. Add Mirror VFD to library. * Write-only operations over a network. * Uses TCP/IP sockets. * Server and auxiliary server-shutdown programs provided in a new directory, `utils/mirror_vfd`. * Automated testing via loopback ("remote" of localhost).
* Merge pull request #2318 in HDFFV/hdf5 from ↵David Young2020-01-291-9/+6
|\ | | | | | | | | | | | | ~DYOUNG/werror:reduce-werror-diffs-1 to develop * commit 'fa1b2f6ef35c459c9f74ead885c119ae7f61c056': Reduce differences between my -Werror branch and `develop`:
| * Reduce differences between my -Werror branch and `develop`:David Young2020-01-291-9/+6
| | | | | | | | | | | | | | | | Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC shadowed declaration warnings about index(3). Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
* | testpar/t_2Gio.c: Fix a typo that I think was introduced by aDavid Young2020-01-291-6/+9
|/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2]. fortran/src/H5Pf.c: move conditional compilation controlled by H5_NO_DEPRECATED_SYMBOLS outside of a function for readability. fortran/src/H5match_types.c: put a variable's declaration under the same conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its use. For now, skip compilation of some unused debug dump routines in the JNI. While I'm in the JNI, delete a set-but-unused variable. src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS so that it's not declared but unused or vice versa. test/cache_common.h: add an #include in to get some symbols we need to avoid implicit declaration warnings. test/dsets.c: use a more conventional conditional-compilation syntax. test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized variables before use. test/vfd.c: pass the expected type of `void **` to posix_memalign(3) instead of `int **`. testpar/t_bigio.c: explicitly compare with 0 instead of using ! when "equal to 0?" is the question not "is false?" Repair some indentation while I'm here. testpar/testpar.h: repair misaligned line-continuation backslashes in a macro that probably should be a function so that we don't have to fiddle with the line continuation to begin with. tools/src/h5repack/h5repack_main.c: fix some compiler fussing about enums. tools/test/perform/pio_engine.c: the compiler fusses if you cast a function call returning double directly to off_t. It's ok if you cast a variable that's a double to off_t, however. Write and use a new function, sqrto(), to avoid the cast warnings.
* Fixed stack and frame size warnings. Not complete, but fixes most ofDana Robinson2020-01-151-82/+114
| | | | the easier cases.
* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-041-2/+2
| | | | the Autotools and CMake.
* Merge branch 'develop' of ↵Jacob Smith2019-09-231-13/+112
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Untangle #ifdef mess in ROS3 code.Dana Robinson2019-08-201-55/+13
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| * Squashed commit of the following:Larry Knox2019-07-251-13/+154
| | | | | | | | | | | | | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
* | Merge branch 'develop' of ↵Jacob Smith2019-07-221-0/+27
|\ \ | |/ | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Updates to warnhist script, along with a few cleanups, and add some commentsQuincey Koziol2019-07-101-0/+27
| | | | | | | | to warning cleanups that are a bit obscure.
* | Minor formatting adjustments.Jacob Smith2019-07-221-32/+53
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* | Add test that uses the family member FAPL setting.Jacob Smith2019-05-241-0/+112
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* C and POSIX call cleanupDana Robinson2019-01-111-21/+23
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* Normalization with vol_integration (test code and H5Xtest.c)Dana Robinson2018-09-201-11/+10
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* HD prefix and whitespaceAllen Byrne2018-08-281-11/+11
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* Fixed typo in vfd.c from 'updated VFD feature flag' checkin.Dana Robinson2017-05-301-1/+1
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* Added feature flag checks for a few other VFDs in test/vfd.c.Dana Robinson2017-05-261-10/+116
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* * Added new public H5FDdriver_query() API call.Dana Robinson2017-05-241-0/+48
| | | | | | * Changed return type of H5FD_driver_query() to herr_t. * Updated swmr.c to use H5FDdriver_query() instead of the private call. * Added some flags tests to vfd.c.
* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* Fixed a few memory problems in test/cache_logging.c andDana Robinson2016-11-231-1/+1
| | | | test/h5test.c (which show up in test/vfd.c).
* [svn-r30306] Updated vfd test to be better about fapls and h5_reset().Dana Robinson2016-08-191-72/+110
| | | | | | | | | | | Prevents the test from segfaulting in other sub-tests when a previous test fails. Tested on: 64-bit Ubuntu Linux 16.04 LTS w/ gcc 5.4.0 Autotools serial + direct VFD (vfd test only) Also tested with a forced error to ensure that the test no longer segfaults and confirmed that all test files are cleaned up.
