[Rd] problem with Rmpi 0.5-5 and openmpi

Tue Apr 8 11:53:10 CEST 2008

See

http://www.open-mpi.org/community/lists/users/2007/10/4192.php

Does the version of Rmpi you used have the suggested patch?

On Mon, 7 Apr 2008, Peter Pearman wrote:

> Dear knowledgeable experts :-),
>
> I am trying to get openmpi, Rmpi and SNOW running on a Myrinet/GM
> cluster.  I'm not an IT expert, but I surely could use a working
> installation of Rmpi and SNOW.
>
> I try to load the Rmpi library and get the following:
>
> > library(Rmpi)
> [master:07230] mca: base: component_find: unable to open osc pt2pt: file
> not found (ignored)
> --------------------------------------------------------------------------
> [0,0,0]: Myrinet/GM on host master was unable to find any NICs.
> Another transport will be used instead, although this may result in
> lower performance.
>
> Then if I start a cluster, only nodes on Master can be seen and initiated
>
> Here is environment, configuration and installation information:
>
>
> # configuration of openmpi
> ./configure --prefix=/opt/openmpi --with-gm=/opt/gm/2.1.21/2.6.11-21smp
> --with-sge=/opt/sge --disable-mpi-f90
>
> #installation of Rmpi
> /usr/local/bin/R CMD INSTALL Rmpi_0.5-5.tar.gz \
> --configure-args=--with-mpi=/opt/openmpi
>
> R version 2.6.1 (2007-11-26)
>
> #master environment
> pearman at master:~> env
> LESSKEY=/etc/lesskey.bin
> NNTPSERVER=news
> INFODIR=/usr/local/info:/usr/share/info:/usr/info
> MANPATH=/opt/sge/man:/usr/local/man:/usr/local/share/man:/usr/share/man:/usr/X11R6/man:/opt/gnome/share/man:/opt/c3-4/man
> HOSTNAME=master
> GNOME2_PATH=/usr/local:/opt/gnome:/usr
> XKEYSYMDB=/usr/X11R6/lib/X11/XKeysymDB
> HOST=master
> TERM=xterm
> SHELL=/bin/bash
> PROFILEREAD=true
> HISTSIZE=1000
> SSH_CLIENT=::ffff:10.15.1.179 51565 22
> QTDIR=/usr/lib/qt3
> OLDPWD=/opt/openmpi/bin
> SSH_TTY=/dev/pts/6
> GROFF_NO_SGR=yes
> JRE_HOME=/usr/lib/jvm/java/jre
> USER=pearman
> LS_COLORS=no=00:fi=00:di=01;34:ln=00;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=4
> 0;31:ex=00;32:*.cmd=00;32:*.exe=01;32:*.com=01;32:*.bat=01;32:*.btm=01;32:*.dll=01;32:*.tar=00;
> 31:*.tbz=00;31:*.tgz=00;31:*.rpm=00;31:*.deb=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.zip=00
> ;31:*.zoo=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.tb2=00;31:*.tz2=00;31:*.tbz2=00;31
> :*.avi=01;35:*.bmp=01;35:*.fli=01;35:*.gif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mng=01;35:*.mov=01;
> 35:*.mpg=01;35:*.pcx=01;35:*.pbm=01;35:*.pgm=01;35:*.png=01;35:*.ppm=01;35:*.tga=01;35:*.tif=01
> ;35:*.xbm=01;35:*.xpm=01;35:*.dl=01;35:*.gl=01;35:*.aiff=00;32:*.au=00;32:*.mid=00;32:*.mp3=00;
> 32:*.ogg=00;32:*.voc=00;32:*.wav=00;32:
> LD_LIBRARY_PATH=/opt/openmpi/lib:/opt/sge/lib/lx24-amd64
> XNLSPATH=/usr/X11R6/lib/X11/nls
> HOSTTYPE=x86_64
> PAGER=less
> XDG_CONFIG_DIRS=/usr/local/etc/xdg/:/etc/xdg/:/etc/opt/gnome/xdg/
> C3_PATH=/opt/c3-4
> MINICOM=-c on
> MAIL=/var/mail/pearman
> PATH=/opt/openmpi/bin:/opt/sge/bin/lx24-amd64:/opt/mpich/1.2.6..14b/x86_64/gcc//bin:/opt/gm/2.1
> .21/2.6.11-21smp/bin:/opt/c3-4:/home/pearman/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/u
> sr/games:/opt/gnome/bin:/opt/kde3/bin:/opt/pathscale/bin
> CPU=x86_64
> JAVA_BINDIR=/usr/lib/jvm/java/bin
> INPUTRC=/etc/inputrc
> PWD=/home/pearman
> JAVA_HOME=/usr/lib/jvm/java
> LANG=en_US.UTF-8
> PYTHONSTARTUP=/etc/pythonstart
> SGE_ROOT=/opt/sge
> SDK_HOME=/usr/lib/jvm/java
> C3_RSH=ssh
> TEXINPUTS=:/home/pearman/.TeX:/usr/share/doc/.TeX:/usr/doc/.TeX
> JDK_HOME=/usr/lib/jvm/java
> SHLVL=1
> HOME=/home/pearman
> LESS_ADVANCED_PREPROCESSOR=no
> OSTYPE=linux
> LS_OPTIONS=-N --color=tty -T 0
> XCURSOR_THEME=crystalwhite
> WINDOWMANAGER=/usr/X11R6/bin/kde
> GTK_PATH=/usr/local/lib/gtk-2.0:/opt/gnome/lib/gtk-2.0:/usr/lib/gtk-2.0
> GM_PATH=/opt/gm/2.1.21/2.6.11-21smp
> G_FILENAME_ENCODING=@locale,UTF-8,ISO-8859-15,CP1252
> LESS=-M -I
> MACHTYPE=x86_64-suse-linux
> LOGNAME=pearman
> GTK_PATH64=/usr/local/lib64/gtk-2.0:/opt/gnome/lib64/gtk-2.0:/usr/lib64/gtk-2.0
> CVS_RSH=ssh
> XDG_DATA_DIRS=/usr/local/share/:/usr/share/:/etc/opt/kde3/share/:/opt/kde3/share/:/opt/gnome/sh
> are/
> MPICH_PATH=/opt/mpich/1.2.6..14b/x86_64/gcc/
> ACLOCAL_FLAGS=-I /opt/gnome/share/aclocal
> SSH_CONNECTION=::ffff:10.15.1.179 51565 ::ffff:10.30.1.15 22
> PKG_CONFIG_PATH=/opt/gnome/lib64/pkgconfig
> LESSOPEN=lessopen.sh %s
> INFOPATH=/usr/local/info:/usr/share/info:/usr/info:/opt/gnome/share/info
> LESSCLOSE=lessclose.sh %s %s
> G_BROKEN_FILENAMES=1
> JAVA_ROOT=/usr/lib/jvm/java
> COLORTERM=1
> _=/usr/bin/env
>
>
> pearman at master:~> which mpirun
> /opt/openmpi/bin/mpirun
>
> Also note:  mpich is also installed and is also in the PATH, after openmpi
>
> BTW.  I have seen a number of posts concerning the pt2pt error message.
>  Still, I was unable to understand how they might apply to fixing the
> current problem.
>
> Help would be greatly appreciated.
>
> Peter
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595