Archive of Occasional Messages about Computing

Contents have been selected (and will be edited) to reflect items that are (hopefully) still relevant.

01/21/05 - course webpages, undergrad use of DoIT InfoLabs

--Course web pages are now generally available in a number of ways. The entire raw list of pages (from past and currents semesters)can be found at:

http://www.stat.wisc.edu/courses

and all individual pages (from past and current semesters) can be accessed directly with:

http://www.stat.wisc.edu/courses/stNNN-IIII

where NNN is the course number and IIII is the instructor's login ID.

Courses for this semester ONLY can be accessed with:

http://www.stat.wisc.edu/~stNNN-S

where NNN is the course number and S is the section number. Or you can find the list of current courses with links at:

http://www.stat.wisc.edu/Department/Courses/2004.2.html

--Generally, undergraduates taking introductory Statistics courses do not have accounts on the Statistics computing system or access to Statistics computers. They should be encouraged to use the resources available through DoIT and the University to do their work. This includes Email, personal web pages and access to computing through the InfoLabs. The InfoLabs have the type of software that students will typically need, including R, SAS, Minitab and Matlab. You can find information about the location and capabilities of the InfoLabs at:

http://www.doit.wisc.edu/computerlabs/software.asp

We will arrange for undergrad students majoring in Statistics to get some access to the Statistics computing resources as needed. Special arrangements may also be needed to serve graduate students not in Statistics (and some undergrads) but taking graduate level courses in Statistics. Please mail lab@stat.wisc.edu if you have special needs in that respect, and we can discuss options.

01/31/05 - default Stat people web pages

--Links have been created on the www.stat.wisc.edu - People - Students page that by default link to student ~/public/html page. If you put and index.html file in that directory, it will come up when the link is used. If you have a public/html directory, but no index.html file in the directory, the list of what is in the directory will be shown when the link is used. This is not a good thing, so you should put in an index.html file in the directory. If you have not yet created and html directory under your public directory, you should do so. Otherwise and error message comes up when the link is used. For information on creating your personal home page, see:

http://www.stat.wisc.edu/Computing/personalhomepageinfo.htm

02/17/05 - Slides for Stat Seminars, R on Condor tutorial slides

--The slides for the "R on Condor" tutorial that was presented by Xianhong Xie on Wednesday, February 16th are now available at the Seminars web page on the Statistics site (www.stat.wisc.edu). Follow Seminars to the appropriate place.

--In the future it will be possible to post slides from seminars on the seminars page. We can generally convert them to pdf formats that are easy to deal with. If any of the past speakers are willing to share their slides, I can put them up.

03/25/05 - duplex and color printing in Stats, Condor for Stats, using statforum, using lab@stat.wisc.edu

--The printer in 1205/1207 (pr1207) has been replaced with a new unit that includes duplexing. It should be more consistent and reliable than the old printer. Please use the duplex mode whenever possible to save paper. If you want to print single-sided, please see the CSL documents on how to specify the simplex queue.

--A duplexer unit has been added to the printer in B248 (prb248). Please use the duplex mode whenever possible to save paper. If you want to print single-sided, please see the CSL documents on how to specify the simplex queue.

--A reminder that the color printer is available for use in 1205/1207 (statcolor). There are options of paper or transparency printing as well as duplex color printing (on paper). You need an authorized account on internal, University funds, to use the color printer. There is a page charge to recover costs for supplies. A color image on paper is $.15 per side, and a color image on transparency is $.80. This is a lot less than the cost at Bob's or Kinkos, so please take advantage of this local capability.

--Condor is installed on Statistics and CS machines to provide a large-scale computing resource for both of our departments. Typically, Condor jobs should have a minimal impact on the interactive users of the Statistics computers. However, if you see a case where a Condor job is "locked" on your machine after you log in (use "top" to see the machine utilization), please let us know by sending mail to "lab@stat.wisc.edu". This is errant behavior and we need to report it to the condor administrators to fix the problem. Please do not attempt to remove Condor jobs from your system without checking with us first. It will be to everyone's benefit to permit the well behaved jobs to run to completion.

--If you have a computer problem related to hardware or software function, please send your Email message to "lab@stat.wisc.edu". That way the problem will be logged and tracked. Always include your machine name and location. If you send mail directly to me or to Colleen, it can't be tracked properly and we will probably ask you to resend the message again through lab@stat.wisc.edu.

--If you have a question about solving a statistics problem when using software like R or Condor, you should send your message to "stat-forum@stat.wisc.edu". You should join the stat-forum mailing list to get authorized to both send and receive stat-forum messages. You can subscribe at:

https://lists.cs.wisc.edu/mailman/listinfo/stat-forum

04/21/05 - Stat technical reports

--The Statistics web site has a page to access departmental technical reports. To keep the page up-to-date, it is necessary for technical report authors to inform Denise and me about the publication of new reports. At this point, we have no records on reports 1095, 1096, 1097 and 1098. If you are the author or co-author of one of these reports, please inform Denise and me about the details, and provide a copy of the report in pdf format or a link to where the report can be viewed.