* [svn-r30297] Changed FAIL_STACK_ERROR to TEST_ERROR in test/vfd.c.Dana Robinson2016-08-181-51/+51
| | | | | Tested on: 64-bit Ubuntu Linux 16.04 LTS w/ gcc 5.4.0 Autotools serial, vfd test only
* [svn-r30184] Converted h5_fileaccess() to H5Pcreate() in the sec2 test.Dana Robinson2016-07-141-1/+2
| | | | | Tested on: 64-bit Ubuntu Linux 16.04 LTS w/ gcc 5.4.0 Autotools serial, vfd test only w/ various VFDs
* [svn-r30163] Changed a h5_fileaccess() call to H5Pcreate() in the core VFD test.Dana Robinson2016-07-091-1/+2
| | | | | | | | | | Since it only tests the core VFD, there's no need to get a VFD-dependent fapl. Tested on: 64-bit Ubuntu Linux w/ gcc 5.3.1 vfd test w/ all VFDs tested by make check-vfd
* [svn-r30148] Expanded core VFD test in vfd.c. Minor tidying to sec2 VFD test ↵Dana Robinson2016-07-061-189/+295
| | | | | | | also. Tested on: 64-bit Ubuntu Linux w/ gcc 5.3.1 Autotools serial
* [svn-r27768] Description:Quincey Koziol2015-09-141-181/+199
| | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* [svn-r24993] Purpose:Dana Robinson2014-04-091-0/+13
| | | | | | | | | | | | | | | Adds write tracking to the core VFD, which can be configured via the H5Pset/get_core_write_tracking() API call. When enabled and writing to the backing store is enabled, this feature will track writes and only write out the changed bytes on flush/close. Tested on: 32-bit LE linux (jam) w/ Fortran and C++ 64-bit BE linux (ostrich) 64-bit Darwin 12.5.0 (kite) All were tested using the core VFD w/ paging on (core_paged in the VFD list). Make check-vfd was also tested on jam.
* [svn-r23219] Description:Quincey Koziol2013-02-021-101/+118
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring reviewed changes from Coverity branch back to trunk (QK & JK): r20457: Coverity issue 691: return of H5duo could be negative. Fixed by using STDOUT_FILENO and redesign parse_command_line and main to cleanup file allocations. The output_file var is null when using stdout. In cleanup do not close output_file if NULL. r20510: Initialize ufid = -1 and predicate HDclose call on ufid != -1 r20511: Purpose: Fix coverity issue 1715 Description: Free "file" and nested data on failure in H5FD_core_open. r20512: Initialize ifid = -1 and predicate HDclose call on ifid != -1 r20514: Initialize h5fid = -1 and predicate HDclose call on h5fid != -1 r20516: Added else branch to the if (ret_value < 0) check. r20522: Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor potential buffer overwrite bugs, or coverity errors. Fixed by replacing strcpy and sprintf with strncpy and snprintf. r20523: fixed coverity issues 68, 1120, 1116i r20524: Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence. r20601: Purpose: Fix coverity issues 1703-1705 Description: Modified the cleanup code in test_free in accum.c to reset allocated buffers to NULL after they are freed, and modified the error cleanup code to check if these buffers are NULL before freeing them. Also fixed some unrelated warnings in accum.c. r20602: Use HDsnprintf and HDstrncat r20603: Purpose: Fix coverity issues 808-809 Description: Modified test_core in vfd.c to check the returns from malloc, and keep track of whether points and check are allocated by setting them to NULL when they are not. Added code to free points and check on error if they are not NULL. Also fixed unrelated warnings in vfd.c. r20604: Use HDstrncpy. r20605: Use HDstrncpy and HDstrncat. r20606: Purpose: Fix coverity issue 807 Description: Modified long_compact in stab.c to keep track of whether objname is allocated by setting it to NULL when it is not. Added code to free objname on error if it is not NULL. r20607: Changed string function calls to use versions that specify the string length to fix coverity issues 832 and 839. Tested on: Mac OSX/64 10.8.2 (amazon) (Too minor to require h5committest)
* [svn-r22411] reduce compiler warnings by removing unreferenced variables and ↵Allen Byrne2012-05-251-2/+1
| | | | | | adding cast Tested: local linux
* [svn-r21366] JIRA HDFFV-2748 replace use of _WIN32 in source. Created new ↵Allen Byrne2011-09-061-63/+62
| | | | | | defines H5_HAVE_WIN32_API and H5_HAVE_VISUAL_STUDIO defines to use. These can be properly set during configurration. Tested: windows and local linux - reviewed internally
* [svn-r21017] This is a follow-up checkin for r21015 (bug fix for Issue ↵Raymond Lu2011-06-221-0/+1
| | | | | | | | 2598). I added two minor changes: 1. put the output file for vfd.c test in the list for cleanup in Makefile.am; 2. put the data file in the list in CMakeLists.txt. Tested on jam - simple change.
