AMBER Archive (2005)

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

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Mon Jan 17 2005 - 10:09:03 CST

Hi, Gilles

Is your ${TMPDIR} localized storage or a global storage? The REM
implementation you are running requires every node has the access to the
same disk storage.

Guanglei

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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu