Category Archives: Linux

Very helpful PDF manipulation tools on Linux

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

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

Continue reading

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

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

Installing Lumerical FDTD on a linux cluster

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

Continue reading

Building NumPy and SciPy with Intel Composer 2013 and the MKL

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

Continue reading

The Infiniband troubleshooting quick reference

Glossary of Infiniband Terminology:

  • GID: Global Identifier
  • HCA: Host Channel Adapter
  • LID: Local Identifier
  • TCA: Target Channel Adapter

Infiniband Fundamentals:

InfiniBand Troubleshooting:

Man pages for useful diagnostic tools: