Mon Nov 17 12:04:33 PST 2008

More on hex

I have pulled out the CPU expansion board from hex and sent it back to the vendor, who is going to try to get a replacement from the manufacturer. In the meantime, hex is running with eight cores (four CPUs) and 16 GB of RAM, and it seems to be stable.

Please let me know about any problems, and check back here for updates.

Posted by Claire Connelly | Permalink | Categories: News, System Maintenance, Amber

Wed Jun 4 17:00:03 PDT 2008

CTAN and CentOS Mirrors Moved off

I have moved the current CentOS and CTAN mirrors off and on to our new mirror server,

The new base URLs for these mirrors are


For the time being, I have set up redirects so that attempts to retrieve data from URLs pointing to yum will automatically be redirected to

At some point the machine that the old mirror server runs on may be retired or repurposed, so if you're using our CentOS mirror to update your machines or our CTAN mirror to download TeX-related material, I would encourage you to change the URLs in your YUM configuration files to point to the new location.

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

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

Sat Jul 7 14:37:07 PDT 2007

Fedora Mirror Changes

We have stopped mirroring the Fedora development tree until we can add more disk space to our mirror system.

With the release of Fedora 7 (which we are also not mirroring), the Fedora Project merged the Extras repository into what was "Core", dramatically increasing the size of the distribution. As a result, Fedora development also picked up all the packages from Extras.

While having a larger selection of packages available in Fedora is generally a good thing, our primary operating system is still CentOS, and with the release of CentOS 5, disk space was starting to get a bit tight. With Fedora's merger of Extras, we can no longer maintain an active mirror of Fedora until we obtain additional resources.

Note that there are various possibilities in the works. There is a move to create a Claremont-Colleges-wide Linux Users Group, which might pick up some of the mirroring. The mathematics department may be making some new hardware acquisitions that will allow us to shuffle some things around and give us additional disk space. And I'm still hoping to get the college on board with the idea of providing some services, including public mirrors, to the FOSS community.

Keep an eye on this blog for more information about all these possibilities, and about changes to the mirror status.

Posted by Claire Connelly | Permalink | Categories: mirror, News

Sat Jul 7 13:36:41 PDT 2007

Reboot Complete

As anticipated, the system ran fsck to check the disks on most of the home-directory partitions, taking on the order of half an hour to complete.

The partitions came up clean and the system rebooted. The tape drive is working again, and I am flushing the previous day's backups to tape.

We now resume normal service. However, if you come across any problems, please let us know by sending e-mail to

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

Fri Jul 6 17:45:15 PDT 2007

System Outage, Saturday, 2007 July 7, 1:00 PM

The Facts

The department's main server will be rebooted Saturday afternoon to clear a stuck IO process.

Services affected will include

  • Logins on department Linux and Macintosh machines
  • File services to Linux and Macintosh machines
  • Print services for Linux
  • E-Mail (incoming and outgoing)
  • Web service for personal accounts (~user URLs)

Length of Outage: Approximately one hour.

A Bit More Detail

The SCSI driver for our tape drive is stuck in a low-level IO loop that can't be interrupted. As we can't use the tape drive until this process is cleared, and the only way to clear it is by rebooting, we need to reboot the server.

The minimum time for a reboot of this system is around ten minutes based on various hardware tests and initializations. The actual reboot will probably take longer, especially if the system needs to run checks on disk partitions, in which case the reboot time could extend to around forty minutes or so. Rebooting can also reveal unforeseen consequences of some configuration changes, which can add additional delays before all services are available.

I will send messages to all logged-in users about ten minutes before I start the reboot. If you happen to log in shortly after the reboot, don't expect that the system will remain up unless the department's system blog has been updated with a message stating that the system is back up and maintenance is complete.

As usual, we apologize for any inconvenience that this downtime will impose, but occasional maintenance is required to keep the system running.

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

Fri Apr 13 17:23:00 PDT 2007

End of Life for Fedora Legacy (and Our Mirror of It)

As of February 9th, 2007, the Fedora Legacy Project, which provided security updates for versions of Red Hat Linux and Fedora Core Linux that were no longer being supported by Red Hat itself, shut down operations.

