[Paraview-developers] ParaView 5.5.0-RC3 problem importing h5py?

[Utkarsh Ayachit]

Shawn,

The superbuild doesn't mangle HDF5 or any of the 3rd parties it builds.

Utkarsh

On Thu, Mar 15, 2018 at 9:11 AM, Shawn Waldon <shawn.waldon at kitware.com> wrote:
> Hi Jean,
>
> I'm curious why this doens't work.  In VTK/ParaView we mangle all the HDF5
> symbols so that it shouldn't conflict with an external HDF5 (like the one
> from h5py).  In theory you should be able to load both with nothing
> conflicting, and the VTK list has helped us find conflicting symbols and
> write scripts for symbol mangling so none are missed.  Was there a symbol
> conflict or was the OS being "smart" and refusing to load two versions of
> the same library even though they have completely different symbols?
>
> Shawn
>
> On Thu, Mar 15, 2018 at 8:29 AM, Daan van Vugt <daanvanvugt at gmail.com>
> wrote:
>>
>> Hi Jean,
>>
>> Glad you solved this. I found it to be faster and less work to build the
>> right h5py instead of recompiling ParaView.
>> See https://github.com/Exteris/paraview-python-file-reader for
>> instructions (copied below for convenience).
>>
>>
>> # run this script in ParaView-5.4.1-Qt5-OpenGL2-MPI-Linux-64bit or
>> equivalent or set PV_DIR
>> export PV_DIR=$(pwd)
>>
>> # Install python2 with ucs2
>> https://stackoverflow.com/questions/38928942/build-python-as-ucs-4-via-pyenv
>> export PYTHON_CONFIGURE_OPTS=--enable-unicode=ucs2
>> pyenv install -v 2.7.11
>> pyenv local 2.7.11
>>
>> # Install pip
>> wget https://bootstrap.pypa.io/get-pip.py && ~/.pyenv/shims/python
>> get-pip.py
>>
>> # Install the same numpy paraview uses (as of writing)
>> ~/.pyenv/versions/2.7.11/bin/pip install --user numpy==1.8.1
>>
>> # Install hdf5 of the same version as paraview (not enough files included
>> in binary paraview distribution to build against)
>> # Paraview 5.2 - 5.4.1 are using 1.8.13, I have not checked the rest
>> # We then take the install summary
>> cd ~
>> wget
>> https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.13/src/hdf5-1.8.13.tar.bz2
>> tar jxf hdf5-1.8.13.tar.bz2
>> cd hdf5-1.8.13
>> ./configure
>> make -j
>> make install # in ~/hdf5-1.8.13/hdf5
>>
>> # Install h5py against the paraview hdf5 libraries
>> export HDF5_DIR=~/hdf5-1.8.13/hdf5
>> ~/.pyenv/versions/2.7.11/bin/pip install --no-binary=h5py --user h5py
>>
>> # Copy it to your paraview folder to make a portable version, or leave it
>> in your local site-packages
>> mv ~/.local/lib/python2.7/site-packages/h5py
>> $PV_DIR/lib/python2.7/site-packages/
>> # Create symlinks to the paraview library files (since we built against
>> slightly different hdf5 the name is different)
>> cd $PV_DIR/lib/paraview-*
>> ln -s libhdf5.so.8.0.2 libhdf5.so.8
>> ln -s libhdf5_hl.so.8.0.2 libhdf5_hl.so.8
>>
>> # Clean up
>> rm -r ~/hdf5-1.8.13.tar.bz2 ~/hdf5-1.8.13
>>
>>
>> Daan
>>
>> On Thu, Mar 15, 2018 at 10:45 AM, Favre Jean <jfavre at cscs.ch> wrote:
>>>
>>>
>>> I have resolved the issue.
>>>
>>> PV5.4 uses HDF5 1.8.13 in VTK/ThirdParty/hdf5
>>> PV5.5 uses HDF5 1.10.1
>>>
>>> recompiling ParaView with -DVTK_USE_SYSTEM_HDF5:BOOL=ON ensures that I
>>> pick up a version of HDF5 compatible with what h5py imports.
>>>
>>> Thanks for listening. :-)
>>>
>>> Jean
>>>
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>>
>>
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>
>
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