02.04.2005 18:09

Broken Shell Startup Scripts

One of the MCM/ICM contest participants just brought a problem with the shell startup scripts to my attention. The basic problem was that there were no .tcshrc or .login files in the home directories for accounts created since mid-September, which, coincidentally, was when I upgraded our main server from Red Hat Linux 9 to CentOS.

The result was that new accounts weren't sourcing the global.tcshrc and global.login scripts, which meant that their PATHs and other important variables and aliases weren't being initialized properly.

I've fixed the problem. The longer term solution is to actually modify the default startup scripts on the machines, which is the ``right'' way to do things, and I will get around to doing that before too terribly long. I hope.

In the meantime, all should be back to normal. Remember, if you can't run standard software such as MATLAB, Maple, Java, and Acrobat Reader, please let me know. Making things work, and fixing them when they break, is why I'm here. But I don't use every tool available on the system, and I'm not always aware when things break.

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

01.19.2005 14:42

elijah and ramandu back!

To my amazement, New Egg came through incredibly quickly and elijah and ramandu are now back on line with shiny new video cards and readable screens. Enjoy!

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

01.18.2005 14:03

elijah and ramandu have bad video cards...

Both elijah and ramandu have bad video cards. As a result, they're pretty much unusable interactively until I can find replacements, get them ordered, installed, and configured. Sorry for the inconvenience.

You can help avoid equipment downtime in the future by actually reporting it!

Yes, it's true, now that my office is no longer inside the lab, I don't get into the lab as much these days. That means that I rely on you, the users of the Scientific Computing Lab, to let me know when something's a bit funky. If the machine is reachable on the network and responds to various network-oriented tests, I'll have little reason to assume it's not working fine. But you can tell me if its keyboard is sticky, or the mouse is wonky, or the video is all wavy, or some other problem that's only obvious from sitting directly in front of the machine is present. Please tell me. I won't get mad (unless you tell me you deliberately poured a soda into the keyboard to see what would happen -- please don't do that). And the sooner I know about the problem, the sooner I can try to get it fixed.


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

01.18.2005 12:32

Epidemiological Risks to Our Computational Infrastructure

Over a long break, students, staff, and faculty scatter around the country and the globe, visiting friends and family, and encountering new variants of diseases that they bring with them on their return.

Those of us who took our computers with us may well be exposing other computers at the college to similar risks. If your anti-virus software wasn't up to date before you left, plugging into dad's company's network, your brother's LAN party system, or your high-school friend's DSL line may have infected your machine with a virus or worm that you've brought back to share with everyone else at Mudd.

Now that you're back, take a minute to make sure that your anti-virus software is updated, and run a full scan on your machine. Make sure that there's nothing (unintentionally) weird going on with your machine.

You might not care what infects your machine, but your neighbors (and CIS) might.

Sophos Anti-Virus

If you don't already have anti-virus software on your machine, CIS provides Sophos anti-virus software for the Mudd community.

They have detailed instructions for installing it for Windows.

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

01.12.2005 13:33

New LaTeX Packages Added

I've added some additional LaTeX packages to the system for the creation of presentations. Beamer and FoilTeX allow you to create PowerPoint-like presentations using LaTeX, with transitions, backgrounds, templates, and so forth.

You should be able to use these packages by opening your document with the appropriate \documentclass command or by loading packages with \usepackage. If you need to look at the source code, you will find it under /shared/local/share/texmf/tex/latex. Documentation can be found under /shared/local/share/texmf/doc.

As usual, we welcome suggestions for LaTeX packages of general interest for shared installation -- if there's a LaTeX package that you find useful, let us know about it and we'll look into installing it so that everyone can take advantage of it!

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

12.19.2004 02:47

Systems Back...

The power finally came back on at about 12:30 AM, six-and-a-half hours after F&M's estimate, and eight-and-a-half hours after CIS's.

Most of the servers came back up fine, but the backup server was recalcitrant. I got it running manually, but will have to spend some more time looking into it when I get back.

Workstations should all be up and running normally; please let me know if you notice unusual behavior.

I fixed some wacky X configs in the lab and swapped one monitor for one of the ones that seemed to be bad -- looks like we may need to replace some video cards in some of the machines. Again, I'll look into it when I get back.

There are a few more details I'll need to attend to tomorrow. It's nearly 3:00 AM now, and I think I'll go to bed. Cheers.

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

12.15.2004 13:23

CVS Emacs Available for Play

For those of you who like to live dangerously, or at least like to dance around a bit near the edge, I have installed a recent (today's, actually) CVS GNU Emacs for you to play with.

