Very helpful PDF manipulation tools on Linux

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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:

PDFjam is a small collection of shell scripts which provide a simple interface to much of the functionality of the excellent pdfpages PDF file package (by Andreas Matthias) for pdfLaTeX. These scripts take one or more PDF files (and/or JPG/PNG graphics files) as input, and produce one or more PDF files as output. They are useful for joining files together, selecting pages, reducing several source pages onto one output page, etc., etc.

When root cannot run X applications from a local terminal

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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

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The cause of init: Id “co” respawning too fast, and how to fix it

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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: Continue reading →

Opportunity for postdoctoral research associate in high performance computing

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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.

Updated GROMACS tutorials

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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. Continue reading →

Installing Lumerical FDTD on a linux cluster

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Most of the time, RPM (especially in conjunction with yum) is a decent package management solution. However, I can think of two common circumstances when you don’t want to let RPM install a package:

  • You don’t have root permissions on a system such as a shared cluster
  • You are an administrator on a shared cluster and you can’t risk having a package over-write system-critical files

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pickle, hickle and HDF5

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Danny Price recently left a comment to let me know about a new Python package he’s developing called hickle. The goal of “hickle” is to create a module that works like Python’s pickle module but stores its data in the HDF5 binary file format. This is a promising approach, because I advocate storing binary data in HDF5 files whenever possible instead of creating yet another one-off binary file format that nobody will be able to read in ten years. The immediate advantage of using HDF5 to store picked Python objects is that HDF5 files are portable across many platforms, while “pickled” objects may not be readable on a different platform. Continue reading →

Building NumPy and SciPy with Intel Composer 2013 and the MKL

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Since Python is widely used as a high-productivity language for scientific computing, Intel has created a page showing how to build NumPy with Intel compilers and the Math Kernel Library (MKL). I would like to clarify a few items regarding building NumPy on a 64-bit Red Hat Enterprise Linux 5.4 system. Since this is a production system, I don’t want to replace the Python 2.4 binary -2.7.3-intel-composer-2013that ships with RHEL 5.4. Instead, I created a directory called

/apps/python/python/-2.7.3-intel-composer-2013

and set

PYTHONPATH=/apps/python/python-2.7.3-intel-composer-2013
LD_LIBRARY_PATH=/apps/python/python-2.7.3-intel-composer-2013/lib:$LD_LIBRARY_PATH

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