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 > [EMAIL PROTECTED]:~> 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 > [EMAIL PROTECTED],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 > > > [EMAIL PROTECTED]:~> 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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Brian D. Ripley, [EMAIL PROTECTED] 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 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
