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* Merge pull request #1806 from vchoi-hdfgroup/to_merge_echidna_fixesvchoi-hdfgroup2022-06-082-22/+12
|\ | | | | To merge echidna fixes
| * Committing clang-format changesgithub-actions2022-06-082-5/+3
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| * Merge branch 'to_merge_echidna_fixes' of ↵vchoi2022-06-083-35/+37
| |\ | | | | | | | | | https://github.com/vchoi-hdfgroup/hdf5 into to_merge_echidna_fixes
| * | (1) Modify test/vfd_swmr_bigset_writer.c to use h5_retry routines instead of ↵vchoi2022-06-082-21/+13
| | | | | | | | | | | | | | | | | | "for loop for NUM_ATTEMPTS" times. (2) Clean up test/vfd_swmr.c
* | | Merge pull request #1802 from vchoi-hdfgroup/to_merge_echidna_fixesvchoi-hdfgroup2022-06-078-46/+110
|\ \ \ | | |/ | |/| To merge echidna fixes
| * | Committing clang-format changesgithub-actions2022-06-073-35/+37
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| * Fixes for:vchoi2022-06-078-38/+100
| | | | | | | | | | | | | | | | | | | | | | | | (1) H5O_refresh_metadata(): address failure when make check-passthrough-vol: use H5VL_object_data() to retrieve the vol object. (2) H5FD__vfd_swmr_open(): use HADDR_UNDEF as maxaddr when opening the underlying hdf5 file; otherwise it will casue problem when the hdf5 file is opened with the core driver. (3) src/H5Fvfd_swmr.c and vfd swmr tests: --Use long long for constant define in H5Fvfd_swmr.c and when snprintf the updater file's sequence number --Modify test/vfd_swmr.c to accommodate endianness of machine and also long long for sequence number --Modify vfd_swmr_bigset_writer.c, vfd_swmr_common.c, vfd_swmr_gfail_writer.c, vfd_swmr_gperf_writer.c to use long long for constant define
| * Merge pull request #67 from HDFGroup/feature/vfd_swmrvchoi-hdfgroup2022-06-0620-537/+1162
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* | Merge pull request #1800 from vchoi-hdfgroup/merge_john_tarballvchoi-hdfgroup2022-06-0420-537/+1162
|\ \ | | | | | | Merge john tarball
| * | Committing clang-format changesgithub-actions2022-06-032-33/+32
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| * | Merge branch 'merge_john_tarball' of https://github.com/vchoi-hdfgroup/hdf5 ↵vchoi2022-06-0313-222/+183
| |\ \ | | | | | | | | | | | | into merge_john_tarball
| | * | Committing clang-format changesgithub-actions2022-06-0313-255/+215
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| * | | Correct spelling errors.vchoi2022-06-032-5/+5
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| * | Merge in VFD SWMR changes by John Mainzer.vchoi2022-06-0320-492/+1157
| |/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Commit log message from John: Returned VFD SWMR to using the VFD SWMR reader VFD only in the reader case. In passing, added a private VFD SWMR reader VFD fapl entry that is pushed and popped off the FAPL during file open, and removed the code that set the VFD SWMR reader VFD as the driver in the FAPL when VFD SWMR is configured. This was necessary, as there is no mechanism to prevent the user from overwriting this entry on the FAPL before file open. While we don't use it now, it also gives us a mechanism for allowing the user to specify an underlying VFD for VFD SWMR. Modified code to compare file opens to compare the terminal VFDs, not the top level VFDs. Failure to do this allowed multiple opens of the same file with the same VFD but with different pass through VFDs to appear to be treated as different files -- with the obvious file corruption issues. To support this, added a new VFD ctl op code to return a pointer to the instance of H5FD_t associated with the terminal VFD. Note that this change does not address the case of the same file being opened twice with different terminal VFDs -- that will have to be addressed another day. Overview of major changes from John: 1) Reworked file open so that the VFD SWMR reader VFD is only used when a file is opened VFD SWMR reader. This required the following changes: a) Removed code to set the driver in H5Pset_vfd_swmr_config() b) Added a private fapl entry for the VFD SWMR reader VFD c) Modified H5F_open to test for VFD SWMR reader opens, and push the vfd swmr reader vfd FAPL entry on the VFD stack if so. In this case the entry is popped off the VFD stack on exit so as to avoid any net modification from the supplied FAPL. 2) Removed dedup code, and augmented H5FD_cmp() to provide the necessary functionality. This required the following changes: a) Added the get terminal VFD op code to the H5FD ctl call. This allows duplicate file opens with the same VFD but different overlying pass through VFDs to be recognized. Updated ctl callback in VFDs as required to support the new op code. b) Modified H5FD_cmp to use the above ctl op code to allow it to recognize duplicate file opens with the same VFD but with different overlying passthoguh VFDs. This is necessary to recognize duplicate VFD SWMR reader and regular opens. Note that this does not allow us to recognize duplicate opens with different terminal VFDs.
