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

[Shawn Waldon]

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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