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base repository: hpc-io/pdc
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base: 0.5
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head repository: hpc-io/pdc
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compare: stable
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  • 9 commits
  • 425 files changed
  • 9 contributors

Commits on Jul 22, 2024

  1. Copy the full SHA
    6999ac7 View commit details

Commits on Dec 3, 2024

  1. Sync develop to stable (v.0.6) (#216)

    * Performace improvement for vpicio (#211)
    
    * Paritial fix for the region transfer/wait performance issue
    
    * Committing clang-format changes
    
    * Improve the async processing for vpicio_mts_all, also fix a few compile issues
    
    * Committing clang-format changes
    
    * Minor change
    
    * Continue to optimize start_all performance for vpicio, add a few time related convinient functions
    
    * Committing clang-format changes
    
    * Fix hanging issue in CI testing
    
    * Committing clang-format changes
    
    * Disable debug prints
    
    * Revert back for non-all ops
    
    * Better pthread management
    
    * Better pthread management
    
    * Fix timeout issue with CI testing and clang-formatting
    
    * Committing clang-format changes
    
    * Test
    
    * Trigger test
    
    * Committing clang-format changes
    
    * Trigger CI
    
    * Committing clang-format changes
    
    * Trigger CI
    
    * Switch to static partition for vpicio
    
    * Replace vpicio_mts with new implementation
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * Multi-thread fix and request merging (#205)
    
    * Update getting_started.rst (#184)
    * Removing gres option for ctest (#182)
    * Removing gres option from scripts
    * Update check for core
    
    ---------
    
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Fix an issue with region transfer request
    * Committing clang-format changes
    * Merge small requests when they are contiguous and 1D, change srun commands in run scripts to detect Perlmutter compute nodes
    * Merge only for REGION_LOCAL partition
    * Committing clang-format changes
    * Fix a bug that causes some tests to fail
    * Fix a couple of issues with start/wait all
    * Committing clang-format changes
    * Add aggregation support for contiguous read operations
    * Committing clang-format changes
    * Fix compile issue when multithread is enabled
    * Committing clang-format changes
    * minor change with test code
    * Committing clang-format changes
    * Remove metadata mutex for multi threading
    * Committing clang-format changes
    * Fix mutex
    * Committing clang-format changes
    * Fix an issue when closing an obj
    * Sync develop to stable (v.0.5) (#201)
    * Update getting_started.rst (#184)
    * Removing gres option for ctest (#182)
    * Removing gres option for ctest
    * Removing gres option from scripts
    * Update check for core
    
    ---------
    
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * enable cache by default (#187)
    * Removing PDC macro (#189)
    * Removing gres option for ctest
    * Removing gres option from scripts
    * Update check for core
    * Remove PDC macro
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * BDCATS fix (#193)
    * Fix issues with bdcats_batch
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * Update mpi_test.sh (#197)
    * Update .gitlab-ci.yml (#195)
    * Updates for latest integration with Jacamar and Gitlab tokens in CI
    * VPICIO bugfix (#196)
    * Fix VPICIO bug
    * Add more checks and error out when no server is selected
    * Committing clang-format changes
    * Add VPICIO and BDCATS to MPI test
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Fix vpicio_mts (#199)
    
    ---------
    
    Co-authored-by: Houjun Tang <htang4@lbl.gov>
    Co-authored-by: Hyunju Oh <oh.693@osu.edu>
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * Committing clang-format changes
    * Fix rebase issue
    * Add timers
    * Committing clang-format changes
    * Add explict transfer start (all) with MPI communicator
    * Committing clang-format changes
    * MPI fix
    * remove debug msg
    * Committing clang-format changes
    * Add function comment for doc
    * Revert script changes
    * Committing clang-format changes
    * Revert script changes
    * Committing clang-format changes
    * Revert script setting
    
    ---------
    
    Co-authored-by: Hyunju Oh <oh.693@osu.edu>
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * Update CMakeLists.txt to bump version number (#202)
    
    * Update CMakeLists.txt to bump version number
    
    * Update clang-format-check.yml
    
    * IDIOMS Update & BULKI v0.1 (#203)
    
