AMBER Archive (2005)

Subject: Re: AMBER: Sander Replica Exchange exits with unit 6 error

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Jan 17 2005 - 08:45:56 CST

is there any way to run the test interactively to see if it is
something with LoadLeveler or if it is a problem with AMBER?
I can't reproduce that problem myself.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Jordi Rodrigo wrote:

>Hi Carlos,
>
>As we have already precised, we tried to submit via LoadLeveler, the
>test
>provided for Replica Exchange with Amber8. So here is the script:
>
>md9.in - PyrFurDuplex gb test run, igb = 1
> &cntrl
> imin = 0, nstlim = 100, dt = 0.001,
> ntx = 5, tempi = 0.0, temp0 = 267.0,
> ntt = 1, tol = 0.000001, saltcon = 0.2,
> ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> ntpr = 1,
> scee = 1.2, cut = 99.0,
> ntr = 0, tautp = 0.1, offset = 0.09,
> nscm = 1000, igb = 1, numexchg = 5,
> irest = 1, ntave = 0,
> /
>
>The input coordinates and topology files are the one provided with
>amber8.
>
>Here is complete LoadLeveler script:
>
>#@ cpu_limit = 00:10:00
>#@ job_name = Amber_RE
>#@ data_limit = 1.5Gb
>#@ notify_user = toto_at_mail.adress
>#@ notification = complete
>#@ stack_limit = 2Gb
>#@ output = $(job_name).$(jobid)
>#@ error = $(job_name).$(jobid)
>#@ shell = /bin/ksh
>#@ job_type = parallel
>#@ total_tasks = 4
>#@ environment = MP_PROCS=$(total_tasks)
>#@ queue
>
>set -x
>export AMBERHOME=$WORKDIR/amber8
>export PATH=${AMBERHOME}/exe:$PATH
>cd ${TMPDIR}
>cp $AMBERHOME/test/rem/* .
>mpirun -np 4 $AMBERHOME/exe/sander -O -rem 1 -ng 2 -i rem.in -c md14.x
>-o mdout.rem -p prmtop -remlog rem.log
>
>cp ${TMPDIR}/* $HOME/MyDirectory
>
>Thank you very much for your help,
>
>Gilles et Jordi
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