CVS Emacs has some really cool features. Among them, it's prettier, with a GTK interface and a much better scrollbar. And it finally supports drag-and-drop, so you can drag a URL from Mozilla directly into an Emacs buffer. Other features I've run across include defaulting to the last search-and-replace operation with query-replace (M-%), some nice new AUC-TeX and RefTeX features, and a bunch of stuff related to MIME handling with MH-E that no one but me is likely to care about, but trust me, it's good stuff.

To give it a whirl, add


to your PATH with a command such as

setenv PATH /shared/local/emacs-cvs/bin:${PATH} (for {t,}csh)
or export PATH /shared/local/emacs-cvs/bin:${PATH} (for bash)
(Hardcore sh and ksh users presumably already know what they need to do.)

You can add those commands to your startup files (.tcshrc or .cshrc for tcsh or csh, respectively; .bashrc for bash; .profile for sh; etcetera).

I will rebuild the release periodically, and, because it's development code, it may break. If it does, you can revert to the old system Emacs by removing the CVS Emacs path from your path.

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

12.06.2004 23:06

Upcoming Power Outage

F & M has announced a power outage on Saturday, December 18, from 6:00 AM through 4:00 PM. Because of the length of this outage, the department's servers will be unavailble during this time period.

As a result, web services, along with e-mail, printing, and file services, will be unavailble. All workstations will be powered off.

I will be shutting down workstations located in the Scientific Computing and Clinic Labs the night before the outage. I will also shut down any faculty workstations left running at that time.

You can guarantee the integrity of your data by logging out of your workstations prior to 6:00 PM on Friday, December 17.

I will plan to be on campus Saturday evening to get servers and lab workstations running again. (Probably around 6:00 PM.)

Thanks for your cooperation.

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

11.30.2004 10:31

Change Your Passwords!

We have discovered a compromise made through a less-than-secure CGI script on the math cluster. The compromise was originally made in early September, and includes password information.

Please change your password immediately!

I am currently running cracking tools to locate especially vulnerable accounts; accounts with weak passwords will be locked and will require you to stop by my office (Olin B159) with photo ID to get your account unlocked and start with a new password.

Good passwords are

  • As long as possible -- 6 to 8 characters, minimum
  • Obscure -- don't use dates, names, or words found in a(ny) dictionary
  • Use a mix of upper and lower-case characters (A-Z, a-z), numbers (0-9), and symbols (!@#$%^&*()_+{}[]:;"'`~<>,./?|\)

Change your passwords using the passwd command on any math workstation.

If you need help generating an appropriate password, the mkpasswd command can generate strong passwords. Yes, they may look confusing, but type them a few times and you'll remember them.

Also, please be sure to let me know if you notice any strange activity, files, or directories in your account, or if you have problems logging in.

The CGI scripts responsible for the problem are being rewritten from scratch to make sure that they are secure.

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

11.29.2004 19:51

Security Update for PuTTY, WinSCP

A security hole that allows ssh servers to run arbitrary code on Windows machines connecting with ssh was discovered recently.

If you have a version of PuTTY older than version 0.56 or WinSCP older than version 3.7.1, you should upgrade immediately.

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

11.29.2004 14:21

Eudora Considered Harmful

Eudora is a terrible e-mail client.

I don't just mean that in an abstract sense. I'm not that fond of graphical MUAs in general -- remember, I use nmh, a slight update to an e-mail system invented by the RAND Corporation back in the seventies. But I did use Netscape's mail client for about a year when I was stuck running Mac OS 7.5.X and Mac OS 8 and survived okay. (Then I started running Linux on my Mac and went right back to MH.)

But I had to use Eudora at one of my previous jobs, and I hated it. Something about the whole interface grated with me, although I was never quite able to put my finger on it.

But now I'm having problems when I send mail to people using Eudora. My mail is totally RFC 2822 compliant -- it uses MIME, the right formats, the right headers, and so on. But Eudora doesn't like it. Eudora thinks that MIME parts are attachments. And if it doesn't recognize a particular kind of attachment, it whines to the user, warning them about the dangers of opening attachments.

In contrast, the same message opened up in a more reasonable, but similarly pretty, MUA, such as Thunderbird appears exactly as you'd expect -- the MIME parts are displayed inline when they should be (such as when they're plain text) and appear as clickable icons otherwise.

Oh, yes, and then there's the fact that Thunderbird is free, and comes with no ads, whereas the college has people using the ad-sponsored version of Eudora (???!!!), so there are issues with the ads being hidden.

Also, Thunderbird leaves the message alone -- messages in a mailbox are just as they were received. Eudora, however, rewrites the message -- it splits out attachments as separate files (stored separately) and rewrites the message into a sort of pseudo-HTML, with links to the attachment files. So good luck moving your mail from Eudora to another MUA without some hoop jumping.