09/29/05 - warning about safe computing

--We are getting reminders from campus IT folks to redouble efforts to protect our systems. This is particularly important for computers that you own and manage. But parts also apply to the computers that are provided by Statistics. On all computers, you need to be careful about spam, scams and phishing attacks. Don't answer unsolicited mail, or open web sites embedded in mail, where there are requests for private information.

11/03/05 - using statforum, using lab@stat.wisc.edu

--This is a reminder: If you have a computer problem related to hardware or software operation, please send an Email message describing the problem to "lab@stat.wisc.edu". That way the problem will be logged and tracked. Always include your machine name and location. If you send mail directly to me or to Colleen, it can't be tracked properly and we will ask you to resend the message again through lab@stat. If you come and see us in the 1280 office, we will likely ask the same thing so that we can keep an electronic track of the problems we work on.

--If you have problems related to the use and function of Statistics computing applications, like R or SAS, I encourage you to get advice through the stat-forum list. You should join the forum at:

https://lists.cs.wisc.edu/mailman/listinfo/stat-forum

and then you can Email to:

stat-forum@stat.wisc.edu

and you will receive discussion messages from the forum. You can look at the archives of messages at:

https://lists.cs.wisc.edu/archive/stat-forum/

12/30/05 - dangers of using /scratch and /tmp

--DON'T USE /scratch OR /tmp There have been recent disturbing cases where users are keeping important files in /scratch without providing a backup. THIS IS A REALLY BAD IDEA! You have at least a chance of losing everything you are keeping in /scratch (almost a certainty for files in /tmp). If you don't plan to back up important files you might keep there, YOU SHOULD NOT USE /scratch! I don't know if I can emphasize this more strongly...DON'T USE /scratch OR /tmp!

04/07/06 - laptop use with Stat monitors, running out of disk quota

--With the availability of the new LCD monitors and included cables (for DVI connection), it will be possible in some cases to provide "dual use" for the monitors. Monitors labeled VG710b and VA712b (new units) allow dual connection. Most of the desktop computers in the "chi" series permit use of the DVI connection which is needed for dual use. For desks with that combination, a second analog VGA connection will be available to attach a notebook computer to the LCD monitor. Switching between the desktop (chi) machine and the laptop is easy (push the "2" button on the monitor). If you have a laptop and would like to use the local LCD monitor as a dual laptop/desktop display, please contact me and I will evaluate the situation.

--If you start getting odd behavior in your Stat account, one of the first things to check it your quota:

fs listquota

If it is at 100%, you need to eliminate files. If you do any type of programming, including R work, it is possible you have "core" error dump files in your account that are taking lots of space. To find out, go to your home directory and "find" all the files that have "core" in the name:

cd ~
find . | grep core

You can then go to the appropriate directories and delete the files that are error dumps. They usually have a name similar to:

core.15432

After deleting the core files, look at your quota again with fs listquota and see if it has gotten better.

07/05/06 - using projectors in 1210 (and 133)

--Projectors in 1210 (and 133) have new, permanently installed remote controls. When you use the remote, make sure you always press the "proj" button before using other functions on the remote. For example, to turn the projector on, press "proj" then "on". To turn it off, press "proj" then "off", then "off" a second time. If you can't get the remote to turn the projector off, please leave it alone, and it will turn itself off after 2 hours. For your safety and to avoid moving the projector, don't climb on the table or desks to try to reach the switches on the projector. WARNING: the projector turns off automatically 2 hours after it is turned on, so if you have a really long session of multiple presentations, you may want to turn the projector off temporarily between breaks. Otherwise, it may turn itself off in the middle of a presentation. If that happens, just wait the 3 to 5 minute cool-down period until you can turn the projector back on.

10/02/06 - using the wireless mic in 133

--Most lecturers won't need it, but there is a wireless microphone and amplifier in 133. The mic should be left on the (amplifier) near the west wall of the room. To use the mic, you may have to turn on the amplifier and wireless receiver (the red lights need to be on on the two units). The mic has an on/off/standby switch. Slide it to "on" to use it. But make sure you turn it OFF when you are done, otherwise the AA battery will die. If you really plan to use it, bring your own AA battery just in case. Make sure you put the mic back on top of the (amplifier).

12/04/06 - renting additional disk quota for research use

--Access to additional disk quota - The Department currently has flexibility to provide some additional AFS disk quota to students, faculty and staff. Quotas have been increased to 1G for students and to 2G for faculty and staff. Please only use the amount of AFS disk space you need. The quota specifies individual upper limits. We do not actually have enough disk space if everyone uses all of their quota space. So please be conscientious in your use of AFS space. Clean out unneeded files.

If you need AFS disk storage beyond your quota limit, additional space can be rented in 5Gb increments for $30/5Gb per year. Students can work with their advisers on renting space. Contact Denise to provide funding information for this.

