[Nek5000-users] Submitting Job Nek Enabled Moab

[nek5000-users at lists.mcs.anl.gov]

Friedrich,

Make sure your LD_LIBRARY_PATH has the path to szip libraries. If you
do "ldd nek5000", you should be able to see whether the shared
libraries are resolved at runtime. Make sure that all libraries are
loaded before running nek5000 driver.

Vijay

On Tue, Oct 28, 2014 at 7:12 AM,  <nek5000-users at lists.mcs.anl.gov> wrote:
> Hi All,
>
>
> I am currently experiencing issues when trying to run jobs on my hpc system.
>
>
> I have installed moab (with hdf5 and zoltan) as recommended on the nek5000
> webpages -
> https://nek5000.mcs.anl.gov/index.php/Building_and_Using_Nek_/_MOAB.
>
>
> When I do this the simulation will run if I acquire resources form the
> system and then run the job using nekmpi [casename] [np]. However if I then
> attempt to submit this same simulation to the queue using:
>
>
> #!/bin/bash
>
> #PBS -l nodes=1:ppn=12,pvmem=1900mb,walltime=01:00:00
>
> #PBS -V
>
>
> cd $PBS_O_WORKDIR
>
> nekmpi pipe 8 > log
>
> exit 0
>
>
> I submit the job and it fails citing:
>
>
> mv: cannot stat `pipe.log.8': No such file or directory
> mv: cannot stat `pipe.sch': No such file or directory
> node6.8452Error re-mmapping shared memory: Cannot allocate memory (err=9)
> node6.8452Error re-mmapping shared memory: Cannot allocate memory
> [node6:08452] Open MPI detected an unexpected PSM error in opening an
> endpoint: Error re-mmapping shared memory: Cannot allocate memory
> --------------------------------------------------------------------------
> mpiexec has exited due to process rank 7 with PID 8452 on
> node node6 exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpiexec (as reported here).
> --------------------------------------------------------------------------
>
>
> I thus decided there may be issues with moab so I installed according to the
> moab webpages -
> http://trac.mcs.anl.gov/projects/ITAPS/wiki/BuildingAndUsingMOAB.
>
>
> When I submit the job now I see a different error:
>
>
> mv: cannot stat `pipe.log.8': No such file or directory
> mv: cannot stat `pipe.sch': No such file or directory
> ./nek5000: error while loading shared libraries: libsz.so.2: cannot open
> shared object file: No such file or directory
>
>
> The above error I feel is somehow linked to either netcdf or hdf5 but I
> cannot see how or why as they both installed correctly (as far as I can
> tell).
>
>
> Thank you for any help,
>
>
> Friedrich
>
>
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