> Well, score one for perisitence!
Dad kept saying something like that to me... Mom called it "stubborn." :-)
> Can you post the final wrapper you came up with (again)? Maybe we can
> get a web page up for people with similar problems.
Of course. I might want to clean it up a little more before posting it on the web, but it's below for the curious. I can probably even come up with something that will work similarly with qsub (with our version of qsub, anyhow) to generate a temporary script file and submit. It should be easy enough to write.
> This is actually somewhat disconcerting...looks like a problem with
> gfortran, but one that doesn't seem to have other bad consequences. I'll
> get Thomas to look at this when he returns from Germany.
Ok. I save all my diff output, so if he wants I can send other results.
My wrapper for scasub (Scali sub) with PBS:
=============== do_scasub_pbs_parallel.c =========================
// See READ ME below
#include <stdio.h>
#include <stdlib.h>
#include <stddef.h>
#include <string.h>
int main(int argc, char *argv[]){
int a=0;
char command[4001];
// *** READ ME ***
// Change the following command to match your situation if need be.
// The short walltime is usually more than sufficient and might get
// you into a short queue. gm0 is for myrinet -- alter if needed
strcpy(command,"/opt/scali/bin/scasub -qsparams \"-W block=true -l walltime=00:10:00\" -mpimon -network gm0,smp -np 2 -npn 2 ");
for(a=1;a<argc;a++){ sprintf(command,"%s %s",command,argv[a]); }
strcat(command,"\n");
system(command);
return 0;
}
========================================
then:
gcc do_scasub_pbs_parallel.c -o do_scasub_pbs_parallel
setenv DO_PARALLEL '/path/to/do_scasub_pbs_parallel'
(etc.)
Note, again, that this wrapper does exactly what you -think- should happen with:
setenv DO_PARALLEL '/opt/scali/bin/scasub -qsparams "-W block=true -l walltime=00:10:00" -mpimon -network gm0,smp -np 2 -npn 2'
$DO_PARALLEL /path/to/amber10/bin/sander.MPI -O -i mdin -c 01.ann10.xyz -o noesy.out
(for example)
...but that doesn't, at least not for me. I don't know why.
:-) Lachele
--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: David A. Case
[mailto:case.scripps.edu]
To: amber-developers.scripps.edu
Sent: Tue, 15 Apr
2008 15:12:08 -0400
Subject: Re: amber-developers: Testing Parallel
> On Tue, Apr 15, 2008, Lachele Foley wrote:
>
> > Ok... I used my excessive C wrapper to get around the quote thing. Using
> > block=true has three advantages over the interactive method (for me --
> > neither is really -better-): [1] I get nice, neat, individualized output
> > from the scheduler in each test directory; [2] it tests the system in a
> > manner very close to how the users will be running; [3] I only have to run
> > one set of tests (rather than test amber parallel and then test submission
> > to queue).
>
> Well, score one for perisitence! Can you post the final wrapper you came up
> with (again)? Maybe we can get a web page up for people with similar
> problems.
>
> > possible FAILURE: check out.0.dif
> > /scratch2/sysadmin_test/amber10/test/softcore/complex
> > 77c77
> > < Total charge of 0.1305 removed
> > ---
> > > Total charge of ************ removed
> > ---------------------------------------
>
> This is actually somewhat disconcerting...looks like a problem with
> gfortran,
> but one that doesn't seem to have other bad consequences. I'll get Thomas
> to look at this when he returns from Germany.
>
> ...dave
>
>
Received on Fri Apr 18 2008 - 21:19:38 PDT
