[gmx-users] mdrun with mpich

[David van der Spoel]

Pradeep Kota wrote:
> 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,

compile LAM without fortran, there's a flag for it

> kota.
> 
> On 2/2/06, *Itamar Kass* <ikass at cc.huji.ac.il 
> <mailto: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 <mailto: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 <mailto:kotanmd at gmail.com>
>         *To:* Discussion list for GROMACS users
>         <mailto: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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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