From: daniel aguayo (bioquimico_at_gmail.com)
Date: Fri Jan 08 2010 - 17:46:30 CST
Dear Axel,
Tks for your advice. Actually we are working namd with the command
"reloadcharges"
to avoid restart the simulation with The exec command calling a script that
do some analysis
to choose the charges.. (calling APBS and some awk and other stuff).
Tks a lot.
Daniel Aguayo V.
On Fri, Jan 8, 2010 at 6:31 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Jan 8, 2010 at 3:48 PM, daniel aguayo <bioquimico_at_gmail.com>
> wrote:
> > Dear All
>
> dear daniel,
>
> > We are trying to execute an external bash script between "run"
> stages
> > (example below) with the exec tcl command. But when the exec process is
> > executed the CPUs are on 100% usage with namd2 process.. then our script
> > cant run well. Can someone give us a shortcut to stop namd for starving
> CPU
> > or
> > we just have to deal with this issue?
>
> it is often quite problematic to call "exec" from within a parallel
> program.
> particularly some implementations of MPI on top of infiniband or myrinet
> seem to be affected by it.
>
> i assume you are running namd from a batch shell script. if yes, why don't
> you simply use 2 namd config files and launch namd twice and call
> your shell script in between? that would sidestep this issue and is
> - in my personal opinion - a cleaner way to do this to begin with.
>
> cheers,
> axel.
>
> >
> > BTW: namd is running on a multiple CPU / nodes with OPENMPI.
> >
> > Tks a lot ...
> >
> > Daniel Aguayo V.
> > CBSM - UTAL
> >
> >
> > #######
> >
> > run 500000
> > output dend_1n_eq
> > set ruta [exec pwd ]
> > if { [catch {exec "$ruta/buildfilesprueba.sh"} fid] } {
> > puts "Error \n$fid"
> > puts "Information about it: $::errorInfo"
> > exit 1
> > }
> > run 50000
> >
> > ########
> >
> >
> >
> >
> > --
> > saludos desde el fin del mundo
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
-- saludos desde el fin del mundo
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