<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi Folks,<br>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.<br>Thanks in advance<br>Rama<br>********************<br>JOB FILE<br>*********************<br><br>#!/bin/bash<br>#PBS -l nodes=1:ppn=2<br>#PBS -l walltime=00:20:00 <br>#PBS -j oe<br>#PBS -q debug<br><br><br>set -x<br><br>#move to my $SCRATCH directory<br>cd $SCRATCH<br>#RAMA STUFF ON WARHOL<br><br>#export PATH=$PATH:/usr/local/packages/gromacs4/bin/<br>#export
PATH=$PATH:/usr/local/packages/intel/icc/11.0/074/lib/intel64/<br><br><br>exefile="/usr/local/packages/gromacs4/bin/mdrun_mpi"<br>projDir="MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes"<br>projName="4402_PR_0.5ns_Protein.tpr"<br><br>#copy executable to $SCRATCH<br>cp $HOME/${projDir}/${projName} ./<br>#cp /usr/local/packages/intel/icc/11.0/074/lib/intel64/libimf.so ./<br><br>#run my executable<br>mpirun ${exefile} -deffnm ${projName} <br>cp $SCRATCH/${projName}.* ${HOME}/${projDir}/*<br><br><br>***********************<br>ERROR FILE<br>***********************<br>+ cd /scratch/gullapal<br>+ exefile=/usr/local/packages/gromacs4/bin/mdrun_mpi<br>+ projDir=MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes<br>+ projName=4402_PR_0.5ns_Protein.tpr<br>+ cp /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_PR_0.5ns_Protein.tpr ./<br>+ mpirun /usr/local/packages/gromacs4/bin/mdrun_mpi -deffnm
4402_PR_0.5ns_Protein.tpr<br>/usr/local/packages/gromacs4/bin/mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No s<br>uch file or directory<br>/usr/local/packages/gromacs4/bin/mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No s<br>uch file or directory<br>+ cp '/scratch/gullapal/4402_PR_0.5ns_Protein.tpr.*' /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402<br>_nopep.job /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_PR_0.5ns_Protein.tpr /usr/users/9/gullapa<br>l/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_pr_index.ndx /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_<br>Struc_PosRes/4402_topol.top /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/include_files /usr/users/9/gu<br>llapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/pr.mdp
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_<br>PosRes/Step1_nopep_Posre.gro<br>cp: target `/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/Step1_nopep_Posre.gro' is not a directory<br><br><br><br><br><br><br></td></tr></table><br>