[gmx-users] mdrun with mpich
Pradeep Kota
kotanmd at gmail.com
Thu Feb 2 15:51:37 CET 2006
thanks for the info, Mr.David.. but when i try to compile gromacs, it
returns an error. the following is an excerpt from the output of 'make'.
/usr/local/lib/libfftw3f.a(the-planner.o) definition of _fftwf_the_planner
in section (__TEXT,__text)
/usr/local/lib/libfftw3f.a(version.o) definition of _fftwf_cc in section
(__TEXT,__cstring)
/usr/local/lib/libfftw3f.a(version.o) definition of _fftwf_codelet_optim in
section (__TEXT,__cstring)
/usr/local/lib/libfftw3f.a(version.o) definition of _fftwf_version in
section (__TEXT,__cstring)
/usr/bin/libtool: internal link edit command failed
make[4]: *** [libgmx.la] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
i think Mr.Jack Howarth had already pointed the same thing out, sometime
back. any suggestion!?
regards,
kota.
On 2/2/06, Pradeep Kota < kotanmd at gmail.com> 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.
> regards,
> kota.
>
> On 2/2/06, David van der Spoel < 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> > 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>
> > > <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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> > >
> > ------------------------------------------------------------------------
> > >
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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 <http://xray.bmc.uu.se/%7Espoel>
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
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>
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