[Dock-fans] Multiprocessor Test Job

Scott Brozell sbrozell at scripps.edu
Tue Jul 29 20:15:50 PDT 2008


Hi,

[scott]$ ./script_clean
[scott]$ ll
 4 -rw-r--r-- 1 scott kuntz   734 Mar 27  2006 0README
 4 -rw-r--r-- 1 scott kuntz  3955 Mar  2 00:15 mpi.in
 4 -rwxr-xr-x 1 scott kuntz    49 Jun 15  2006 script_clean
 4 -rwxr-xr-x 1 scott kuntz   982 Jun 15  2006 script_demo
[scott]$ ./script_demo
Environment variable DOCK_PROCESSES is not defined.
    Using 4 MPI processes for DOCK.
Environment variable MPICH_HOME is defined.
    Using MPICH mpirun from /home/terry/mpich2-install/bin
Starting MPI DOCK.
Initializing MPI Routines...
Initializing MPI Routines...
Initializing MPI Routines...
Initializing MPI Routines...
[scott]$ ll
 4 -rw-r--r-- 1 scott kuntz   734 Mar 27  2006 0README
24 -rw-r--r-- 1 scott kuntz 23819 Jul 29 18:59 1VRT_scored.mol2
 4 -rw-r--r-- 1 scott kuntz  3955 Mar  2 00:15 mpi.in
12 -rw-r--r-- 1 scott kuntz  8417 Jul 29 18:59 mpi.out
 8 -rw-r--r-- 1 scott kuntz  6539 Jul 29 18:59 mpi.out.1
 8 -rw-r--r-- 1 scott kuntz  6540 Jul 29 18:59 mpi.out.2
 8 -rw-r--r-- 1 scott kuntz  6637 Jul 29 18:59 mpi.out.3
 4 -rwxr-xr-x 1 scott kuntz    49 Jun 15  2006 script_clean
 4 -rwxr-xr-x 1 scott kuntz   982 Jun 15  2006 script_demo

The run takes 2.5 minutes on a Xeon(TM) CPU 3GHz with TWO processors.
I'll email you a tarball.

Scott

On Mon, 28 Jul 2008, Scientific Software Division @ USF-RC wrote:

> Unfortunately, the only problem with that tutorial is that it doesn't 
> come with the expected output. If I had that, then I would be all set.
> 
> Sudipto Mukherjee wrote:
> > Paul,
> >
> > You could use the sample MPI job listed under dock6/tutorials/mpi_demo 
> > under your dock6 installation. This tutorial should work out of the 
> > box for DOCK6.
> >  
> > Regards
> > Sudipto Mukherjee
> > Graduate Student, Robert C. Rizzo Lab
> > Dept. of Applied Math & Statistics, Stony Brook University
> >
> > ----- Original Message ----
> > From: "Scientific Software Division @ USF-RC" <scisoft at rc.usf.edu>
> > To: dock-fans at docking.org
> > Sent: Monday, July 28, 2008 2:30:50 PM
> > Subject: [Dock-fans] Multiprocessor Test Job
> >
> > I was wondering if there was anyone out there who would be willing to
> > let me have a sample multiprocessor Dock6 job with  expected output. The
> > test suite on the Dock6 website is only for Dock5. Thanks for any help.
> >
> > - Paul Tittle
> >   Research Computing @ USF



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