12/08/06 - Dangers of using /scratch and /tmp

--Please, Please do not save important files on /scratch (or /tmp) unless you are doing consistent and frequent backups. We have had many disk failures on chi computers (and others). It is difficult and sometimes impossible to recover files from /scratch after a crash. In a recent case in CS, a faculty member needed to spend about $600 to an outside recovery service to recover critical files from /scratch, and it could have cost over $800. If you are not prepared to spend that much to recover important files from /scratch, please do not save them there without making frequent, consistent backups.

01/11/07 - don't leave CDs in drives, fix Gnome screen saver settings

--Please do not leave CDs (or DVDs) in the CD/DVD drives on the Statistics computers. If your CD gets stuck, please let the Stat Computing staff know right away (mail lab@stat.wisc.edu). Also, before inserting them in Statistics computer drives, please check your CDs near the inner rim to make sure they are clean. If there is any sticky residue near the center, toss the CD or clean it completely.

--Please check your screen saver settings to make sure your screen saver eventually goes into energy saving mode (turns off signal to monitor). This should be part of the screen saver preferences in gnome and I think only gnome users are having a problem. I see monitors that are continuously showing the screen saver images, and that is bad. It means the fluorescent tubes in the flat panel monitors are always lit which shortens their life. If you have questions about getting your computer into full energy saving mode, send a note to lab@stat.wisc.edu and we will help you get it set up correctly.

01/12/07 - details to fix Gnome screen saver settings

--Here are the instructions to "fix" the screen saver on Gnome so that your monitor goes into power save mode:

When in Gnome, go into the Applications->Preferences->Screensaver preference. Select the "Advanced" tab that shows options for "Display Power Management". Enable Power Management and select a reasonable delay to use in all the boxes, maybe 30 minutes max. If you look in the "Display Modes" tab, you'll see a "Blank After" entry that sets a time to "Blank" the screen to a black background. Unfortunately, this does not reliably put the monitor into a low power.

01/22/07 - don't abuse parallel job execution and printing, how to set up laptops in Stats

--Some gentle reminders...Please do not run multiple large jobs across multiple public computers. These are resources shared by everyone in the department. Also, please be careful about the number of pages printed. There have been reports of large printouts that are multiple copies, and printouts that are not picked up. The cost for paper and toner is becoming prohibitive for the department and it is likely that we will eventually need to impose quotas to control costs. But the preferred solution is still to have everyone make the most judicious use of the printing resource as is possible

--I have posted updated methods for setting up laptops and home computers to connect to the Statistics network. These methods allow you to run Statistics workstation applications through your notebook. Please check the updates at:

http://www.stat.wisc.edu/twiki/bin/view/StatDocs/StatLaptop

03/19/07 - updating FVWM configuration

--Please update your FVWM desktop configuration. Please consider using the Statistics update at:

http://www.stat.wisc.edu/twiki/bin/view/StatDocs/StatUnixdesktop

If you have any questions or problems in updating your desktop, please send mail to lab@stat.wisc.edu

09/19/07 - rules for using Stat computers, limits for multimedia

--Here are some computing rules-of-the-road for new folks in the department (and a reminder to everyone else):

-Keep thinXX (thin clients) turned off when not in use
-Don't shut down or reset winstatXX Statistics computers
If there is a problem, write an Email to lab@stat.wisc.edu
If it is time-critical or you can't Email, see us in 1280 MSC
-Don't leave open, logged-in sessions on the thin clients in 1274
This is a security breach and is dangerous for your account integrity
-Don't lock the screens of Statistics thin clients in 1274
If there is a critical need for this, Email lab@stat or see us in 1280
-Don't abuse printing - only print one copy of what you need. No books!
-Don't leave screen saver animation running in the GNOME desktop
This wastes power and shortens life for the flat-screen monitors
To set energy save mode, see:

http://www.stat.wisc.edu/twiki/bin/view/StatDocs/StatUnixdesktop#WARNINGS!

--It is not possible to liste to on-line music or watch on-line videos (with sound) with Statistics using a thin-client connected to a desk server (deskXX). It just won't work. Many of you have your own Windows or Mac laptops, and those computers will give you the best results for working with Multimedia.

11/21/07 - thin client servers

--All of the thin clients have deskXX servers "behind" them. If you are using an ltermXX or thinXX, please keep in mind that you can do essentially all your computing on the associated desk server. At this time, some desk servers are not heavily used. I will be configuring the desk, public and bigmem servers for Condor jobs to increase utilization.

01/14/08 - using thin client stations and servers, recovering disk space is out of quota

--Linux thin-client terminals are installed in 1274 (lterm01 to lterm06). Instructions for using the thin clients are on sheets attached to the computer cases. Instructions are also on the SCL web FAQ pages at:

http://www.stat.wisc.edu/twiki/bin/view/StatDocs/StatThinClients

Please connect to the public01-03 preferred server as noted on each thin-client monitor.

