[gmx-users] mdrun with mpich

[Pradeep Kota]

Thank you for your response, itamar..but the cluster isolated from the
internet for security reasons. i dont think there is any chance to use fink
on the head node either. any other alternatives?
regards,
kota.

On 2/2/06, Itamar Kass <ikass at cc.huji.ac.il> wrote:
>
> Why not using fortan?
> install it using Fink and let lam have it.
>
>    Itamar.
>
> ===========================================
> | Itamar Kass
> | The Alexander Silberman
> | Institute of Life Sciences
> | Department of Biological Chemistry
> | The Hebrew University, Givat-Ram
> | Jerusalem, 91904, Israel
> | Tel: +972-(0)2-6585194
> | Fax: +972-(0)2-6584329
> | Email: ikass at cc.huji.ac.il
> | Net: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html<http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html>
> ============================================
>
> ----- Original Message -----
>  *From:* Pradeep Kota <kotanmd at gmail.com>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Thursday, February 02, 2006 4:43 AM
> *Subject:* [gmx-users] mdrun with mpich
>
> Dear users,
>     I have compiled gromacs on our dual core mac os x G5 cluster, and
> tried running a simulation on a 540 residue protein for 1 ns on 8
> processors. i used mpich as the mpi environment for parallelising gromacs.
> it worked fine, and the job was split properly and assigned to nodes. now,
> the cpu usage per processor is not more than 50% on any of the processors.
> and the total running time for this was 13hrs. though output is written
> properly onto the specified output file, mdirun doesnot terminate even after
> running through all the steps. it still shows two mdrun_mpi processes
> running on the head node, with a 0% cpu usage. was going through gmx-users
> mailing list and somehow figured out that mpich is not a good idea for
> running gromacs. so, i wanted to switch over to lam. now when i complie
> gromacs using lam, it is not able to link the libraries properly. so, i
> tried reinstalling lam on my cluster. now, lam keeps complaining about not
> being able to find a fortran compiler. i should not need a fortran compiler
> unless i'm using SUN or SGI for this purpose..(am i going wrong here?). what
> flags do i need to compile lam with, in order to compile gromacs
> successfully? any help is very much appreciated..
> thanks in advance,
> regards,
> kota.
>
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