Re: CPU usage when exec function is used

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 08 2010 - 15:31:16 CST

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.

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