MCSR Parallel-O-Gram

MATLAB 2012b has been released. For standalone users (that is, most individual faculty, staff and students who are installing MATLAB on their personal or work computers), the Activation Key needed to install the new version is unchanged. Thus, the installation instructions in my.olemiss.edu are current and correct.

The license server for lab installations has been updated to support 2012b, so lab administrators who use this server may update their images at any time. There is a new File Installation Key for lab computers for this new version. We will have the documents in the myOleMiss portal updated soon. In the meantime, interested lab managers may contact MCSR staff for the latest File Installation Key for 2012b.

This semester MCSR will offer several workshops on the University of Mississippi campus to help train users to utilize the servers and software we administrate.

Each workshop will be offered twice during a single week, on Wednesday and Thursday at 3pm. Each workshop will be approximately one hour long. With one noted exception, all workshops will be held in room 107 of Weir Hall.

Introduction to the UNIX Command Line, September 5th and 6th
Introduction to MATLAB, September 19th and 20th
Intermediate UNIX Command Line, September 26th and 27th (Weir 104)
Introduction to Python, October 3rd and 4th
Introduction to R, October 10th and 11th
Introduction to LaTeX, October 17th and 18th
Introduction to Regular Expressions, November 7th and 8th
Introduction to MPI, November 28th and 29th

Go to olemiss.edu/workshop to view or register for any of these workshops. Training is free, as always.

If you have questions, or would like to suggest a workshop topic, please email us at assist@mcsr.olemiss.edu.

Sequoia, MCSR’s Altix XE Infiniband Cluster, is back in service and available to users.  During the outage, several changes were made to the system:

1.  26 new nodes were added, bringing the total cluster to 124 compute nodes and 1304 compute cores.

2.  The /ptmp filesystem where most users do their work was moved to a new device. The new device offers more space, faster performance, and better reliability relative to the old device.  All user data in /ptmp has been moved over; the change in devices should be completely seamless.  Please do let us know if there’s anything you think we may have missed.

3.  Pursuant to point 2, the /ptmp and /home areas on sequoia are now located on different devices.  This should be familiar to users who have used redwood and earlier systems.  We encourage you to do most of your work in the /ptmp area.

4.  The filesystem that is mounted as /ptmp on sequoia is mounted as /hpc_ptmp on hpcwoods. What this means, in short, is that you can transfer files directly between your computer and sequoia.  Just use command-line or GUI tools to connect to hpcwoods and transfer files in /hpc_ptmp/$USER/file.  Then when you log into sequoia, that same file will be present as /ptmp/$USER/file; there is no need to do any sftp or scp command to move the files between hpcwoods and sequoia.

As always, please contact MCSR Staff at assist@mcsr.olemiss.edu with any questions or concerns.

There is a new version of Abaqus, v. 6.12-1, available. The UM license server for Abaqus has been updated, and Abaqus itself has been upgraded on sequoia. An example PBS script for running Abaqus on sequoia is located on sequoia in

/home/bwhopkin/sample_jobs/sequoia_abaqus_example/6.12

The UM concurrent-usage license allows Abaqus to be installed on any UM-owned computer. If you’re a new or current Abaqus user at UM and would like a copy of the new version, contact MCSR staff at assist@mcsr.olemiss.edu for installation media.

Unfortunately, the UM Abaqus license does not allow non-UM users of MCSR servers to access this program.

The University has renewed the campus MATLAB license. All users of the MATLAB campus license will need to reactivate your MATLAB installation to use the new license unless you installed after April 1st, 2012.

To reactivate your current Windows or Mac OS X installation: start MATLAB, then choose Help->Licensing->Update Current Licenses. Choose “License 585993: Total Academic Headcount Campus – TAH Designated Computer”. Click OK a series of times. Restart MATLAB for the changes to take effect.

Instructions for reactivating network and lab installations can be found on the MATLAB page on myOleMiss.

If you have any questions about MATLAB reactivation, please contact MCSR at assist@mcsr.olemiss.edu or 915-3036.

If you’ve been using MATLAB under the University of Mississippi’s Total Academic Headcount license (ie, if you obtained MATLAB by following the instructions in the MyOleMiss portal), you’ve likely been seeing a warning that the current license will expire at the end of March. While technically true, this is a bit misleading, and there is no cause for concern. The license does formally expire each March 31st. However, it then enters a 30-day grace period; the software will work, unrenewed, until April 30th. A renewal purchase is in progress and will be complete next week, well in advance of this cutoff date. Thus, the warnings about the license expiring at the end of March can simply be ignored.

MCSR has scheduled the following workshops for this semester:

Introduction to UNIX – Part 1, Thursday, February 9th, 3pm, Weir 107
Introduction to UNIX – Part 2, Thursday, February 16th, 3pm, Weir 107
Programming in Python for Beginners, Thursday, March 1st, 3pm, Weir 107
Version Control with Subversion, Wednesday, March 7th, 3pm, Weir 107
Introduction to MPI and PBS, Thursday, March 22nd, 3pm, Weir 107
Introduction to LaTeX, Thursday, March 29th, 3pm, Weir 107
Scientific Computing in Python, Wednesday, April 4th, 3pm, Weir 107
Introduction to R, Thursday, April 12th, 3pm, Weir 107

Go to olemiss.edu/workshop to view or register for any of these workshops. Training is free, as always.

If you have questions, or would like to suggest a workshop topic, please email us at assist@mcsr.olemiss.edu.

Redwood, MCSR’s SGI Altix 3700 supercomputer, is down today. We will inform you when the problem has been identified and solved and the system is available for use.

While adding nodes yesterday, we were forced to regenerate RSA keys for sequoia (both the head node and all of its compute nodes). If you’ve been getting error messages like this:

IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that the RSA host key has just been changed.
The fingerprint for the RSA key sent by the remote host is
8c:fe:12:eb:7a:c6:41:bf:b7:b9:
f1:67:ad:69:06:0d.
Please contact your system administrator.
Add correct host key in /home/r1260/.ssh/known_hosts to get rid of this message.
Offending key in /home/r1260/.ssh/known_hosts:2
RSA host key for sequoia has changed and you have requested strict checking.
Host key verification failed.

this is simply a symptom of the new key generation. You are not being hacked; there is no man-in-the-middle attack in progress.

To correct the problem, we’ve run a script that automatically deleted everyone’s known_hosts file. Thus, from this point forward you will not see the above error message, but probably will see a message like this:

The authenticity of host ‘sequoia (130.74.110.18)’ can’t be established.
RSA key fingerprint is 8c:fe:12:eb:7a:c6:41:bf:b7:b9:f1:67:ad:69:06:0d.
Are you sure you want to continue connecting (yes/no)?

Just type yes (the whole word) at the prompt and connect as normal. This will only come up once; once you’ve accepted the new key all subsequent connections will happen normally.

Because we deleted the whole known_hosts file, you will need to type ‘yes’ when connecting to redwood for the first time after today as well.

Please contact MCSR staff at assist@mcsr.olemiss.edu with any questions.

Sequoia, MCSR’s Altix XE Infiniband cluster, will be unreachable tomorrow as we add compute nodes. We expect to return the cluster to production by midday Thursday.