    * fix cmake mercury_util not found issue
    
    * update for Julia support
    
    * fix hdf5.h not found for src/tools
    
    * update container config
    
    * add libhdf5-dev for Github Actions
    
    * update CMake for HDF5 in tools
    
    * update logic for finding HDF5
    
    * update
    
    * remove use system hdf5
    
    * delete useless find library
    
    * update findHDF5
    
    * Feature/dart (#11)
    
    Update to avoid fixing compilation issue on src/tools (due to : HDF5 cannot be found)
    
    * Use cc on Perlmutter (#161)
    
    Dr. Tang fixed a compilation issue in NERSC CI where HDF5 cannot be detected even if the cray-parallel-hdf5 module is loaded on Perlmultter.
    
    * update with fixes on tools and llsm example
    
    * add gitignore for llsm
    
    * update gitignore
    
    * Feature/dart (#12)
    
    * fix formatting
    
    * update clangformat10
    
    * update base dockerfile
    
    * Add clang-format10 to docker container. Also fixed clang-format.
    
    Add clang-format10 to docker container. Also fixed clang-format.
    
    * Fix pdc ls (#154)
    
    * pdc import, export, ls compiled successfully
    
    * removed requested files
    
    * formatting issues
    
    * changed install tools
    
    * gets checkpoint files
    
    * grabbing checkpoint files from within sub-directories, minor comments
    
    * Committing clang-format changes
    
    * Committing clang-format changes
    
    * Fix a few issues with pdc_ls
    
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: nickaruwang <nickwan0318@gmail.com>
    Co-authored-by: Nick Wang <66816536+nickaruwang@users.noreply.github.com>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * update documentation
    
    * update document 
    
    update document
    
    * sync branch 
    
    sync branch
    
    * no UUID module is required
    
    * update document and make UUID an optional package
    
    * update docker repo name
    
    * updating docker repo name and make UUID optional
    
    * Complete support for Docker and Github Codespace  (#157)
    
    Include support for Docker and Github Codespace so we can run our dev environment with the support of Docker.
    
    * SQLite and RocksDB support for KVtags (#165)
    
    SQLite and RocksDB support for KVtags
    
    * fix round for tag delete
    
    * update test
    
    * bulki update
    
    * BULKI base type worked
    
    * BULKI all tests done
    
    * new index code
    
    * update
    
    * update new test
    
    * update csv bench
    
    * update
    
    * update script
    
    * adding python scripts for generating large metadata set for LLSM application
    
    * update json schema
    
    * better json validator
    
    * update importer
    
    * update code for non-MPI compatibility
    
    * update llsm converter
    
    * update LLSM data converter
    
    * split files
    
    * update .gitignore
    
    * update
    
    * add timing info
    
    * update
    
    * update tag size
    
    * detect object creation failure
    
    * update
    
    * update object name with date
    
    * update for robustness
    
    * update
    
    * update JMD_DEBUG option
    
    * update output for overall output
    
    * update inttypes.h
    
    * update
    
    * update extractor
    
    * update inttypes.h
    
    * update converter
    
    * update importer information
    
    * Update getting_started.rst (#184)
    
    * Removing gres option for ctest (#182)
    
    * Removing gres option for ctest
    * Removing gres option from scripts
    * Update check for core
    
    ---------
    
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * fix issue
    
    * fixed search issues
    
    * update for infix
    
    * update
    
    * index persistence still needs improvement
    
    * update
    
    * enable cache by default (#187)
    
    * Removing PDC macro (#189)
    
    * Removing gres option for ctest
    * Removing gres option from scripts
    * Update check for core
    * Remove PDC macro
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * update
    
    * range query done'
    
    * range query local test passed
    
    * multi-condition in progress
    
    * clean up code
    
    * add comments
    
    * new benchmark
    
    * update
    
    * update range query test
    
    * update cmake:
    
    * update
    
    * update
    
    * update
    
    * update
    
    * someta range query
    
    * someta range query
    
    * someta range query
    
    * fix value serialization
    
    * update
    
    * update double free
    
    * update
    
    * update
    
    * update
    
    * fixed pointer issue
    
    * rb_tree delete fixed, now need to check index persistence
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * update
    
