Wed Jun 4 15:06:43 PDT 2008

Systems Work: Saturday, June 7, and Sunday, June 8


I will be doing some systems work this weekend, June 7--8.

Work will probably begin around 11:00 AM on Saturday, June 7, and will continue for several hours. If necessary, additional work may be done on Sunday, June 8, within a similar block of time.

What Will Be Affected

The work will disrupt most of our networked services, including e-mail, file service, interactive sessions, and the web server for periods of several minutes to an hour over the course of the work.

I also want to make sure that all of our Macs are running the latest security updates, so will be updating these machines during this time period as well.

What You Should Do

If you're using a Mac or Linux system that mounts file systems from our servers, before you leave on Friday evening,

  • Save all open files;
  • Close all applications;
  • Log out;
  • Leave your machine running.


This work is necessary for us to ensure the security and improve the stability of the overall system. In particular, I am hoping that ongoing issues with our web server will be resolved as a result of this work.

I will do my best to keep as much of the system functional as possible for as much of the time as I can, but there will still be some outages.

Additional Background

Last semester we had some serious issues with interactions between the NFS support on our new file server and on our workstations and older servers, exacerbated by the HVAC failure. I was able to stabilize things, but we still see some flaky behavior (especially From the web server, which needs to be rebooted periodically).

On the Linux server side, I plan to update to the latest kernel releases and do some experimentation to see if everything will work together happily. I will need to reboot various servers and workstations an arbitrary number of times to explore all the possible interactions.

For Macs, I will install the latest updates, most of which require the machines to be rebooted. As Tiger (Mac OS X 10.4) has problems when an NFS server disappears and reappears, these machines would need to be rebooted anyway.

Comments/Problems/Other Issues

As usual, if there are problems with the scheduling of this work, requests or any other comments, please let me know.

Updates/Status Reports

As usual, updates on the status of the systems and progress reports will be posted to the ``sysblog'', on our web server at>

Thanks for your cooperation!

Posted by Claire Connelly | Permalink | Categories: Mail, News, System Maintenance, Linux, Macintosh, Website, Amber

Thu Oct 12 13:39:23 PDT 2006

Package Requirement for Clinic and Thesis Classes

If you're planning on working on your thesis or Clinic report using systems not run by the department, you will need to download the cmtty package to use these classes.

The cmtty package specifies Computer Modern Typewriter as the default monospace typeface when typesetting theses or Clinic reports. Computer Modern Typewriter is more compact and better formed than Courier, which is the default monospace font with many of LaTeX's font packages.

The package is licensed under the GNU General Public License, and you are welcome to use it for any of your own projects under that license.

Posted by Claire Connelly | Permalink | Categories: News, LaTeX, Website

Mon Jan 23 12:22:50 PST 2006

PHP Support Ends

As announced in November, 2005, support for the use of PHP, a popular, but problematic, web-programming language, has now ceased.

Any pages that relied on the Apache PHP module being available will no longer render properly.

If the lack of PHP poses a problem for you, please let me know and we can look into alternatives that pose less of a security risk for our system.

Posted by Claire Connelly | Permalink | Categories: System Maintenance, Website

Mon Jan 23 12:12:38 PST 2006

Amber Cluster Documentation Now Available

I have converted and updated the old Beowulf cluster documentation to match the mathematics and computer-science departments' current cluster, Amber.

I have not yet been able to test and verify all of the example code provided on the old site, but the code that does work properly is included, along with links to upstream documentation.

Please note the new policies and account-request process. Amber accounts require a standard math-cluster account (as Amber nodes are, basically, standard math cluster nodes with some additional software).

If you have comments or questions, please send them to beowulf at

Posted by Claire Connelly | Permalink | Categories: Website, Amber

11.14.2005 10:25

End of Support for PHP

I am in the process of converting the only system pages that make use of PHP to a form that does not use PHP. Once that conversion is complete (probably by the end of the day on Monday, 2005 November 14), I will be removing all support for the use of PHP on the department's web server(s).

PHP is a server-side programming language that allows developers to write web pages with computer code embedded in them. It is widely used in the hobbyist market for writing web log, bulletin board, and forum-type applications. Unfortunately, PHP appears to be insecure by design, as numerous security holes continue to be found in the core PHP Apache module even though the system is about ten years old and has undergone several major rewrites and reimplementations.

Note that I am not speaking of insecure code written in PHP -- such buggy code is trivial to produce in any language. But we are still seeing numerous flaws in the Apache module that implements the core language itself. Such flaws can open up the entire server to attack, and the risks are greater than the benefits.

Posted by Claire Connelly | Permalink | Categories: System Maintenance, Website

09.19.2005 14:22

Sample Thesis/Clinic Available

The revamped combined sample thesis and Clinic report is now available for download and use.

This document provides you with

  • A typeset example showing various features provided by LaTeX and the hmcthesis or hmcclinic classes
  • An exemplary document to show you what ``good'' LaTeX code should look like

The sample document can be downloaded from, which is the new canonical home for this material. In addition to links to download the files in ZIP or tar.gz format, there are basic instructions on how to typeset the sample files to generate a sample thesis, sample clinic report, or both.

Remember, if you're working on your TeX system, you'll also need to be sure that you have the latest version of the hmcthesis or hmcclinic class files. The class files can be found by going to and following the links to the appropriate pages.

