This post shows how I set up MATLAB to perform parallel calculations on a multi-core server which is part of an existing cluster that is managed using Torque and Moab. I did this without making any changes to the cluster submission system. The installation documentation for the MATLAB Parallel Computing Toolbox and Distributed Computing Server is poor. The instructions make a lot of assumptions that don’t fit into an existing “production” cluster environment. For example, they assume that a GUI is available to configure the cluster (this step is not required for my method!) Further, the instructions give the impression that MATLAB components must be “installed” on both the head node and compute nodes by an administrator. THIS IS FALSE! Ordinary users can run concurrent (multicore) MATLAB jobs without administrative privileges!

In my last post, I showed how to install PHPUnit with PHP 5.3 on a CentOS 5.9 system. Today, I will tackle the much simpler task of installing PHPUnit on a CentOS 6.4 system. The task is easier since PHP5.3 is standard on CentOS 6. On my system, PEAR was already installed. Steps: 1. Install the PHPUnit channel for PEAR:

yum install php-channel-phpunit

2. Set channel to auto-discover:

I recently had to install PHPUnit on a CentOS 5.9 system.  This turned out to be a little more complicated than I had anticipated, so I wrote down the procedure in case I had to do it again. Here are my notes: 1. Install php53 packages, not php (php packages install the old 4.x series) 2. Install PEAR, PHP’s component management system.  Here is the complete Yum log for a PEAR installation: Jun 03 22:49:56 Installed: php53-common-5.3.3-13.el5_8.x86_64 Jun 03 22:49:57 Installed: php53-cli-5.3.3-13.el5_8.x86_64 Jun 03 22:49:58 Installed: php53-5.3.3-13.el5_8.x86_64 Jun 03 22:51:24 Installed: php53-devel-5.3.3-13.el5_8.x86_64 Jun 03 22:51:25 Installed: 1:php-pear-1.4.9-8.el5.noarch 3. Install php53-xml: Jun 03 23:30:40 Installed: php53-xml-5.3.3-13.el5_8.x86_64 4. Install php54-xml and restart httpd to get the DOM extension for PHP 5. Install PHPUnit with PEAR:

You can do some really cool stuff with Ghostscript on the command line on a computer running Linux or OS X. However, it’s hard to remember all that stuff when you don’t use it very often. I recently learned about a set of command-line PDF manipulation tools called PDFjam. If you are a  geek like me, you probably already have pdfLaTeX installed.  I can’t summarize the capabilities any better than the description on the PDFjam site:

I run XWindows on a CentOS 5.9 box as a non-root user. To perform administrative tasks, I occasionally log in as root using “su” in a terminal window. However, I found that I was unable to start any GUI applications as root. I got the following error:

Xlib: connection to ":0.0" refused by server
Xlib: No protocol specified
E233: cannot open display Xlib: connection to ":0.0" refused by server
Xlib: No protocol specified

This can happen when xhost isn’t configured to allow local, non-network connections. As the user who started the xwindows session (not root) run:

I recently found the following message in the system logs for one of the compute nodes in the STOKES cluster:

init: Id "co" respawning too fast: disabled for 5 minutes

This caught my attention, because this OS image on this particular node should be identical to the image that is deployed on the rest of the nodes in the cluster. Why was it the only one producing this strange warning message? I searched the web and learned that the following line in /etc/inittab is causing the warning:

GROMACS produces graphical output in the form of .xvg files. These are designed to be viewed with a classic UNIX/Linux plotting program called Grace. If you happen to be using Linux and you have Grace installed, it is very easy to plot the data with the command

xmgrace my_file.xvg

If you aren’t using Linux, plotting .xvg files is quite a bit more difficult. Gnuplot is the only free plotting program that I have found that can handle .xvg files. Gnuplot is available for Windows (there is a direct download link near the top of the download page), but I will caution you that Gnuplot is not easy to learn. It has a command-line interface, and there are no point-and-click options to do basic operations such as labeling the axes of the plot. If you are using Gnuplot, you can plot the contents of an .xvg file with the command:

My current employer, the STOKES Advanced Research Computing Center (STOKES ARCC), is hiring a postdoctoral research associate to conduct research in high performance computing with an emphasis on next-generation networking technologies. The ARCC has internal funding that will be used to upgrade our research network to the Internet2 Innovation Platform standard. We are also seeking external funding to extend the research network across the UCF campus. We are looking for a candidate with an interest in topics such as defining a “Science DMZ,” Internet2, GENI, perfSONAR, software-defined networks, etc. Please use the link above to apply for the position. Feel free to contact me if you have questions-my contact information is on the about page.

I have published up-to-date versions of two classic GROMACS tutorials on GitHub. The Getting Started section of the GROMACS online documentation contains some helpful tutorials.  Unfortunately, these tutorials have not been updated in a while. They also don’t explain how to set up an efficient workflow to run large molecular dynamics simulations on a shared cluster using a resource manager such at Torque. I have created a set of files that implement the speptide tutorial from the GROMACS documentation.You can use my files and follow along with the explanations in the GROMACS manual. The speptide directory has two subdirectories: one for MDP files (which control the simulations) and one for simulation files. I have found this to be an efficient setup because many MD experiments involve simulating multiple variants of a molecule (such as mutants of a protein) and comparing the results. All variants should be run with the same parameters, so the same MDP files are used for each simulation. Keeping the MDP files in their own directory and creating symbolic links from the run directory to the MDP files ensures that all simulations are run with identical parameters. In the run directory, there is a Bash script called setup_GROMACS_job.sh. At the top of the script, the user sets variables to set simulation parameters such as the box size. The script can be run with the command