As a result, no updates have been forthcoming from that time onwards. In the interest of freeing up mirror space for active projects, we have stopped mirroring the files from this project, and removed them from our mirror server.

If you are still using one of the operating systems that the Fedora Legacy Project was supporting, we strongly urge you to upgrade your systems to a more recent -- and supported -- operating system.

Depending on your needs, we suggest that you consider CentOS, a rebuild of Red Hat's Enterprise Linux product, Debian GNU/Linux, or Fedora Core Linux. All three OSs have had recent releases or will release soon (5 for CentOS; 4 for Debian; 7 is due soon from Fedora).

For server systems, we recommend CentOS or Debian. For desktop systems that have to work, CentOS or Debian are also good choices. For more experimental systems, Debian or Fedora are your best bets. Installing Debian and switching to the testing or unstable "releases" will give you access to very recent software, with different levels of potential bugginess. For Fedora, you can run the most recent release or run the development version.

All of the mentioned versions of these operating-system distributions are available on our mirror server.

Posted by Claire Connelly | Permalink | Categories: mirror, News

Sat Jan 20 18:05:56 PST 2007

Repairs Complete

I have completed the repairs to our primary server, and everything should be working as usual. If not, please let me know!


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

Fri Jan 19 16:10:42 PST 2007

System Offline for Maintenance Saturday, 2007 January 20

We have a hardware problem with our main server, esme, which requires me to take the machine offline in order to replace some parts.

I will shut the server down at 2:00 PM tomorrow, Saturday, January 20. The work will either take about twenty minutes or will require much more extensive part swapping, which could take several hours. Please check this blog (which will remain available) for updates and notification about everything being back on line.

Because the problem is with our primary server, e-mail, logins, and printing will not be available during the outage. Home directories will also not be available, so class websites hosted out of professors' home directories (which is most of them) will also not be available during the outage. Our web server is a separate machine and will remain available, with all content not kept in home directories.

Sorry for the inconvenience and short notice; I've only just received the necessary parts.


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

Tue Jan 16 16:32:14 PST 2007

MATLAB 2007a Preview Available

I have installed a preview release of MATLAB R2007a on our system for testing. The official release of this software should occur in March, 2007.

R2007a includes a number of bug fixes and some new features. Release notes with more detailed information are available within the help files for this release; run MATLAB, then choose Help->MATLAB Help; then click on Release Notes for MATLAB 2007a.

Testing R2007a

You can run the R2007a release by typing


at a shell prompt. The preview release includes all toolboxes, so there isn't a separate installation for the research and classroom licenses.

Running the Test Version All the Time

From now on, I expect that we will be maintaining links to a testing version of MATLAB at all times. When a newer version is not available, the links will simply point to the current release.

If you want to run the most cutting edge version of MATLAB that we have available, you can add one of the testing paths to your PATH environment variable. I recommend that you put the testing path near the head of your PATH so that it isn't overridden by the older version that is set automatically by our shell defaults.

The correct magic incantations to add these paths are

  • For csh and variants: % setenv PATH /shared/local/matlab-testing/bin:$PATH
  • For Bourne shell variants: set PATH="/shared/local/matlab-testing/bin:$PATH"; export PATH
  • For bash, zsh, and newer shells, you may be able to do export PATH="/shared/local/matlab-testing/bin:$PATH"

Our Schedule

We are dependent on CIS updating their license servers with the licenses for new releases, so exactly when we'll be able to move to the official release is a bit up in the air. In recent times, I've been able to get them to install the newer licenses in parallel with the older licenses so that we can run the newest release but their labs with older installation don't need to be updated.


Posted by Claire Connelly | Permalink | Categories: Software, News

Thu Nov 16 11:40:34 PST 2006

Wolfram Workbench Available

I have installed Wolfram Workbench, an IDE for working with Mathematica projects on our Linux cluster.

If /shared/local/bin is in your PATH (it is by default), the program can be run by typing WolframWorkbench at a shell prompt.


