Simon's Blog

After 2.5 hours I have finally managed to get Rmpi installed and working on Arch.

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!

Link: http://www4.ncsu.edu/~pfackler/MatCalc.pdf

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!!

I recently upgraded Skype to version 2.1.0.81, and since then I've been having troubles with my web cam (Microsoft Lifecam NX-6000). The camera would work in other applications, and Skype would detect it but couldn't grab the image either in the test or in an actual call. I stumbled upon this post and creating a simple wrapper to change the LD_PRELOAD environment variable seems to have worked. The entire script is:

#/bin/bash

export LD_PRELOAD=/usr/lib/libv4l/v4l2convert.so

/usr/bin/skype

and the camera now works if I run run_skype. Don't forget to make the script executable!

Line numbering is difficult for LaTeX because the line numbers are only known after the text has been typeset. The lineno package does a pretty good job, but it sometimes gets confused and can leave seemingly random sections of the document without numbers. I recently had this problem when submitting a paper for Biometrics using the provided style file. I then stumbled upon this great fix. Simply copy the following text and place it in your LaTeX file before the \begin{document} command:


\newcommand*\patchAmsMathEnvironmentForLineno[1]{%
\expandafter\let\csname old#1\expandafter\endcsname\csname #1\endcsname
\expandafter\let\csname oldend#1\expandafter\endcsname\csname end#1\endcsname
\renewenvironment{#1}%
{\linenomath\csname old#1\endcsname}%
{\csname oldend#1\endcsname\endlinenomath}}%
\newcommand*\patchBothAmsMathEnvironmentsForLineno[1]{%
\patchAmsMathEnvironmentForLineno{#1}%
\patchAmsMathEnvironmentForLineno{#1*}}%
\AtBeginDocument{%
\patchBothAmsMathEnvironmentsForLineno{equation}%
\patchBothAmsMathEnvironmentsForLineno{align}%
\patchBothAmsMathEnvironmentsForLineno{flalign}%
\patchBothAmsMathEnvironmentsForLineno{alignat}%
\patchBothAmsMathEnvironmentsForLineno{gather}%
\patchBothAmsMathEnvironmentsForLineno{multline}%
}


Worked like a charm for me!