[gmx-users] mdrun_mpi issue.

[quantrum75]

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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