[gmx-users] mdrun_mpi issue.

[Mark Abraham]

----- Original Message -----
From: quantrum75 <quantrum75 at yahoo.com>
Date: Wednesday, June 30, 2010 7:12
Subject: [gmx-users] mdrun_mpi issue.
To: gmx-users at gromacs.org

-----------------------------------------------------------
| > 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 

If this installation used to work, then something's changed with the system setup. Consult your sysadmins or compiler docs on how to set LD_LIBRARY_PATH and/or LD_RUN_PATH environment variables so that run-time linking works like it needs to. Or, set up fully static linking.

Mark

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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> 
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