Latest news and a timeline of activities


NAS (nas-0-0) issues       Tuesday, 8th December 2015 @ 10:35 am

Update: 2015-12-09 @ 8:25 am

Superior is accessible as before. Please feel free to log in and submit your jobs. They may wait in queue for a while but will soon start running.

Thank you all your patience while we worked on this issue, and apologies for the inconvenience.

Update: 2015-12-08 @ 4:50 pm

Thanks to timely support from our hardware vendor and in-house storage team, we were able to identify the cause of the problem. Hardware components and data checked out ok.

The cause of sluggishness in Superior, as noted this morning, resulted from the unresponsiveness of the storage node serving /research/ partition. Storage node became unresponsive as a result of one user's simulation attempting to write a single 25+TB file to disk. The user and research advisor will be notified of it very soon.

To prevent further write activity to the node while we complete the troubleshooting, all currently running/waiting simulations have been terminated. Login nodes have also been locked temporarily. Superior should be available for use from about 9 am tomorrow (Wednesday, 12/9/2015).

Thank you for your patience, and apologies for the inconvenience.

Update: 2015-12-08 @ 7:51 am

Please note that the previously experienced sluggish performance has re-surfaced again this morning (10:30 am). Cause of the sluggishness is the unresponsiveness of the storage node serving /research/ partition. Currently running simulations will, however, hang (or at least end up in Eqw status, and in turn, be terminated).

Please do not panic: Data seems to be intact and safe; Hardware vendor and our storage team are aware of it, and we are working towards a solution.

We expect Superior to be functional again by 5 pm today, if not sooner. Should there be delay, we will keep you informed.


NAS (nas-0-0) issues       Thursday, 3rd December 2015 @ 7:51 am

Update: 2015-12-04 @ 10:00 am

Thanks to timely support from our vendor, and overnight work from our in-house storage team, the NAS node serving /research/ partition has been restored to its full functionality. You can access Superior and continue your work.

Please note that any simulation that still shows up as running is very likely stale. Check the output files and if they aren't being updated, you will need to delete the job and re-submit it to the queue.

We believe that this incident isn't/will not be a systemic problem. As has been noted any number of times before, there is no backup in Superior and you are responsible for your data.

Thank you all again for your patience and co-operation over the past 24+ hours.

Update: 2015-12-03 @ 3:00 pm

Vendor showed up this morning and inspected the node: all hard drives and other components checked out ok. They replaced the RAID controllers one at a time. The storage node booted up successfully but was unable to mount the /research/ partition. Vendor is performing a thorough check today to ensure no other hardware component is cause of this problem and chances of data loss are minimized.

We are continuing to work with them. Should there be difficulty in mounting the /research/ partition even after the vendor has completed their end of the check, our storage team experts will work on it. We'll know more about ETA for using Superior early tomorrow (Friday, 12/4) morning. Thank you for your continued patience.

Update: 2015-12-03 @ 7:51 am

Previously experienced sluggish performance re-surfaced again early this morning (~1:30 am). Cause of the sluggishness is the unresponsiveness of the storage node serving /research/ partition. Further investigation has revealed a failing/failed hardware RAID controller in this storage node. Currently running simulations will, however, hang (or at least end up in Eqw status).

Please do not panic: Data seems to be intact and safe; Hardware vendor has been notified and is in possession of a replacement hardware RAID controller; Vendor will be on site to replace the RAID controller and bring the node back to its working status.

We expect Superior to be functional again by 8 am tomorrow (Friday, 12/4), if not sooner. Should there be delay, we will keep you informed.


Sluggish performance       Tuesday, 1st December 2015 @ 4:40 pm

Superior was sluggish over the past hour or so (e.g., very slow to respond to even the basic commands, etc.). Cause of this sluggishness was found to be the brief unresponsiveness of the storage node serving /research/ partition.

Though storage node is working properly now, we are looking into the cause of its brief unresponsiveness. In the meanwhile, please make sure that your currently running simulations are indeed running.


