HPC Questions and Answers

General HPC Questions

How do I make a General Request/Consultation?🤔

OIT provides general request services or for assessments for individuals and research groups who wish to deploy research computing and advanced cyberinfrastructure techniques (e.g. high-performance computing, visualization, advanced networking and data collaboration, and advanced technology-enhanced workflow development). You can make a General Request/Consultation here.

How to include CIRT managed charged services into budget statement?

The faculties plan to include the budget for CIRT-managed charged services in the budget statement. Please list it under the category of 'Other Direct Costs.' For example, purchased HPC storage services can be allocated to the 'Materials/Supplies: MERCED HPC storage and maintenance' category within the 'Other Direct Costs' section. Here is the sample NIH data management documentations and budget justification.

When/where are the HPC Walk-in Clinic hours?

Bring your laptop, your code and your questions to the clinic and get expert help, right on the spot. Experienced graduate students are encouraged to come help your peers by mentoring them in HPC tips and tricks. Faculty are also welcome to join. Among others, Yue Yu (Sr. Research Computing Facilitator) will be available to meet with and help members of the campus research computing community at these sessions.

Click Here for Office Hour Location and Time

How do I change password on research cluster?

• You can request for changing your password on MERCED/any CIRT managed research cluster by submitting a general research request here.
• Please provide the name (and/or IP address) of the cluster on which you need your password updated.

Error Logging into research cluster/ error sshing into cluster

• When accessing the research clusters from an off-campus location, please ensure you are logged into UC Merced VPN to access your research cluster. VPN allows faculty, students and staff to connect to research computing resources from home or other off campus networks.

• If you still run into errors logging into the cluster, please submit a general research request here.

I am a student in a PI group. How can I request for Pinnacles and/or MERCED cluster access?

You can start the step-1 access process, but in order to receive an account, you need approval from a UC Merced PI. Every account on Pinnacles is associated with that of a faculty PI. If you are requesting MERCED cluster access you must attach a valid COA number, to the ticket process, this COA number is usually distributed by the PI.

I am a student who changed PIs do I need to update my PI information?

Yes, submit a ticket to update your PI and to change user groups.

My access request for Pinnacles and/or MERCED was denied – what are my next steps?

CIRT can schedule a consultation with the faculty to specifically address the comments from Committee on Research Computing (CoRC).

I have several users doing different projects, can I use different COA# for them?

Yes, please make sure keep the COA# information updated. Each user can also have different COA#, if the user is doing multiple projects. If you have any questions, feel free to open a ticket here.

How do I move Big Data?

*Visit our Data Transfer to get more information on transferring Big Data.

I want access to free resources. How can I get access to them?

Remember, if you stay below or at your baseline allocation, you will not incur any fees. However, you can obtain access to other free compute resources such as our new NSF-MRI Pinnacles cluster, and XSEDE resources – and my team can provide consultation for how to access these resources. Schedule a consultation here.

Pinnacles - Questions

I am in the process of purchasing a condo-model nodes for Pinnacles, do I have to go through the access process?

No

I am a UC Merced PI, but my collaborators are not from UC Merced, how do I request Pinnacles access to my collaborator ?

All accounts on Pinnacles cluster need to be associated with that of a UC Merced faculty PI. If your collaborator is a non-UC Merced collaborator, then, they would need a UC Merced NetID to access VPN and login to Pinnacles cluster. Usually, department MSOs provide UC Merced NetIDs for collaborators.

MERCED - Questions

Are the costs the same regardless of whether we purchased our own nodes or not?

The costs and the charges are for general Slurm partitions on MERCED cluster.

What is the approval process for any work that would be run on the machine? Given that money is involved, I hope you have a way for PIs to approve charges it is made and consequently before the run is made.

The MERCED recharge system operates on a pay-per-use basis. Currently, we do not have the technical controls in place to require PI approval for research user jobs.

The MERCED computational cycle accounting system is based on core-hours, where one core-hour represents a single compute core used for one hour along with 2GB of RAM. The total cost in core-hours for a computation is calculated as follows:

Total Cost ($) = Number of cores × Job duration in wall clock hours × Billing rate per core-hour

The UC rate per core-hour is $0.01.

Faculty can request usage information per user whenever they need additional details on an invoice. Additionally, we are happy to provide training to your researchers on how to utilize the FREE Pinnacles resources and estimate the usage costs for jobs running on MERCED cluster.

What if I have multiple grant with multiple COAs, can I use all of my COA numbers?

Yes, we can set up multiple Slurm accounts so that when users submit jobs to the MERCED cluster, they are required to select a specific account. This ensures that the usage for the project is charged to the designated COA number.

Can I purchase core-hours in advance?

Since recharge services are pay-per-use services, users cannot purchase core-hours in advance. However, you can purchase “condo-model” CPU/GPU compute node(s) for Pinnacles for seamless access to compute resources after Jan 1, 2022. Request for a Pinnacles condo-model purchase here.

Can faculty charge recharge services directly to a grant?

Grant funds have restrictions on how the funding can be spent, and every grant is unique. So, as long as recharge service is allowable expense under the grant, then faculty can charge recharge services directly to the grant. Each grant has a unique COA#. Please ensure that you inform CIRT team your updated COA number information.

I want to ensure that my research group does not exceed a certain amount of Core Hour usage on MERCED.

You can send a request to the CIRT team at cirt@ucmerced.edu to gather information on monthly usage at any time.

Job/Software - Questions

How do I install software on a CIRT Managed cluster?

• If the software package or version you need is not available in the list of provided software, you may compile and install it yourself. The recommended location for user-installed software is the $HOME path.
• If the software installation requires root (sudo) access and/or if you need further assistance installing the software, you can request service here.

My Jobs are running unusually slow, failing with errors, I need to cancel a currently running job

Jobs can be running unusually slow for many reasons that can be relating to the about number of tasks assigned to the job, number of nodes, and the memory being allocated to the job. These three factors are just a few common factors that can be leading to an unusually slow job, and all of these are dependent on what is being computed(i.e. a parallel python script or a simple list of unix commands). It is important to understand what the code is anticipated to execute and how that will be done with the resources you are requesting. This will allow for the user to better less/more computing resources to get the computations/calculations done in an effecient manner.

To get information about troubleshooting a job failing with errors visit our Job Management Page

To cancel a job: scancel <jobid> or skill <jobid>