| * Merge pull request #66 from HDFGroup/feature/vfd_swmrvchoi-hdfgroup2022-05-250-0/+0
| |\ | |/ |/| Merge pull request #1786 from vchoi-hdfgroup/feature/vfd_swmr
* | Merge pull request #1786 from vchoi-hdfgroup/feature/vfd_swmrvchoi-hdfgroup2022-05-191-0/+320
|\ \ | |/ | | Feature/vfd swmr
| * Merge pull request #65 from vchoi-hdfgroup/new_vds_feature_vfd_swmrvchoi-hdfgroup2022-05-161-0/+320
| |\ | | | | | | New vds feature vfd swmr
| | * Committing clang-format changesgithub-actions2022-05-161-28/+25
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| | * Add test to verify multiple opens of the same file with different VFDs.vchoi2022-05-161-0/+323
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| | * Merge pull request #64 from vchoi-hdfgroup/feature/vfd_swmrvchoi-hdfgroup2022-05-134-7/+74
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| * | Merge pull request #63 from HDFGroup/feature/vfd_swmrvchoi-hdfgroup2022-05-1346-780/+2220
| |\ \ | |/ / |/| | Feature/vfd swmr
* | | Check for parallel HDF5 before running SWMR acceptance tests (#1764)Dana Robinson2022-05-114-7/+74
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* | | New vds feature vfd swmr (#1743)vchoi-hdfgroup2022-05-069-345/+1219
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 1) Add feature flag H5FD_FEAT_SUPPORTS_VFD_SWMR to sec2, core and stdio drivers 2) Disable file locking for VFD SWMR reader in H5F_open() 3) Add checking of VFD SWMR feature flag in test/page_buffer.c and test/vfd_swmr.c. Skip tests if the driver does not support VFD SWMR feature. 4) Add new tests + cleanups to test/vfd_swmr.c. * Committing clang-format changes * Fix failing check for Windows: Add the VFD SWMR feature flag also to test_windows() (which is sec2) in test/vfd.c. * Committing clang-format changes Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* | | Merge pull request #1671 from vchoi-hdfgroup/new_vds_feature_vfd_swmrvchoi-hdfgroup2022-04-2139-445/+944
|\ \ \ | | | | | | | | New vds feature vfd swmr
| | | * Committing clang-format changesgithub-actions2022-05-061-4/+4
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| | | * Merge branch 'new_vds_feature_vfd_swmr' of ↵vchoi2022-05-067-217/+216
| | | |\ | | | | | | | | | | | | | | | https://github.com/vchoi-hdfgroup/hdf5 into new_vds_feature_vfd_swmr
| | | | * Committing clang-format changesgithub-actions2022-05-067-217/+216
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| | | * | Fix failing check for Windows:vchoi2022-05-061-1/+10
| | | |/ | | | | | | | | | | | | Add the VFD SWMR feature flag also to test_windows() (which is sec2) in test/vfd.c.
| | | * Merge branch 'new_vds_feature_vfd_swmr' of ↵vchoi2022-05-061-7/+8
| | | |\ | | |_|/ | |/| | | | | | https://github.com/vchoi-hdfgroup/hdf5 into new_vds_feature_vfd_swmr
| * | | Committing clang-format changesgithub-actions2022-04-211-7/+8
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| | | * 1) Add feature flag H5FD_FEAT_SUPPORTS_VFD_SWMR to sec2, core and stdio driversvchoi2022-05-069-288/+1154
| | |/ | |/| | | | | | | | | | | | | | | | 2) Disable file locking for VFD SWMR reader in H5F_open() 3) Add checking of VFD SWMR feature flag in test/page_buffer.c and test/vfd_swmr.c. Skip tests if the driver does not support VFD SWMR feature. 4) Add new tests + cleanups to test/vfd_swmr.c.
| * | Merge branch 'new_vds_feature_vfd_swmr' of ↵vchoi2022-04-2122-156/+163
| |\ \ | | | | | | | | | | | | https://github.com/vchoi-hdfgroup/hdf5 into new_vds_feature_vfd_swmr
| | * | Committing clang-format changesgithub-actions2022-04-2122-162/+169
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| * | | 1) Fix spelling errorsvchoi2022-04-212-12/+12
| |/ / | | | | | | | | | 2) Fix couple routine names due to FUNC_ENTER_PACKAGE.
| * | Modifications to:vchoi2022-04-2139-401/+892
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | A) Allow automatic generation of metadata file names for VDS support B) Allow VFD SWMR reader to open an existing HDF5 file either before the VFD SWMR writer has opened it or after it has closed. C) Remove the usage of H5P_FILE_ACCESS_ANY_VFD. D) Add H5FD_FEAT_SUPPORTS_VFD_SWMR feature flag. E) Do not map H5FD_MEM_GHEAP to H5FD_MEM_DRAW when vfd swmr IS enabled; map H5FD_MEM_GHEAP to H5FD_MEM_DRAW when vfd swmr is NOT enabled. For details regarding #A and #B above, see version 9 of the RFC.
