[gmx-users] mdrun with mpich
David van der Spoel
spoel at xray.bmc.uu.se
Thu Feb 2 15:36:18 CET 2006
Pradeep Kota wrote:
> Thank you for your response Mr.David. I compiled lam successfully
> without fortran support. all i wanted to know was whether it would make
> any difference to the running time of gromacs. I am curious because, it
> is well-known that fortran loops are faster than loops of other
> languages..so, i wanted to clarify ! moreover, i would want to know how
> different this is, from mpich.
> thanks for the support.
this is not the case for gromacs, except on old architectures like DEC
alpha. For G5 and x86 processors C is fastest due to assembly code.
> regards,
> kota.
>
> On 2/2/06, *David van der Spoel* <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> 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>
> > <mailto: 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>
> <mailto: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
> <mailto:kotanmd at gmail.com>>
> > *To:* Discussion list for GROMACS users
> > <mailto:gmx-users at gromacs.org <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.
> >
> >
> ------------------------------------------------------------------------
>
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > <mailto: gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use
> the
> > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> > <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> > <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> <http://www.gromacs.org/mailing_lists/users.php>
> > <http://www.gromacs.org/mailing_lists/users.php>
> >
> >
> >
> >
> ------------------------------------------------------------------------
>
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> 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
> <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> <mailto:spoel at gromacs.org> http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> <http://www.gromacs.org/mailman/listinfo/gmx-users>
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list