SLURM Logo

This year, the HPCC moved over to SLURM. Overall, I think the new scheduler is nice but it required me to relearn a bunch of things I have gotten to know by reflex.

One nice new feature is that I can manage our own Buy-in account. The CMSE department has multiple buy-in nodes. For example, the command to show everyone on the CMSE account is:

sacctmgr show association account=cmse

If I want to add someone to the CMSE buy-in account I just do the following:

sacctmgr add user account=cmse name=colbrydi

Then if I want to delete someone from he CMSE buy-in account is just as easy:

sacctmgr delete user account=cmse name=colbrydi

The HPCC staff also provides the following useful powertools that users can access by running module load powertools:

priority_status or buyin_status - equivalent commands that shows all of your buy-in nodes and who is currently running on them.

To use the buy-in account you need to specifically use the account option in the job script (I think). For example, the following SBATCH commands should request one of the Volta GPU cards on the cmse account:

#SBATCH --gres=gpu:1  
#SBATCH --nodelist=nvl-001
#SBATCH --time=08:00:00
#SBATCH --account=cmse

Many of our people want to use the Volta over Jupyterhub run though the webrdp website. To do this, you would log into webrdp, open a terminal on the webrdp desktop, ssh to one of the dev nodes and then issue the following command:

salloc --gres=gpu:1  --x11 --nodelist=nvl-001 --time=08:00:00 --mail-type=BEGIN --account=cmse

Once the job starts, you would just type jupyter notebook assuming you have it installed.

Hope you find these notes useful.

  • Dirk

Understanding Research Technology Support and Where it Fails

Tue 26 March 2019 by Dr. Dirk Colbry

Image of a Microscope

I was invited to give a talk to a newly formed IT Research Support group here on MSU campus. As the name suggests, the purpose of this group is to find the best ways to help researchers use technology to do their science.

This talk was a patchwork of many …

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Using an X11 Virtual Frame Buffer to run GUI jobs in batch mode on the HPC.

Thu 20 December 2018 by Dr. Dirk Colbry

X11 Logo

I have an example program that came with BCCD called Pandemic which I wanted to run on our local HPCC. Unfortunately Pandemic requires X11 to run and I would get a segmentation fault every time I ran it in the batch system.

This blog post shows how I used the …

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Emerging Technologies (FPGAs) @ 2018 ACI-REF VR

Fri 10 August 2018 by Dr. Dirk Colbry

Picture from Panel

Today is the last day of the 2018 ACI-REF Virtual residency workshop here in Norman Ok. It was a great week with a lot of great people. I highly recommend the workshop for anyone in the area of Advanced Computing Instruction especially those do some Research and Education Facilitation in …

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Deciding Which Technologies to Adopt, and When @ 2018 ACI-REF VR

Wed 08 August 2018 by Dr. Dirk Colbry

Image used in presentation representing the technology adoption wave

I had fun leading a discussion on Deciding Which Technologies to Adopt, and When at the 2018 ACI-REF Virtual residency event in Norman Oklahoma. Since many of the participants were virtual I experimented with doing a Brainstorming exercise over zoom. We had local volunteers on typing in comments from our …

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Teams of CI Professionals: Recruitment & Retention, Management, Team-building, and Motivation Panel @ 2018 ACI-REF VR

Tue 07 August 2018 by Dr. Dirk Colbry

Image from Panel

Thank you Aaron Bergstrom (U North Dakota) for facilitating the panel discussion on Teams of CI Professionals: Recruitment & Retention, Management, Team-building, and Motivation at the 2018 ACI-REF Virtual residency. My fellow panel members included:

  • Jerry Perez, U Texas Dallas
  • Derek Leydig, Pennsylvania State U
  • Claire Mizumoto, U California San Diego …
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Installing RStudio on the MSU HPCC

Fri 06 July 2018 by Dr. Dirk Colbry

Rstudio

These instructions are for installing RStudio on the HPCC. RStudio provides a variety of installers on their website https://www.rstudio.com/products/rstudio/download2/. However, the HPCC uses an older version of Linux and the precompiled binaries are not compatible. Trying to install RStudio from the source code is …

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Managing Inconsistent Runtimes on the HPCC

Fri 29 June 2018 by Dr. Dirk Colbry

One of our postdocs stopped by my office today to talk about a problem with inconsistant runtimes on our HPCC. This user is running a lot of jobs with 512 cores (current cpu limit is 520). The problem is that it is really difficult for the user to estimate the …

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Inverse Problems Seminar

Mon 04 June 2018 by Dr. Dirk Colbry

I was invited to give a talk at the inverse seminars symposium:

https://inverseproblems2018.org/

At first I was a little nervous since I don't consider myself an expert in inverse problems so I did not fully understand what they wanted me to present. However after talking to the organizers …

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