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.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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Received on Mon Jan 17 2005 - 14:53:00 PST