Posted by Claire Connelly | Permalink | Categories: Software, News

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

Tue Jan 10 11:36:46 PST 2006

Stevenote: New Macbook, iMac, iLife, iWork, Mac OS X 10.4.4

Apple's CEO, Steve Jobs, gave the keynote at MacWorld 2006 this morning. The highlights of his presentation were

  • The iMac being updated with the new Intel Core Duo processor; it's the same machine in every respect except for the processor. According to Jobs, the top of the line iMac, with a 2 GHz Intel processor, is twice as fast as the 2 GHz PowerPC G5 version. Now sells for $1499 educational (base price).
  • New versions of iLife and iWork. It seems like the iWork apps (Pages and Keynote) were updated a bit, but there are no new apps. The iLife bundle has updates to iMovie, iDVD, and GarageBand (including a new Podcast Studio for making your own podcasts). It also has a brand new app, iWeb, which allows you to create and maintain websites. As this app is brand new, there's no feedback on what sorts of HTML it produces, but we can hope that Apple has done the right thing and is creating clean, valid XHTML or XML and valid CSS. Both of these packages are $79.
  • Of most interest, as usual, was Jobs's ``one more thing'' -- a new laptop computer using the Intel Core Duo processor, the MacBook Pro. This computer is essentially a drop-in replacement of the existing 15" G4 PowerBook -- it has the same size and weight as the PowerPC version. But it runs four times faster than the top of the line PowerPC version, and presumably also picks up some advantages in terms of battery life and heat production by using Intel's mobile CPUs, which are optimized to reduce power use and heat production. The MacBook Pro also features a built-in iSight camera and microphone (like the iMacs) and has a clever new power connector that makes it slightly less likely that someone will trip over your power cord and yank your machine off a table or desk. The MacBook Pro has two models, both with the new 15.4" screens with the same resolution as the older 17" PowerBook. The 1.67 GHz Core Duo model starts at $1799 educational; the 1.83 GHz machine starts at $2299 educational.
  • Finally, Mac OS X 10.4.4 was announced for release via Software Update. The new OS version includes all the support necessary for the new Intel machines, and throws in some bug fixes and new widgets for those of with older machines.

For anyone disappointed that they missed out on getting a new Intel-based machine in the most recent round of purchases, let me point out that as the processor has changed, older PowerPC software has to run through an emulator that Apple calls Rosetta. Rosetta is meant to be reasonably fast (especially with the newer, faster processors), but you would still see a significant performance hit when running older software.

Apple's own software is now shipping as ``universal binaries'', as is software produced by various smaller companies. Many of the larger players, however, such as Microsoft and Adobe, have yet to ship universal versions of their products. Even if they started shipping these today, they would probably update the very newest versions of their software -- older versions that work just fine would not be updated. The same issues apply for much of the software provided by CIS, most of which is not the very latest-and-greatest version.

My personal comments on the MacBook Pro: It looks very, very cool. I was very interested in the improved screens on the last refresh, in which the 15" and 17" PowerBooks had dramatic increases in the number of pixels that they could display (the 15" model ended up with the same number of pixels the old 17" PowerBook had; the new 17" PowerBook had the same number of pixels as Apple's 20" desktop display).

But the 15" PowerBook and MacBook Pro are still pretty big machines. Both weigh 5.6 pounds, a full pound more than the 12" model. If you're a big guy, 5.6 pounds isn't that much, but if you're me, 5.6 pounds is a lot, especially combined with the rest of the stuff I end up carrying around. I think I'll have to see it before I'm completely sold on it, and I'm hoping that Apple will figure out that there are a lot of people who need or want performance but who don't need a huge screen and the extra weight that brings you. (Hey, I plug my 12" laptop into a 20" monitor when I need a bigger screen -- it works great.)

Also, beware the lure of the first generation of Apple products. Traditionally, Apple has been on the cutting edge with the coolest new gadgets. Unfortunately, also traditionally, these first-generation models have almost always had various issues that affect their performance in some way. The sound advice is to let other people be the first adopters, and pick up new stuff after Apple's had a chance to work out some of the bugs.

