Hi Folks,
I am trying to run a simulation under GMX 4.0.5. When I do a qsub of my job, it
does not seem to run and gives me an error saying the library libimf.so is not
available. I tried subsequently giving/copying the library into the run path
with still the exact same error. I am attaching the .job file and error file
for your perusal. I d be glad for any ideas since I tried quite a few without
much help.
Thanks in advance
Rama
********************
JOB FILE
*********************
#!/bin/bash
#PBS -l nodes=1:ppn=2
#PBS -l walltime=00:20:00
#PBS -j oe
#PBS -q debug
set -x
#move to my $SCRATCH directory
cd $SCRATCH
#RAMA STUFF ON WARHOL
#export PATH=$PATH:/usr/local/packages/gromacs4/bin/
#export PATH=$PATH:/usr/local/packages/intel/icc/11.0/074/lib/intel64/
exefile="/usr/local/packages/gromacs4/bin/mdrun_mpi"
projDir="MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes"
projName="4402_PR_0.5ns_Protein.tpr"
#copy executable to $SCRATCH
cp $HOME/${projDir}/${projName} ./
#cp /usr/local/packages/intel/icc/11.0/074/lib/intel64/libimf.so ./
#run my executable
mpirun ${exefile} -deffnm ${projName}
cp $SCRATCH/${projName}.* ${HOME}/${projDir}/*
***********************
ERROR FILE
***********************
+ cd /scratch/gullapal
+ exefile=/usr/local/packages/gromacs4/bin/mdrun_mpi
+ projDir=MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes
+ projName=4402_PR_0.5ns_Protein.tpr
+ cp
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_PR_0.5ns_Protein.tpr
./
+ mpirun /usr/local/packages/gromacs4/bin/mdrun_mpi -deffnm
4402_PR_0.5ns_Protein.tpr
/usr/local/packages/gromacs4/bin/mdrun_mpi: error while loading shared
libraries: libimf.so: cannot open shared object file: No s
uch file or directory
/usr/local/packages/gromacs4/bin/mdrun_mpi: error while loading shared
libraries: libimf.so: cannot open shared object file: No s
uch file or directory
+ cp '/scratch/gullapal/4402_PR_0.5ns_Protein.tpr.*'
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402
_nopep.job
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_PR_0.5ns_Protein.tpr
/usr/users/9/gullapa
l/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_pr_index.ndx
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_
Struc_PosRes/4402_topol.top
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/include_files
/usr/users/9/gu
llapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/pr.mdp
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_
PosRes/Step1_nopep_Posre.gro
cp: target
`/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/Step1_nopep_Posre.gro'
is not a directory
--
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