EQSIM benchmark code and fixes #213
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* 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>
…k is less than the 4GB chunk limit
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Nov 4, 2024
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Nov 26, 2024
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* 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>
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