    * BDCATS fix (#193)
    
    * Fix issues with bdcats_batch
    
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * update
    
    * clean up code
    
    * update test sh
    
    * IDIOMS persistence DONE
    
    * update
    
    * remove old kvtag benchmarks
    
    * update
    
    * update
    
    * update changes
    
    * dart info
    
    * update
    
    * multi data type for the same key, supported now
    
    * Monitoring changes from feature/dart to develop (#18)
    
    Major changes: 
    * IDIOMS -> affix-based query benchmark
    * IDIOMS -> Simulation Test
    * IDIOMS -> Multi data type supported for the same key
    * IDIOMS -> Range Query and Exact Query for Numeric Values
    * IDIOMS -> benchmark for numeric values (exact search and range query)
    * IDIOMS -> Index Persistence
    * BULKI -> A data serialization and deserialization mechanism.
    
    * fix CMakeLists.txt
    
    * update
    
    * update format
    
    * update BULKI interface order
    
    * BULKI API sorted
    
    * add idioms ci test
    
    * Feature/dart (#20)
    
    1. add documentation about BULKI and IDIOMS query conditions
    2. add ci test for IDIOMS
    3. optimized BULKI to save space on its metadata fields.
    
    * Feature/dart (#22)
    
    update version
    
    * update
    
    * update
    
    * update
    
    * remove unnecessary .bin file
    
    * update
    
    * update
    
    ---------
    
    Co-authored-by: Houjun Tang <htang4@lbl.gov>
    Co-authored-by: nickaruwang <nickwan0318@gmail.com>
    Co-authored-by: Nick Wang <66816536+nickaruwang@users.noreply.github.com>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    Co-authored-by: Hyunju Oh <oh.693@osu.edu>
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    
    * Fix region transfer with object static partitioning (#214)
    
    * Update pdc_region_transfer.c
    
    * Committing clang-format changes
    
    * Update .gitlab-ci.yml
    
    Fix issue with Perlmutter CI libfabric module
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * EQSIM benchmark code and fixes (#213)
    
    * Update getting_started.rst (#184)
    
    * Removing gres option for ctest (#182)
    
    * Removing gres option for ctest
    * Removing gres option from scripts
    * Update check for core
    
    ---------
    
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * enable cache by default (#187)
    
    * Benchmark code for EQSIM data
    
    * Committing clang-format changes
    
    * Minor adjustments
    
    * Committing clang-format changes
    
    * Updates
    
    * Committing clang-format changes
    
    * Change vpicio to use local server partitioning, add some debug prints
    
    * Committing clang-format changes
    
    * Add metadata query to benchmark code
    
    * Committing clang-format changes
    
    * Add ZFP compression for read and write
    
    * Committing clang-format changes
    
    * Add a option to use more ranks to read data so total data of each rank is less than the 4GB chunk limit
    
    * Committing clang-format changes
    
    * Add a data query code for EQSIM data
    
    * Committing clang-format changes
    
    * Minor adjustments for the HDF5 read code
    
    * Committing clang-format changes
    
    * Fix an issue with periodic data flush, minor changes to benchmark code
    
    * Committing clang-format changes
    
    * fix an issue with 3d read segfault
    
    * Committing clang-format changes
    
    * Fix compile issue
    
    * Update .gitlab-ci.yml
    
    * Update sleep time
    
    * Replace function
    
    * Replace function
    
    * Minor updates and doc changes
    
    * Committing clang-format changes
    
    * Update
    
    ---------
    
    Co-authored-by: Hyunju Oh <oh.693@osu.edu>
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    ---------
    
    Co-authored-by: Houjun Tang <htang4@lbl.gov>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Hyunju Oh <oh.693@osu.edu>
    Co-authored-by: Hyunju Oh <hjoh16@login15.chn.perlmutter.nersc.gov>
    Co-authored-by: Zhang Wei <zhangwei217245@lbl.gov>
    Co-authored-by: nickaruwang <nickwan0318@gmail.com>
    Co-authored-by: Nick Wang <66816536+nickaruwang@users.noreply.github.com>
    8 people authored Dec 3, 2024
    Copy the full SHA
    5fe5929 View commit details

