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
job submission on HPC [SOLVED]
Moderators: fgoudreault, mcote
Forum rules
Please have a look at ~abinit/doc/config/build-config.ac in the source package for detailed and up-to-date information about the configuration of Abinit 8 builds.
For a video explanation on how to build Abinit 7.x for Linux, please go to: http://www.youtube.com/watch?v=DppLQ-KQA68.
IMPORTANT: when an answer solves your problem, please check the little green V-like button on its upper-right corner to accept it.
Please have a look at ~abinit/doc/config/build-config.ac in the source package for detailed and up-to-date information about the configuration of Abinit 8 builds.
For a video explanation on how to build Abinit 7.x for Linux, please go to: http://www.youtube.com/watch?v=DppLQ-KQA68.
IMPORTANT: when an answer solves your problem, please check the little green V-like button on its upper-right corner to accept it.
Re: job submission on HPC [SOLVED]
You need to configure LD_LIBRARY_PATH to point to the libraries you built Abinit with, e.g.:
You'll have to do it for each library your cluster complains about.
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.
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain
Simune Atomistics
Donostia-San Sebastián, Spain