Re: your mail

From: Jarrod Smith <>
Date: Thu 22 Mar 2001 16:38:16 -0600

David Case wrote:
> On Thu, Mar 22, 2001, wentaofu wrote:
> >
> > Thank you for your pervious answer about compiling AMBER6.0 using MPICH.
> > Since there is a bug on the sander_classic using MPICH, I am compiling
> > AMBER6.0 on our SGI 2100 4 processor machine running IRIX6.5. We are using
> > the shared memory "Machine.sgi" file to make it compiled with parallelism.
> > But, when we test run sander_classic on the machine, we find it runs only on
> > one processor even using "setenv MP_SET_NUMTHREADS 4". Is there anything we
> > need to change on the Machine.sgi file to make it can be compiled with
> > parallelism? Thanks!
> >
> I don't know of any reason why sander_classic should not run on multiple
> processors when compiled with shared memory. I'm forwarding your question
> to the amber mail-reflector: that's always the best place to ask questions
> of this sort.

Look very carefully in the Machine.sgi file. There is some logic in
there that looks for some parallel fortran libraries (which are part
of the ftn_dev.sw IRIX package). If the system does not have these
libraries installed, then Machine.sgi silently sets NPROC to 1, and
you don't get a parallel binary. You get a single-threaded binary
that will ignore MP_SET_NUMTHREADS.

Jarrod A. Smith
Research Asst. Professor, Biochemistry
Asst. Director, Center for Structural Biology
Computation and Molecular Graphics
Vanderbilt University
Received on Thu Mar 22 2001 - 14:38:16 PST
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