[OMPI users] Error run mpiexec
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 -srun.tpr InputGeneric run input: tpr tpb tpa xml -orun.trr Output Full precision trajectory: trr trj -xrun.xtc Output, Opt. Compressed trajectory (portable xdr format) -crun.gro Output Generic structure: gro g96 pdb xml -erun.edr Output Generic energy: edr ene -grun.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 -tpirun.xvg Output, Opt. xvgr/xmgr file -eirun.edi Input, Opt. ED sampling input -eorun.edo Output, Opt. ED sampling output -jrun.gct Input, Opt. General coupling stuff -jorun.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 -pirun.ppa Input, Opt. Pull parameters -porun.ppa Output, Opt. Pull parameters -pdrun.pdo Output, Opt. Pull data output -pnrun.ndx Input, Opt. Index file -mtxrun.mtx Output, Opt. Hessian matrix -dnrun.ndx O
Re: [OMPI users] Error run mpiexec
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 -srun.tpr InputGeneric run input: tpr tpb tpa xml -orun.trr Output Full precision trajectory: trr trj -xrun.xtc Output, Opt. Compressed trajectory (portable xdr format) -crun.gro Output Generic structure: gro g96 pdb xml -erun.edr Output Generic energy: edr ene -grun.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 -tpirun.xvg Output, Opt. xvgr/xmgr file -eirun.edi Input, Opt. ED sampling input -eorun.edo Output, Opt. ED sampling output -jrun.gct Input, Opt. General coupling stuff -jorun.gct Output, Opt. General coupling stuff -ffout run.xvg Output, Opt. xvgr/xmgr file -devout run.xvg Output, Opt. xvgr/xmgr file -runav
Re: [OMPI users] Error run mpiexec
Hi, In my /usr/bin I have lrwxrwxrwx 1 root root25 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 $PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games I don't know what happening Thanks Mario Jose --- Em seg, 21/7/08, Ralph Castain escreveu: > De: Ralph Castain > Assunto: Re: [OMPI users] Error run mpiexec > Para: mariognu-outs...@yahoo.com.br, "Open MPI Users" > Data: Segunda-feira, 21 de Julho de 2008, 11:00 > If you look closely at the error messages, you will see that > you were > executing LAM-MPI, not Open MPI. If you truly wanted to run > Open MPI, > I would check your path to ensure that mpiexec is pointing > at the Open > MPI binary. > > Ralph > > On Jul 21, 2008, at 7:47 AM, mariognu-outs...@yahoo.com.br > wrote: > > > Hi all, > > > > First, excuse my english, it isn't good :) > > > > Well, I have 2 machines, one a Xeon with 2 cpu (64bit) > and a Pentium > > 4 with only one cpu. At the 2 machines I have > installed Ubuntu 8 > > Server and all packages to open-mpi and gromacs. > > > > I use gromacs for my works > > > > Ok, in the 2 machines, at my users folder, I have a > file like this: > > machine1 cpu=2 > > machine2 > > > > Machine1 is Xeon (192.168.0.10) and Machine2 is > Pentium 4 > > (192.168.0.11) > > > > My file /etc/hosts is configured too. > > > > When I run mpiexec in machine2, I have like this: > > mariojose@machine2:~/lam-mpi$ 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 > > a
Re: [OMPI users] Error run mpiexec
Hi > > mpiexec.openmpi -n 3 hostname > Here you forgot to specify the hosts, so all processes run on the local machine; see: http://www.open-mpi.org/faq/?category=running#mpirun-host Jody
[OMPI users] Problem with WRF and pgi-7.2
Hi, When compiling WRF with PGI-7.2-1 with openmpi-1.2.6
The file buf_for_proc.c fails. Nothing specail about this file
sticks out to me. But older versions of PGI like it just fine. The
errors PGI complains about has to do with mpi.h though:
[brockp@nyx-login1 RSL_LITE]$ mpicc -DFSEEKO64_OK -w -O3 -
DDM_PARALLEL -c buf_for_proc.c
PGC-S-0036-Syntax error: Recovery attempted by inserting
identifier .Z before '(' (/home/software/rhel4/openmpi-1.2.6/
pgi-7.0/include/mpi.h: 823)
PGC-S-0082-Function returning array not allowed (/home/software/rhel4/
openmpi-1.2.6/pgi-7.0/include/mpi.h: 823)
PGC-S-0043-Redefinition of symbol, MPI_Comm (/home/software/rhel4/
openmpi-1.2.6/pgi-7.0/include/mpi.h: 837)
PGC/x86-64 Linux 7.2-1: compilation completed with severe errors
Has anyone else seen that kind of problem with mpi.h and pgi? Do I
need to use -c89 ? I know PGI changed the default with this a while
back, but it does not appear to help.
Thanks!
Brock Palen
www.umich.edu/~brockp
Center for Advanced Computing
bro...@umich.edu
(734)936-1985
