[CIG-SHORT] Error Installing Pylith on Cluster

[Brad Aagaard]

Xiao,

You should be using the CLUSTER option in the installer, not 
DESKTOP-LINUX-OPENMPI.

Load the xml2 and openmpi modules as mentioned by your sysadmin.

If you are using the Intel Fortran compilers, then see the note at the 
end of the INSTALL document under troubleshooting regarding potential 
problems with netcdf and HDF5 with ifort. This should resolve the 
problem noted by your sysadmin.

Regards,
Brad


On 12/12/2014 10:52 AM, Xiao Ma wrote:
> Hi,
> Brad- I am using an stalled version which is on the my campus cluster.
> I am forwarding the following message from the Administer of the cluster
> *********************************************************
> Hi Xiao,
>
> Open MPI requires libxml2 to be available at build time (so I assume you are
> using the "DESKTOP-LINUX-OPENMPI" option in the attached INSTALL document).
> libxml2 is available via modules:
>
> module load libxml2/2.9.1
>
> Your software build also requires unzip, load it with:
>
> module load unzip/unzip60
>
> I should mention that a generic build of Open MPI may not run correctly when
> running on multiple nodes in a batch job on the campus cluster. You can
> check
> this once you have your software installed. Also, the version of Open MPI
> that
> Pylith used is 1.4.5, which is old. So I tried to build Pylith using the
> Open
> MPI 1.6.5 built with the Intel compiler and Python 2.7.8 already on the
> system
> (following the "DEFAULT" option in the INSTALL document):
>
> module load openmpi/1.6.5-intel-14.0
>
> module load python/2.7.8
>
> ./configure CC=icc CXX=icpc FC=ifort --with-make-threads=2
> --enable-force-install --prefix= …
> make
>
> Unfortunately, I got the error:
> ifort: error #10236: File not found: 'libnetcdff.so.5'
>
> I did a google search, and found a discussion at
> https://geodynamics.org/pipermail/cig-short/2014-October/001861.html. This
> references the INSTALL file for the solution, but that is already in
> libtool.
>
> Thanks,
>
> Susan
> Susan John
> Campus Cluster User Services
> *************************************************
> Thanks,
> Xiao
>
>
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>