ARSC HPC Users' Newsletter Issue 432 2014-05-14

ARSC HPC Users' Newsletter Issue 432 2014-05-14

A publication of the Arctic Region Supercomputing Center.

1 FASST This Weekend!

1.1 Summary

This weekend is the annual Butrovich Building Fire and Alarm Safety Systems Test (FASST). Power in the building will be disabled intermittently. Most major ARSC systems are scheduled to be offline from 10am Saturday (May 17) to 11pm Sunday (May 18). This protects ARSC equipment from unexpected power drops and allows us to complete various hardware maintenance tasks.

The systems we will take offline include (but are not limited to)

  • All of the compute and login nodes for our Penguin Computing cluster (pacman)
  • All of the compute and login nodes for our Cray XK6m-200 supercomputer (fish)
  • All of the Linux workstations in the Duckering 234 lab. These systems are pacman login nodes and depend on resources housed in Butrovich.
  • The archival storage system (bigdipper, a.k.a. $ARCHIVE)
  • The high-performance Lustre file system (digdug, a.k.a., $CENTER)
  • The LSI Compute Portal and secure filesystem. (LSI systems are scheduled to come back online Monday May 19 at noon.)
  • All ARSC-hosted virtual machines.

1.2 Process

While the downtime is scheduled for 10am Saturday, in reality, properly powering down ARSC systems is a multi-stage process, with many cross-system dependencies. So it is unlikely that any particular system will go offline at the exact moment expected.

ARSC technicians will be taking advantage of the FASST shutdown to perform a lot of maintenance, such as replacing motherboard batteries, moving rack equipment, and adjusting cable configurations.

Our pacman cluster has hundreds of compute nodes and runs at high heat levels. Whenever pacman is powered down, the dramatic temperature changes can cause internal electronics to bend and break, especially networking cards. Inevitably, not all nodes will come back on-line immediately, or other startup problems may occur. We appreciate your patience as we work through any hiccups in the restart process.

1.3 Tuxedo Replaced by Pacman

During this downtime, the "tuxedo.inbre.alaska.edu" LSI login cluster will be retired. Replacing the service provided by the tuxedo login cluster will be "pacman.arsc.edu", the Penguin Computing Cluster hosted by the Arctic Region Supercomputing Center on the UAF campus.

The pacman system is a 2816 core system offering both interactive logins and batch job submissions from the cluster itself and the LSI Compute Portal. The pacman system supports long runtime batch jobs and a 128 core node with 2 TB of RAM for bioinformatics applications.

For information on how to access pacman and the 128 core node dedicated to the use of bioinformatics applications, please communicate with ARSC User Support.

1.4 The Eerie Darkness

Normally, the Butrovich machine room is brightly lit and filled with flashing computer lights. The high powered fans, which pull heat out of the computer racks, are so noisy that you can hardly hear yourself think.

Tim Slauson, student employee for ARSC, tells of his experience stuck in the Butrovich machine room during a power outage.

[It was] during an October '12 outage to Butro when the main power feed to that building was getting upgraded. We decided to take the opportunity to move a bunch of patches and some fiber trunk lines. We were told that systems and lights would still be operational thanks to a UPS grid that we were assured was good for two hours, and that after those two hours we would have emergency lights to work under. I met Jeff [Harrison] down in the data center at 7:20 on Sunday morning (2012-10-14), grabbed a flashlight (a good idea even with full lighting, because the [cable space under the floor] is dark), and he gave me a paper with the desired mappings and disconnects listed. Main power was down at this point, so I started working with the cables right away. About 20 minutes later, the UPS grid failed far short of its two-hour estimate and everything in the data center fell silent. We still had emergency lighting, but that was spotty so I took out my flashlight. And a good thing that was! Not too shortly afterward, when I was working under the tiles in front of the 6509 [router] cabinets, the emergency lighting failed too! I ended up doing the last hour of my shift down in the floor with one hand moving cables out of the way, one hand pulling cables, and the flashlight in my teeth.

Fortunately for us, Tim was not eaten by a Grue. But our dedicated ARSC employees are willing to take any risk to ensure you get top-quality High Performance Computing!

2 ARSC Mirrors ArchAssault Linux

The ARSC public mirror, accessible via http://mirrors.arsc.edu and ftp://mirrors.arsc.edu, is now mirroring ArchAssault Linux. As described at https://archassault.org/

The ArchAssault Project is an Arch Linux derivative for penetration testers, security professionals and all-around Linux enthusiasts. This means we import the vast majority of the official upstream Arch Linux packages, and these packages are unmodified from their upstream source. While our Arch Linux base is primarily untouched, there are times where we have to fork a package to be able to better support our vast selection of tools. All of our packages strive to maintain the Arch Linux standards, methods and philosophies.

