[SOLVED] Paraview shared library (libhdf5.so.101) mismatch

mrchef88 · 2018-09-21 11:08:03

I've installed the latest paraview package from the community repo, but it returns the following shared library error when trying to run it:

$ paraview
/usr/lib/paraview: error while loading shared libraries: libhdf5.so.101: cannot open shared object file: No such file or directory

Searching for that library reveals:

$ sudo updatedb
$ locate libhdf5.so
/usr/lib/libhdf5.so
/usr/lib/libhdf5.so.103
/usr/lib/libhdf5.so.103.0.0

Both paraview and hdf5-openmpi (a dependency for paraview which owns those libhdf5.so.*, and thus I assume might have once provided libhdf5.so.101) are up to date:

$ pacman -Q paraview
paraview 5.5.2-4

$ pacman -Q hdf5-openmpi
hdf5-openmpi 1.10.3-1

So my thinking was that the paraview package has been built/linked against the wrong hdf5 version. What's slightly strange, however, is that libhdf5.so.103 is linked to /usr/lib/paraview, but paraview seems to want libhdf5.so.101 as well.

$ ldd /usr/lib/paraview | grep libhdf5
        libhdf5.so.103 => /usr/lib/libhdf5.so.103 (0x00007f1f98e04000)
        libhdf5_hl.so.100 => /usr/lib/libhdf5_hl.so.100 (0x00007f1f96034000)
        libhdf5.so.101 => not found

"pkgfile libhdf5.so.101" returns empty.

Is anyone else having the same issue?

Last edited by mrchef88 (2018-09-21 12:56:19)

eschwartz · 2018-09-21 11:46:40

$ pkg-list-linked-libraries paraview libhdf5
==> checking linked libraries for paraview-5.5.2-4-x86_64.pkg.tar.xz ...
/usr/lib/libvtkxdmf2-pv5.5.so.1
  NEEDED               libhdf5.so.103
/usr/lib/libvtkPVVTKExtensionsH5PartReader-pv5.5.so.1
  NEEDED               libhdf5.so.103
/usr/lib/libvtkIOVisItBridge-pv5.5.so.1
  NEEDED               libhdf5.so.103
/usr/lib/libvtkIOTRUCHAS-pv5.5.so.1
  NEEDED               libhdf5.so.103
/usr/lib/libvtkIOAMR-pv5.5.so.1
  NEEDED               libhdf5.so.103

Don't use ldd, use lddtree (from the pax-utils package) to see what needs libhdf5.so.101

Stefan Husmann · 2018-09-21 12:15:44

Please file a bug report against paraview.

mrchef88 · 2018-09-21 12:56:04

Eschwartz wrote:

Don't use ldd, use lddtree (from the pax-utils package) to see what needs libhdf5.so.101

Thanks for that, I wasn't aware that tool existed (also, if I might add, that's a nifty looking script you have).

Using lddtree quickly led me to the root cause and the solution:

$ lddtree /usr/lib/paraview
   -- output snipped --
            libvtkPVVTKExtensionsCGNSReader-pv5.5.so.1 => /usr/lib/libvtkPVVTKExtensionsCGNSReader-pv5.5.so.1
                libcgns.so.3.3 => /usr/lib/libcgns.so.3.3                        
                    libhdf5.so.101 => None
  -- output snipped --

i.e. The CGNS Library (libcgns.so.3.3) as provided by the cgns package. Turns out I still had the "cgns-git" AUR package installed from back when it wasn't in the community repo.

Upgrading to the cgns package from the community repo solved the issue. Thanks so much!

Stefan Husmann wrote:

Please file a bug report against paraview.

Indeed, that was my next step, but I guess I wasn't yet convinced it was their issue (or, rather, that I hadn't done something silly)

Thanks all. I'll mark this as solved.

WorMzy · 2018-09-21 13:00:15

Stefan Husmann wrote:

Please file a bug report against paraview.

Please don't recommend people do this unless it has been confirmed that there is actually a bug. In this case, there wasn't, so a bug report would be a waste of everyones time.

eschwartz · 2018-09-21 13:13:51

Stefan Husmann wrote:

Please file a bug report against paraview.

*puts on official bugwrangler hat*

Please don't advise community members to violate the rules.

It is understood and begrudgingly accepted that people aren't perfect and invalid bugs will be inadvertently submitted.

Once I've already responded to a thread in order to help troubleshoot an issue and point to problems outside of paraview itself, it becomes obvious that any such bug would be invalid, and the bug submission would no longer be an inadvertent one. Deliberately filing bugs just to waste my time, is definitively against the rules.

eschwartz · 2018-09-21 13:16:00

mrchef88 wrote:

Eschwartz wrote:
Don't use ldd, use lddtree (from the pax-utils package) to see what needs libhdf5.so.101
Thanks for that, I wasn't aware that tool existed (also, if I might add, that's a nifty looking script you have).

It is indeed a very nifty script, I've made it publicly available at https://github.com/eli-schwartz/dotfile … -libraries if you're interested in it.

Using lddtree quickly led me to the root cause and the solution:
$ lddtree /usr/lib/paraview
   -- output snipped --
            libvtkPVVTKExtensionsCGNSReader-pv5.5.so.1 => /usr/lib/libvtkPVVTKExtensionsCGNSReader-pv5.5.so.1
                libcgns.so.3.3 => /usr/lib/libcgns.so.3.3                        
                    libhdf5.so.101 => None
  -- output snipped --
i.e. The CGNS Library (libcgns.so.3.3) as provided by the cgns package. Turns out I still had the "cgns-git" AUR package installed from back when it wasn't in the community repo.
Upgrading to the cgns package from the community repo solved the issue. Thanks so much!

Great, happy to help.

Arch Linux

#1 2018-09-21 11:08:03

[SOLVED] Paraview shared library (libhdf5.so.101) mismatch

#2 2018-09-21 11:46:40

Re: [SOLVED] Paraview shared library (libhdf5.so.101) mismatch

#3 2018-09-21 12:15:44

Re: [SOLVED] Paraview shared library (libhdf5.so.101) mismatch

#4 2018-09-21 12:56:04

Re: [SOLVED] Paraview shared library (libhdf5.so.101) mismatch

#5 2018-09-21 13:00:15

Re: [SOLVED] Paraview shared library (libhdf5.so.101) mismatch

#6 2018-09-21 13:13:51

Re: [SOLVED] Paraview shared library (libhdf5.so.101) mismatch

#7 2018-09-21 13:16:00

Re: [SOLVED] Paraview shared library (libhdf5.so.101) mismatch

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