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

11.18.2004 17:55


So NanoBlogger appears to be somewhat similar to the weblog script I wrote for myself, only it's written in the Bourne Again Shell (bash) rather than Perl, and has more of an interface. (My script expects you to format the entries properly and save them in the right place -- all it does is format them.)

I think I'll try using this tool for a while. It might be a nice way to get some notes up and organized, as well as keep a bit of track of what I've been up to. On the other hand, it might be a big annoyance.

It might even inspire me to get off my butt and freshen up my own blog script....

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

11.18.2004 17:49

Firefox 1.0

Much to my surprise, Firefox 1.0 seems to work on my machine. I've been having problems getting any recent version of Mozilla itself to work -- rebuilding packages from Fedora has resulted in mysterious ``nothing happens'' errors, which have left me without a fully functional web browser, which is not a good thing.

But Mozilla's prepackaged Firefox seems to work fine, so I'm happy for now!

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

2004 Apr 29 1:25 PM

Added CD Burner to SciCompLab

As the end of the semester rapidly approaches, you may be considering creating more portable archives of your files (especially if you're graduating -- remember that accounts of graduating students expire on July 1!)

Happily, I bought and installed a 52X CD-ROM burner in tumnus, one of the machines in the scientific computing lab. Anyone sitting at the console of this machine should be able to create and burn CDs using gtoaster or xcdroast.

See Burning CDs for more information on how to burn CDs with this drive.

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

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 shell.math.hmc.edu 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 Dec 30 12:00 PM

Upgrade Status

Printing is back. Tape backup system restored. Spamassassin running again. Other backend services restored/adjusted.

Lab and faculty machines are now rebooted. If you have problems reaching them, with file access, or with anything else that doesn't seem to work the way it used to, please let me know ASAP. Thanks.

Please remember that during the remainder of the break access may still be suspended temporarily while I do minor maintenance. Significant service breaks will be announced here and by e-mail at least a day before they happen.

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

2003 Dec 29 10:00 PM

Upgrade Status

Incoming and outgoing mail working. Authentication working. UPS working. NFS working. Time to go home. More testing and configuration tomorrow.

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

2003 Dec 29 8:15 PM

Upgrade Status

Packages installed. Rebooting.

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

2003 Dec 29 8:10 PM

Upgrade Status

Partitioning and configuration complete; installing packages.

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

2003 Dec 29 7:55 PM

Upgrade Status

Start OS install.

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

2003 Dec 29 7:15 PM

Upgrade Status

Begin installing BIOS updates.

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

2003 Dec 29 6:45 PM

Upgrade Status

fscking /home partitions. (Machine had been up for 160 days.)

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

2003 Dec 29 6:30 PM

Upgrade Status

Backups complete.

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

2003 Dec 29 5:00 PM

Upgrade Status

Services suspended. Final backups underway.

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

2003 Dec 29 1:00 PM

Upgrade Status

Temporarily restored mail and printing service while prebackup copies complete.

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

2003 Dec 29 11:00 AM

Upgrade Status

Many services have been shutdown in preparation for the final backups. These services include:

  • Log in
  • Electronic mail
  • Printing

Mail should be picked up by an alternate server and delivered when our main server is up again.

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

2004 Dec 15 12:00 PM

Server Upgrade

I will be performing an upgrade of the operating system on the department's main server, esme, on December 29, 2003. The upgrade itself should be fairly straightforward, but I am reserving the following two days for reconfiguring services and testing. Access to the department's systems will be undependable during this time period.

Services affected will include: file service (home directories), remote login, e-mail, and printing. I will be shutting down nonessential workstation systems during the outage.

I plan to temporarily relocate the core of the department's website to the web server, so access to the website should continue during the service outage (with the exception of personal websites located in ~/public_html directories).

Because the web server will remain available, you will be able to check in on progress on the computing support page, <http://www.math.hmc.edu/computing/> (i.e., right here).

I will be performing other work during the break that may make access unreliable or impossible. I will send out mail in advance of such work, but it's safe to assume that if you can't log in to a workstation (directly or remotely), it's work-related. Feel free to send me e-mail if an outage lasts for longer than a couple of hours (or call me, if e-mail is affected).

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

2003 Jun 18 3:23 PM

New OpenOffice; StarOffice Going Away

I've installed version of OpenOffice on the department's server. If you're already an OpenOffice user, you'll find that starting one of its programs will cause the installer to start. You'll need to go through the same steps you went through when you first installed OpenOffice -- for a refresher, be sure to check our OpenOffice installation page.

