I and others who use ___@ieee.org email addresses have a serious problem in which we occasionally fail to receive certain email messages that are sent our ieee.org addresses. This is a serious problem, and I’ve finally found a solution.
How to fix your IEEE email alias so that it delivers all messages Read More »
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
Using the MATLAB Distributed/Parallel Computing Toolbox without modifying your cluster Read More »
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
PHPUnit on CentOS 6 Read More »
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)
Installing PHPUnit on CentOS 5.9 Read More »
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
Very helpful PDF manipulation tools on Linux Read More »
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:
When root cannot run X applications from a local terminal Read More »
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 cause of init: Id “co” respawning too fast, and how to fix it Read More »
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
How to plot .xvg files from GROMACS on Windows Read More »
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
Opportunity for postdoctoral research associate in high performance computing Read More »
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
Updated GROMACS tutorials Read More »