AMBER Archive (2007)

Subject: Re: AMBER: Compile Amber9 for MVAPICH

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 06 2007 - 14:23:07 CST

On Tue, Feb 06, 2007, Mike Hanby wrote:
>
> I've compiled MVAPICH on my system (so I can utilize the Infiniband
> cards) using the Intel 9.1 compilers.
> For parallel I ran:
>
> ./configure -mpich -p4
>
> And then add -I/share/mvapich/include to the CPPFLAGS variable
>
> The make parallel appears to finish without errors however when I
> attempt to run:
>
> sander.MPI -help
>
> I get a bunch of segmentation faults. Any idea what I should look at?
> Is the configure option correct (-mpich)?
>

I don't know anything about MVAPICH, so this is really a wild guess, but it is
at least worth trying: sander.MPI needs to be run under the control of
"mpirun". It calls mpi_init() etc. before processing any command-line flags.
So you should at least try something like

    mpirun -np 1 sander.MPI -help

I assume(?) you also tried obvious things like "make test.parallel". And that
you have run the MPI test cases that are probably supplied with the MVAPICH
distribution, or otherwise know that your MPI implementation is working.
Information along these lines would be helpful, but you may have to compile
with traceback turned on to get much useful information.

Others with specific experience with Infiniband may wish to chime in here....

...good luck...dac
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