Commits on Jan 10, 2025

  1. migrate CI (#219)

    migrate CI to new instance
    jeanbez authored Jan 10, 2025
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    83bde6a View commit details

Commits on Jan 17, 2025

  1. Sync develop to stable (#221)

    * Update CI message (#220)
    
    * include CODEOWNERS
    
    * include status messages
    
    * improve message
    
    * fix metric name (#222)
    
    * Update .gitlab-ci.yml
    jeanbez authored Jan 17, 2025
    Copy the full SHA
    b8ad03f View commit details

Commits on Feb 4, 2025

  1. Fix a thread race issue (#224)

    * Fix a thread race issue that may cause memory error when larger than cache max size data is transferred
    
    * Add a test that writes more data than server cache size
    
    * Fix CI run command
    houjun authored Feb 4, 2025
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    1c78dab View commit details

Commits on Feb 5, 2025

  1. Revert "Fix a thread race issue (#224)" (#225)

    This reverts commit 1c78dab.
    houjun authored Feb 5, 2025
    Copy the full SHA
    c307e18 View commit details

Commits on Apr 1, 2025

  1. Synchronize with develop (#242)

    * Fix cache flush (#226)
    
    * Fix a thread race issue that may cause memory error when larger than cache max size data is transferred
    
    * Add a test that writes more data than server cache size
    
    * Fix CI run command
    
    * Update nersc.yml (#238)
    
    * Since PDCinit returns a uint64_t, 0 should indicate failure (#233)
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Check the return value of `PDC_Client_init` in `PDC_init` (#230)
    
    * Check that return value of PDC_Client_init in PDC_init
    
    * Change return to 0
    
    This will make is simpler when merging #233 (comment)
    
    ---------
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Change `printf` to PDC logger (#232)
    
    * Changed all printf to use pdc logger
    
    Also removed large blocks of comments and chanegd the pdc logger
    to print the file name, function, and line number.
    
    * Change typo of LOG_INFO to LOG_ERROR
    
    * Correct grammar from fail -> failed
    
    * update grammer succesfully close -> successfully closed
    
    * switch type of LOG_INFO to LOG_ERROR
    
    * Add logging docs and fix some LOG_INFO->LOG_JUST_PRINT
    
    * update clang formatting
    
    ---------
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Malloc correct size for pdc_obj_metadata_pkg (#237)
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * PDCregion_transfer_create validate client buf, local region, and remote regions (#236)
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    ---------
    
    Co-authored-by: Houjun Tang <htang4@lbl.gov>
    Co-authored-by: Noah Lewis <47840925+TheAssembler1@users.noreply.github.com>
    3 people authored Apr 1, 2025
    Copy the full SHA
    0884588 View commit details
  2. use latest cmake in CI (#243)

    * install latest cmake
    * fix mercury version to match the docs
    * try fix
    jeanbez authored Apr 1, 2025
    Copy the full SHA
    89268e8 View commit details

Commits on Jul 21, 2025

  1. Synchronize with develop (#256)

    * Add pdc_logger.h to installation (#245)
    
    * sync with gitlab (#248)
    
    * Fix restart issue (#228)
    
    * Fix cache flush (#226)
    
    * Fix a thread race issue that may cause memory error when larger than cache max size data is transferred
    
    * Add a test that writes more data than server cache size
    
    * Fix CI run command
    
    * Fix restart issue
    
    * Update nersc.yml (#238)
    
    * Since PDCinit returns a uint64_t, 0 should indicate failure (#233)
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Check the return value of `PDC_Client_init` in `PDC_init` (#230)
    
    * Check that return value of PDC_Client_init in PDC_init
    
    * Change return to 0
    
    This will make is simpler when merging #233 (comment)
    
    ---------
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Change `printf` to PDC logger (#232)
    
    * Changed all printf to use pdc logger
    
    Also removed large blocks of comments and chanegd the pdc logger
    to print the file name, function, and line number.
    