Meanwhile, I'm working on cleaning up some older software. OpenOffice is an improved version of StarOffice, which we currently have installed, so StarOffice is on the chopping block. If you use StarOffice (soffice) and haven't installed OpenOffice, please install OpenOffice and use that instead. I will be removing StarOffice at the end of June.

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

2003 Jun 14 12:00 PM

Memory Upgrades for SciCompLab

We have doubled the RAM in the OptiPlex GX400 and Precision Workstation machines in the Scientific Computing Lab to 512 MB each. The increase should give users a bit more headroom for large computational jobs, and might also make some other things a bit more zippy.

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

2003 May 21 4:46 PM

Power Outage

Mathematics department computer systems will be unavailable from roughly 10:00 PM Saturday, 2003 May 24 through noon on Sunday, 2003 May 25 while Southern California Edison does some work that requires shutting off power to the Claremont Colleges campuses.

Please be sure to log out of all department computers before 10:00 PM on Saturday. I will be logging in remotely to shut down all Linux workstations at that time.

Please shut down any Windows computers, printers, or other electrical equipment you have in your office that might be damaged by a power outage.

Systems may be available after 7:00 AM on Sunday when the Colleges' generators start running, depending on whether the servers are still running at that time. You can check server status by

  • sshing to shell.math.hmc.edu. If your home directory is available, things are working.
  • Checking the department's website. If it loads, the servers are up.

I will be in around 11:00 AM on Sunday to start any servers that were powered down during the power outage.

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

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

2003 Apr 28 11:23 AM

Spamassassin Installed

I have installed Spamassassin, a spam-filtering package, on the department's mail server. I've added some information about SpamAssassin to the e-mail section of the department'ssupport area.

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

2003 Apr 28 11:22 AM

Accounts Expiring

Accounts for Harvey Mudd students who are graduating in 2003 will expire on 2003 July 1, as will all accounts belonging to non-Mudd students. Please be sure to copy anything that you want to keep to some other location before July 1.

Guest accounts and student accounts whose expirations have been extended will also expire on 2003 July 1.

If you need access to your account after July 1, brief access will be granted on a case-by-case basis. Password resets will require you to see the systems administrator in person, with a photo ID.

If you need longer-term access, please talk with a faculty member about getting an extension. You should fill out another account-request form (PDF) and obtain the necessary signatures. Renewed guest accounts will be good until 2004 July 31.

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

2002 Oct 1 12:19 PM

Scientific Computing Lab Upgraded

The machines in the Scientific Computing Lab have been upgraded to Red Hat Linux 7.3. As a result, there are several changes that will affect your interaction with the systems:

  • KDE is now available as a desktop choice. You can choose the KDE desktop by selecting it from the Session menu on the GDM login panel.
  • The printing backend has changed from LPRng to CUPS. CUPS is more flexible and powerful than LPRng, and is being adopted by several distributions (including Red Hat) and other operating systems (such as Mac OS X) as their default printing backend.
  • The XPP client has been added. Use xpp anywhere you would ordinarily use lpr, and you'll get a graphical print dialog similar to the ones you get with Mac OS or Windows.
  • dvips behavior has changed so that dvips, by default, produces a PostScript file rather than dumping output to your default printer.

    To get the old behavior, edit your ~/.tcshrc and add the following line:

    alias dvipsp 'dvips -o|lpr'

  • The Enlightenment window manager is no longer available.
  • The Evolution mail/calendar client is available.

There are many other changes -- subtle and otherwise -- that I can't easily summarize here. For more information, you may want to read Red Hat's release notes for 7.3.

If you notice any problems, please let me know by sending mail to system@math.hmc.edu.

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

2002 Sep 14 10:59 AM

Mail Changes

Because the server has changed, your e-mail client configuration may no longer work. pop.math.hmc.edu provides both POP and IMAP service. (SSL-protected access is in the works.)

The outgoing (SMTP) mail server is esme.math.hmc.edu. However, esme will only accept mail sent from the department's subnet. If you're planning to use a dialup connection, you should use your Internet server provider's SMTP server. If your ISP is Mudd, through CIS, you should use CIS's mail server, thuban.ac.hmc.edu. You should also use thuban if you're using a wireless card.

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

2002 Sep 14 10:58 AM

New Server

One of my major projects this summer was to research, obtain, and install a new server to replace the department's file server. The new machine was brought on line in mid-August, and provides considerably more disk space to the user community (which doesn't mean you should go crazy!).

The department's old server will be rebuilt so that it can replace the current web server (and probably provide additional services). The web server will probably become a remote-access server.

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

New Machine-Naming Scheme

You may notice some machines in the cluster or Clinic lab with names you don't recognize. New machines are now named after characters from Terry Pratchett's ``Discworld'' series of novels. There are currently more than twenty books set in the Discworld, so we should have a good stock of names available.

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