LAMMPS 2015.10.20       Thursday, 22nd October 2015 @ 8:51 am

A newer stable version of LAMMPS, labeled 2015.10.20, has been compiled and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers using LAMMPS 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.


MAPLE 2015.1       Wednesday, 2nd September 2015 @ 10:23 am

A single license of MAPLE 2015.1 (Features) with MATLAB R2014b support/integration has been installed and is now available for use -- a courtesy of Dr. Benjamin Ong.

For interactive work, please use a qloginx session and MAPLE can be launched using xmaple command. Necessary batch submission script can be generated using qgenscript.


COMSOL 5.1 Update 2       Tuesday, 7th July 2015 @ 9:28 am

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       Friday, 17th April 2015 @ 9:30 am

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       Monday, 30th March 2015 @ 11:00 am

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       Thursday, 25th December 2014 @ 7:30 pm

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)       Thursday, 25th December 2014 @ 12:30 pm

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       Thursday, 25th December 2014 @ 8:45 am

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       Wednesday, 3rd September 2014 @ 8:44 am

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)       Tuesday, 29th July 2014 @ 12:43 pm

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       Wednesday, 16th July 2014 @ 9:00 am

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.


Superior in review with insideHPC       Friday, 20th June 2014 @ 9:49 am

insideHPC, a renowned platform that distils news and events in the world of HPC and presents them in bite-sized nuggets of helpfulness as a resource for supercomputing professionals, did an interview reviewing Superior's performance during the past year.

Read the complete interview here.


R 3.1.0 (Spring Dance)       Tuesday, 3rd June 2014 @ 3:13 pm

R 3.1.0 (Spring Dance; Release Notes) has been compiled and is now available. 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.


Quantum ESPRESSO 5.1       Tuesday, 3rd June 2014 @ 12:28 pm

Quantum ESPRESSO 5.1 (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 ensure that the results are consistent before proceeding ahead with subsequent, production quality attempts.


CONVERGE 2.2.0 β       Tuesday, 3rd June 2014 @ 9:39 am

CONVERGE 2.2.0 β, a computational fluid dynamics software suite, has been installed and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers specifically licensed and authorized to use this software suite are strongly recommended to run test simulations to ensure reproducibility of results from elsewhere before proceeding ahead with subsequent, production quality attempts.


CALYPSO 3.6       Saturday, 10th May 2014 @ 11:30 am

CALYPSO 3.6 has been compiled and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers specifically authorized to use this software suite are strongly encourage to run a test/example simulation with our installation and ensure that the results are consistent before proceeding ahead with subsequent, production quality attempts.


VASP 5.3.5       Saturday, 10th May 2014 @ 10:15 am

VASP 5.3.5 (Release Notes) has been compiled and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers specifically authorized to use this software suite are strongly recommended to re-run a previously successful simulation with this newer version and ensure that the results are consistent before proceeding ahead with subsequent, production quality attempts.


MuSTI adds 64 more processors       Thursday, 8th May 2014 @ 2:01 pm

Multi-Scale Technologies Institute (MuSTI) has added four more CPU based compute nodes to Superior, forming musti.q (a higher priority queue for MuSTI researchers with a lower priority access to everyone else) and taking the overall compute capacity to nearly 31 TFLOPS.

Multi-scale technologies are those that bring together functional elements to form systems where the relative size of components within the system spans from the nano through the micro and into the macro domain. The systems focus of the MuSTI emphasizes the challenges associated with integrating technologies that have relative feature sizes orders of magnitude apart and operating characteristics that are size dependent. This presents many problems that must be addressed by interdisciplinary teams of researchers using specialized equipment.