The thin clients use little energy when running, and they shut down when not in use. They are very quiet with slow-running fans and no hard disk. Please check these out and let me know how they work for you.

--If you seem to be running out of AFS disk space for no reason, it may be that your "Trash" folders at ~/Desktop/Trash and/or ~/.Trash are full of useless stuff. Please check those directories and see what's there. Delete the contents if you need space. If you do programming in C, Fortran and R, it is also possible for you to generate "core" files when run-time errors occur. These files are typically not very useful, but take up lots of space. To find core files, go to your home directory and "find" all the files that have "core" in the name:

cd ~
find . | grep core

You can then go to the appropriate directories and delete the files that are error dumps. They usually have a name similar to:

core.15432

03/07/08 - using laptop as primary desk station

--If you typically bring a notebook computer to your desk, please talk to me about how to use it as your main access station to the Statistics servers. Eventually, the primary Department computational resources will be provided on servers. Department stations remaining at desks will typically be thin clients with no local computing power. They will be low cost, energy efficient, and specifically configured to access server computers. Other services, like web access to multimedia and audio, will be deemphasized or unavailable. Your notebook computer will do as well for accessing the Departmental servers. And a notebook will have the capabilities needed for full access to web services, including multimedia. Arrangements for connection of a notebook at your desk include access to the 100Mbit wired network, and use of the flat panel monitor at the desk location. The department may also be able to loan you a locking cable to secure your notebook while it is at your desk.

03/26/08 - changes for using the new RHEL5 operating system, screensaver for FVWM (can't use xlock anymore)

--We have upgraded to the new RHEL5 Operating System, and now, if you run the default windows manager (FVWM2) rather than the slower, graphics manager (GNOME), you can no longer use a number of X applications. Information about some of this is at the CSL FAQ page for RHEL5:

http://www.cs.wisc.edu/twiki/bin/view/CSDocs/RhelFiveFaqs

-The main loss is xlock for locking an FVWM screen. You now need to run:

/s/std/bin/gnome-screensaver

initially to start the screensaver daemon (under FVWM only). Then run:

/s/std/bin/gnome-screensaver-command -a

when you actually want to start the screensaver (again, under FVWM only)

-You can use other GNOME utilities under FVWM. Suggestions for many are in the CSL FAQ page. You may also want to run "nautilus" in one of your FVWM virtual windows if you want access to the GNOME point-and-click file manager while using FVWM.

-"nedit" is no longer directly available under RHEL5. You should plan to use "gedit" instead. There is still a version of nedit available in the "unsup" area if you really feel you need it. You can get it at:

/unsup/nedit-5.4.0/nedit

However, keep in mind that support for nedit could go away suddenly.

07/25/08 - adding private packages to R

--To add private libraries and packages to the new version of R (R-2.7.1), create the special directories that you need at:

~/R/i686-pc-linux-gnu-library/2.7

for use on 32 bit systems (deskXX, publicXX, chiXX), and

~/R/x86_64-unknown-linux-gnu-library/2.7

for use on 64 bit systems (powerXX, bigmem01, research servers). When you install the libraries and packages, they will be created in your special directory.

It is no longer practical to include the large and growing list of packages in the R repository as a default. So it is more likely now that you will need to add private packages for special requirements. If a number of users in the department also need such a package, I will consider adding it into the base installation.

08/21/08 - texmaker GUI TeX editor, Keeping thin clietns shut down

--There is a new editor for TeX available under Linux. You can access Texmaker at:

/s/texmaker/bin/texmaker

Please check it out and send comments to lab@stat.wisc.edu

--Thin clients should be turned off whenever they are not in use. There are no background jobs running on thin clients, so they are only doing useful work when you are connected through the thin client to a server. There is no hard disk in a thin client so it is not possible to do damage if the thin client is turned off. If something doesn't work on a thin client, the best response is to turn it off and turn it back on. If the problem persists after doing that one or two times, then let SCL staff know so we can check it out. Since there is no hard disk (and for other reasons), there is less to go wrong with a thin client.

09/19/08 - SAS runs on 64 bit servers, thin client failsafe session to fix out of quota

--It is now possible to run SAS on the 64 bit servers (power01, power02 and bigmem01). It still runs in 32 bit mode, so it will not be possible to build problems with larger arrays that take advantage of the bigger memory. Please try it and let me know if there are any issues with performance.

--Thin clients now have a "Failsafe" session option that can be selected on startup. When you are asked to type "G" if you want the Gnome desktop, you also have the option to type "F" for the failsafe session. Anything else will start the basic (FVWM2) desktop. The failsafe window is red and opens to the left of the "black" window. You need to move your pointer into the red window to enter your password and use the failsafe session. The failsafe session is handy if you are not getting a login from a regular session, and the thin client keeps turning off when you try. Usually this means that you are out of disk quota or that you do not have authorization to log into the server you chose. If you are out of disk quota, the failsafe session will usually give an error message about not being able to write a file. You can check your quota with the command:

fs lq
or
fs listquota

If you are over quota (>>100%), you will need to remove some files using the failsafe session before you will be able to log in with a regular session.

