[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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> >>
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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
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