Research focuses on engineered systems and components such as nanoelectronics, nanosensors and systems, and associated materials. MuSTI is home to interdisciplinary nano- and micro-technologies education programs -- such as an interdisciplinary minor in Nanoscale Science and Engineering. The establishment of MuSTI is based on Michigan Tech's focus on applied research, established practices of interdisciplinary research, capabilities in testing, and strong engineering and science programs.


qsummary       Thursday, 8th May 2014 @ 1:15 pm

A new tool, qsummary, is now available and it can be used in one of the following two ways:

qsummary
qsummary USERNAME

qsummary displays useful information about all completed jobs by the currently logged in user (i.e., you).

qsummary USERNAME displays same information for a specified user.


Updated qgenscript       Thursday, 8th May 2014 @ 8:05 am

Researchers will need to generate fresh submission scripts using the updated qgenscript. The new scripts are designed to considerably reduce the wait time and improve the overall performance.

The old scripts will not work.


IDL 8.2 SP1       Wednesday, 16th April 2014 @ 3:00 pm

IDL 8.2 Service Pack 1 is now available for use. The necessary variables will be set up from within a qlogin session.

Researchers are strongly recommended to run test simulations to ensure reproducibility of results from elsewhere before proceeding ahead with subsequent, production quality attempts.


MCCCS Towhee 7.0.6       Monday, 7th April 2014 @ 8:37 am

MCCCS Towhee 7.0.6, a Monte Carlo molecular simulation code, has been compiled and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers are strongly recommended to run test simulations to ensure reproducibility of results from elsewhere before proceeding ahead with subsequent, production quality attempts.


CONVERGE 2.1.0       Thursday, 27th March 2014 @ 8:03 am

CONVERGE 2.1.0, a computational fluid dynamics software suite, has been installed and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers specifically licensed and authorized to use this software suite are strongly recommended to run test simulations to ensure reproducibility of results from elsewhere before proceeding ahead with subsequent, production quality attempts.


Annual proactive maintenance       Friday, 21st March 2014 @ 9:18 am

In order to ensure Superior continues to operate consistently at a high level, ITS will be performing proactive maintenance work starting at 8 am on Monday, 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 work station so that analysis, visualization, and manuscript preparation work can still be continued.

Superior will be accessible as before starting at 8 am on Thursday, 8th May 2014.


XSEDE Research Allocation       Saturday, 15th March 2014 @ 11:30 am

XSEDE is now accepting Research Allocation Requests for the allocation period, July 1, 2014 to June 30, 2015. The submission period is from March 15, 2014 through April 15, 2014. Interested researchers may review the new XSEDE systems and important policy changes before submitting the request through the XSEDE User Portal.

Researchers needing assistance in writing a proposal can contact it-help@mtu.edu.


VASP 5.3.3 Non-Collinear Spin       Wednesday, 12th March 2014 @ 11:23 am

A new variant of VASP 5.3.3 that supports Non-Collinear Spin calculations has been compiled and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers specifically licensed and authorized to use this software suite are strongly recommended to read through the thread on VASP discussion forum and understand what it does before proceeding ahead with subsequent, production quality attempts.


R 3.0.3 (Warm Puppy)       Tuesday, 11th March 2014 @ 10:45 pm

R 3.0.3 (Warm Puppy; 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.


Gnuplot 4.6.5       Monday, 10th March 2014 @ 2:30 pm

Gnuplot 4.6.5 (Release Notes; Demo) has been compiled and is now available for use.

Researchers interested in integrating plotting features into their work flow may contact it-help@mtu.edu.


MATLAB R2013b       Thursday, 6th March 2014 @ 9:37 am

MATLAB R2013b 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.


CRYSTAL 14       Tuesday, 4th March 2014 @ 9:39 am

CRYSTAL 14 has been installed and is now available for use. Necessary job submission script can be generated via qgenscript.

Researchers specifically licensed and authorized to use this software suite 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.


LAMMPS 2014.02.27       Tuesday, 4th March 2014 @ 9:19 am

A newer, parallel, version of LAMMPS (marked 20140227) 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.


