Hdf5 filter testing

requested review from @mwestphal

Errors:

commit 1676e379 cannot be merged; it is marked as a work-in-progress (WIP).

Please rewrite commits to fix the errors listed above (adding fixup commits will not resolve the errors) and force-push the branch again to update the merge request.

mentioned in issue paraview#22329 (closed)

added 2 commits

cc03e35b - hdf5: fix szip linking with the proper variables
0c65c5f6 - WIP: test only hdf5

Compare with previous version

Errors:

commit 0c65c5f6 cannot be merged; it is marked as a work-in-progress (WIP).

Please rewrite commits to fix the errors listed above (adding fixup commits will not resolve the errors) and force-push the branch again to update the merge request.

added 1 commit

11d61d13 - WIP: test only hdf5 and mpi

Compare with previous version

Errors:

commit 11d61d13 cannot be merged; it is marked as a work-in-progress (WIP).

Please rewrite commits to fix the errors listed above (adding fixup commits will not resolve the errors) and force-push the branch again to update the merge request.

+2, but we may want to inform upstream.

https://github.com/HDFGroup/hdf5/issues/3637

Do: merge

mentioned in commit a26c4439

merged

mentioned in commit ben.boeckel/paraview-superbuild@a842259c

mentioned in merge request paraview-superbuild!1121 (merged)

I may have a related issue on MacOS since this change:

2023-10-28T06:55:28.2507240Z [ 77%] Linking C shared module lib__nch5misc.dylib
2023-10-28T06:55:28.3429890Z ld: warning: dylib (/usr/local/lib/libzstd.dylib) was built for newer macOS version (12.0) than being linked (10.9)
2023-10-28T06:55:28.4034120Z [ 78%] Building C object plugins/CMakeFiles/h5noop.dir/H5Znoop.c.o
2023-10-28T06:55:28.4134090Z Undefined symbols for architecture x86_64:
2023-10-28T06:55:28.4235720Z   "_SZ_BufftoBuffCompress", referenced from:
2023-10-28T06:55:28.4336290Z       _H5Z__filter_szip in libhdf5.a(H5Zszip.c.o)
2023-10-28T06:55:28.4436960Z   "_SZ_BufftoBuffDecompress", referenced from:
2023-10-28T06:55:28.4537600Z       _H5Z__filter_szip in libhdf5.a(H5Zszip.c.o)
2023-10-28T06:55:28.4638050Z   "_SZ_encoder_enabled", referenced from:
2023-10-28T06:55:28.4738220Z       _H5Z_init in libhdf5.a(H5Z.c.o)
2023-10-28T06:55:28.4838960Z ld: symbol(s) not found for architecture x86_64
2023-10-28T06:55:28.4940030Z clang: error: linker command failed with exit code 1 (use -v to see invocation)
2023-10-28T06:55:28.5040080Z make[5]: *** [plugins/lib__nch5misc.dylib] Error 1
2023-10-28T06:55:28.5140470Z make[4]: *** [plugins/CMakeFiles/h5misc.dir/all] Error 2
2023-10-28T06:55:28.5240740Z make[4]: *** Waiting for unfinished jobs....
2023-10-28T06:55:28.5341740Z [ 78%] Building C object libsrc/CMakeFiles/netcdf3.dir/posixio.c.o
2023-10-28T06:55:28.6271490Z [ 79%] Building C object plugins/CMakeFiles/h5noop.dir/H5Zutil.c.o
2023-10-28T06:55:28.7618700Z [ 80%] Linking C shared module lib__nch5noop.dylib
2023-10-28T06:55:28.8674400Z ld: warning: dylib (/usr/local/lib/libzstd.dylib) was built for newer macOS version (12.0) than being linked (10.9)
2023-10-28T06:55:28.9266720Z Undefined symbols for architecture x86_64:
2023-10-28T06:55:28.9267850Z   "_SZ_BufftoBuffCompress", referenced from:
2023-10-28T06:55:28.9269400Z       _H5Z__filter_szip in libhdf5.a(H5Zszip.c.o)
2023-10-28T06:55:28.9275620Z   "_SZ_BufftoBuffDecompress", referenced from:
2023-10-28T06:55:28.9279700Z       _H5Z__filter_szip in libhdf5.a(H5Zszip.c.o)
2023-10-28T06:55:28.9284860Z   "_SZ_encoder_enabled", referenced from:
2023-10-28T06:55:28.9286270Z       _H5Z_init in libhdf5.a(H5Z.c.o)
2023-10-28T06:55:28.9296710Z ld: symbol(s) not found for architecture x86_64
2023-10-28T06:55:28.9316960Z clang: error: linker command failed with exit code 1 (use -v to see invocation)
2023-10-28T06:55:28.9341940Z make[5]: *** [plugins/lib__nch5noop.dylib] Error 1
2023-10-28T06:55:28.9344930Z make[4]: *** [plugins/CMakeFiles/h5noop.dir/all] Error 2
2023-10-28T06:55:30.4939010Z [ 80%] Built target netcdf3
2023-10-28T06:55:30.4947050Z make[3]: *** [all] Error 2
2023-10-28T06:55:30.4952710Z CMake Error at /Users/runner/work/f3d-superbuild/f3d-superbuild/fsbb/superbuild/sb-netcdf-build.cmake:47 (message):
2023-10-28T06:55:30.4953660Z   Failed with exit code 2

I reproduce simply with cmake -DBUILD_SHARED_LIBS=OFF -DENABLE_netcdf=ON ../src/selftest. I Will open an issue.

mentioned in issue #70 (closed)

#70 (closed)

EDIT: Sorry I just realized @mwestphal already reported the issue above.

It looks like this change forces a link to zstd system lib.
There are also link errors related to szip.
It's only happening on macos though.

Please take a look at this log: https://github.com/f3d-app/f3d-superbuild/actions/runs/7164851701/job/19505672622?pr=124#step:3:3635

Relevant error is:

ld: warning: dylib (/usr/local/lib/libzstd.dylib) was built for newer macOS version (12.0) than being linked (10.9)
  Undefined symbols for architecture x86_64:
    "_SZ_BufftoBuffCompress", referenced from:
        _H5Z__filter_szip in libhdf5.a(H5Zszip.c.o)
    "_SZ_BufftoBuffDecompress", referenced from:
        _H5Z__filter_szip in libhdf5.a(H5Zszip.c.o)
    "_SZ_encoder_enabled", referenced from:
        _H5Z_init in libhdf5.a(H5Z.c.o)
  ld: symbol(s) not found for architecture x86_64
  clang: error: linker command failed with exit code 1 (use -v to see invocation)

Any idea?

mentioned in commit bob.obara/cmb-superbuild@2ab05153

mentioned in commit bob.obara/cmb-superbuild@37431a73

Hdf5 filter testing

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