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Fix region transfer with object static partitioning #214

Merged
merged 3 commits into from
Nov 26, 2024
Merged

Fix region transfer with object static partitioning #214

merged 3 commits into from
Nov 26, 2024

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houjun
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@houjun houjun commented Nov 1, 2024 •
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#215

Description

Fix a bug when all dim lengths of an object are smaller than the number of servers when object static partitioning (default) is used.

What changes are proposed in this pull request?

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality not to work as expected; for instance, examples in this repository must be updated too)
  • This change requires a documentation update

Checklist:

  • My code modifies existing public API, or introduces new public API, and I updated or wrote docstrings
  • I have commented my code
  • My code requires documentation updates, and I have made corresponding changes to the documentation
  • I have added tests that prove my fix is effective or that my feature works
  • New and existing unit tests pass locally with my changes

@houjun houjun changed the title Update pdc_region_transfer.c Fix region transfer with object static partitioning Nov 4, 2024
@houjun houjun marked this pull request as ready for review November 4, 2024 16:45
jeanbez
jeanbez requested changes Nov 4, 2024
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We need to either merge the #213 first which corrects the libfabric dependency in Perlmutter or also fix it here for the CI to complete.

@houjun
Update .gitlab-ci.yml
13c909e 
Fix issue with Perlmutter CI libfabric module
@jeanbez jeanbez merged commit 25db7c1 into develop Nov 26, 2024
8 checks passed
jeanbez added a commit that referenced this pull request Dec 3, 2024
@jeanbez @houjun
@github-actions @hyunjuooh @zhangwei217245 @nickaruwang
Sync develop to stable (v.0.6) (#216)
5fe5929 
* 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 <[email protected]>
Co-authored-by: Jean Luca Bez <[email protected]>

* 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 <[email protected]>
Co-authored-by: Jean Luca Bez <[email protected]>

* 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 <[email protected]>
Co-authored-by: Jean Luca Bez <[email protected]>
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 <[email protected]>

* Fix vpicio_mts (#199)

---------

Co-authored-by: Houjun Tang <[email protected]>
Co-authored-by: Hyunju Oh <[email protected]>
Co-authored-by: Hyunju Oh <[email protected]>
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 <[email protected]>
Co-authored-by: Hyunju Oh <[email protected]>
Co-authored-by: Jean Luca Bez <[email protected]>
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 <[email protected]>
Co-authored-by: Nick Wang <[email protected]>
Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Jean Luca Bez <[email protected]>

* 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 <[email protected]>
Co-authored-by: Jean Luca Bez <[email protected]>

* 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 <[email protected]>
Co-authored-by: Jean Luca Bez <[email protected]>
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 <[email protected]>
Co-authored-by: nickaruwang <[email protected]>
Co-authored-by: Nick Wang <[email protected]>
Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Jean Luca Bez <[email protected]>
Co-authored-by: Hyunju Oh <[email protected]>
Co-authored-by: Hyunju Oh <[email protected]>

* 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 <[email protected]>
Co-authored-by: Jean Luca Bez <[email protected]>

* 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 <[email protected]>
Co-authored-by: Hyunju Oh <[email protected]>
Co-authored-by: Jean Luca Bez <[email protected]>
Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>

---------

Co-authored-by: Houjun Tang <[email protected]>
Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Hyunju Oh <[email protected]>
Co-authored-by: Hyunju Oh <[email protected]>
Co-authored-by: Zhang Wei <[email protected]>
Co-authored-by: nickaruwang <[email protected]>
Co-authored-by: Nick Wang <[email protected]>
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@jeanbez jeanbez jeanbez approved these changes

@zhangwei217245 zhangwei217245 zhangwei217245 approved these changes

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@houjun @zhangwei217245 @jeanbez