    * Change typo of LOG_INFO to LOG_ERROR
    
    * Correct grammar from fail -> failed
    
    * update grammer succesfully close -> successfully closed
    
    * switch type of LOG_INFO to LOG_ERROR
    
    * Add logging docs and fix some LOG_INFO->LOG_JUST_PRINT
    
    * update clang formatting
    
    ---------
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Malloc correct size for pdc_obj_metadata_pkg (#237)
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * PDCregion_transfer_create validate client buf, local region, and remote regions (#236)
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    ---------
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    Co-authored-by: Noah Lewis <47840925+TheAssembler1@users.noreply.github.com>
    
    * Fix return metadata dtype (#246)
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Region info transfer struct type and helper functions (#247)
    
    * Fix cache flush (#226)
    
    * Fix a thread race issue that may cause memory error when larger than cache max size data is transferred
    
    * Add a test that writes more data than server cache size
    
    * Fix CI run command
    
    * checkpoint
    
    * Switch variables such as count_0, start_0, and size0... to arrays
    
    This will reduce code duplication, reduce bugs, and make it easier
    to switch to support n-dimnesional data.
    
    * clang format
    
    * checkpoint
    
    * created better function names and documentation
    
    * remove
    
    * Committing clang-format changes
    
    * clang format
    
    * remove file
    
    * change for use helper function
    
    * fix bug with incorrect helper function call
    
    ---------
    
    Co-authored-by: Houjun Tang <htang4@lbl.gov>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Fix issues with PDC tools (#249)
    
    * Fix issues with PDC tools
    
    * Correct LOG_ERROR to LOG_INFO
    
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Fix printing in `PGOTO_ERROR` and `PGOTO_ERROR_VOID` (#250)
    
    Print new line by default in `PGOTO_ERROR` and `PGOTO_ERROR_VOID`
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Group Tests Into Folders (#252)
    
    * Fix cache flush (#226)
    
    * Fix a thread race issue that may cause memory error when larger than cache max size data is transferred
    
    * Add a test that writes more data than server cache size
    
    * Fix CI run command
    
    * Grouped commons tests into folders
    
    This commit also changes the src/tests/CmakeLists.txt to build tests
    within their new folders
    
    * add deprecated folder remove buf_map folder
    
    * Update run_multiple_mpi_test.sh
    
    * Update dependencies-macos.sh
    
    * Update dependencies-macos.sh
    
    ---------
    
    Co-authored-by: Houjun Tang <htang4@lbl.gov>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    Co-authored-by: Jean Luca Bez <jeanlucabez@gmail.com>
    
    * Return the same obj_id if the obj is just created or already opened (#254)
    
    * Return the same obj_id if the obj is just created or already opened
    
    * Committing clang-format changes
    
    * Update doc
    
    * Update dependencies-macos.sh
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * add option to choose interface (#255)
    
    * add option to connect to a given network interface
    * Committing clang-format changes
    * fix conflict
    * include header
    * enable output on failure
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * Fix multithreading compilation (#259)
    
    * fix multhreading compilation
    
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Fix segmentation fault of calling `PDCobj_create_mpi` twice with duplicate object name (#262)
    
    * Validate sucess of PDC_obj_create and PDC_find_id in PDCobj_create_mpi
    
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Use `PDC_malloc`, `PDC_free`, `PDC_calloc`, and `PDC_realloc` (#260)
    
    * checkpoint
    
    * replace free with PDC_free and calloc with PDC_calloc
    
    * Committing clang-format changes
    
    * fix more mallocs to PDC_malloc
    
    * more PDC_free fixes
    
    * Committing clang-format changes
    
    * Update ubuntu-cache.yml
    
    * remove eno1
    
    * fix realloc
    
    * Committing clang-format changes
    
    * Update ubuntu-no-cache.yaml
    
    * Fix several bugs with error checking with object dim allocation
    
    * Committing clang-format changes
    
    * fix bug
    
    * Committing clang-format changes
    
    * Update ubuntu-no-cache.yaml
    
    * Update ubuntu-cache.yml
    
    * Set default value of ndim to 1 in PDCprop_create when using PDC_OBJ_CREATE
    
    * Committing clang-format changes
    
    * Malloc when defaulting to ndim size 1.
    Only free hostname when we PDC_malloc the memory
    because pointers returned by getenv are not malloced
    and could point to static memory.
    
