HMC Mathematics Computing Weblog

TeX Live 2009 Released!

Claire Connelly — 2009-11-10T16:25:44-08:00

TeX Live 2009, a complete TeX system for use on Linux, Mac OS X, and Windows, has been released!

This release contains the latest versions of the various TeX binaries, as well as a wide variety of LaTeX packages, fonts, and other support files. Major new features include the cross-platform TeXworks editor, modeled on the TeXshop editor on Mac OS X; and new versions of the AMS PostScript Type 1 fonts, including the Computer Modern family, and an updated set of Euler fonts incorporating new designs from Hermann Zapf.

We currently have TeX Live 2009 installed on our Linux systems, but not as the primary TeX system; using it requires you to add /shared/local/texlive/2009/bin/i386-linux (on ponder) or /shared/local/texlive/2009/bin/x86_64-linux (on the other Linux systems) to your path. TeX Live 2009 will become the default TeX system on the Linux machines in the near future (once it has propagated to more mirrors).

TeX Live 2009 is available on our mirror server from http://mirror.hmc.edu/ctan/systems/texlive/. There are DVD ISO images that can be downloaded (in the Images directory) as well as a network installable version (in the tlnet directory).

For Mac OS X users, the MacTeX-2009 package should be available soon from our mirror server, in http://mirror.hmc.edu/ctan/systems/mac/mactex/. (Note that the mactex-20090320* packages are not the new release; the new release, with a date similar to 20091108 should appear soon.

New Release of `hmcpset`Homework LaTeX Class

Claire Connelly — 2009-10-06T10:14:39-08:00

Current versions of PDFTeX resulted in problems with the PDFTeX-detection code in the hmcpset homework LaTeX class, making it unusable.

A new release of the hmcpset class, 0.5, addresses this issue by substituting the use of the ifpdf package for the offending code. That version is now the current version for users of the department's Linux cluster and is available for download from the class's support page, at http://www.math.hmc.edu/computing/support/tex/classes/hmcpset/.

As the older version of the class is unusable with current TeX systems (e.g., TeX Live 2008 or TeX Live 2009), we encourage users to download the newer version as soon as possible.

As usual, please report problems to system@math.hmc.edu.

New Scientific Computing Lab Combination

Claire Connelly — 2009-08-31T16:02:44-08:00

We've changed the combination for the door to the Scientific Computing Lab. Anyone with an account can find out the new combination by logging into a department machine and reading the contents of the file /shared/local/scicomp-combo.

Upcoming Scientific Computing Lab Outage

Claire Connelly — 2009-08-07T16:49:49-08:00

We will be taking the entire Scientific Computing Lab offline for a few days. During this outage all of the machines in the lab will be rebuilt with a generic OS install in preparation for replacement. We will then pull the machines out and make them available for scavenging in the hall behind Big Beckman.

With the machines out of the lab, we will have the room cleaned thoroughly, and then we will install the new machines in preparation for the fall, 2009, semester.

The exact dates for this outage have not yet been determined, but early during the week of August 10–14 is the likely target for decommissioning, with the new machines being installed later that week or during the next week.

Stay tuned for more news, or check our Twitter feed!

New SciComp Lab Machines Coming

Claire Connelly — 2009-06-02T16:04:47-08:00

The department has been able to negotiate a deal with CIS to replace the machines in our Scientific Computing Lab with new workstations. (We traded our share of an IBM grant for money to use for other systems.)

We will be replacing the current mix of machines in the lab with twelve new Dell OptiPlex 960n systems, each with a 3 GHz Core 2 Duo processor, 4 GB of RAM, an ATI Radeon HD 3450 video card, and a 22" widescreen LCD monitor. These machines will run the latest release of the CentOS Linux distribution (currently 5.3).

We expect to have the machines in hand in mid-June, with deployment to follow soon after.

File Server Reboot: 5:00 PM, Wednesday, June 3, 2009

Claire Connelly — 2009-06-02T15:55:34-08:00

We will be rebooting the department's main file server, gytha, to apply some security updates and improve the stability of our web server.

