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Subject: Re: [OMPI users] Error run mpiexec
From: mariognu-outside_at_[hidden]
Date: 2008-07-21 10:27:21


Hi,

In my /usr/bin I have
lrwxrwxrwx 1 root root 25 2008-07-17 10:25 /usr/bin/mpiexec -> /etc/alternatives/mpiexec
-rwxr-xr-x 1 root root 19941 2008-03-23 03:36 /usr/bin/mpiexec.lam
lrwxrwxrwx 1 root root 7 2008-07-17 10:25 /usr/bin/mpiexec.openmpi -> orterun

I try to run

mpiexec.openmpi -n 3 mdrun_mpi.openmpi -n 3 -v -deffnm run

But only machine 1 the cpu is working in 100%. The machine2 not.

I run

mpiexec.openmpi -n 3 hostname

And I have

machine1
machine1
machine1

My path

mariojose_at_machine1:~/lam-mpi$ echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games

I don't know what happening

Thanks

Mario Jose

--- Em seg, 21/7/08, Ralph Castain <rhc_at_[hidden]> escreveu:

> De: Ralph Castain <rhc_at_[hidden]>
> Assunto: Re: [OMPI users] Error run mpiexec
> Para: mariognu-outside_at_[hidden], "Open MPI Users" <users_at_[hidden]>
> Data: Segunda-feira, 21 de Julho de 2008, 11:00
> If you look closely at the error messages, you will see that
> you were
> executing LAM-MPI, not Open MPI. If you truly wanted to run
> Open MPI,
> I would check your path to ensure that mpiexec is pointing
> at the Open
> MPI binary.
>
> Ralph
>
> On Jul 21, 2008, at 7:47 AM, mariognu-outside_at_[hidden]
> wrote:
>
> > Hi all,
> >
> > First, excuse my english, it isn't good :)
> >
> > Well, I have 2 machines, one a Xeon with 2 cpu (64bit)
> and a Pentium
> > 4 with only one cpu. At the 2 machines I have
> installed Ubuntu 8
> > Server and all packages to open-mpi and gromacs.
> >
> > I use gromacs for my works
> >
> > Ok, in the 2 machines, at my users folder, I have a
> file like this:
> > machine1 cpu=2
> > machine2
> >
> > Machine1 is Xeon (192.168.0.10) and Machine2 is
> Pentium 4
> > (192.168.0.11)
> >
> > My file /etc/hosts is configured too.
> >
> > When I run mpiexec in machine2, I have like this:
> > mariojose_at_machine2:~/lam-mpi$ mpiexec -n 3 hostname
> > machine1
> > machine2
> >
> -----------------------------------------------------------------------------
> > 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 n0).
> >
> > 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.
> >
> -----------------------------------------------------------------------------
> > machine1
> > mpirun failed with exit status 252
> >
> > When I run in machine1 I have like this:
> >
> > mariojose_at_machine1:~/lam-mpi$ mpiexec -n 3 hostname
> > machine1
> > machine1
> > machine2
> >
> -----------------------------------------------------------------------------
> > 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 n0).
> >
> > 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.
> >
> -----------------------------------------------------------------------------
> > mpirun failed with exit status 252
> >
> > I don't know why I have this message. I think that
> is a error.
> >
> > I try run with gromacs, if anybody use gromacs and can
> help me I
> > like very much :) .
> >
> > mariojose_at_machine1:~/lam-mpi$ grompp -f run.mdp -p
> topol.top -c
> > pr.gro -o run.tpr
> > mariojose_at_machine1:~/mpiexec -n 3 mdrun -v -deffnm run
> >
> > It's works Ok. I see that cpu of 2 machines woks
> in 100%. It look
> > well for me. But I have a error em I run mdrun_mpi
> that is a binary
> > to work in cluster.
> >
> > mariojose_at_machine1:~/lam-mpi$ grompp -f run.mdp -p
> topol.top -c
> > pr.gro -o run.tpr -np 3 -sort -shuffle
> > mariojose_at_machine1:~/lam-mpi$ mpiexec -n 3 mdrun_mpi
> -v -deffnm run
> > NNODES=3, MYRANK=0, HOSTNAME=machine1
> > NNODES=3, MYRANK=2, HOSTNAME=machine1
> > NODEID=0 argc=4
> > NODEID=2 argc=4
> > NNODES=3, MYRANK=1, HOSTNAME=machine2
> > NODEID=1 argc=4
> > :-) G R O M A C S (-:
> >
> > Gyas ROwers Mature At Cryogenic
> Speed
> >
> > :-) VERSION 3.3.3 (-:
> >
> >
> > Written by David van der Spoel, Erik Lindahl,
> Berk Hess, and
> > others.
> > Copyright (c) 1991-2000, University of
> Groningen, The
> > Netherlands.
> > Copyright (c) 2001-2008, The GROMACS
> development team,
> > check out http://www.gromacs.org for more
> information.
> >
> > This program is free software; you can
> redistribute it and/or
> > modify it under the terms of the GNU General
> Public License
> > as published by the Free Software Foundation;
> either version 2
> > of the License, or (at your option) any
> later version.
> >
> > :-) mdrun_mpi (-:
> >
> > Option Filename Type Description
> >
> ------------------------------------------------------------
> > -s run.tpr Input Generic run input:
> tpr tpb tpa xml
