El 06/08/12 19:00, Prabu Manoharan escribió:
> Hi,
>
> I am new to amber. I recently installed amber12 in mac OS X 10.5
> server based on the input I got from amber mailing list. I also tested both
> serial and parallel runs. Both methods worked. For parallel run I gave
> below command. But it only runs on the master node. (The job I am trying to
> run is on a mac cluster of 15 nodes, with 8 cores for each node).
>
> mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i min.in -o polyAT_wat1.out -c
> polyAT_wat.inpcrd -p polyAT_wat.prmtop -r polyAT_wat1.rst
>
>
> Then I used the SGE scripts to submit the parallel job (the SGE script is
> given below). But my job is not running on any of the node not even in the
> master node. I also provided the error output below the SGE script.
>
>
> #!/bin/bash
>
> ## ------ EMBEDDED SGE ARGUMENTS ----
> #$ -N amber_job
> #$ -pe mpich 1
> #$ -cwd
> #$ -S /bin/bash
> ## ------------------------------------
> # export all environment variables to SGE
> #$ -V
>
> MPIRUN=$AMBERHOME/bin/mpirun
> sander=$AMBERHOME/bin/sander.MPI
> export RSHCOMMAND=/usr/bin/ssh
>
> echo " i got $NSLOTS slots to run on!"
> $MPIRUN -np $NSLOTS -machinefile $TMDIR/mpd.hosts $sander -O -i min.in -o
> polyAT_wat2.out -c polyAT_wat.incprd -p polyAT_wat.prmtop -r polyAT_wat2.rst
>
>
> *Error output*
>
>
> dyld: Library not loaded: /Volumes/data/common/amber12/lib/libmpl.1.dylib
> Referenced from: /common/amber12/bin/mpirun
> Reason: image not found
> /common/sge/default/spool/node006/job_scripts/676: line 17: 620 Trace/BPT
> trap
> (core dumped) $MPIRUN -np $NSLOTS -machinefile $TMDIR/mpd.hosts
> $sande
> r -O -i min.in -o polyAT_wat2.out -c polyAT_wat.incprd -p polyAT_wat.prmtop
> -r p
> olyAT_wat2.rst
>
>
> I have also added below lines to my .bash_profile file.
>
> export AMBERHOME=/common/amber12
> export PATH="$AMBERHOME/bin:$PATH"
> export MPI_HOME=$AMBERHOME
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:$AMBERHOME/lib
>
> I am not able to figure out what went wrong.
>
> Thanks in advance
>
Hi,
Not sure, but it seems that the path to the library is not the same in
the machine where you compiled amber
/Volumes/data/common/amber12/lib/
than in the nodes where you are trying to execute the programs:
/common/amber12/lib/
Also, OSX does not (always) acknowledge the environment variable
LD_LIBRARY_PATH
better use DYLD_LIBRARY_PATH
HTH,
--
Miguel
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Received on Mon Aug 06 2012 - 12:00:03 PDT
