Featured researcher and project(s)

Dr. Thomas Oommen
Assistant Professor, GMES

Learn more about how computing is used in his research endeavors.

Dr. Maximilian Seel
Professor, Physics

Learn more about how computing is used in his research endeavors.


COMSOL 5.1 Update 2


COMSOL 5.1 Update 2 (Release Highlights) with MATLAB R2014b LiveLink has been installed and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers authorized to use COMSOL (and any additional modules purchased with research funds) are strongly recommended to re-run a previously successful simulation with this newer version and make sure that the results are consistent before proceeding ahead with subsequent, production quality attempts.

COMSOL 4.3b with MATLAB R2013b LiveLink has been retired (not removed).



Annual proactive maintenance


In order to ensure that Superior continues to operate consistently at a high level, IT will be performing proactive maintenance work starting at 8 am on Tuesday, 5th May 2014.

All nodes -- including the front end, login and storage nodes -- will need to be powered down. Any running simulation at that time will be automatically terminated without further notice.

As such, researchers are requested to complete (or at least checkpoint) their simulations, and transfer any necessary data to a local workstation so that analysis, visualization, and manuscript preparation work can still be continued.

Superior should be accessible as before starting at 8 am on Friday, 8th May 2014.



VASP Implicit Solvation Model


An additional variant of VASP to facilitate implicit solvation model computations has now been compiled (for version 5.3.3) and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers are strongly recommended to verify the results for simpler/inexpensive systems with available literature before proceeding ahead with subsequent, production quality attempts for bigger/complex systems.



VASP Spin Orbit Coupling


An additional variant of VASP to facilitate spin orbit coupling computations has now been compiled (for versions 5.3.3 and 5.3.5) and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers are strongly recommended to verify the results for simpler/inexpensive systems -- preferably with both versions when permissible -- with available literature before proceeding ahead with subsequent, production quality attempts for bigger/complex systems.



R 3.1.2 (Pumpkin Helmet)


R 3.1.2 (Pumpkin Helmet; Release Notes) has been compiled and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers are strongly recommended to re-run a previously successful simulation with this newer version and make sure that the results are consistent before proceeding ahead with subsequent, production quality attempts.

Unless there is a request from researchers to do otherwise, 3.1.1 (Sock it to me) will be retired on Friday, 27th March 2015.



MATLAB R2014b


MATLAB R2014b (Release notes) has been installed and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers are strongly recommended to re-run a previously successful simulation with this newer version and make sure that the results are consistent before proceeding ahead with subsequent, production quality attempts.

Unless there is a request from researchers to do otherwise, R2013b will be retired on Friday, 27th March 2015.



Phonopy 1.9.0.1


Phonopy 1.9.0.1 -- a set of tools for performing phonon calculations based on the supercell approach -- has been compiled and is now available for use from within a qlogin session.



R 3.1.1 (Sock it to Me)


R 3.1.1 (Sock it to Me; Release Notes) has been compiled and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers are strongly recommended to re-run a previously successful simulation with this newer version and make sure that the results are consistent before proceeding ahead with subsequent, production quality attempts.



Data Center Switch Upgrade


Telcom will be upgrading the software on the data center switches, and as such, Superior will be inaccessible during 6-7 am on Thursday, July 17th 2014.

Running simulations will be unaffected.


  1. Open ServiceDesk Plus Portal
  2. Log in with ISO credentials
  3. Use a brief but descriptive ISSUE TITLE in the Subject field

Including as much information as possible (for e.g., command sequence/work flow that is causing the issue, job ID, full path to the folder where the simulation was started from, as is error messages, screenshots, etc.) will help diagnose and resolve the issue in a timely manner.

Named after the greatest of the great lakes, Lake Superior, and built with Rocks Cluster Distribution 6.1.1 (with CentOS 6.3), Superior is a shared high performance computing cluster.

It is used for a variety of research projects including the ones that involve confidential and sponsored data, and provides 32 TFLOPS of CPU and 13 TFLOPS of GPU computing capacity.

It has 1 front end, 2 login nodes, one 48 TB RAID60 NAS node with 33 TB usable space for use by every researcher, two more 48 TB RAID60 NAS nodes with 33 TB usable sapce each for a specific research project, 92 CPU compute nodes [each having 16 CPU cores (Intel Sandy Bridge E5-2670 2.60 GHz) and 64 GB RAM] and 5 GPU compute nodes [each having 16 CPU cores (Intel Sandy Bridge E5-2670 2.60 GHz), 64 GB RAM and 4 NVIDIA Tesla M2090 GPUs].

A gigabit ethernet backend network serves the administrative needs of this cluster, and a 56 Gb/s InfiniBand network serves its computing needs.

Rocks Cluster Distribution Originally started by National Partnership for Advanced Computing Infrastructure and San Diego Supercomputer Center and called NPACI Rocks, Rocks Cluster Distribution is aimed at making every aspect (deploy, manage, upgrade and scale) of high performance computing clusters easy.

National Science Foundation Rocks is supported by the National Science Foundation, under grants OCI-0721623 and OCI-1032778.


Supercomputing for aerospace: http://t.co/Hx1c4KPXxp [via @insideHPC]



Supercomputing the human heart: http://t.co/CwrlyUqd5s [via @insideHPC]



Making sense of cyberinfrastructure: http://t.co/PRQqwlnE5g [via @HPCWire]



OpenCL for performance: http://t.co/IEt1IaPaSs [via @insideHPC]



Path towards code modernization: http://t.co/PRQqwlnE5g [via @HPCWire]



Collaborative cancer cloud: http://t.co/Gay8pGtSbx @Intel [via @insideHPC]



Investigations of model human origins using @XSEDEScience: http://t.co/05rbCEXDRD [via @HPCWire]



IBM LinuxOne: http://t.co/lwq2BuPiW1 @IBM



Particle trajectories in a laminar static mixer: http://t.co/kYBKAyjt2j [via @COMSOL_Inc]



Innovation keeps supercomputers cool: http://t.co/kctDBqrk9j [via @insideHPC]



Roles of simulation and nature in a study of phase change: http://t.co/OH0mK1oNuC [via @COMSOL_Inc]



New mathematics advances frontier of macromolecular imaging: http://t.co/itar0deO2r @ENERGY @LBNLcs



Taste of water in the morning: http://t.co/LuhJa3Z1so [via @Wired]