    * Committing clang-format changes
    
    * Update README.md
    
    minor change to trigger the pipeline
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    Co-authored-by: Jean Luca Bez <jeanlucabez@gmail.com>
    
    * Fix Sphinx documentation errors and warnings (#265)
    
    * Fix all sphinx warnings and errors. Removed repeat declarations of functions.
    
    * Committing clang-format changes
    
    * remove def of EXTENSION_MAPPING
    
    * gitignore for docs and fix c structs
    
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Replace `docs/README.md` -> steps to build docs (#268)
    
    * Replace docs/README.md -> steps to build docs
    
    * Update README.md
    
    ---------
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Use `FUNC_ENTER` and `FUNC_LEAVE` (#270)
    
    * use func enter and func leave in all functions
    
    * Committing clang-format changes
    
    * fix infinite recursion between memory managment, hash table, and per function timing
    
    * Committing clang-format changes
    
    * add profiling to CI
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * New test macros and code cleanup (#261)
    
    * checkpoint
    
    * Committing clang-format changes
    
    * some tests
    
    * Committing clang-format changes
    
    * checkpoint
    
    * open_obj uses new test macros
    
    * Committing clang-format changes
    
    * read_obj uses TASSERT
    
    * read_obj uses TASSERT
    
    * Committing clang-format changes
    
    * cont_del and cont_getid use test macros
    
    * convert more tests to use macros
    
    * convert more tests to macros
    
    * Committing clang-format changes
    
    * Committing clang-format changes
    
    * clang format
    
    * use test helper in cont_info and cont_add_del
    
    * more tests use macros
    
    * Committing clang-format changes
    
    * use tests macros in more tests
    
    * use PGOTO* macros instead of goto
    
    * clang format
    
    * more log fixes
    
    * logging cleanup and more usage of test macros
    
    * Committing clang-format changes
    
    * clang format and fix CMakeLists for tests
    
    * use tests macros in transfer overlap 2D/3D
    
    * use TASSERT in more tests
    
    * Committing clang-format changes
    
    * use test asserts
    
    * all tests on the CI use TASSERT
    
    * fix printing and newlines in tests
    
    * print time, file name, function name, and line number in debug print
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * Tests logging typo fix (#273)
    
    * Fixed logging typos
    
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * Rename pdc_server.exe to pdc_server for consistency (#275)
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Update vpicio_mts.c (#276)
    
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Client Propogate `HG_Finalize` error on `PDCclose` (#263)
    
    * all but 4 close errors are fixed
    
    * Committing clang-format changes
    
    * client side HG_Finalize now passes on serial tests
    
    * Committing clang-format changes
    
    * cleanup
    
    * Committing clang-format changes
    
    * Update pdc_region_transfer.c
    
    * free bulk handles during region transfer close
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * Standardize ID Lookup Null Checks and Error Handling (#281)
    
    * cleanup finding id's
    
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    
    * Obj open fix (#279)
    
    * Fix seg fault for PDCobj_open on non-existent object
    
    * Committing clang-format changes
    
    * Remove log from NULL check
    
    * Log message when object metadata isn't found.
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Fix multithread (#274)
    
    * move hash table mutex to hashtable source filse
    
    * Committing clang-format changes
    
    * add multithread compile test
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    * Fix seg fault when mercury initialization fails (#283)
    
    * check for NULL paramterse in hash table
    
    * Committing clang-format changes
    
    ---------
    
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>
    
    ---------
    
    Co-authored-by: Noah Lewis <47840925+TheAssembler1@users.noreply.github.com>
    Co-authored-by: Houjun Tang <htang4@lbl.gov>
    Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
    4 people authored Jul 21, 2025
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