[CIG-SHORT] using a batch system

[Brad Aagaard]

Fengli-

Your environment variable LD_LIBRARY_PATH is not being setup correctly 
on the compute nodes of your cluster. Run "env" (which prints out all of 
the environment variables) on a login node and a compute node to make 
sure they match. You may also want to switch the order of the 
directories when setting LD_LIBRARY_PATH so that the order is

export LD_LIBRARY_PATH=[pylith stuff]:${LD_LIBRARY_PATH}

to make sure the PyLith libraries are found before any system libraries.

Brad


lf1981 at mail.ustc.edu.cn wrote:
> Dear sir :
>   Thanks for you advices. I am sorry to tell you that I had submitted a bad report that count for nothing last time, because my version of Batch system is x86_64 ,but i installed the  pylith-1.4.2-i686 on my Batch system. So when i try to run with a Batch system ,some unfriendliness message troubled me. this time,I installed pylith-1.4.2-linux-x86_64 which suitable for my Batch system as the instructions of User Manual.  I placed the distribution in the directory of /home/hjs/lf/pylith and reset the .bashrc file as follows:
> 
> export PATH=$PATH:/home/hjs/lf/pylith/pylith-1.4.2-linux-x86_64/bin
> export PATH=$PATH:/home/hjs/yangan/citcoms/CitcomS-3.1.1/bin
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/hjs/lf/pylith/pylith-1.4.2-linux-x86_64/lib:/home/hjs/lf/pylith/pylith-1.4.2-linux-x86_64/opt/petsc-dev/linux-gnu-cxx-opt/lib
> export PYTHONPATH=$PATH:/home/hjs/lf/pylith/pylith-1.4.2-linux-x86_64/lib/python2.5/site-packages
> 
>   To check whether it run successfully without a Batch System, I didn't creat the ~/.pyre/pylithapp/pylithapp.cfg file, Just running a case of the example which is a self-contained package. It is running successfully.
>   Then,I want it run with a Batch System,so I created a ~/.pyre/pylithapp/pylithapp.cfg file which contained as follows:
> 
> [pylithapp]
> scheduler=pbs
> launcher =mpich
> [pylithapp.pbs]
> qsub-options = [-a mpich_gm ]
> [pylithapp.launcher]
> command=mpirun.pbs
> [pylithapp.job]
> queue=normal
>   When I try to run a case in the self-contained package with a Batch System, for example in the directory of /home/hjs/lf/pylith/pylith-1.4.2-linux-x86_64/src/pylith/examples/3d/tet4, I run pylith dislocation.cfg--nodes=4 --macros.nodes=4 --macros.job.name=dislocation.cfg
> 
> The  STDIN.e2784 file which contained the debug message showed as follows:
> /home/hjs/lf/pylith/pylith-1.4.2-linux-x86_64/bin/nemesis: error while loading shared libraries: libpython2.5.so.1.0: cannot open shared object file: No such file or directory
> 
> I forgot to tell you that the version of Python on my Batch Systerm is Python 2.3.4, and because the Pylith I installed is binary ,I had not installed other version of Python. Can you see any problems with what I've done and show me how to settle it. Thanks for your help 
> 
>                                                                                                Sincerely  Fengli
>                                                                                                      USTC
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