The reboot will happen at 5:00 PM on Wednesday, June 3, 2009. The outage may last as long as two hours.

Affected Services/Systems

Rebooting gytha will affect almost all services provided by the department, including mail, logins on department Macs and Linux systems, and personal/faculty web pages, as gytha provides all home directories, and those services depend on access to your home directories.

Windows machines and other machines that use CIS servers will not be affected unless you're mounting drives from our servers as well.

Core web pages (those without a ~ in the URL) will not be affected.

Duration and After Effects

The reboot could take as little as 15 minutes or as long as two hours, depending on how many file systems need to be checked; as the machine has been running continuously for 216 days (at this writing), a longer outage is likely.

After the server reboot, desktop Macs running Mac OS X 10.4 (Tiger) will need to be rebooted, as their NFS software does not handle reboots gracefully. Some Linux servers and workstations may also require attention.

What You Should Do

Log out of your account before 5:00 PM on Wednesday, 2009 June 5. I will take down mail services (including incoming and outgoing mail and IMAP and POP services) prior to the reboot, so you don't need to worry about quitting mail clients on home machines or laptops, but you will not be able to send mail through our mail server until the file server is back up and mail services have been restarted.

New Versions of hmcclinic and hmcthesis LaTeX Classes Available

Claire Connelly — 2009-02-26T14:18:59-08:00

I've updated the Clinic and thesis LaTeX classes to explicitly load the booktabs and natbib packages, and to define bibliographic punctuation as described in the Clinic and thesis handbooks; that is, in theses or Clinic reports, you no longer need the lines

              \usepackage{booktabs}
              \usepackage{natbib}
              \bibpunct[:~]{(}{)}{;}{a}{,}{,~}

in the preamble of your document's master file.

The new versions are available on the math Linux cluster (in /shared/local/share/texmf/tex/latex/{hmcclinic,hmcthesis}), where they will be used automatically for typesetting Clinic reports or theses on a math cluster machine.

For use on your own machine, you can download a tar.gz or zip archive from the following URLs:

Clinic Class
Thesis Class

As always, the very latest (development) versions are available from our Subversion repository, at

hmcclinic class: http://vetinari.math.hmc.edu/svn/latex/hmcmath/classes/hmcclinic/trunk
hmcthesis class: http://vetinari.math.hmc.edu/svn/latex/hmcmath/classes/hmcthesis/trunk>

As usual, if you have any questions or problems, please let me know.

Hex Back In Service

Claire Connelly — 2009-02-20T11:05:19-08:00

hex, a compute server operated by the mathematics department and the Quantitative Life Sciences Center, is now back in service.

I got the original machine back on Wednesday and have completed updates and reinstalled it in our machine room. All data from the loaner machine has been restored to the /scratch partition, which is current as of 2009 February 18.

Please report any problems or other issues to system@math.hmc.edu.

Continued Mirror Issues

Claire Connelly — 2009-02-16T12:04:36-08:00

Mixed up in all the issues with the main array (which runs off a dedicated array-controller card) was a failure of one of the hard drives in the software mirror supporting the OS. We saw a few minutes of downtime this morning as I identified and pulled the problem drive. Once I get the replacement drive, there will be a few more minutes downtime while I install the drive and get the mirrors synced up again.

Thanks for your patience.

Mirror Back In Service

Claire Connelly — 2009-02-12T09:27:53-08:00

I've now brought the mirror server, mirror.hmc.edu back online. The array checked out okay, which was good, but getting the machine back up was complicated by the Grub configuration on the OS disks somehow getting lost. Once I'd managed to get that working, and the machine actually booting consistently, I was able to fsck the file systems on the various mirror volumes.

Most of the mirrors were fine, but there was some corruption on the RPMforge mirror, which I cleaned up.

I then ran some resync jobs to get everything up to date. Most of those ran fine, but I wasn't able to get the CentOS mirror updated on that run (too many users on the server), and it was quite late, so I decided to just let the machine be overnight, and to let the morning syncs run. As those seemed to be in order, I restarted the web server and resumed serving mirrors this morning.

As ever, if you encounter any problems, please let me know.