| * | Merge pull request #62 from vchoi-hdfgroup/feature/vfd_swmrvchoi-hdfgroup2022-04-21487-13870/+17058
| |\ \ | | |/ | | | Feature/vfd swmr
| | * Merge pull request #61 from HDFGroup/feature/vfd_swmrvchoi-hdfgroup2022-04-21487-13870/+17058
| | |\ | |/ / | | / | |/ |/| VFD SWMR: Merges from develop (#1670)
* | VFD SWMR: Merges from develop (#1670)Dana Robinson2022-04-21487-13870/+17058
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Cleans up SWMR test scripts (both legacy and VFD) * Brings over format source changes for Java * Normalization of HL, Fortran, C++, Java w/ develop * Removes the STATIC flavor of FUNC_ENTER macros (#1622) * Removes the STATIC flavor of FUNC_ENTER macros * Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426) * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes unused definitions from module headers (#1624) * Misc stuff from develop (includes some parallel things) * Brings over SWMR test quiet mode changes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Merge pull request #60 from HDFGroup/feature/vfd_swmrvchoi-hdfgroup2022-04-04826-28719/+34697
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* | VFD SWMR: Normalization with develop and cleanup (#1559)Dana Robinson2022-03-3146-5373/+1538
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brought over plugin and test script changes * Removes remaining register keywords (#1481) * Fixed warnings in the aux process code * Minor fixes from develop * Minor changes from develop, fixed format warnings * Formatted source * Added HD prefix to timespec_get * Cleanup in new files * Removes the MANIFEST file and unused release files (#1497) * Removes the MANIFEST file and unused release files * Updated tar command * checkposix corrections * More checkposix fixes * Ripped out unused instrumentation functionality * Brought over cache tagging changes from develop * Changes to tagged metadata expulsion iteration * Fixed typo * Brought over H5O__free() changes from develop * Brings (unused) parallel page buffer test in line with develop * Moved the functionality in supervise.subr to test_vfd_swmr.sh * Tools VFD parameter updates * Committing clang-format changes * H5F VFD SWMR refactoring * Committing clang-format changes * Misc changes * Acceptance test cleanup * HD prefix * H5_get_option instead of getopt * Some bool fixes * Changes to VFD SWMR acceptance tests * Minor cleanup * Use AC_MSG_RESULT/AC_MSG_ERROR/AC_MSG_WARN instead of echo (#1532) * Merges from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* | VFD SWMR: Normalization with develop (#1506)Dana Robinson2022-03-23126-9566/+3109
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brought over plugin and test script changes * Removes remaining register keywords (#1481) * Fixed warnings in the aux process code * Minor fixes from develop * Minor changes from develop, fixed format warnings * Formatted source * Added HD prefix to timespec_get * Cleanup in new files * Removes the MANIFEST file and unused release files (#1497) * Removes the MANIFEST file and unused release files * Updated tar command * checkposix corrections * More checkposix fixes * Ripped out unused instrumentation functionality * Brought over cache tagging changes from develop * Changes to tagged metadata expulsion iteration * Fixed typo * Brought over H5O__free() changes from develop * Brings (unused) parallel page buffer test in line with develop * Moved the functionality in supervise.subr to test_vfd_swmr.sh * Tools VFD parameter updates * Committing clang-format changes * H5F VFD SWMR refactoring * Committing clang-format changes * Misc changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* | VFD SWMR: normalization with develop (#1472)Dana Robinson2022-03-06774-14074/+30344
| | | | | | Much normalization with develop. Still needs tools changes wrt VFD plugins.
| * Merge pull request #58 from HDFGroup/feature/vfd_swmrvchoi-hdfgroup2022-02-1950-46/+1670
| |\ | |/ |/| VFD SWMR: Aux process changes (#1451)
* | VFD SWMR: Aux process changes (#1451)Dana Robinson2022-02-1850-46/+1670
| | | | | | | | | | | | | | | | | | | | | | * Removed the aux process submodule * Directly added aux process files after submodule delete * Updated Akadio copyright on appropriate files * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
| * Merge pull request #56 from HDFGroup/feature/vfd_swmrvchoi-hdfgroup2022-02-1751-190/+942
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* | Merge pull request #1445 from derobins/vfd_swmr/licenseDana Robinson2022-02-1746-78/+227
|\ \ | | | | | | Updated VFD SWMR's Akadio license
| * | Updated the submodule to point to the correct commit so the tests passDana Robinson2022-02-171-0/+0
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| * | Updated VFD SWMR's Akadio licenseDana Robinson2022-02-1745-78/+227
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* | Merge pull request #1333 from raylu-hdf/raylu_aux_processraylu-hdf2022-01-318-11/+215
|\ \ | | | | | | Changes Related to the Auxiliary Process
| * | Enable submodule checkout for vfd_swmr.Ray Lu2022-01-281-0/+2
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