From luke at stat.uiowa.edu  Tue Apr  8 20:39:29 2008
From: luke at stat.uiowa.edu (Luke Tierney)
Date: Tue, 8 Apr 2008 13:39:29 -0500 (CDT)
Subject: [Rd] problem with Rmpi 0.5-5 and openmpi
In-Reply-To: <47FA1901.10904@wsl.ch>
References: <47FA1901.10904@wsl.ch>
Message-ID: <Pine.LNX.4.64.0804081332330.13353@nokomis.stat.uiowa.edu>

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
> 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
>

-- 
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:      luke at stat.uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu



[Rd] problem with Rmpi 0.5-5 and openmpi
Luke Tierney