In case you don't have authorization, you will get a message in the failsafe session that lets you know. You will need to start over and select a server which you are authorized to use.

To end a failsafe session, move your pointer back to the black window and hit ctrl-c (or use one of the other thin-client shutdown methods.

10/16/08 - Mac laptop setup with Stats, stop using Gnome on thin clients, laptops as primary desktops

--There is now a FAQ page for users of Mac OS/X laptops (and home computers) with instructions on how to connect to the Stat computing and printing services. You can find the instructions at:

http://www.stat.wisc.edu/twiki/bin/view/StatDocs/StatLaptop

If you find errors or problems in the instructions, please let me know.

--I will reiterate my recommendation that Gnome NOT be used on thin clients. Gnome is generally slower than the basic desktop alternative (FVWM2). But the more serious problem is that it tends to break over time, causing unpredictable behavior (loss of command bars and application functionality, for example). Gnome also tends to leave orphaned processes running on the servers. The processes are hard to cleaned out. These issues can be manually resolved by removing specific user files from /tmp and/or by rebooting the servers. But that is time consuming and potentially disruptive.

If you have been using Gnome, please consider switching to the basic desktop manager . If you want a usable pull-down menu to access applications, you can execute the command:

/p/stat/bin/Applications

If you want to be able to lock the display, you can execute the command:

/usr/bin/gnome-screensaver

once at the start of your session, and

/usr/bin/gnome-screensaver-command -a

whenever you want to lock the screen

If you want a file system display that looks like Gnome (though it can look a little messy), you can execute the command:

nautilus

--I will also reiterate my recommendation that students and faculty consider using laptop computers as their primary access station at their desks. MS Windows and Mac OS/X laptop computers can provide the server access that thin clients do, but in a more familiar and flexible environment. This also resolves the issue of using Gnome vs. the basic Linux desktop environment. Instead, you use the familiar MS Windows or Mac OS/X environment, and access the servers with terminal sessions from there. When thin clients are removed in favor of user-owned laptops, the 100Mbit wired Ethernet is available for high-speed connection, and the desktop monitor can be used to expand the laptop to dual-screen operation. The department can also provide a keyboard, mouse and lock to use with your laptop.

If you bring in your laptop most days, please consider this option. The public thin clients in 1274 are available for use in cases where you do not have your laptop at your desk.

I can help set up laptops for this use. Please check with me.

--After you are done using a thin client in 1274, please make sure you have fully shut it down. You can do this with ctrl-c in the black window, or ctrl-alt-Backspace, or just hold the power button down on the computer for about 5 seconds. Please do not lock the thin clients in 1274 and walk away. If there is no one at the station, I am not sure what the status is and it is possible that I will shut it down. You could lose work.

1/29/09 - Win XP Office update, Scanner easier to use

--While I was out in January, an update for the Statistics Windows XP systems was initiated. I completed the update today (1/29/09) and the changes are now implemented for the 1274, 1335 and B248 Win XP systems (winstat01, winstat02 and winstat06). The most notable change is that Microsoft Office is now at the new Office 2007 version. This version looks considerably different that the previous version, so it may take some time to get used to. Office 2007 can also create files that are incompatible with the older versions of Office you might have on your notebooks or home computers. When in doubt, please save files in the old format from Office 2007 (in the Save As menu selection). If you want to be able to read files with the new format on your "older" versions of Office, you can install a converter on your laptop or home computer. For Windows computers, you can check:

http://office.microsoft.com/en-us/word/HA100444731033.aspx

For Mac OS X, you can check:

http://www.microsoft.com/mac/downloads.mspx

or

http://www.apple.com/downloads/macosx/system_disk_utilities/microsoftofficeopenxmlfileformatconverter.html

--The Acrobat packages were also updated on the Win XP systems. Acroread 9.0 is now on all the updated systems. And winstat01 also has the full Acrobat 9.0 Pro installed. The new Acrobat Pro makes the scanner in 1274 much easier to use. From within Acrobat Pro, select:

File->Create PDF->From Scanner->Configure Presets

in Scanner: select HP Precision Scan Pro 1.0 in Paper Size: select Letter

Hit OK, then, on "Save Changes", hit OK (this may need to be done only once)

Put what you want to scan on the glass. Or if you have multiple loose pages, put them in the page feeder (Blue Lever to 1, insert pages, Blue Lever to 3 - put in max of 9 pages at a time - you can feed more later). Then:

File->Create PDF->From Scanner->Black & White Document

Your page(s) will scan, and a box will come up. Select "Scan is Complete" if done, or "Scan More Pages" to keep going. When done, Acrobat Pro will bring the pages into a PDF file and do its best to recognize the content with character recognition. You can then save the PDF file as you wish.

