Volume 11, Number 2, June 2014

University of Minnesota
Supercomputing Institute
Editor: Tracey Bartlett

The Users Bulletin provides a summary of new policies, procedures, and events of interest to MSI users. It is published quarterly.

1. New MSI User Forums: There are three new MSI User Forums:

chem: for users of chemistry applications
python: for Python users
matlab: for MATLAB users

A list of MSI user forums and links to the forum pages can be found on the MSI website.

These forums are a way for researchers to exchange ideas and ask questions on specific topics. For instance, the chem forum involves numerical modeling of a wide variety of chemistry applications, including NAMD, HOOMD, LAMMPS, Gromacs, Gaussian, NWChem, Turbomole, GAMESS, Amber, Vasp, CHARMM, MOLCAS, Schrodinger, ADF, MCCCS, MOPAC, Molpro, and Orca. 

Questions and discussions in the forums are encouraged, but not limited to, topics like:
• Commercial, community, and user-generated software.
• Developing and running models, doing analysis, and post-processing results.
• Parallel computation on MSI's High Performance Computing (HPC) resources.
• Usage, sharing, and potential expansion of commercial licenses.

You can post a question or start a discussion. See a question you can answer? Help your peers with feedback, suggest new ideas, and vote on the best and worst answers.

MSI staff will also use these forums to announce changes and events of interest, including:
• Availability of new software
• Changes and expansion of HPC systems and storage
• Upcoming tutorials (including requests for topics of interest to you)
• Organizing visits from commercial vendors
• Organizing user group meetings at MSI

As the variety and extent of conversations grow, these forums should also become an valuable resource for finding answers to problems others have run into.

2. Supplemental SU and Storage Request Deadline: The MSI HPC Allocation Committee considers requests for supplemental allocations each quarter. The next quarterly deadline for submitting requests for supplemental SUs and storage allocations is July 1, 2014.

To request additional HPC SU allocations or additional storage, please use the online Supplemental Request Form. The request must be sent by the PI or the Group Administrator.

Questions concerning the form or the request process can be sent to the Research Programs Administrator at rpa@msi.umn.edu.

3. Calhoun Decommissioning: On July 2, 2014, Calhoun will be decommissioned. MSI is entering a construction phase in our main data center to prepare for the new HPC system, which will be delivered in the fall of 2014. The physical space, power, and cooling used by Calhoun must be reconfigured to meet the requirements of the new system.

To continue to provide the same functionality currently available on Calhoun, a very long queue with up to a 30-day duration will be implemented on Itasca by July 2. We will also be providing some additional features on the Itasca system to improve the overall throughput of jobs. We strongly recommend that you begin to transition your work to other MSI systems in advance of the July 2 deadline. 

If you have questions or need assistance, please contact MSI Help through the online Help Request form, via email to help@msi.umn.edu, or by calling 612-626-0802.

4. Windows Remote Desktop Servers: As part of our migration from our Windows remote desktop servers, Iron and Copper, to Citrix XenDesktop, we have added a new virtual desktop at xen.msi.umn.edu. The "Node-Locked Software" desktop is a single, shared machine hosting software that, due to licensing limitations, cannot be installed on our regular virtual desktops.

With the availability of this functionality, the Cambridge Structural Database, Scaffold, and ProteinPilot software packages are now available on xen.msi.umn.edu, through the "Node-Locked Software" desktop option. To comply with the vendors' license requirements, we will remove these software packages from Iron and Copper during the July maintenance period.

The following information may be useful:
How to connect to Citrix Pools
How to access an MSI Windows server from a Windows machine
General information about the Windows Application Servers

Please send any questions or concerns to MSI Help through the online Help Request form, via email to help@msi.umn.edu, or by calling 612-626-0802.

5. COMSOL Multiphysics Workshop: COMSOL staff will be providing a workshop on COMSOL Multiphysics at MSI on June 19, 9:30-12:30. The workshop includes an overview and hands-on practice. More information and registration is available on the MSI website

6. Intel Xeon Phi Workshop: Intel will present a workshop on modernizing code to take advantage of parallel architectures found in the Intel Xeon processor and the Intel Xeon Phi Coprocessor. This all-day workshop will be held Thursday, September 11, in 402 Walter Library, 8:30am - 4pm. Lunch is provided. The workshop is free, but registration is required. The MSI website has complete information and a link to the registration website.

7. Virtual School of Computational Science and Engineering (VSCSE) Courses: The VSCSE will be presenting a course entitled "Data Intensive Summer School" on June 30 - July 2, 2014, and a "Science Visualization Course" on August 25 - 26, 2014. While these courses are not being held on the University of Minnesota campus, there are several locations throughout the country that still have openings. More information and registration can be found on the VSCSE website.

8. Software Renewals and Discontinuations: 
a. MSI will soon be removing some older Gaussian modules. Anyone still using these modules will need to transition to newer versions of Gaussian. Please see the MSI Forums for more information.
b. In order to align software resources to the needs of researchers, MSI’s software working group regularly reviews software at MSI. The Software Renewal page contains information about which software packages are coming up for renewal and which ones will not be renewed. You can also provide feedback and requests for MSI software purchases.

9. Journal Covers: MSI displays the covers of journals that feature MSI-related research in our public area. If you have authored a cover article, we would appreciate it if you would send us a PDF of the journal cover. We will print it and display it in our Commons area.

10. Jobs Available at MSI:
a. Infrastructure Support Systems Administrator
b. Project Manager/Systems Analyst

11. Useful Webpages: Looking for help with your research? MSI has a number of complementary services:

a. Software application and database development

b. Interdisciplinary informatics and bioinformatics
c. Visualization
d. High-performance computing
e. Network and general computing

12. Useful email addresses:
a. Address for requesting technical assistance: help@msi.umn.edu
b. Address for submitting citations for articles, papers, posters, book chapters, and other publications supported in whole or in part by MSI resources: submissions@msi.umn.edu
c.
 Address for submitting videos of your research or suggestions for research articles: videoclips-articles@msi.umn.edu