PBS and PGI interactions?
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 8 05:10:05 EDT 2001
On Sat, 7 Apr 2001, Don Morton wrote:
>I seem to come from an older school where we used NQS on Cray T3E's
>to run ANY parallel job, whether it was written in PVM, MPICH, EPCC
>MPI, PGI HPF, etc. In fact, Cray's "mpprun" command seemed to
>abstract away the details of dealing with various parallel libraries.
>You launched a job from a shell node - you could run an interactive job
>for maybe 30 minutes, and the allocation of those nodes would be
>coordinated with NQS. Anything longer required a batch NQS job
>and, again, you could use the same submission paradigm whether you
>were using PGI HPF, MPICH, etc.
>Has anybody worked on this in the realm of clusters? My guess is that
>most of these issues can be resolved through high-level scripts, but
>I know it ain't easy. If someone has explored this, I'd love
>to hear about it. If not, I'll put a student or two to work on it.
>In my opinion, you just can't make clusters accessible to the general
>scientific public without such mechanisms. :)
I think PBS has all the basic functionaity, but you probably have to write
your own PBS scheduler. You just have to tell the queuing system that you
need N nodes. But maybe someone on the list has done it already and is
willing to share their code. If you are going to do it yourself (and are
willing to share your code), then do it in C please...
It shouldn't be that hard, except for the bit that you recall about
automaticaly going from interactive to batch. Correct me if I'm wrong.
Dr. David van der Spoel Biomedical center, Dept. of Biochemistry
s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden
e-mail: spoel at xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel
phone: 46 18 471 4205 fax: 46 18 511 755
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