Removed References section as the links were all going to a login page which our credentials don't work on.
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|=== Reference Documentation ===
* [[https://wiki.hpcc.msu.edu/display/hpccdocs/HPCC+Quick+Reference+Sheet|HPCC Quick Reference Sheet]]
* [[https://wiki.hpcc.msu.edu/pages/viewpage.action?spaceKey=hpccdocs&title=Documentation+and+User+Manual|Documentation and User Manual]]
* [[https://wiki.hpcc.msu.edu/pages/viewpage.action?pageId=1343596|iCER Products and Services (Buy-in and Storage)]]
MSU Institute for Cyber-Enabled Research (ICER) High-Performance Computing Cluster (HPCC)
Oakland University has 4 buy-in nodes as part of the MSU Institute for Cyber-Enabled Research (ICER) High-Performance Computing Cluster (HPCC). Oakland University faculty can get priority access on the buy-in nodes, but also access resources on the entire cluster.
To utilize Oakland University's ICER nodes, you will need 2 accounts:
- MSU Community ID
- MSU ICER NetID
Instructions for obtaining these accounts can be found below.
MSU Community ID
Your MSU Community ID will grant you sign-in access to various community web portals. In the case of Oakland University, your MSU Community ID is needed to request an account for the HPCC and follow-up requests (such as a Primary Investigator requesting shared research space for a research group) through https://contact.icer.msu.edu. The MSU Community ID username will be your Oakland University e-mail address.
The first step is to request an MSU Community ID at https://community.idm.msu.edu/selfservice/.
- Follow the link to "Create a Guest Account (Community ID)"
- Make sure to use your real name and Oakland University e-mail address when submitting the request.
You should receive an e-mail from firstname.lastname@example.org with a subject of "MSU Community ID Account Created - Please Complete Setup" to your Oakland e-mail address.
- Follow the link in that e-mail to create a password for your MSU Community ID account.
MSU iCER HPCC NetID
This account will be used to access the HPCC through SSH (Secure Shell) via gateway.hpcc.msu.edu. The user account will be a randomized set of letters and numbers (e.g. fgiz3dm4).
- Once you have an MSU Community ID you need to request an account for the iCER HPCC.
- On the "Community ID", fill out the Principal Investigator name (optional) and Click "Submit".
- If you are a student please put the name of the faculty or staff member you are working with in the Principal Investigator name (optional) field.
- iCER will create the account and you will receive confirmation of the creation in your OU e-mail account.
When you have your accounts, you will be able to log into OU's buy-in nodes on cluster at iCER with the directions at https://wiki.hpcc.msu.edu/display/ITH/Connect+to+HPC+System and https://wiki.hpcc.msu.edu/#DocumentationandUserManual-SystemAccess.
The cluster is primarily accessed by means of the Secure Shell (SSH) network protocol. An SSH connection can be opened to hpcc.msu.edu from a terminal prompt (Mac/Linux) or a program like PuTTY (Windows). Windows users may find using MobaXterm more feature rich then PuTTY and supports graphical applications. See https://wiki.hpcc.msu.edu/display/ITH/Install+SSH+Client for details.
Your initial connection will be to gateway.hpcc.msu.edu (e.g. ssh email@example.com ). From the gateway you can further SSH to a dev node (e.g. ssh dev-intel16).
One of the first things you may wish to do if you are new to the cluster is to load the powertools modules and view the available examples and commands:
module load powertools powertools getexample
Job Submission examples
Once on the gateway system you may wish to view some of the examples to get and understanding of job submission. To get the examples try the following, lines beginning with a # are comments and should not be executed:
# Assuming you are already on gateway.hpcc.msu.edu via SSH. # SSH to a dev node ssh dev-intel16 # Load the powertools module module load powertools # Get the helloworld example getexample helloworld # change to the helloworld directory cd helloworld # Look over the README file cat README # Run the README file to compile the helloworld.c and submits the jobs with qsub ./README # Check the status of your submission qstat -u $USER
See the following documentation link regarding File Systems on the cluster https://wiki.hpcc.msu.edu/display/ITH/File+Systems
Note that scratch space is not available on the gateway, files older than 45 days are automatically deleted, and files on scratch are not backed up. When on a node in the cluster other than the gateway you can reference the scratch space with $SCRATCH.
# Example of changing to your scratch directory cd $SCRATCH # Print name of current working directory pwd /mnt/ls15/scratch/users/fgsjdke2
The 4 buy-in nodes that we have are part of the "laconia (intel16)" cluster and are considered "Intel16 — Large Memory" nodes as referenced in Compute Resources
You should be able to check the status of the nodes and the jobs running on them with the following:
module load powertools priority_status -g oakland-university
- Laconia (intel16), Intel16 — Large Memory Node Names