Re: amber-developers: Testing Parallel

From: Volodymyr Babin <vbabin.ncsu.edu>
Date: Tue, 15 Apr 2008 16:22:00 -0400 (EDT)

I am not entirely sure it does work as expected for argc > 2.
I would also avoid things like sprintf(command, "%s", command).
I am also not completely sure something like this is really necessary
(cannot help though: have no clue about [t]csh). You could try
something like:

#!/bin/sh

/opt/scali/bin/scasub -qsparams \"-W block=true -l walltime=00:10:00\"
-mpimon -network gm0,smp -np 2 -npn 2 $*

(i.e., escape from [t]csh to, e.g., /bin/sh; this is what system()
call does).

With best wishes,
  Volodymyr

> 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
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