Wed Nov 30 17:38:14 PST 2005

Maple Updated to 10.02 (and x86_64 Support)

I have updated the version of Maple installed on our server to 10.02. It's set as the default, so just typing maple or xmaple should launch the latest version.

If you have problems, (1) please tell me, and then (2) run the previous version by specifying the full path to the maple or xmaple executables, as in /shared/local/maple10.01/bin/{maple|xmaple}.

I noticed that there was support for the AMD 64/x86_64 64-bit processors in the update, but found that I didn't have the original installation media for the 64-bit version of Maple. I got a copy from CIS, so we now have both 32-bit and 64-bit versions of Maple available for your use (assuming you're using one of the 64-bit workstations the department has, of course).

To be honest, I'm not sure what having the 64-bit version buys you, as Maple is a symbolic math application rather than a major number cruncher, but 64-bits must be cooler than 32-bits, right?

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

Thu Nov 24 22:49:24 PST 2005

Server Reboot Successful

I came in today and rebooted our main server, esme. As I had expected, the home partitions needed checking. Once that process had finished, however, the machine came back up and was running just fine.

I was able to move the new tape library onto esme and verify that it works. Very cool.

While I was working with the machine, I took the opportunity to update various firmware packages (BIOS, SCSI RAID, etc.). As far as I can tell, those updates worked fine, too.

I rebooted the scientific-computing laboratory machines. Faculty and Clinic workstations should probably also be rebooted; I will look at rebooting the Clinic machines over the next couple of days. Faculty should reboot their machines sometime next week (ideally when I'm in the office, just in case there are any issues).

Thanks for everyone's patience and cooperation. As usual, if you notice any problems with the systems, please send mail to describing the problems you're having.

Posted by Claire Connelly | Permalink | Categories: System Maintenance

11.23.2005 10:38

Server Reboots Over Thanksgiving Holiday

I will be rebooting the department's server systems over the Thanksgiving holiday. Exactly when, I'm not sure, but our main server, which provides file, print, mail, and some other services, hasn't been rebooted in over 200 days. As there's been a major update (from CentOS 3.5 to CentOS 3.6) during that period, we're more than due for a reboot.

If you were planning on running processes over the Thanksgiving holiday, please contact me immediately. As of right now, no one has spoken to me about any such processes (which, you'll recall, is a requirement of the department's long-jobs policy), so I'm assuming it's safe for me to reboot the systems whenever it's most convenient for me to do so.

Posted by Claire Connelly | Permalink | Categories: System Maintenance

11.16.2005 14:20

New Tape Library Arrives!

This summer, we learned about a matching grant program run by IBM. Mudders who had gone on to work at IBM had donated money to be given to Mudd, with IBM matching those funds. Altogether, the donation was around $40,000.

After the department chairs hashed out who would get how much of the pool of funds, the mathematics department opted for a 3581 Tape Autoloader, a device that contains a single Ultrium LTO 3 drive and a robotic tape carousel that can hold eight Ultrium 3 tapes.

Each Ultrium 3 tape can hold 400 GB of data uncompressed, or up to 800 GB of data if compression is used. Our current backup system, which uses DLT IV tape, can hold 40 GB uncompressed, 80 GB compressed per tape, so the new system represents a tenfold increase in capacity.

The eight-cartridge carousel also means less tape changing -- the system can be set up to cycle through the tapes in order or to select particular tapes based on the ``slot'' in which they're loaded.

I'm currently in the process of testing the new tape system. It's installed in our rack, but actually getting the servers to talk to it and make it do what we want is going to require a bit of fiddling. I hope to have it online by next semester.

This new tape library clears the way for increasing our disk-space capacity. Now that we can back up larger amounts of data, we can start working toward obtaining additional disk space, knowing that we will be able to protect that data.

This IBM 3581 Tape Autoloader, with rack-mount kit and a SCSI cable, sells for $9,293. We would like to say ``Thank you, IBM,'' and especially to thank the Mudders now working there for contributing to this fund.

Posted by Claire Connelly | Permalink | Categories: System Maintenance

11.14.2005 17:06

Appropriate-Use Policy Updated

I have reviewed and updated the department's Appropriate-Use Policy, which governs the usage of the department's computer resources.

The changes are not significant; they're more along the line of clarifying the existing text based on my actual experiences since drafting the original document (in late summer, 2002) in preparation for adding a second document that will spell out some additional requirements for users who want to use our Amber parallel cluster.

The change log is as follows:

First significant overhaul of the departmental appropriate-use policy.

Change format a bit to include use of lastpage.sty and svn.sty so that each page indicates where it fits in the complete document and contains the date of last revision.

Make various minor typographical, spelling, and terminological fixes.

Clarify the definition of faculty sponsor to indicate that such an individual must be a member of the mathematics department or the department's systems administrator (which allows, for example, CS faculty who have students who need to use the Amber cluster to authorize those students to do so).

Emphasize that leaving files with permissions wide open does not mean that those files can be changed without direct permission from the owner.

Broaden the harassment policy to include other potential media beyond those listed.

Add a section on installation of software by users. This section formalizes our ``ask us to install X if you think it would be useful'' policy.

Expand the discussion of disk-space usage to give additional guidance on determining appropriate amounts of usage for an individual, to authorize temporary large uses when the material will be removed prior to backups running, and to encourage users to discuss their disk-space needs with the systems-administration staff.

