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-- B. Lachele Foley, PhD '92,'02 Assistant Research Scientist Complex Carbohydrate Research Center, UGA 706-542-0263 lfoley.ccrc.uga.edu ----- Original Message ----- From: Ross Walker [mailto:ross.rosswalker.co.uk] To: amber-developers.scripps.edu Sent: Mon, 14 Apr 2008 17:09:57 -0400 Subject: RE: amber-developers: Testing Parallel > Hi Lachele, > > Most pbs invocations allow you to request interactive use - this is how I > test things. So you do something like: > > qsub -I -V -l walltime=02:00:00 -l nodes=2:ppn=2 > > Then you end up, after a wait, with a shell on one of the nodes. Then you > can do: > > setenv DO_PARALLEL 'mpirun -np 4 -machinefile $PBSNODEFILE ' > setenv AMBERHOME '/foo/bar/amber10' > cd $AMBERHOME/test > make test.parallel > > when you are done you then type 'exit' to quit the interactive session. If > you cluster doesn't currently have this enabled then I'd ask the person in > charge if they could enable it for you. > > Good luck, > > Ross > > /\ > \/ > |\oss Walker > > | Assistant Research Professor | > | San Diego Supercomputer Center | > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk | > | http://www.rosswalker.co.uk | PGP Key available on request | > > Note: Electronic Mail is not secure, has no guarantee of delivery, may not > be read every day, and should not be used for urgent or sensitive issues. > > > -----Original Message----- > > From: owner-amber-developers.scripps.edu > > [mailto:owner-amber-developers.scripps.edu] On Behalf Of Lachele Foley > > Sent: Monday, April 14, 2008 13:12 > > To: amber-developers.scripps.edu > > Subject: Re: amber-developers: Testing Parallel > > > > > Your machine's queue situation seems odd. > > > > Do lots of people use pbs? I've been reading the fine > > manual, and I can't see how > > > > $DO_PARALLEL $TESTsander anything > > > > is going to work. To use qsub without a job script involves > > starting up a little mini-qsub shell that requires a cntrl-D > > at the end. Quoting the manual from the "Jobs Without a Job > > Script" section ("<ret>" means "hit return"): > > > > qsub <ret> > > [directives] > > [tasks] > > ctrl-D > > > > The amber parallel test suite does not easily lend itself to > > generating a job script or to doing this command-line thing. > > How do folks who use pbs use the tests? Until now, I just > > looked at the output, shuddered, ran an old job of mine, > > checked the output then went on to the next thing on my list. > > I could certainly whip up some rebel engineering (see below) > > to get around it, but does everyone do that? I admit to not > > being the world's best reader, so I might have missed > > something. This is PBS Pro 8.0. Maybe later versions are different. > > > > > Anyway, try > > > set echo > > > set verbose > > > then your two command invocations to see the differences. > > > My guess is that "-W block=true" -> '-W block=true' > > > might work and wont hurt. > > > > I tried that. And similar variations. And bash, csh, ash, > > zsh, ksh... None worked. Thanks, though. Good idea. > > > > Unwilling to be done in by a quote mark: > > > > ======= begin excessive palliative engineering ================= > > ]$ more amber_parallel_test.c > > #include <stdio.h> > > #include <stdlib.h> > > #include <stddef.h> > > #include <string.h> > > > > int main(int argc, char *argv[]){ > > int a=0; > > char command[4001]; > > > > strcpy(command,"/opt/scali/bin/scasub -qsparams \"-W > > block=true\" -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; > > } > > $ gcc amber_parallel_test.c > > $ setenv DO_PARALLEL ./a.out > > $ $DO_PARALLEL $sander -O -i mdin -c 01.ann10.xyz -o noesy.out > > > > ======= end excessive (and successful) palliative engineering > > ================= > > > > I suspect my string handling could be swifter, but it works. > > > > Sigh. > > > > :-) Lachele > > -- > > B. Lachele Foley, PhD '92,'02 > > Assistant Research Scientist > > Complex Carbohydrate Research Center, UGA > > 706-542-0263 > > lfoley.ccrc.uga.edu > > > > > > ----- Original Message ----- > > From: Scott Brozell > > [mailto:sbrozell.scripps.edu] > > To: amber-developers.scripps.edu > > Sent: Mon, 14 > > Apr 2008 16:04:41 -0400 > > Subject: Re: amber-developers: Testing Parallel > > > > > > > Hi, > > > > > > On Mon, 14 Apr 2008, Lachele Foley wrote: > > > > > > > More fun with parallel tests: mostly FYI, but with questions. And > > > apologies in advance for whatever I forgot to notice or check... > > > > > > > > Another issue for parallel testing with us is that the > > tests are run like > > > so: > > > > > > > > =====start abbreviated pseudo-script======= > > > > set up some environment stuff and check sanity > > > > run the parallel job > > > > check the output for differences > > > > =====end abbreviated pseudo-script======= > > > > > > > > On our system, jobs go away to the scheduler by default > > (like running in > > > the background). So, the tests frequently check for output > > that hasn't > > > happened yet -- or, in the noesy case, delete the input > > file before the job > > > runs. I can get the scheduler to run "in the foreground" > > (or "wait" or > > > "block" -- choose your favorite terminology). But, I seem > > to be having a > > > quote-character issue. Can someone who knows the shell > > better than me > > > suggest a fix (SHELL is tcsh)? > > > > > > > > This works: > > > > [lachele.keats noesy]$ /opt/scali/bin/scasub -qsparams > > "-W block=true" > > > -mpimon -network gm0,smp -np 2 -npn 2 $sander -O -i mdin -c > > 01.ann10.xyz -o > > > noesy.out > > > > 44368.keats > > > > > > > > This doesn't: > > > > [lachele.keats noesy]$ echo $DO_PARALLEL > > > > /opt/scali/bin/scasub -qsparams "-W block=true" -mpimon > > -network gm0,smp > > > -np 2 -npn 2 > > > > [lachele.keats noesy]$ $DO_PARALLEL $sander -O -i mdin -c > > 01.ann10.xyz -o > > > noesy.out > > > > qsub: script file:: No such file or directory > > > > > > > > I don't think using plain qsub is a good idea, either, > > but if someone > > > wants to explore that option, say so. Brief reasons: qsub > > seems to want a > > > separate script file (=rewrite tests) and scaMPI complains > > if not using > > > scasub. Possibly can work around both, and happy to accept > > suggestions. > > > > > > > > > > Your machine's queue situation seems odd. > > > Anyway, try > > > set echo > > > set verbose > > > then your two command invocations to see the differences. > > > My guess is that "-W block=true" -> '-W block=true' > > > might work and wont hurt. > > > > > > Scott > > > > > > > > > > >Received on Fri Apr 18 2008 - 21:19:22 PDT