[gmx-users] mdrun with mpich

David van der Spoel spoel at xray.bmc.uu.se
Sun Feb 5 09:27:36 CET 2006


Pradeep Kota wrote:
> 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.

you are still running an MPICH exacutable here. lamboot is used for LAM 
only. Are you inadvertedly mixing LAM and MPICH?



> 
> thanks in anticipation,
> 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:
>      > 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> < 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>
>      > <mailto: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>
>      >     <mailto: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>>
>      >>  <mailto: 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>>
>      >         <mailto: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>
>      >         <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>
>      >         <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>
>     <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
>      >         spoel at gromacs.org <mailto:spoel at gromacs.org>
>     <mailto:spoel at gromacs.org <mailto:spoel at gromacs.org>>
>      >         http://xray.bmc.uu.se/~spoel
>     <http://xray.bmc.uu.se/%7Espoel <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
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://xray.bmc.uu.se/~spoel
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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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