AMBER Archive (2003)

Subject: Re: AMBER: Re: AMBER7 & mpich : (no-attachment version)

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Aug 07 2003 - 02:40:06 CDT

Hello,

Without knowing the details of your situation, and using /bin/sh
this sequence will run the sander tests on 4 nodes.

    DO_PARALLEL="mpirun C "
    localmachinefile=./machinefile
    lamboot -v $localmachinefile
    make test.sander

    lamhalt $localmachinefile
    if [ $? -ne 0 ]
    then
        wipe -v $localmachinefile
    fi

cat $localmachinefile
bohr11
bohr11
bohr12
bohr12

Since LAM-MPI mpirun is in your path, probably man lamboot will work.
A google search will find the LAM home page.

Scott

On Thu, 7 Aug 2003 takanori.kanazawa_at_pharma.novartis.com wrote:

> Dear Scott, Dear Amber users,
>
> Thanks a lot for this kind help.
> I have successfully built Amber with LAM-MPI and it's likely I can run
> parallel sander jobs
> if I can boot LAM( I now have problem with this).
> Thanks a lot again to everyone who helped me with the problems.
>
> Best regards
> Takanori Kanazawa
>
>
>
>
>
> Scott Brozell <sbrozell_at_scripps.edu>
> 2003/08/05 08:58
>
>
> To: Takanori Kanazawa/PH/Novartis_at_PH
> cc:
> ·ļĢ¾: Re: AMBER7 & mpich : (no-attachment version)
>
>
> Hello,
>
> I no longer have the previous emails, but I noticed that your mpi error
> message came from LAM-MPI not MPICH.
> You should determine the correct path for the MPICH mpirun command
> or build Amber with LAM-MPI.
>
> Scott Brozell
>
> On Tue, 5 Aug 2003 takanori.kanazawa_at_pharma.novartis.com wrote:
>
> >
> > Thanks a lot to everyone who responded to my question.
> >
> > Yes, I do have the input file. And the problem is not fixed yet.
> > I would greatly appreciate any further comments or suggestions.
> >
> > Best regards,
> > Takanori Kanazawa
> >
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