UT System Research Cyberinfrastructure

The UT System Research Cyberinfrastructure (UTRC) project is underway and progress is being made toward providing researchers at UT System institutions access to enhanced compute, storage, and networking infrastructure. The new TACC resource Lonestar began production on February 1 and is available to UT System researchers through UTRC. Researchers at several institutions have already applied for allocation and have begun processing.

Jay Boisseau, TACC Director, and other TACC staff members will visit UT Arlington on Monday, April 25th to meet with members of our research community and staff who may benefit from access to this resource. Jay will present an overview of the TACC resources and services available to us through the UTRC project and a summary of the research projects underway at TACC. We will have a Q&A session for UT Arlington researchers to discuss our current projects, existing computing resources, future needs, and how TACC can possibly be of assistance.

Please join us in the Palo Pinto room, E.H. Hereford University Center, on Monday the 25th of April from 2:00 to 5:00 pm.

2:00 – 2:30 TACC Resources and Services – Jay Boisseau
2:30 – 3:00 TACC R&D Projects – TACC Staff
3:00 – 3:30 UT Arlington HPC Resources and Utilization – OIT Staff
3:30 – 4:00 HPC Research Spotlight – Frank Lu, Luca Massa
4:00 – 4:30 HPC Research Spotlight – Peter Kroll
4:30 – 5:00 Open Discussion, All

OIT will provide light refreshments.

High Performance Computing for NextGen Sequence Analysis

April 14, 2011 – 9 a.m. – 5 p.m. (CT)
Austin, TX

This one–day workshop is intended to introduce life scientists to high performance computing at the Texas Advanced Computing Center (TACC) with a specific emphasis on NextGen Sequence analysis. Attendees will learn how to utilize an array of computational and software resources that TACC offers for Computational Biology. Topics to be covered include large-scale computing, data management, loading and running applications. An introduction to general sequence analysis concepts along with specific, real-world examples will also be provided. A hands-on lab session will give attendees an opportunity to work with TACC systems on NextGen sequence data sets.
The class is intended for biologists and advanced programming skills are not required. However, a working knowledge of Unix is expected.

Please visit the following URL for course registration and additional details: http://www.tacc.utexas.edu/user-services/training/classes/compbio/

Lonestar

The new Lonestar system is the latest in the line of leadership high performance computing systems provided by the Texas Advanced Computing Center (TACC) toresearchers in the state of Texas. Two things make this system unique: one is the comprehensive computing capabilities provided by the system. Whether you need to run large scale parallel computing jobs, shared memory computations, remote visualization tasks, GPGPU computing, or high throughput computations, Lonestar has the capabilities you need. The second aspect is the broad partnership involved in deploying this system, with funding provided by the National Science Foundation, The University of Texas System, Texas A&M University, Texas Tech University, The University of Texas at Austin, the Institute for Computational Engineering and Sciences at The University of Texas at Austin and a number of research centers. If you need large scale computation for your research, and you work in higher education in Texas, Lonestar is the system for you!

Join the staff of TACC for a 90 minute webinar on March 24 to learn about the capabilities of Lonestar. An overview of the system itself will be provided, along with information about how to apply for an account, and information about upcoming in-depth training opportunities. This course is targeted at all researchers in Texas Higher Education or the TeraGrid community interested in learning about TACC resources.

To register for this event, please visit:

http://www.tacc.utexas.edu/user-services/training/classes/lonestar-presentation/

Modernizing System Administration

If you haven’t heard by now, Luke Kanies Wants to Modernize System Administration. Yes, the puppet master speaks!

We’ve been using Puppet at UT Arlington for the past several years. I had initially looked into using CFEngine for configuration enforcement and change management, but a good friend of mine turned us on to Puppet. Puppet has really transformed the way my administrators think about setting up and maintaining systems. There’s a lot less direct SSH’ing into a system, messing with a configuration file (and hoping that you’ve edited the same file the same way on every system), and adding/starting/restarting the service that uses that configuration file. There’s also a lot more control in how we do things — and just like that, viola, we have a documented change control process!

Obtaining user information from LDAP using Perl

This is much simpler that the PHP example listed a few weeks ago. It demonstrates some of the advantages of Perl (namely, just about anything you want to do is already built as a module by someone who’s been where you are). Please refer to http://search.cpan.org for Net::LDAP and Net::LDAPS module documentation and usage examples.

In this example, we’ll bind to the LDAP server using an application account (in the cn=applications,dc=uta,dc=edu branch of our directory server) and search the account branch (cn=accounts,dc=uta,dc=edu) for all users (uid=*). We’ll fetch the NetIDs (uid), e-mail addresses (mail), and the common names (cn) for each account.

#!/usr/bin/perl -w

use strict;
use Net::LDAPS;
use Data::Dumper;

my $bind_dn       = 'cn=mavapp,cn=applications,dc=uta,dc=edu';
my $bind_password = 'mavAppPass';
my $ldaps         = Net::LDAPS->new('ldap.cedar.uta.edu');
my $mesg          = $ldaps->bind( $bind_dn, password => $bind_password );

my $result  = $ldaps->search(base => "cn=accounts,dc=uta,dc=edu",
                                            filter => "(uid=*)",
                                            attrs => ['uid','mail','cn'] );

my $entries = $result->as_struct();

# How many entries did we find?
print scalar $entries . " entries returned\n";

# Print them out
foreach my $dn ( keys %{$entries} ) {
   foreach my $attr ( keys %{$entries->{$dn}} ) {
      foreach my $val ( @{$entries->{$dn}->{$attr}} ) {
         print "$attr - $val\n";
      }
   }
   print "\n";
}

This last section could be simplified using the Data::Dumper module as:

print Dumper( $entries );

My code’s compiling, leave me alone.

Read the rest of this entry »

Much of SCO’s case was just dismissed. Novell owns UNIX copyright.

Wow!
You’ve got to check out this ruling handed down this afternoon in the SCO v. Novell case.

CONCLUSION

For the reasons stated above, the court concludes that Novell is the owner of the UNIX and UnixWare copyrights. Therefore, SCO’s First Claim for Relief for slander of title and Third Claim for specific performance are dismissed, as are the copyright ownership portions of SCO’s Fifth Claim for Relief for unfair competition and Second Claim for Relief for breach of implied covenant of good faith and fair dealing. The court denies SCO’s cross-motion for summary judgment on its own slander of title, breach of contract, and unfair competition claims, and on Novell’s slander of title claim. Accordingly, Novell’s slander of title claim is still at issue.

Read the rest of this entry »

Obtaining user information from LDAP using PHP

This ought to be in a FAQ somewhere, I certainly get asked it enough: “How can I retrieve attributes from LDAP of users who log into my web application?” Well, I’ll break it down with an example that retrieves information about a user that submits their uid & password to a form. Note that this code could be simplified to handle authentication only by determining if the ldap_bind() succeeds or not — it’s usually enough to simply be able to bind to verify someones identity.

I’ll make my comments after each section of code. Read the rest of this entry »

Sysadmin Appreciation Day

Hey, system adminstrators: Tom Limoncelli “appreciate[s] you!” And I do too!

The Last Friday Of July is System Administrator Appreciation Day

Let’s face it, System Administrators get no respect 364 days a year. This is the day that all fellow System Administrators across the globe, will be showered with expensive sports cars and large piles of cash in appreciation of their diligent work. But seriously, we are asking for a nice token gift and some public acknowledgement. It’s the least you could do.

Consider all the daunting tasks and long hours (weekends too.) Let’s be honest, sometimes we don’t know our System Administrators as well as they know us. Remember this is one day to recognize your System Administrator for their workplace contributions and to promote professional excellence. Thank them for all the things they do for you and your business.

Nominate Your IT Hero for SysAdmin of the Year 2007.

Have your (Perl) Pie and eat it too!

Undoubtedly one of the most frequent tasks a system administrator, or developer, faces involves making inline changes to a file or set of files. This can range from the very complex edit to the very trivial.

Let’s say you have a series of PHP pages in your web site that access your MySQL server. What happens if you need to change the name of your MySQL server? Would you go into each file individually, search for the line (or lines) of code to edit and save the file? This can be tedious, error-prone and time consuming.

The ’sed’ (string editor) command is often used to accomplish this, where sed is passed a file name and a regular expression for the string substitutions. Output from sed is sent to standard output (usually the terminal) which means that you must redirect it to another file and then copy the new file over the original. This effectively changes the original but requires a lot of excess steps. There’s got to be a better way, right? Yes, ‘perl’ can do it in one shot — Read the rest of this entry »