adding Adios2 io support #113

seegyoung · 2024-09-09T17:48:55Z

support for serial adios2 file I/O (set Omega_h_USE_ADIOS2 ON)
MPI only with single process at the moment
testing with kokkos and coda not included

jacobmerson · 2024-09-10T03:33:31Z

/runtests

github-actions · 2024-09-10T03:45:34Z

Test Result: failure (details)

jacobmerson

Hi Seegyoung, from what I see so far it looks like things are on the right track.

However, it seems like there are some missing files in your commit. I don't see the Omega_h_adios2.hpp file, or where the write_adios2 code is located.

cmake/FindADIOS2.cmake

src/CMakeLists.txt

src/osh2bp.cpp

cwsmith · 2024-09-10T13:47:56Z

Thank you @seegyoung. Looks good.

If it isn't there already, and while partitioned mesh support is under development, we should add a check to the adios writer and reader to ensure that the mesh is serial.

seegyoung · 2024-09-11T20:06:11Z

I will update based on all the input from both of you.

src/adios2_io.cpp

jacobmerson · 2024-09-16T21:47:51Z

@seegyoung I still don't see the definitions for write_value and read_value for adios2.

seegyoung · 2024-09-17T04:34:40Z

Sorry about the trouble - missing files are added

cwsmith · 2024-09-17T13:24:59Z

@seegyoung Would you please remove the romulus-config.sh file? We maintain build instructions for various systems in the wiki: https://github.com/SCOREC/omega_h/wiki

seegyoung · 2024-09-17T13:33:04Z

OK I will do.

jacobmerson · 2024-12-03T18:33:50Z

Hi Seegyoung, did you have a chance to address the comments from Cameron and I?

seegyoung · 2024-12-06T07:57:23Z

Yes, it was removed on September 17th. Thanks for checking with me.

jacobmerson · 2024-12-12T20:19:56Z

@seegyoung can you update this pull request with your changes? I do not see the requested updates.

seegyoung · 2024-12-13T03:40:38Z

I am not good at GitHub so I don't know what to do to resolve the issue and what's the source of the issue. Can someone can do this for me please?

cwsmith · 2024-12-13T18:49:31Z

If you have changes that are committed into your local copy of the branch (i.e., on the SCOREC filesystem) you can run 'git push' to upload them to github. This PR will automatically be updated.

I'm available to discuss via WebEx if needed. Please send me an email and we can pick a time.

jacobmerson

@seegyoung i have added additional comments. Please address them and update this pull request.

cmake/FindADIOS2.cmake

src/Omega_h_adios2.hpp

src/adios2_io.cpp

src/bp2osh.cpp

src/Omega_h_adios2.hpp

src/Omega_h_adios2.cpp

src/Omega_h_adios2.hpp

src/Omega_h_adios2.cpp

src/Omega_h_adios2.hpp

cwsmith

Looks good. Thank you. A few comments are below.

src/CMakeLists.txt

src/Omega_h_adios2.cpp

src/adios2_io.cpp

Co-authored-by: Cameron Smith <[email protected]>

cwsmith · 2025-01-30T17:29:41Z

@seegyoung Thanks for the updates. It looks like the mesh object is passed into the [read|write]_[value|array](...) (and related functions) to extract MPI communicator info. Instead of passing the mesh there, I think it would be cleaner to pass the Omegah comm object (i.e., mesh->comm()). This makes it clear there is no 'mesh' dependency in those functions.

seegyoung · 2025-01-30T20:06:53Z

That sounds good. I will do so.

jacobmerson · 2025-01-31T19:38:40Z

@cwsmith does Omega_h have logging or print functions that we should be using to be XSDK compliant? I didn't find anything with a quick check.

cwsmith · 2025-01-31T19:49:49Z

@jacobmerson Good question. Adios2 is not a part of the xSDK (https://xsdk.info/release-1-1-0/). I did a couple of quick searches through the adios2 docs (https://adios2.readthedocs.io/en/v2.10.2/) and didn't find anything obvious.

jacobmerson · 2025-02-03T05:44:42Z

src/CMakeLists.txt

+    target_include_directories(omega_h PRIVATE "${ADIOS2_INCLUDE_DIRS}")
+    target_link_libraries(omega_h PUBLIC "${ADIOS2_LIBRARIES}")


@cwsmith @seegyoung should we be using the adios2 target here? Or, do we need to handle this with the library variables because of bob.cmake?

I think Cameron can answer this

jacobmerson · 2025-02-03T05:45:57Z

I just had one remaining question on the CMakeLists.txt, that hopefully Cameron will know more about. Once we resolve I'm ready to merge.

seegyoung added 4 commits August 25, 2024 02:19

support for Omega_h_USE_ADIOS2 added

c786f61

checking in adios2 dev

788e45c

adding osh2bp and bp2osh to utils

906c8bc

minor changes

dcdfe09

seegyoung requested review from cwsmith and jacobmerson September 9, 2024 17:49

seegyoung added the enhancement New feature or request label Sep 9, 2024

jacobmerson requested changes Sep 10, 2024

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cwsmith reviewed Sep 10, 2024

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cwsmith added the adios2 label Sep 10, 2024

adding missing header file and sanity check

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jacobmerson reviewed Sep 16, 2024

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adding adios2 impl (cpp) and config.sh for romulus

ad95f00

config.sh removed

a76e37a

resolve conflicts

cb35d7f

jacobmerson reviewed Dec 23, 2024

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adding prefix option in adios2 read/write

5627b34

seegyoung added 2 commits December 29, 2024 21:28

writing multiple meshes with prefix

1971fe0

writing multiple meshes added to adios2_io test

aae867b

jacobmerson requested changes Dec 31, 2024

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seegyoung added 6 commits January 15, 2025 23:47

fixing ctest error with adios2_io

f0099e7

removing unnecessary function declaration

6285327

adding static

6abf57a

removing FindADIOS2.cmake

d7a31ea

addressing requested changes

e937e83

adding adios namespace

70bb5b9

cwsmith requested changes Jan 27, 2025

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seegyoung and others added 2 commits January 29, 2025 22:53

Update src/CMakeLists.txt

8a2be97

Co-authored-by: Cameron Smith <[email protected]>

addressing comments

b11dda0

removing mesh from read/write_value

cbc88b6

cwsmith approved these changes Jan 31, 2025

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jacobmerson reviewed Feb 3, 2025

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jacobmerson self-requested a review February 3, 2025 05:46

jacobmerson approved these changes Feb 3, 2025

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seegyoung merged commit d09d2bb into master Feb 3, 2025
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adding Adios2 io support #113

adding Adios2 io support #113

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		target_include_directories(omega_h PRIVATE "${ADIOS2_INCLUDE_DIRS}")
		target_link_libraries(omega_h PUBLIC "${ADIOS2_LIBRARIES}")

adding Adios2 io support #113

adding Adios2 io support #113

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