From pearman at wsl.ch  Mon Apr  7 14:52:17 2008
From: pearman at wsl.ch (Peter Pearman)
Date: Mon, 07 Apr 2008 14:52:17 +0200
Subject: [Rd] problem with Rmpi 0.5-5 and openmpi
Message-ID: <47FA1901.10904@wsl.ch>

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



[Rd] problem with Rmpi 0.5-5 and openmpi
Peter Pearman