Tweak licensed software section to make it flow better.

Clarify that account revocation could be permanent.

Add the additional stick of law-enforcement involvement in extreme situations.

Add questions and comments section, with the systems-administration staff's e-mail address.

Please feel free to take a look at the actual document to see what's changed for yourself. If you've never bothered to read the AUP, now might be a good time to see what you agreed to when you signed your account-request form.

I would maintain that the core of the document is ``Be nice to other people''.

I have also updated the department's computing-policy web pages as part of this effort.

Posted by Claire Connelly | Permalink | Categories: System Policy

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

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

11.11.2005 10:43

Unexpected Power Outage in SciCompLab

As I've mentioned before, work is underway to replace the "brains" of the air conditioning system in the department's machine room and hook it into the general HVAC monitoring system.

Among the other things we keep in that room is a magic button that cuts the power for the servers in that room, a relic of the days when water-cooled mainframe computers might need to be shut down all at once to prevent electrocution.

These days, of course, our systems are air cooled. And they're all on UPS power, which means that hitting the panic button just switches them onto battery power. But the button is still there, waiting to be pressed....

Which is what happened this morning. The Physical Plant folks working on the air conditioning accidentally triggered the power cutoff. To make matters worse (and more confusing), the cutoff doesn't just affect the power in our machine room, but also the power in the scientific-computing lab, the publications room, and, I believe, at least one or two of the biology labs nearby.

Our servers, with their UPSs, were fine. But any jobs that were running on the scientific-computing lab machines were stopped when the power went out and the machines crashed. The machines rebooted, as they were set to, but they didn't restart your jobs -- you'll have to restart them yourselves.

Before you do that, however, I encourage you to review the department's policy on long jobs. Let me summarize for you: You're not supposed to leave processes running when you're not sitting in front of a machine unless you check with me first. The lab machines are meant for use by people sitting in front of them first, with people logging in remotely to run interactive jobs next. Long, unattended jobs should be run so that they don't dominate the processing power of the machine when someone is trying to do things at the console.

That means that you should

  1. Tell me that you have a job that needs to run for a long period of time.
  2. Run your job with the nice command, as in

    nice -n 19 your_process_name

Ideally, you should also write your code so that it periodically writes out its status and results, and can resume by reading in that information and starting from where it left off. Writing such code is a bit more difficult, but it might save you from having to redo hours of computations when the power fails, someone reboots the machine because its running too slowly, or other unforeseen events stop your job from running.

If you're still looking for reasons to tell me about your long jobs, let me point out that I routinely update packages on the lab machines for security issues, and some of those updates require a reboot to take effect. If I don't know your job is running, I might reboot the machine without checking with you first. Letting me know means that I can maintain a list of machines to avoid rebooting without notice.

Please remember that the lab machines are a shared resource, and sharing requires that everyone using them behave responsibly and respect the other users.

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

11.02.2005 15:01

A/C Work in Progress

It turns out that there are some significant issues with the air-conditioning unit in the mathematics department machine room. They're being looked into by F&M and the CUC Physical Plant HVAC people.

There should be no disruption of services, but should it become necessary for something major to be done, I will let people know as far in advance as I can. I would also hope that we could arrange for any significant disruption to occur on a weekend or over a break period.

Thanks for your patience during this work.

Posted by Claire Connelly | Permalink | Categories: System Maintenance

11.02.2005 14:54

Amber Cluster Move Complete

The Amber cluster has been successfully moved into its new home. Tim and I will probably be doing some additional shuffling around over the next few weeks or months, but we should be able to either make those disruptions short enough as to be unnoticeable or announce the disruptions in advance.

There may still be some issues that users might notice that I'm not seeing; if you have any issues, please report them to

Thanks for your patience and cooperation!

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

11.01.2005 11:19

Amber Cluster Move Scheduled

The mathematics and computer-science departments' Beowulf cluster, Amber, is going to be moving from the mathematics department's machine room to the much more commodious CS machine room.

We will be moving the cluster sometime tomorrow, Wednesday, 2005 November 2.

If all goes perfectly, the cluster move will be simple and quick. If things get a bit more complicated, we will have to disassemble and reassemble the cluster, which means disconnecting sixteen computers (power & Ethernet), moving them in groups of three or four, then reconnecting everything in the new location, which will require at least an hour, maybe longer.

To make the process as easy as possible, we're asking that anyone who is actively using the cluster stop their work by 10:00 AM on Wednesday. We will post here when the cluster is back up.

(People who are authorized to use the Amber cluster have already received e-mail messages at their math addresses with this information, and will also receive a message when the cluster is running again.)

The Amber cluster has sixteen Dell PowerEdge 400SC nodes, each with a 2.8 GHz Pentium 4 processor and 1 or 1.25 GiB of RAM. The nodes communicate over a gigabit Ethernet switch. The cluster is running CentOS 3 with various additional cluster-related software packages (notably LAM/MPI). Use of the cluster is limited to faculty, students, and staff of the colleges who are doing computationally intensive research, especially research that requires or can take advantage of parallel-computing techniques.

Amber cluster nodes were purchased with funds from several CS faculty members. Systems integration and support is provided by the mathematics department.

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