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bpls fails to read HDF5 files #4225

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jodreyer opened this issue Jul 5, 2024 · 1 comment
Open

bpls fails to read HDF5 files #4225

jodreyer opened this issue Jul 5, 2024 · 1 comment

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@jodreyer
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jodreyer commented Jul 5, 2024

When trying to analyze a h5 file written with ADIOS2 using bpls test.h5 it bails out with the following error message:

Failed to open with HDF5 engine: [] [ADIOS2 EXCEPTION] : ERROR: this version didn't compile with HDF5 library, can not use HDF5 engine

This error occurs with ADIOS2 >= 2.10.0. The version 9.2.0 does not show this error instead it lists the content of the file as expected.
I checked with readelf -d bpls and also ldd bpls that the program is linked with libhdf5.so.
In my case libhdf5.so.200 from /usr/lib64/mpi/gcc/openmpi4/lib64.

To Reproduce
I compiled both version from source using:
git clone https://github.com/ornladios/ADIOS2.git
git checkout v9.2.0 or git checkout v2.10.0
mkdir build
cd build
cmake ..
make
cd bin
bpls ../../../test.h5

Expected behavior
As the result from cmake showed that both HF5 and MPI are ON I expected to be able to list the content of the HDF5 file using bpls.

Desktop (please complete the following information):

  • OS/Platform: [OpenSuSE Tumbleweed ]
  • Build [e.g. compiler version gcc 13.3.0, cmake 3.29.6, build type: dynamic ]
@pnorbert
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pnorbert commented Jul 5, 2024

I am not able to reproduce this issue on ubuntu. I am a bit suspicious about the location of that libhdf5.so.200 file.

  • How did you install HDF5 and which version?
  • What is the output of bpls -Vv?
  • In your ADIOS2 build directory, what is the output for
    $ grep ADIOS2_HAVE_HDF5 source/adios2/common/ADIOSConfig.h

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