2/10/09 - Change in thin client desktop interface

--In late fall, 2008, Comp Sci modified the default desktop interface for Linux stations. This has caused some issues with the desktop interface used on the Statistics thin clients. Today I made changed that hopefully enhances the functionality of the FVWM (simpler) and GNOME desktop interfaces specifically used with the Statistics thin clients. It also separates the Statistics default configuration from the Comp Sci default. The interfaces now include the Statistics application pull-down menu by default. It appears in the upper left corner of the desktop. The GNOME interface now shows a terminal window by default. Hopefully these changes are not too disruptive for Statistics users.

2/19/09 - Upgrading 64 bit servers to run 32 bit applications - New default version for accelerated R

--All of the Statistics 64 bit computers have been upgraded to allow use of 32 bit applications (such as SAS). This includes the bigmemXX computers that are publicly available, and the research computers belonging to faculty and faculty groups (darwinXX, dots01, starXX, diabetesXX, herculesXX, zeusXX, diabetesXX, toncuk, mars01, durga and athena). All of the programs accessible from the Statistics pull-down menu (/p/stat/bin/Applications) on the 32 bit computers can now be run on 64 bit computers. The 64 bit "Applications" menu includes an additional entry for accelerated R that is only available on the 64 bit systems.

Please keep in mind that there are some differences with the 64 bit systems that you must deal with. Compilations for code (c for example) will default to 64 bits and will need 64 bit libraries. Local libraries for R will need to go into:

~/R/x86_64-unknown-linux-gnu-library

rather than

~/R/i686-pc-linux-gnu-library

and will need to be reinstalled for 64 bits. The 64 bit systems with larger memory permit use of larger array sizes for R, Matlab and other applications than is possible with the 32 bit systems. But be careful not to specify array sizes that will exceed the real memory capacity of the systems. You may not get an error, but the computer performance will be very poor due to excessive use of disk "swap" for virtual memory access.

--As mentioned above, the new pull-down "Applications" menu on 64 bit systems now includes an entry to start accelerated R. This version is specifically compiled to run on 64 bit Intel processors and has optimizations to take advantage of the Intel architecture. I do not recommend using this R version on the AMD compute servers (toncuk and durga). There is also a new path to get to the default version of accelerated R. Currently, the default is (R-2.9.1). So:

/unsup/Ra/bin/R

is currently equivalent to:

/unsup/R-2.9.1a/bin/R

The R version is typically updated in September or January. And the next version is likely to be R-2.9.1. But if you use the /unsup/Ra/bin/R command, you will automatically use the updated accelerated R. For "regular" R, you can continue to use /unsup/R/bin/R to get the default version.

3/4/09 - New bigmem02 server - Docs for Ubuntu Netbooks - Reading Microsoft Office 2007 files

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A second bigmem server (bigmem02) (has been) installed. This server has 8 "cores" and 64G memory to run larger computational tasks. bigmem01 (also with 8 cores) has been upgraded from the current 32G of memory to 48G of memory. These two servers provide for the general/public 64 bit computing needs of the department. As mentioned before, the power01 and power02 servers will be "repurposed" at the end of the spring semester to provide desk services to the "new" thin clients created by converting the remaining chiXX computers to diskless systems. publicXX computers will continue to be available for the general/public 32 bit computing needs of the department.

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New documentation has been added to help owners of Linux based Netbooks to connect to Statistics computing systems:

http://www.stat.wisc.edu/twiki/bin/view/StatDocs/StatLaptop

This version of the documentation is specific to "regular" Ubuntu installations as opposed to some of the special Linux OS implementations found on a variety of netbooks. If you need help with versions that are not documented, please email lab@stat.wisc.edu.

Netbooks are a low-cost, portable alternative for student computing. They can be particularly convenient for TAs that make slide presentations in classes.

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The new Microsoft Office 2007 can produce documents that are not compatible with old versions of Microsoft Word. The Microsoft Word available on the Stat Linux systems cannot read the new format, identified with the ".docx" file extension. If you want to view .docx files you have some options:

1) On the Stat Linux computers, you can use OpenOffice for viewing. You can select "Open Office" from the Statistics pull-down menu, or start OpenOffice from a terminal command line with:

ooffice

2) You can view the .docx files by using the Stat Windows computers in 1274, B248 or 1335. These computers now have MS Office 2007 installed as the default version

3) You can use your own computer to view the .docx files if you have MS Office 2007 locally installed, or if you install a converter to allow importing Office 2007 documents into older versions of MS Word. You can find several options for converters by searching on:

".docx converters"

Including an official Microsoft solution at:

http://office.microsoft.com/en-us/word/HA100444731033.aspx

4/10/09 - New Stats applications pull-down menu - MS Natural Keyboards available

--If you use the Statistics pull-down menu for thin clients, you may have noticed that it changed. The new pull-down is more compact (so it can be used on Netbooks with 1024X600 resolution), and it is multilevel. Hopefully that isn't a problem. But if you still want to use the old, one level pull-down, you can start it with:

/p/stat/bin/Apps

--I have 3 Microsoft "Natural" keyboard (kind of ergonomic) that can be installed on Statistics desktop client computers. If you are interested in using this type of keyboard, please check with me. First come-first served.