* [svn-r21015] Bug fix for Issue 2598 - In v1.6 library, there was EOA for the ↵Raymond Lu2011-06-221-1/+172
| | | | | | | | | | | | | whole MULTI file saved in the super block. We took it out in v1.8 library because it's meaningless for the MULTI file. v1.8 library saves the EOA for the metadata file, instead. But this caused some backward compatibility problem. v1.8 library couldn't open the file created with v1.6 library. I fixed the problem by checking the EOA value to detect the file created with v1.6 library. Tested on jam, koala, and heiwa.
* [svn-r20551] Description:Quincey Koziol2011-04-191-2/+2
| | | | | | | | | Correct 'FILE **' back to 'FILE *' for H5Fget_vfd_handle call. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc 4.6 & debug FreeBSD/64 8.2 (freedom) w/gcc 4.6 & debug Solaris 2.6 (linew)
* [svn-r20548] Fixed bug in test/vfd.c (HDFFV-5936) that caused STDIO VFD test ↵Dana Robinson2011-04-181-11/+3
| | | | | | to fail on some platforms. The problem was that the test was a clone of the SEC2 test. The SEC2 test accepts a file descriptor (int) via a void pointer from H5Fget_vfd_handle() whereas the STDIO test needs to accept a FILE pointer. Storing the FILE pointer in an integer failed on some systems. The STDIO test now stores the file handle in FILE pointer and checks it for NULL instead of < 0.
* [svn-r20462] The basic STDIO VFD test in test/vfd.c fails on 64-bit Solaris ↵Dana Robinson2011-04-101-0/+9
| | | | | | 5.10 (SPARC) and 32-bit Darwin 10.7.0 (Intel). This check-in skips the STDIO test on all platforms while we investigate. Bug report HDFFV-5936 filed in JIRA.
* [svn-r20459] Purpose:Dana Robinson2011-04-081-68/+323
| | | | | | | | | | | | | | | Progress on bug 2138 (bugzilla) / HDFFV-4298 (JIRA) Description: - Added basic VFD tests (i.e. cloned the SEC2 test) for the Windows, STDIO and log VFDs. - Added H5Pget_driver() sanity check to all VFD's tests. - Added log output file to list of files to clean up in Makefile.am. Tested on: - h5committest script platforms (jam, amani, heiwa) - Windows 7 (32- and 64-bit)
* [svn-r18197] Description:Quincey Koziol2010-01-301-1/+1
| | | | | | | | | Trim trailing whitespace from source code files with this command: find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//' Tested on: None - eyeballed only
* [svn-r17980] Description:Quincey Koziol2009-12-101-5/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes into the trunk: (also other minor cleanups) r17955: Fix Coverity item 24. Add missing error condition to H5AC_ext_config_2_int_config. r17956: Fix Coverity item 24. Improve error checking in H5A_compact_build_table_cb. r17957: Fix Coverity item 150. Fix warning in H5A_compact_build_table_cb. r17958: Fix Coverity item 117. Fix error handling in H5B_shared_new. r17959: Fix Coverity item 209. Added an assertion for leaf->shared in H5B2_cache_leaf_dest. r17960: Fix Coverity item 208. Added an assertion for internal->shared in H5B2_cache_internal_dest. r17961: Fix Coverity item 89. Reworked the code to avoid array overrun in H5C__autoadjust__ageout__insert_new_marker. r17962: Fix for coverity Resource_leak 195,203,204,205. r17963: Fix Coverity item 44. Prevented potential NULL dereference in H5D_btree_debug. r17964: Fix Coverity issues #197, 198 & 199: memory not being released. (Also clean up other resource leaks in nearby and/or similar code). r17965: Fix Coverity issue #151: release resources on error r17966: Fix Coverity issue #187: Remove leftover code remnant from prior bugfix which was causing resource leak of open files. r17967: Fixed Coverity issues # 193 & 194. Removed unnecessary memory allocation and added comparison of length of path parameter to the size of the destination buffer in h5import.h/h5import.c. r17968: Fix Coverity item 144. Fixed memory leak on error in H5D_chunk_copy. r17969: Fix for coverity Resource_leak #196. r17970: Coverity 167-173: Initialized pointer of buffers. In error handling, closed types and free memory. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17723] Bug fix:Albert Cheng2009-10-221-2/+3
| | | | | | | | | | The file failed to compiled in AIX which flags syntax error. Fixed by making the statements more explicitly compare with NULL and added a missing trailing semi-colon. Tested: Tested in AIX (Up at LLNL) only. The changes are trivial and should be portable to all platforms.
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