> > -o run.trr Output Full precision
> trajectory: trr trj
> > -x run.xtc Output, Opt. Compressed trajectory
> (portable xdr
> > format)
> > -c run.gro Output Generic structure:
> gro g96 pdb xml
> > -e run.edr Output Generic energy: edr
> ene
> > -g run.log Output Log file
> > -dgdl run.xvg Output, Opt. xvgr/xmgr file
> > -field run.xvg Output, Opt. xvgr/xmgr file
> > -table run.xvg Input, Opt. xvgr/xmgr file
> > -tablep run.xvg Input, Opt. xvgr/xmgr file
> > -rerun run.xtc Input, Opt. Generic trajectory:
> xtc trr trj
> > gro g96 pdb
> > -tpi run.xvg Output, Opt. xvgr/xmgr file
> > -ei run.edi Input, Opt. ED sampling input
> > -eo run.edo Output, Opt. ED sampling output
> > -j run.gct Input, Opt. General coupling
> stuff
> > -jo run.gct Output, Opt. General coupling
> stuff
> > -ffout run.xvg Output, Opt. xvgr/xmgr file
> > -devout run.xvg Output, Opt. xvgr/xmgr file
> > -runav run.xvg Output, Opt. xvgr/xmgr file
> > -pi run.ppa Input, Opt. Pull parameters
> > -po run.ppa Output, Opt. Pull parameters
> > -pd run.pdo Output, Opt. Pull data output
> > -pn run.ndx Input, Opt. Index file
> > -mtx run.mtx Output, Opt. Hessian matrix
> > -dn run.ndx Output, Opt. Index file
> >
> > Option Type Value Description
> > ------------------------------------------------------
> > -[no]h bool no Print help info and quit
> > -nice int 19 Set the nicelevel
> > -deffnm string run Set the default filename
> for all file
> > options
> > -[no]xvgr bool yes Add specific codes
> (legends etc.) in the
> > output
> > xvg files for the xmgrace
> program
> > -np int 1 Number of nodes, must be
> the same as
> > used for
> > grompp
> > -nt int 1 Number of threads to start
> on each node
> > -[no]v bool yes Be loud and noisy
> > -[no]compact bool yes Write a compact log file
> > -[no]sepdvdl bool no Write separate V and dVdl
> terms for each
> > interaction type and node
> to the log
> > file(s)
> > -[no]multi bool no Do multiple simulations in
> parallel
> > (only with
> > -np > 1)
> > -replex int 0 Attempt replica exchange
> every # steps
> > -reseed int -1 Seed for replica exchange,
> -1 is
> > generate a seed
> > -[no]glas bool no Do glass simulation with
> special long
> > range
> > corrections
> > -[no]ionize bool no Do a simulation including
> the effect of
> > an X-Ray
> > bombardment on your system
> >
> >
> > Back Off! I just backed up run2.log to ./#run2.log.5#
> >
> > Back Off! I just backed up run0.log to ./#run0.log.12#
> > Getting Loaded...
> > Reading file run.tpr, VERSION 3.3.3 (single precision)
> >
> > Back Off! I just backed up run1.log to ./#run1.log.12#
> >
> >
> -------------------------------------------------------
> > Program mdrun_mpi, VERSION 3.3.3
> > Source code file: ../../../../src/gmxlib/block_tx.c,
> line: 74
> >
> > Fatal error:
> > 0: size=672, len=840, rx_count=0
> >
> >
> -------------------------------------------------------
> >
> > "They're Red Hot" (Red Hot Chili
> Peppers)
> >
> > Error on node 1, will try to stop all the nodes
> > Halting parallel program mdrun_mpi on CPU 1 out of 3
> >
> > gcq#220: "They're Red Hot" (Red Hot
> Chili Peppers)
> >
> >
> -----------------------------------------------------------------------------
> > One of the processes started by mpirun has exited with
> a nonzero exit
> > code. This typically indicates that the process
> finished in error.
> > If your process did not finish in error, be sure to
> include a "return
> > 0" or "exit(0)" in your C code before
> exiting the application.
> >
> > PID 15964 failed on node n0 (192.168.0.10) with exit
> status 1.
> >
> -----------------------------------------------------------------------------
> > mpirun failed with exit status 1
> >
> > I don't know what is problem.
> >
> > Anybody can help me ?
> >
> > Thanks
> >
> > Mario Jose
> >
> >
> > /* WE ARE FREE */
> > Hack to learn, don't learn to hack.
> >
> > /* Free Software Foundation */
> > "Free software" is a matter of liberty, not
> price
> > GNU's Not UNIX. Be free, use GNU/Linux
> > www.gnu.org
> > www.fsf.org
> >
> > /* Free Culture */
> > free-culture.org
> > creativecommons.org
> >
> > /* ... Hoarders may get piles of money,
> > That is true, hackers, that is true.
> > But they cannot help their neighbors;
> > That's not good, hackers, that's not good ...
> >
> > Richard Stallman (www.stallman.org) */
> >
> > /* Human knowledge belongs to the world */
> >
> >
> > Novos endereços, o Yahoo! que você conhece.
> Crie um email novo
> > com a sua cara @ymail.com ou @rocketmail.com.
> > http://br.new.mail.yahoo.com/addresses
> >
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users

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