----- Original Message -----
From: quantrum75 <[email protected]>
Date: Wednesday, June 30, 2010 7:12
Subject: [gmx-users] mdrun_mpi issue.
To: [email protected]
-----------------------------------------------------------
| > 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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