OSG Newsletter – June 2013

Using the OSG to diagnose, treat, and eventually prevent disease


Dr. Shi-Jian Ding, an assistant professor in the University of Nebraska’s College of Medicine, is a researcher in the field of proteomics – the large scale study of proteins and their functions. Ding is currently involved in two projects. The first involves studying epigenetic memory during the stem cell reprogramming process and the second involves studying nuclear matrix proteins, which play an important role in DNA. Collaborating with another colleague, Ding seeks to understand how protein PTMs regulate in a nuclear matrix that triggers a DNA damage response.

With the help of the University of Nebraska’s Holland Computing Center (HCC), directed by Dr. David Swanson and integrated with the Open Science Grid, the team has modified OMMSA so they can now search as many modifications as needed. But, this isn’t possible without the resources of the Open Science Grid.
Read more.

Introducing the new HTCondor and Open Science Grid Release Manager

Tim Theisen

Please welcome Tim Theisen to the University of Wisconsin OSG Software team.

Tim is a Madison native, who graduated from the University of Wisconsin-Madison with both a Bachelor’s and a Master’s of Science in Electrical Engineering.

Tim has 30 years of software development experience- he wrote Ghostview, an X11 PostScript previewer. At the UW-Madison, he deployed an AFS-distributed file system. At Persoft, he led a team that developed a web-to-host terminal emulation product using a Java applet. At TomoTherapy, he totally revamped the packaging of the HPC and GPU clusters that are shipped with the TomoTherapy radiation treatment product- which simplified cluster installation and maintenance. He also designed, implemented, tested and released the TomoTherapy GPU laptop demonstration platform. (This release was a single DVD that a sales or marketing person could install and use.)

An avid downhill skier, Tim is a member of the National Ski Patrol and is an Outdoor Emergency Care and Toboggan instructor.

~ Tim Theisen

Introduction to the CILogon Basic Certificate Authority

The CILogon Basic CA is a service that allows students at universities with existing single sign-on systems to use their campus credentials to get a certificate issued by the CILogon Basic CA instantly. This certificate is only issued if the campus single sign-on system verifies the user’s credentials.

If you manage an OSG VO and your university is already on the list of sites on the CILogon Basic CA web page, http://cilogon.org/osg, then you can have your VO members get CILogon Basic CA certificates now. Note that in addition to getting a certificate, it will also have to be registered with your VO’s VOMS service. This provides an additional security check on all certificate registrations.

If you run an OSG site, the OSG Security Team is looking for sites willing to accept CILogon Basic CA certificates from users for access to your resources. In most cases, this only involves installing the cilogon-ca-certs rpm.

The downside to the CILogon Basic CA for some is that there is one provider, protect.net, which will let anyone with a valid email address request an account. This is not a problem for grid services, since in addition to a valid certificate, a grid user will need a DN mapping entry in their VO’s VOMS server or gridmap files before they can access any grid resources. If, however, other services such as web pages are restricted to any valid client certificate, then those permissions might want to be revisited with CILogon Basic CA certificates installed, since they will likely include more than research-related individuals.

~Kevin Hill

Pacman end-of-life milestone

On May 31, 2013 OSG reached the end-of-life for the use of Pacman as a package manager for distributing OSG middleware. This milestone came after a long campaign to upgrade OSG sites still utilizing Pacman as an installation tool to a new format: Red Hat Package Manager (RPM). Pacman was the only packaging tool used by OSG for distributing middleware from the beginning of the project until the fall of 2011, when the first RPM release was completed. For the past few years packaging of software has been released in both formats- RPM and Pacman. As of May 31st, Pacman distributions for OSG middleware will no longer be updated.

At the time this article was written, most OSG sites have either been updated to the RPM packaging or have scheduled an update. OSG Operations will continue to host Pacman files until all sites are upgraded. The OSG Production and Software teams would like to thank Saul Youssef at Boston University for his time and dedication to the Pacman tool. His support of this tool has had a heavy impact on how OSG has packaged and distributed middleware since its inception.

For more about Pacman, see:

For documentation about the OSG RPM release, see:

Operations Final EOL Notification:

~ Rob Quick