Intel compilers unavailable       Friday, 20th December 2013 @ 3:30 pm

In light of the message below, Intel Cluster Studio 2013.0.028 (ICS) that provides icc, icpc, ifort, mpiicc, mpiifort, etc. is temporarily unavailable.

While pre-compiled software suites might continue to run as before, researchers will experience errors when attempting to compile newer (versions of) software suites.

Monday, 23rd December 2013 @ 5:10 pm:
Intel compilers are available as before.


A message from CTO       Friday, 20th December 2013 @ 3:00 pm

A number of computers on campus have been compromised; as a result, some username/password combinations have been recorded and sent off campus. If you have received notification that you need to reset your password please proceed immediately to login.mtu.edu and do so.

If you have used the same password for other sites you should reset those as well. Please note that this compromise involved a number of Linux servers and that SSH (secure shell) access to them may be temporary blocked or rerouted as those machines are being secured.

Detailed information is here.


k-Wave 1.0       Thursday, 5th December 2013 @ 9:55 am

k-Wave (1.0), a MATLAB toolbox for the time-domain simulation of acoustic wave fields, is now available for use.

This software suite/toolbox inherits all of MATLAB's features (array jobs, parallel and using GPU when applicable, etc.). Necessary job submission script can be generated via qgenscript.

An optimized C++ version of k-Wave that maximizes computational performance for large simulations will soon be made available as well.


MOLPRO 2012.1.3       Wednesday, 27th November 2013 @ 3:00 pm

A pre-compiled version of MOLPRO (2012.1 patch level 3; serial and parallel) is available for use. Array Jobs feature is available for this software suite. Necessary job submission script can be generated via qgenscript.


GROMACS 4.6.3       Sunday, 3rd November 2013 @ 1:15 pm

Latest stable version of GROMACS (4.6.3) has been compiled and is available for use. Array Jobs feature isn't available yet for this software suite.

Preparatory steps for a given simulation involving editconf, genion, grommp, g_energy, pdb2gmx, etc., will need to be performed within a qlogin session. Steps involving mdrun can be accomplished using qgenscript.

Researchers may refer to the Additional References for a link to extremely well written tutorials. If/When using these tutorials (especially within a 'qlogin' session), researchers should keep in mind that Superior's version has a _d suffix, i.e., editconf_d, genion_d, grommp_d, g_energy_d, mdrun_d, pdb2gmx, etc.


qresources       Thursday, 31st October 2013 @ 9:45 pm

Researchers may use this utility from within qgenscript or by itself to get real time information about the number of licenses (total, in use and available) for each software suite.


Custom serial jobs via qgenscript       Monday, 28th October 2013 @ 7:30 pm

qgenscript now generates the necessary job submission script to run any custom program in serial fashion. It does not, however, support the Array Jobs feature yet.


BASH and Python via qgenscript       Tuesday, 22nd October 2013 @ 3:30 pm

qgenscript now provides an option to generate the necessary job submission script for BASH and Python (version 3.3.2). These do not, however, support the Array Jobs feature yet.

This is intended to help submit post-processing tasks (especially the ones that take longer than 4 hours and as such, do not fit within qlogin session) to the queue, akin to any other simulation.


LAMMPS 2013.10.16       Thursday, 17th October 2013 @ 7:12 pm

A newer version of LAMMPS (tagged 2013.10.16) has been compiled. All previous versions will be available until further notice.


VPN: Fix for on-campus issues       Thursday, 11th July 2013 @ 1:20 pm

Superior is accessible to all on campus users (wired and wireless; linux, Mac and Windows) without needing VPN. All connections from off campus, however, will still need to come through VPN.

Users must note that this is a temporary solution. Once a more permanent solution is in place, all connections -- from on and off campus -- will need to come through VPN.


GLRC Generators Load Test       Wednesday, 26th June 2013 @ 3:57 pm

Starting 8 am on Monday, 8th July 2013, Facilities Management will be connecting a load bank to replicate the full load draw and then manually shutting the main power off to observe how long it takes for the building generators to kick in.