That said, four times faster sounds awfully good.... ;-)

Posted by Claire Connelly | Permalink | Categories: News, Macintosh

11.14.2005 09:29

National Security Letters and You

You may not be aware of the FBI's increasing use of "National Security Letters" to obtain information about the activities of people that they believe -- for whatever reason -- to be "of interest".

These letters instruct recipients to turn over requested information to the FBI without consultation with a lawyer or their employers. If I were to receive such a letter, anything that you might have stored on departmental computer systems could be made available to the FBI -- that includes any files in your home directory, electronic mail, the contents of your web browser's cache, hits on your website -- anything I have access to. Which means anything on the department's systems.

I encourage you to not place me in the position of being able to turn anything over should I be requested to do so. If you have potentially controversial material you would like to share on the web, want to have a weblog where you criticize the U.S. government, or even send e-mail back and forth with others who might be in some way "suspicious", you might want to consider using another Internet site to do so.

Not, mind you, that you'll be safer there -- if you do things that attract government attention, the FBI can just as easily send a National Security Letter requesting information to your off-campus ISP and get the information from them.

For more information about National Security Letters and their use by the government, I would encourage you to check out the ACLU's page on NSLs.

Consider using encryption and anonymizers for your e-mail and web surfing.

You might also want to share your opinions on the U.S.A. P.A.T.R.I.O.T. act and the use of National Security Letters with your U.S. Senators and Congressional Representatives -- for the Claremont area, they are Senator Barbara Boxer (D-CA) and Senator Dianne Feinstein (D-CA) and Congressman David Dreier (R-CA). You can use the tools provided by the Senate and the House to find senators and representatives for your home town if you're not registered to vote in Claremont or if you'd like to communicate with the people who represent your home town as well.

Posted by Claire Connelly | Permalink | Categories: News, System Policy

06.06.2005 11:16

Hell Freezes Over: Mac OS to Run on Intel

Well, it's official. Apple has announced that they will start shipping Intel-based Macintoshes starting next year.

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

03.28.2005 12:28 Article on CentOS

CNet's's Stephen Shankland has an article on RHEL rebuilds. (I'm quoted!)

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

03.11.2005 19:49

Judicial Invasion!

Most students have probably left for spring break by now, but if you still happen to be around, you should be aware that a number of rooms are being used by the MCM and ICM contest judges.

The rooms include

  • The Scientific-Computing Lab (Olin B159)
  • The Math Clinic lab (Beckman B115)
  • The Math Library (Olin B161)
  • Beckman B134 (classroom near the soda machine)

Please let the judges work in peace, and avoid those rooms until Monday.

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

02.04.2005 18:01

MCM/ICM Contest Underway

Once again, Mudders are hard at work wrestling with the questions posed as part of the Mathematical Contest in Modeling (MCM) and the Interdisciplinary Contest in Modeling (ICM).

This year's teams are working in the Scientific-Computing Laboratory (Olin B145), the Mathematics Library (Olin B161), the Mathematics Clinic Lab (Beckman B115), and the CS Conference Room (Beckman B100). Because of the intensity of the competition, participants tend to spend the entire weekend camped out in these rooms, working through the night, catching naps at odd hours, leaving only to grab some books or photocopy journal articles in the library, pay for the delivery of food, or use the bathroom.

To accomodate them, these rooms are reserved for their exclusive use from the start of the competition, 5:00 PM on Thursday, 2003 February 3, to its desperate, exhausting end, at 5:00 PM on Monday, 2003 February 7.

Please respect their insanity for agreeing to participate in the competition, and salute their efforts to keep Mudd ranking high in the competition's results by staying out of those rooms and not making a lot of noise nearby.

Also, as far as computer resources go, don't forget that someone sitting in front of a computer has priority in its use. So please don't start any computer-intensive processes on machines in the Scientific-Computing or Clinic Labs while the contest is going on.

Thanks for your cooperation!