The ARSC public mirror currently includes a variety of interesting software and data projects, including

  • Several Gnu/Linux distributions (CentOS, Fedora, and Ubuntu)
  • The GNU projects repository (e.g., GNU Emacs and GNU Hurd)
  • The Linux Kernel repository
  • Over 800 gigabytes of Project Gutenberg data

3 More Bash Tips

3.1 Invoke an External Editor

In the Gnu Bash shell, there is a helpful command called "edit-and-execute-command", which is invoked with the keyboard sequence C-x C-e (i.e., Control x, followed by Control e). This command will open a temporary file inside of a text editor. When the editor is closed, any text entered in the temporary file will be executed by bash directly in the running shell, with each command and its output echoed to the terminal, as though they had been entered normally.

This is very handy if you have some complex set of commands you need to tweak and run, but you do not want to create a real script file. In other words, you get the full benefit of your editor's navigation, pasting, and macro capabilities, without interrupting your workflow by needing to create and execute a separate script.

You will want to export the EDITOR variable from your .bashrc or .bash_profile to ensure your preferred editor is opened. For example:

export EDITOR=emacs

3.2 Refer to the Previous Command

Gnu Bash has an "event designator", typed as !! (two exclamation marks), which refers back to the text of the previous command. This can be helpful for a work cycle in which you must tweak a command a few times (to get the correct output) and then use the command output as part of another command. For example:

$ ls
data-20140501.txt  data-20140510.txt  data-20140520.txt  data-20140601.txt  data-20140610.txt  data-20140620.txt
data-20140505.txt  data-20140515.txt  data-20140525.txt  data-20140605.txt  data-20140615.txt  data-20140625.txt
$ grep -l somevar *
data-20140501.txt
data-20140515.txt
data-20140520.txt
data-20140610.txt
$ grep -l somevar * | grep 201405
data-20140501.txt
data-20140515.txt
data-20140520.txt
$ cp -v `!!` ../report-data/
cp -v `grep -l somevar * | grep 201405` ../report-data/
`data-20140501.txt' -> `../report-data/data-20140501.txt'
`data-20140515.txt' -> `../report-data/data-20140515.txt'
`data-20140520.txt' -> `../report-data/data-20140520.txt'

(Of course, there are other places !! could be used in the above commands, but this was not necessary owing to the convenience of the C-p shortcut, which brings up the previous command for editing.)

4 Incorporating ARSC Utilization into Grant Budget Proposals

For researchers who are planning to submit a grant and would like to incorporate ARSC utilization into the grant budget proposal, we have created an informational page in the ARSC Knowledge Base:

http://www.arsc.edu/arsc/knowledge-base/incorporating-arsc-utiliz/index.xml

This includes details on how to account for ARSC personnel support, dedicated programming work, and new hardware or software purchases.

5 ARSC Summer Tours Presentations

ARSC will be hosting the seasonal Summer Tours presentations to UAF visitors (and anyone else who is interested) every Wednesday from June 4 to August 13. If you already work around here, this can be an opportunity to give friends, family, or significant others an idea of what we do here at ARSC.

Each presentation takes place in the Butrovich machine room viewing area (in the hallway on the lower level) with a digital slide presentation, talk, and Q&A, which takes about thirty minutes. Afterwards, interested visitors get a brief walk-through tour of the machine room, to show them the ARSC storage equipment and supercomputers (for groups with less than 7 people, 8 years of age and older).

6 Frontier Scientists Articles

We want to draw attention to two interesting articles on Frontier Scientists from Azara Mohammadi, a Publications staff member here at ARSC. The first article (from March) tells the story of Soumik Basu, a PhD candidate who moved from Kolkata, India to UAF in order to study climate change in the Arctic region:

Modeling shifting oceanscapes; a collective pursuit

The second article (from April) summarizes the work of Dr. Kate Hedstrom, and several of her colleages, in the field of regional ocean modeling:

Predicting the effect of anomalous sea ice loss and increasing sea surface temperatures on global storm systems

7 More Information

7.1 Editor

Christopher Howard mailto:cmhoward2@alaska.edu

7.2 Credits

Oralee Nudson, ARSC Lead User Consultant. Content reviewer and insider source for ARSC news and tips.

Appreciation goes to Jeremiah Dabney and Tom Bachert for helpful information related to the FASST weekend.

7.3 Publication Schedule

The newsletter is usually released on the third Wednesday of each month.

7.5 Archived Newsletters

7.6 Questions, Comments, and Submissions

mailto:owner-hpc_users@arsc.edu

Need advice? Submit a question about HPC or ARSC software, and we will feature it in a Q&A section in the newsletter.

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