To avoid potential hardware damage in case of loss of power to the data center, Superior will be powered down at 9 pm on Sunday, 7th July 2013. Researchers are strongly encouraged to checkpoint and stop their simulations as running jobs at that time will be terminated without further notice.

Normal operations are expected to resume from 8 am on Tuesday, 9th July 2013.

Monday, 8th July 2013 @ 12:40 pm:
Generators load test was successfully completed well ahead of time. As such, Superior will be available for use as before starting 1 pm.


Power Outage       Wednesday, 12th June 2013 @ 6:42 pm

With flywheel start up scheduled for Thursday, 20th June 2013, Superior will be powered down at 9 pm on Wednesday, 19th June 2013, to prevent potential damage to hardware.

Normal operations will resume from 8 am on Friday, 21st June 2013.

Thursday, 20th June 2013 @ 3:32 pm:
Flywheel start up work went uneventful as expected. Superior is accessible and usable as before from 4 pm on Thursday, 20th June 2013.


Queues       Monday, 10th June 2013 @ 12:05 am

Three queues, short.q, long.q and gpu.q have been created and the queueing system (job submission, notification, etc.) has been successfully tested with several simple cases.

For more information regarding version and compilers used, please refer to Available Resources section.


Compute Nodes       Saturday, 8th June 2013 @ 2:56 pm

compute-0-N (N: 0 - 17) have been added to the cluster and successfully configured.

Saturday, 8th June 2013 @ 11:32 pm:
compute-0-N (N: 20 - 37) have been added to the cluster and successfully configured.

Sunday, 9th June 2013 @ 4:29 pm:
compute-0-N (N: 38 - 55) have been added to the cluster and successfully configured.

Sunday, 9th June 2013 @ 9:50 pm:
compute-0-N (N: 58 - 75) have been added to the cluster and successfully configured.

Sunday, 9th June 2013 @ 10:45 pm:
compute-0-N (N: 82 - 86) have been added to the cluster and successfully configured.


Storage (NAS) Node       Thursday, 6th June 2013 @ 3:30 pm

Storage (NAS) node with 48 TB raw space has been added.

Friday, 7th June 2013 @ 3:46 pm:
/research/ partition with 33 TB RAID6 of usable space has been successfully configured to be accessible from every node.


CS&E Software Suites       Thursday, 6th June 2013 @ 1:30 am

The following computational sciences and engineering (CS&E) software suites have been installed/compiled on Superior. For more information regarding version and compilers used, please refer to Available Resources section:

HPL, HPCC, Crystal, CMake, FFTW, Gaussian, Gnuplot, GULP, LAMMPS, NAMD, Python, Quantum ESPRESSO, R and VASP.

Thursday, 6th June 2013 @ 9:32 am:
Ansys, Mathematica and MATLAB

Friday, 7th June 2013 @ 9:34 am:
LMS Sysnoise and MSC Nastran

Monday, 10th June 2013 @ 10:28 am:
Abaqus

Thursday, 20th June 2013 @ 3:32 pm:
GULP, SIESTA, TBTrans and TranSIESTA


Intel C/C++/FORTRAN Compilers       Wednesday, 5th June 2013 @ 9:28 pm

Intel C/C++/FORTRAN compilers, as part of the Intel Cluster Studio 2013.0.028, have been installed.


Login Nodes       Wednesday, 5th June 2013 @ 8:01 pm

Login nodes for Superior have been successfully installed and these will accept inbound connections only through Michigan Tech's VPN.


Front End Installation & Customization       Wednesday, 5th June 2013 @ 12:45 pm

Front end (a.k.a. the master node or the head node) of superior.research.mtu.edu, housed in the Great Lakes Research Center, has been successfully installed.

Wednesday, 5th June 2013 @ 2:30 pm:
Front end has also been customized to keep it in compliance with policies and procedures from Michigan Tech's Information Technology Services (ITS) and National Security Agency (NSA).