You may want to be a little careful about using R and MPI with Myrinet. We tried to get that to work around 5 years ago and found it more trouble than it was worth (we ended up sending the Myrinet equipment back and getting gigabit ethernet instead).
As I recall, the problem at the time was that the Myrinet libraries used their own malloc (or assumed that their own malloc was used -- I don't recall which), whereas a standard R build would use the system malloc. The resulting combination would work for small allocations. But for large allocations allocated by R using the standard malloc (large meaning allocated by memory mapping) the Myrinet internals would assume these allocations had been allocated by their malloc and start doing things with them that lead to crashes. I'm fuzzy on the details but this should give you an idea of what to look out for. Best, luke 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 > -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