5/11/09 - Using wireless projectors in 133 and 1210

--Both the NEC NP905 projector in room 133 and the NEC LT265 projector in the 1210 Conference Room are now equipped with wireless networking. The same utility software and startup/shutdown procedures work with both projectors.

To use this capability, you must install "Image Express" utility software available from NEC that is specific for Windows XP, Mac OS-X or Windows Vista. For OS-X, there is a version for older Macs (with PowerPC processors) and newer Macs (with Intel processors). You can pick the right version from:

http://www.nec-display.com/dl/en/select/np.html#905

The #905 versions also work for the LT265. You need a working wireless interface on your notebook. And when you use this capability, you will be unable to also access the web (unless you have 2 wireless interfaces).

To try it:
1) Download and install the above software
2) In 133 or 1210, turn on the laptop
3) In 133, turn on the projector with the Philips remote (hit "proj" then "on"). In 1210, turn on the projector with the NEC remote ("On")
4) After the projector warms up, start the software
5) Select the "Easy Connection" option
6) Select the "NP905" projector line for 133. Or the "LT265" or other network card option in 1210. Then hit "Connect"

An image on your laptop screen should be simultaneously projected on the projector screen.

(If you use WiscVPN to authorize access to the UWNet wireless network, you may need to disconnect and exit it before you do step 5.)

When done, "Exit" the software, select the "C2" input on the projector remote, and hit "off" on the projector remote (twice).

There are options to remove a control menu (for Vista and XP systems), change the laptop resolution (for modest increase in speed), and allow multiple laptop users to sequentially share the projector. See the documentation included with Image Express, or check with me for additional information.

8/13/09 - External drive connection for thin clients

--The thin-client software has been modified to allow you to attach more devices to the USB ports for file transfers. You can now attach USB hard drives. You can also attach USB memory card readers. It is possible that some types and configurations of devices will not work. But you can try it and see.

The method to use additional devices is the same as for a USB stick. Before clicking on the "Local_Xfer" button (to open the file transfer program - gftp), plug in the device and power it on (if needed). It is good to wait about 15 seconds to make sure the device is detected by the computer. Then you can click on the "Local_Xfer" file transfer button and provide a password for accessing the deskXX/host computer. When the files window opens, you should be able to find your "usbdeviceX" as the one that has a size other than "3".

Please note that the file transfer program allows file transfers, but it does not support "mounting" of the local drive on the deskXX host. So programs on the host cannot directly read or store data from/to the USB local drive on the thin client.

8/28/09 - R-2.9.1 now default version and guidelines for using thin clients

--The new version of R (R-2.9.1) will become (is now) the default version on Monday Aug 31. You will want to re-installed your personal packages in the 2.9 subdirectories of ~/R/i686-pc-linux-gnu-library (for 32 bits) and ~/R/x86_64-unknown-linux-gnu-library (for 64 bits).

You can run R-2.9.1 as the default version with:

/unsup/R/bin/R

or add /unsup/R/bin to your path and then use the simpler command:

R

The default accelerated version can be run with:

/unsup/Ra/bin/R

You can still run the previous versions with the commands:

/unsup/R-2.8.1/bin/R and /unsup/R-2.8.1a/bin/R (64 bit only)

or you can "downgrade" your path to the /unsup/R-2.8.1/bin or /unsup/R-2.8.1a/bin locations.

--Guidelines for using Stat Thin Clients with servers

All the access stations at students desks have now been converted to thin clients for Linux servers. The following are guidelines that you should follow to make best use of the thin clients:

-> Avoid using the GNOME option on startup (typing "G" for session). GNOME is slower than the "basic" interface and it is prone to errors. It can lock up after a few months of use. And it can fill your disk quota because the Trash bin does not properly empty

-> Use the Failsafe session (typing "F" for session) if the thin client kicks you off after attempting a login. Once you enter your password in the red window, you should be able to see error messages and remove files if you are over quota

-> Turn off the thin client when you are not sitting at it for extended periods. The thin client should typically be powered down overnight. If you use it in the morning, and then go off and stop using it until late afternoon (5 or 6 hours), please turn it off. This saves energy and reduces noise.

-> Since a thin client should normally be turned off, you should run long jobs with batch processing rather than interactively. Learn how to use background jobs where the terminal session can be closed. Learn about using the "nohup" command. Learn how to use the batch commands for R ("nohup R CMD BATCH ... ") and Matlab ("nohup matlab ..."). It is OK to run shorter, interactive jobs while you are able to sit in front of the thin client.

-> Use the deskXX assigned servers for desk services (firefox, thunderbird, etc). For those without assigned deskXX servers, use the public01-04 servers for desk services. Do NOT use bigmemXX compute servers for your desk services. Those should be reserved for computation without competition from firefox and other desk processes. Do NOT use the deskXX servers for big, long-running programs. Try to keep those types of programs on the bigmemXX servers and other research compute servers. Otherwise the compute jobs compete for resources with interactive desk service programs like Firefox and Thunderbird.

