Sync develop to stable (#301)

* 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>

* working to fix CI

* CI on macOS

* CI on macOS

* working on metrics CI

* working on metrics CI

* working on metrics CI

* working on metrics CI

* fix parser for metrics dashboard

* Region transfer all optimization, update vpicio_mts and bdcats_mts, enable IDIOMS in cmake, reduce printfs (#295)

* Improve performance for transfer all, reduce the log messages

* Committing clang-format changes

* Reduce the log warning messages

* update

* Committing clang-format changes

* Update vpicio and bdcats mts version

* Committing clang-format changes

* Update cmakelist and test codes

* Committing clang-format changes

* Update cmakelist

* Add bdcats_mts

* Committing clang-format changes

* remove unnecessary file

* Conditional test with IDIOMS

* Update vpic and bdcats _mts

* Committing clang-format changes

* Minor updates

* Committing clang-format changes

* Fix IDIOMS cmake

---------

Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>

* Change pull_request to pull_request_target event

* Documentation rework (#285)

* created framework for new docs

* worked on getting started example

* section numbers

* update compiliation and running PDC

* started working on hdf5 vol and pdcpy docs

* updated introdution with index for installation types

* worked on first program examples and installation

* worked on first program examples and installation

* worked on first program examples and installation

* message

* checkpoint

* message

* rename services -> using PDC

* using PDC update

* started working on client API

* update C documentation so breathe can extract more docs

* Committing clang-format changes

* more type documentation

* Add more API functions

* update tools

* checkpoint

* checkpoint

* checkpoint

* checkpoint

* test

* Committing clang-format changes

* remove border

* update section numbers

* checkpoint

* Switch core concepts 2.2 with 2.1

---------

Co-authored-by: Avi Maloo <avimaloo24@gmail.com>
Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>

* Installation fix (#293)

* fixes installation issues

* Committing clang-format changes

* remove comment

---------

Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>

* Replace vpicio and bdcats with multiple time step version  (#297)

* Fix a mismatch issue with vpic and bdcats

* Replace old vpicio and bdcats with mts version

* update run cmd

* Update arguments processing

* remove unnecessary code

* remove unnecessary header and timing code

* remove unnecessary code

* Committing clang-format changes

* Remove unnecessary call

* Remove barrier to prevent a deadlock of MPI_Barrier

* Committing clang-format changes

* Trigger CI

---------

Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>

* Update macOS runner version to macos-15 (#299)

* Update macOS runner version to macos-15

MacOS 13 runner has been deprecated

* Set CFLAGS to suppress warnings in macOS dependencies

Add CFLAGS to suppress incompatible function pointer warnings.

* Documentation rework (#298)

* created framework for new docs

* worked on getting started example

* section numbers

* update compiliation and running PDC

* started working on hdf5 vol and pdcpy docs

* updated introdution with index for installation types

* worked on first program examples and installation

* worked on first program examples and installation

* worked on first program examples and installation

* message

* checkpoint

* message

* rename services -> using PDC

* using PDC update

* started working on client API

* update C documentation so breathe can extract more docs

* Committing clang-format changes

* more type documentation

* Add more API functions

* update tools

* checkpoint

* checkpoint

* checkpoint

* checkpoint

* test

* Committing clang-format changes

* remove border

* update section numbers

* checkpoint

* Switch core concepts 2.2 with 2.1

* description of installation targets

* add versions for dependencies

* Add "or later" to HDF5, libfabric, mercury, and python version

---------

Co-authored-by: Avi Maloo <avimaloo24@gmail.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: Noah Lane Lewis <nlewi26@login38.chn.perlmutter.nersc.gov>
Co-authored-by: Houjun Tang <htang4@lbl.gov>

* Object property duplication copy consistency (#291)

* copy consitency in

* Committing clang-format changes

* Copy type in obj dup function

---------

Co-authored-by: github-actions <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Jean Luca Bez <jlbez@lbl.gov>

* Fix metrics CI binary and bump version for release (#300)

* fix metrics CI binary name

* bump version to 0.7 for release

---------

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>
Co-authored-by: Avi Maloo <avimaloo24@gmail.com>
Co-authored-by: Noah Lane Lewis <nlewi26@login38.chn.perlmutter.nersc.gov>

Author: 6 people

.gitlab-ci.yml

@@ -464,7 +464,7 @@ perlmutter-metrics:
         PDC_CLIENT_LOOKUP: "NONE"
         PDC_SERVER: "${PDC_BUILD_PATH}/perlmutter/metrics/bin/pdc_server"
         PDC_SERVER_CLOSE: "${PDC_BUILD_PATH}/perlmutter/metrics/bin/close_server"
-        PDC_CLIENT: "${PDC_BUILD_PATH}/perlmutter/metrics/bin/vpicio_mts"
+        PDC_CLIENT: "${PDC_BUILD_PATH}/perlmutter/metrics/bin/vpicio"
         PDC_JOB_OUTPUT: "pdc-metrics.log"
     script: 
         - hostname

CMakeLists.txt

@@ -55,7 +55,7 @@ endif()
 # Version information
 #------------------------------------------------------------------------------
 set(PDC_VERSION_MAJOR "0")
-set(PDC_VERSION_MINOR "6")
+set(PDC_VERSION_MINOR "7")
 set(PDC_VERSION_PATCH "0")
 set(PDC_PACKAGE "pdc")
 set(PDC_PACKAGE_NAME "PDC")