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

01.26.2005 10:37

PracTeX Journal Launched

The TeX Users Group has launched a new, online journal, PracTeX, devoted to practical, day-to-day use of LaTeX and TeX.

The premiere issue includes articles on using CTAN, creating presentations, documents, and posters from the same LaTeX source, tweaking LaTeX, and a q&a column, Ask Nelly, along with lots of other material.

PracTeX looks like a useful resource for beginners and oldtimers, alike.

While I'm at it, I should mention that we have a CTAN mirror here at Mudd. It's currently located at I'm not currently updating it regularly, but if there's more interest, I can start doing so.

yum also houses the math department's mirrors of CentOS (the Red Hat Enterprise Linux rebuild distribution that we use). Fedora, Red Hat's next generation Linux distribution, and the Fedora Legacy support packages for older Red Hat distributions (we will probably stop mirroring these soon).

All of these mirrors are available for use within CUC. I'm interested in having the CentOS and CTAN mirrors be available to the public, but doing that right would require better hardware than I can currently devote to the mirror right now, I think, as well as an okay from CIS for the bandwidth.

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

01.11.2005 17:15

New Apple Toys

Lots of new toys from Apple today, including the Mac mini, a 3 lb. baby Macintosh for around $500. We already have a full size Mac at home, two Powerbooks, and one iBook, and I'm still tempted by the idea of having one of these for the living room. It looks really cute.

For those of you who've been tempted by a Mac but thought it was too expensive, here's your chance to get your feet wet. It's much nicer than a Windows machine. Once you get TeXShop running, you'll never want to go back. And once you get some of the cool Omni software, you'll wonder why you waited.

Don't be surprised if some of these start showing up on campus soon.

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

11.18.2004 17:44

h.m.c. m.c.

This message is the first post. Whoo-hoo!

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

2003 Aug 22 12:00 PM

Welcome Back!

There have been a number of changes over the summer. The most important are:

Red Hat Linux 9

The Scientific Computing Lab machines have been upgraded to Red Hat Linux 9.

The biggest difference is one you'll notice immediately-RHL9-uses GNOME 2, so everything is shinier and prettier than it used to be. You'll also see a lot of antialiased text.

The main downside is that any customizations you may have made to your GNOME Panels will have been ignored; the system will simply create a new default layout for you, and you'll have to make any changes you want from scratch. Overall, though, I think that the system is an improvement.

Terminal junkies will notice that there's no icon for starting a terminal by default. The terminal menu item is hidden under "System Tools". You can add an icon to your Panel by

  • Right-clicking on a blank spot in the Panel
  • Going to Add to Panel->Launcher from Menu->System Tools->Terminal
  • Releasing the mouse button while "Terminal" is selected

(You can use the same method to add other icons to your Panel.)

Maple 9

Maple 9 came out during the summer, and we installed it in preparation for CIS's switchover this fall. As it happens, RHL9 and Maple 8 didn't get along well; the solution was to move to Maple 9 immediately.

teTeX 2.0 and texdoctk

I was surprised to see that RHL9 only had teTeX 1.0.7, so I built teTeX 2 from Rawhide and installed it. teTeX 2.0 has much newer packages than the older version, as well as some changes to administrative tools that make it easier for me to configure.

teTeX 2 also includes texdoctk , a program that helps you find documentation for teTeX packages. Just type texdoctk at a shell prompt, and you'll get a window with buttons that you can click on to find the documentation you need.

2003 August 22

My Account's Locked!

We may have received incorrect information about students who didn't graduate when first expected. If your account is locked but you're still here, just stop by Claire's office (Olin B159) with something official that says you're still here. We'll move your home directory to the right subdirectory, update the account database, and even let you reset your password.

2003 August 22

I Need an Account!

Account application procedures are the same as they were last year. You will need a faculty sponsor to sign your account request form (PDF). Turn the forms in to Claire in person or in her mailbox. Accounts will be created each night, and will be available for pickup on the next "business day" (Monday-Friday).

See the account policy page for more details about the mathematics department's appropriate-use policy and for links to the account request form (PDF).

You will need photo ID (preferably your own) to pick up your account.

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