-> Firefox is causing some problems at this time, so please start Firefox (for now) with the "firefox -cleanup" option. There can be phantom Firefox processes left around even after you quit firefox. If you know how to check and kill those processes, please do. Otherwise I will start killing them off as the "root" superuser. This means that some Firefox sessions left running overnight will be terminated even if you wanted them to keep running. Turning off the thin clients overnight should help with this issue and avoid unexpected Firefox shutdowns.

9/3/09 - Upgrade your FVWM config, More Firefox issues, Stat computer access if you have H1N1

--If you have not done so before, you can upgrade your basic (FVWM) Linux desktop to include virtual screens and access buttons at the bottom by executing the command:

/p/stat/bin/fvwm_update

Details are at:

http://www.stat.wisc.edu/twiki/bin/view/StatDocs/StatUnixdesktop

--Firefox is causing problems with use of server resources when left running overnight and over several days on Linux servers. This would not be a problems if thin clients were turned off each night as per the thin client guidelines - see previous "Occasional message about computing", archive at:

http://www.stat.wisc.edu/twiki/bin/view/StatDocs/StatOccasMesgs

I am going to start automatically killing Firefox sessions that started running on the previous day or days. Those that started "today" will not be killed. Please be prepared for this. Better yet, please shut down your thin clients overnight.

--If H1N1 pandemic issues arise on campus, it may be very useful for students to have another way to get to the Stat servers rather than coming to MSC to use the thin clients. Please consider acquiring a laptop or home desktop computer that you could use from any location. Laptop (and netbook) prices have fallen to the point that a useful system can be purchased for under $400 (sometimes less).

9/25/09 - Fixing Latex problems, Fixing Firefox problems

--If you have a problem with Latex finding fonts, please execute the following 2 commands in a terminal screen:

chmod 644 ~/.texmf-var/ls-R
mktexlsr ~/.texmf-var

--If you get the automated repeating message that you need to terminate Firefox that has been running since the previous day, BUT you don't have think you had a session of Firefox running since the previous day, please exit Firefox (if you are in it) and execute the following command:

pkill firefox

It would be useful to send me a note when you do this with a description of what might have happened if Firefox suddenly stopped working (or working strangely). Typically this would be a freeze up when you went to a page with some pop-up ads or Flash animations.

10/8/09 - Update to thin client startup screen

--The thin client startup window has been updated. The fonts are bigger and easier to read. And if you make a mistake on entering the server name, you will usually get another chance to enter correctly. This saves a potential full power cycle and an extra 30 seconds of startup.

10/26/09 - Please turnoff thin clients

--Thin clients should be turned off when not in use. At this time, it appears that maybe 10 users in an evening might leave their thin clients running. Some users almost never shut down their thin clients. I estimate that the unnecessary use of energy is 7 kilowatt-hours a week (or more), or about 360 kilowatt-hours a year. Besides the waste of energy, it likely costs the University about $500/year for this unproductive operation, PLUS the wear and tear on the thin clients, PLUS the extra noise produced.

Starting tomorrow, you will get an automated message (around 1PM) if my script detects the likelihood that you have left a thin client on overnight. You should respond by turning off the thin client at the end of the day. I will monitor this, and I will send more specific messages to users that have left thin clients on for several days. Eventually I will send a warning and will shut down thin clients that have still not been turned off by the users.

PLEASE turn off your thin clients if they will not be used for several hours and/or overnight.

12/14/09 - R-2.10.1 will be the default version for spring

--I have completed the installation of R-2.10.1. That will become the default version after the current semester ends. So you should start testing this new version with your applications. As mentioned in an earlier note, the accelerated version will be the default for 64 bit systems, like bigmem01 and bigmem02, and the deskXX systems. The 32 bit systems, publicXX, will continue to use the non-accelerated version by default. Start the new version with:

/unsup/R-2.10.1/bin/R

If you still want the unaccelerated version for 64 bits, you can use:

/unsup/R-2.10.0/bin/Rb

This change also allows you to set a single path:

(for bash shell in .bashrc) PATH = $PATH:/unsup/R-2.10.1/bin

(for tcsh shell in .cshrc.local) set path = ( $path /unsup/R-2.10.1/bin )

Then you can run Accelerated R on 64 bit systems with:

R

and basic (unaccelerated) R with:

Rb

on 64 bit systems, and:

R

on 32 bit systems (by default, unaccelerated).

Please keep in mind that you will need to reinstall your personal R packages and libraries for use with R-2.10.0 by adding a 2.10 directory to your personal library path and then completing reinstalls. For 32 bit systems do:

mkdir -p ~/R/i686-pc-linux-gnu-library/2.10

and for 64 bit systems, do:

mkdir -p ~/R/x86_64-unknown-linux-gnu-library/2.10

-- MikeRedmond - 29 Dec 2009