[gmx-users] mdrun with mpich
Pradeep Kota
kotanmd at gmail.com
Sun Feb 5 06:34:42 CET 2006
Thanks Dr.David. I could compile gromacs successfully. But when i run an md
simulation on four processors, it returns the following error.
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p4_error: latest msg from perror: No such file or directory
p0_2057: p4_error: : -1
-------------------------------------------------------
Program mdrun_mpi, VERSION 3.3
Source code file: futil.c, line: 308
File input/output error:
md.log
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Halting program mdrun_mpi
gcq#1768121632: Thanx for Using GROMACS - Have a Nice Day
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p4_error: latest msg from perror: No such file or directory
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n8952p0_
058: p4_error: : -1
mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------
i had lambooted all the nodes properly and it did not have any problems at
that stage. and as it said, i tried using lamexec too. still no luck. i
tried using other switches with mpirun too..couldnt quite figure out what
the error could be.
thanks in anticipation,
kota.
On 2/2/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Pradeep Kota wrote:
> > 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'.
> >
> seems like you have two different versions of fftw3 installed, or mixed
> single and double precision. Otherwise I don't know.
>
>
>
> > /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 <http://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
> > <mailto: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
> > <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>
> >> <
> >
> 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.
> >>
> >>
> >
> ------------------------------------------------------------------------
> >
> >>
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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 <mailto:spoel at xray.bmc.uu.se>
> > spoel at gromacs.org <mailto:spoel at gromacs.org>
> > http://xray.bmc.uu.se/~spoel <http://xray.bmc.uu.se/%7Espoel>
> >
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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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