AMBER Archive (2009)

Subject: Re: [AMBER] ssh and make test.parallel

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Apr 08 2009 - 02:19:36 CDT


On Mon, Apr 6, 2009 at 10:21 PM, Atro Tossavainen
<atro.tossavainen+amber_at_helsinki.fi> wrote:
>> Do you mean that the flag -openmpi in ./configure (which was ok for
>> openmpi 1.2.6) is no good for version 1.3.1, as I used now?
>
> I wouldn't even dare guess.  The only places in the entire AMBER source
> tree in which I see any mentions of OpenMPI are in the configure_amber
> script and they're not very specific.

./configure_amber --help
Parallel option flags
-openmpi Use OpenMPI (MPI_HOME must be set)

in .bashrc:
MPI_HOME=/usr/local/
export MPI_HOME

>
>> As far as the installation of openmpi 1.3.1 is concerned, the tests passed:
>>
>> ompi_info | grep libnuma
>>   MCA affinity: libnuma (MCA v 2.0, API 2.0)
>>
>> ompi_info | grep maffinity
>>   MCA affinity: first use (MCA as above)
>>   MCA affinity: libnuma as above.
>
> That's not interesting.

I was instructed it is important for dual-opteron. Wrong?

Can you run an actual MPI program (other than
> AMBER)?

Yes, all tests in the "examples" passed

thanks
francesco

>
> --
> Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
> Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
> +358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
> < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
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