AMBER Archive (2005)

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

From: Jordi Rodrigo (rodrigo_at_aspirine.u-strasbg.fr)
Date: Mon Jan 17 2005 - 06:37:00 CST


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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