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@machine1:~/lam-mpi$ echo $PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games I don't know what happening Thanks Mario Jose --- Em seg, 21/7/08, Ralph Castain <r...@lanl.gov> escreveu: > De: Ralph Castain <r...@lanl.gov> > Assunto: Re: [OMPI users] Error run mpiexec > Para: mariognu-outs...@yahoo.com.br, "Open MPI Users" <us...@open-mpi.org> > Data: Segunda-feira, 21 de Julho de 2008, 11:00 > If you look closely at the error messages, you will see that > you were > executing LAM-MPI, not Open MPI. If you truly wanted to run > Open MPI, > I would check your path to ensure that mpiexec is pointing > at the Open > MPI binary. > > Ralph > > On Jul 21, 2008, at 7:47 AM, mariognu-outs...@yahoo.com.br > wrote: > > > Hi all, > > > > First, excuse my english, it isn't good :) > > > > Well, I have 2 machines, one a Xeon with 2 cpu (64bit) > and a Pentium > > 4 with only one cpu. At the 2 machines I have > installed Ubuntu 8 > > Server and all packages to open-mpi and gromacs. > > > > I use gromacs for my works > > > > Ok, in the 2 machines, at my users folder, I have a > file like this: > > machine1 cpu=2 > > machine2 > > > > Machine1 is Xeon (192.168.0.10) and Machine2 is > Pentium 4 > > (192.168.0.11) > > > > My file /etc/hosts is configured too. > > > > When I run mpiexec in machine2, I have like this: > > mariojose@machine2:~/lam-mpi$ 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@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@machine1:~/lam-mpi$ grompp -f run.mdp -p > topol.top -c > > pr.gro -o run.tpr > > mariojose@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@machine1:~/lam-mpi$ grompp -f run.mdp -p > topol.top -c > > pr.gro -o run.tpr -np 3 -sort -shuffle > > mariojose@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 > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users 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
