Original post blogged on b2evolution.

After lots of trying and searching I finally found out that Rmpi is not compatible with the latest version of openmpi which is installed from the Arch repos (version 1.5.3-2). Following the recommendation here I was able to get Rmpi working by reverting to openmpi version 1.4.3, which is in fact the current release.

To do this, I downloaded openmpi 1.4.3 from the Open MPI download page, extracted the tarball, compiled and installed the source in the usual way:

./configure
make
make install


After installation I then followed the directions here with modifications to account for the new install location. Specifically, I ran the command:

sudo ldconfig /usr/local/lib/openmpi/

and then added the line:

export LD_LIBRARY_PATH=/usr/local/lib/openmpi/:$LD_LIBRARY_PATH

to my .bashrc file.

Finally, I was able to install Rmpi in R using the following command:

install.packages("Rmpi",
configure.args =
c("--with-Rmpi-include=/usr/local/include/",
"--with-Rmpi-libpath=/usr/local/lib/openmpi/",
"--with-Rmpi-type=OPENMPI"))


I have now test Rmpi by running the script I posted previously after opening R as:

/usr/local/bin/mpirun -np 1 R --vanilla

and it all seems to work as expected. Phew!

This is a great reference for those who may have forgotten (or keep forgetting) their matrix derivative rules -- like me! The summary at the end is especially useful. Thanks Paul!!


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Worked like a charm for me!

You'll probably also want to add the extra codecs so you can play your favourite music sources. The simplest thing is to install them all at once:

sudo pacman -S gstreamer0.10-bad-plugins gstreamer0.10-ugly-plugins gstreamer0.10-ffmpeg

This will allow you to play mp3 files among other formats. Note: after installing these I received an error message from rhythmbox saying that a Gstreamer plugin was missing until I logged out and restarted X.

You then need to edit the /etc/sudoers file to allow your basic user to run sudo. You can do this by adding a single user to the /etc/sudoers file, but you can also do it with groups. First, add your user to the wheel group with the command:

gpasswd -a wheel
while logged into the root account. Then edit the /etc/sudoers file to allow this group access to sudo. To do this, you need to use the command:
de>
and remove the comment (#) at the start of the line:

%wheel All=(All) All

of from the line:

%wheel All=(All) NOPASSWD: All

if you don't want to have to enter your password every time.

You should now be able to execute commands like pacman from the normal user's account, like:

sudo pacman -S

First you have to edit the machine settings. With the machine off select the machine in the VirtualBox and click settings. Then open the 'Shared Folders' dialog and create a new shared folder -- remember the Folder Name because you'll need this in a sec. The folder I have used is called Archie.

To access the shared folder in the guest machine you simply need to mount the folder. Log-in as root and create a new mount point, like so:

mkdir /media/Archie

The shared folder can then be mounted with the command:

mount -t vboxsf Archie /media/Archie

To avoid having to do this every time you want to move a file, you can have the share mounted automatically on each boot of the guest machine. To do this, you need to edit the /etc/fstab file as root. The suggested line is:

Archie /media/Archie vboxsf defaults 0 0

but I've changed this to:

Archie /media/Archie vboxsf uid=1000,gid=100 0 0

in order that the basic user I created (uid 1000) can easily write files to the share.