Research Computing Resources

Data Usage Agreements

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To acquire data sets from external agencies, often a data security plan must be signed off by an IT department contact.  H&S IT acts as that contact for researchers in the school, with CRC verifying that systems have been set up according to Stanford's and the external agency's standards.  Please contact Jonathan Pilat, H&S CIO, to start that process.

Sherlock Resources for H&S Researchers

Sherlock is Stanford's main shared high performance computing cluster.  The School of Humanities and Sciences has resources in Sherlock and has made them available for any researcher (Faculty, Postdoc, Research Staff, or Student) who is on the research team of an H&S faculty member.  Sherlock can be used for departmental or sponsored research.  It is not intended for classwork.

The school's 'hns' partition has 87 standard compute nodes, including one GPU node and one node with extra memory.  H&S researchers have access to those, along with the centrally provided 'normal' partition.  If you need more computing resources or faster access to those resources, consider purchasing systems for the cluster and becoming a Sherlock "owner".

Getting Started with Sherlock

First, set up an account.  Faculty members can do this by writing srcc-support@lists.stanford.edu and specifying the names and SUNetIDs of the members of their research team.  H&S Faculty members should also specify that they'd like access to the 'hns' partition on Sherlock (this will allow you to compute on the H&S shared resources).

Sherlock is usually accessed via ssh.  Connect using:

ssh <SUNetID>@login.sherlock.stanford.edu

More information on how to connect to Sherlock is available on the getting connected page of the Sherlock website.  Once you've connected you can submit your computing jobs.  There is more information on how to submit jobs in the Sherlock documentation job submittal page.  To use the H&S Sherlock resources, include 

#SBATCH --partition=hns

in the sbatch script to submit your job.

You can also use Sherlock using a browser for some use cases, including Jupyter notebooks and RStudio.   To connect to Sherlock OnDemand, point your browser at https://login.sherlock.stanford.edu.  For more information, see the OnDemand documentation page.

Getting Help

Support for Stanford's central research computing services is handled centrally.  If you can't find the answers you need in SRCC's documentation, please write srcc-support@lists.stanford.edu.  

They also have an office hours service so you can go more in-depth about your particular needs.  Please note that due to the current COVID-19 situation, all office hours are being done remotely, and you will need to sign up for an office hours time.

Getting Training

The H&S IT team collaborates with the Stanford Research Computing Center to provide training to departments, programs, and labs.  We can come to your faculty meeting, graduate student event, or other gathering to give an overview of Sherlock and how to access the H&S resources.  For more information or to schedule an event, please contact Novita Rogers.

Other Research Computing Resources

If the Sherlock resources that H&S provides are not sufficient for your research needs, faculty members can purchase additional dedicated resources on Sherlock.  More information on pricing and capability is available on the Sherlock Server Order Page on the SRCC website.

Sherlock is approved for low and medium risk data as defined by the University.  If you use High Risk Data for research, H&S IT recommends using Nero, a computing cluster specifically designed to compute on and store High Risk Data.  To get started with Nero, please contact srcc-support@lists.stanford.edu and specify that you are interested in using Nero.  You will also need to complete a Data Risk Assessment with the University's Information Security and Privacy offices for each Nero use case.

If you have use cases that are not well served by a shared computing cluster, please schedule an IT Consultation with us.