job submission on HPC [SOLVED]

[Janpreet Sidhu]

Hi
I have installed abinit in parallel on hpc. And it works good in interactive run . But when i try to submit job using "qsub" i got error.
I make abinit.sh file for qsub.
abinit.sh :

#!/bin/bash
#$ -cwd -V
#$ -pe mpich 1
/home/gurinder/mpich-install/bin/mpirun -n 16 ../../abinit/abinit-7.0.5/src/98_main/abinit < tgst.files >& tbasepar_1.log

And then in log file:

../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
../../abinit/abinit-7.0.5/src/98_main/abinit: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 127
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

Please help
Janpreet

[pouillon]

You need to configure LD_LIBRARY_PATH to point to the libraries you built Abinit with, e.g.:

Code: Select all

export LD_LIBRARY_PATH="/path/to/lapack/lib:$LD_LIBRARY_PATH"

You'll have to do it for each library your cluster complains about.