Posted by Claire Connelly | Permalink | Categories: LaTeX, Website

08.16.2005 17:21

LaTeX Class for Mathematics Homework Now Available

Eric Malm '05 put together a nice LaTeX class (hmcpset.cls) for typesetting math homework assignments. The class, along with a template (hw-template.tex) and a sample document (hw-example.tex) is available for your use and enjoyment.

The class file, which helps you typeset homework assignments according to the department's homework guidelines is installed in the shared TEXMF tree at /shared/local/share/texmf/tex/latex/hmcpset/ so it can be used from any department Linux workstation.

If you want to use the class and template on your own TeX system, it can be downloaded from the new home for departmental LaTeX classes.

I am taking over maintenance and development of the class from Eric, so if you have any changes you'd like to see made or bugs fixed, please let me know.

Posted by Claire Connelly | Permalink | Categories: LaTeX, Website

08.02.2005 17:38

New Home for Departmental LaTeX Classes

I have created a new home for the department's LaTeX classes: You will find links to download these classes, along with information about using and customizing them.

I will remove or edit pages referring to older versions of this material so that we can, finally, have a single place to send people to find the most up-to-date versions of these files.

At the moment, there are pages for the hmcclinic, hmcposter, and hmcthesis classes. More will be added when the department adds more classes. (I will be installing the homework class that Eric Malm put together soon.).

As always, the latest version of this code is also available in /shared/local/share/texmf on the math cluster machines. You should be able to use any of these classes without having to do anything special beyond specifying them in your \documentclass command in the preamble of your document.

Posted by Claire Connelly | Permalink | Categories: LaTeX, Website

06.14.2005 16:45

Fedora Core 4 i386 and x86_64 Installers Available

I've downloaded the install images for the i386 and x86_64 architectures for Fedora Core 4. They're available from and, respectively.

Posted by C.M. Connelly | Permalink | Categories: Website

02.21.2005 13:10

RHEL 4 Released; CentOS 4 Imminent

Red Hat released version 4 of their Red Hat Enterprise Linux products last week. RHEL 4 is based on Fedora Core, Red Hat's ``free'' distribution, and includes features such as GNOME 2.8, SELinux, and the 2.6 Linux kernel.

RHEL 4 also drops the Mozilla suite in favor of Firefox and Thunderbird, and changes a whole bunch of other stuff in ways I haven't yet discovered.

CentOS 4 will be coming out soon, incorporating these changes.

I have been running a release candidate of CentOS 4 on a machine in my office, and thus far my impression is that it has many shiny improvements over CentOS 3, but that the changes may cause some issues if they aren't handled carefully. I expect to install CentOS 4 on my workstation and run it for a while before making a decision about rolling the new version of the OS out onto desktops. (Among other things, there's a fair amount of locally built and deployed software that will need to be rebuilt, updated, or replaced before a rollout can happen.)

Exactly when we upgrade workstations to CentOS 4 is unclear at this time, although it's likely that the upgrade will happen this summer at the latest, and probably sooner than that for lab workstations.

I may update the Amber cluster sooner, to see whether the changes affect some problems that have been seen there. Our servers will remain on CentOS 3 until I can see clear evidence that updating them would add enough valuable features to be worthwhile.

As usual, if you have any questions or comments, please feel free to write to me at

Posted by C.M. Connelly | Permalink | Categories: System Maintenance, Linux, Website

2004 Jan 12 4:00 PM

Web Server Changes

We've made the switch to our new web server. The new server is configured to work pretty much like the old one, with the major exception being that users can no longer log onto the server directly. Changes made in your personal web space (~/public_html) will take effect immediately; changes to the ``core'' web space (/home/www) will not take effect until that material is synced with the live website.

Until I get a handle on how frequently automated updates need to happen, please notify me (or the webmaster alias) when you make a change that requires the core site to be updated.

CGI Problems

We are experiencing some problems with CGI scripts pointing to nonexistent binaries (e.g., /usr/local/bin/perl) and compiled programs that do not work on the new server.

I've created a link for perl, but the compiled programs can only be fixed by being recompiled. Please contact me with the location of the source so that I can rebuild these programs.

DNS Changes

Along with the web server switchover and the retirement of naomi, we have made some changes to the alias. Now, instead of pointing to naomi, shell points, round-robin, at the machines in the lab. Thus connecting to shell will give you one machine; a second connection might give you a second machine; a third connection a third machine; and so on. (Depending on your OS's caching policy.)

A nasty side effect is that you may see the WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! warnings from ssh on each attempted connection. This issue can be solved by including the keys for all the machines shell points to in your ~/.ssh/known_hosts file. Details on the fix, as well as the file you'll need, are available on our security page.

The ssh fingerprint information on that page has also been updated.

Posted by C.M. Connelly | Permalink | Categories: System Maintenance, Website

2003 Nov 4 5:02 PM

New Support Material: Mac OS X & Windows

Added some information on using our systems with Mac OS X. There's a similar Windows page, as well.

Posted by C.M. Connelly | Permalink | Categories: Macintosh, Website

2003 May 2 11:15 AM

OpenOffice Installation Instructions

OpenOffice installation instructions available. If you have ideas about other applications that need documentation, let me know.

Posted by C.M. Connelly | Permalink | Categories: System Maintenance, Linux, Website

2002 Oct 1 12:20 PM

TeX and LaTeX Notes

We now have some notes on TeX and LaTeX resources available.

Posted by C.M. Connelly | Permalink | Categories: LaTeX, Website