July 22, 2024
Purpose:
Requirements:
Instructions:
November 13, 2024
An overview of the Scientific Computing (SciC) Linux Clusters with information relating to the service can be found in the Computational Resources section of our website. The cluster webpage also contains links to the account sign-up form, request forms for applications or storage and the support and feedback forms. Review the typical uses for each of the computational resources offered by ERIS to determine the most suitable platform.
Information about using the cluster is found in the Computational Resources and Analyze Data sections of our KnowledgeBase.
Details of our introductory training courses for Linux and SciC Linux Clusters are in the Scientific Computing section of our Training Page
First determine the most suitable platform for your project. Then complete the SciC Linux Clusters account request form, or the corresponding form for the compute platform selected. Estimating the storage, applications and compute time required for your projects will help us provide these services. If you will require access to an existing data folder for your lab / project, find out from the data owner the name of the corresponding group in order to request this access on the account request form.
Once registered your account should be ready in 24-48 hours.
Before connecting to the ERIS cluster with any of the methods described below please ensure you have VPN switched on if you are located offsite.
Opening a command-line terminal session using an SSH client is the most common way to connect to the SciC Linux Clusters. This method requires some familiarity with the Linux operating system.
Once you have chosen the most suitable platform for your project, use the corresponding host:
ERISOne: erisone.partners.org Decommissioned 09/13/2024
ERISTwo: eristwo.partners.org
ERISXdl: erisxdl.partners.org
ssh abc123@yourhost.partners.orgThe first time you connect to SciC Linux Clusters, a message will appear showing the rsa2 key fingerprint. Select "Yes" to proceed if the fingerprint matches the following (as of 09/2024):
SHA256:AYERiujz9FYfiO0DTxmsuybPL2OVroyMaEkQoC41724 no comment (RSA)A remote desktop is ideal for using graphical applications with data stored on the cluster, and for a persistent workspace. On the webpage linked below, you may toggle between available servers.
Web applications allow running jobs, analytics and visualization using only a web-browser. Sections of the quick-start guide below may not apply if you exclusively use to the cluster through a web-browser.
Several labs have web-portals for running analysis pipelines on SciC Linux Clusters. Applications supported by the ERIS Scientific Computing team include
Submit a feature request for other web applications.
Within the SciC Linux Clusters, computers are referred to as "nodes". Find out which node you are currently working on from its host name, which is shown in the terminal prompt, or from the output of the "hostname" command e.g.
hostname
eris2n5.research.partners.org
In order not to overload the front end and so for the benefit of all cluster users, operations on the eristwo login nodes (eris1n2, eris1n3, eris2n4 and eris2n5) should be restricted to job submission, file editing and small-scale file copying. Please note that users are limited to 30 processes, 1 day of continuous compute time, and 8GB of memory per process on these login nodes. Jobs that go beyond these limits will be terminated without warning. On the ERISXdl login nodes (i.e. erisxdl1, erisxdl2, and erisxdl3) only the compute time is limited.
Users can view the limits with the following:
ulimit -a
Any computational and data-intensive work takes place on the compute nodes. Time and resources on these nodes is exclusively granted by a request to the the job scheduler to prevent resource conflicts between jobs. You can request a command-line session immediately on a compute node using the interactive queue. To see the list of hosts, use the bhosts command to see which are available.
To use applications and software provided by the cluster during your jobs, you can take advantage of the cluster's module system. Learn more about loading ready-to-go applications in Loading Applications.
For questions related to the use of SciC Linux Clusters, first check the frequently asked questions in our Knowledge Base. For service request, software installation requests and reporting problems fill the appropriate form from our Forms Library and contact Scientific Computing Support with further queries.
Note that email correspondence from the Scientific Computing support team includes a message header inviting you to check the status of the support requests online. The ticket site http://tickets.partners.org/ does not use your Mass General Brigham ID or password for log-in. Request a new password using your primary email address as the username.
If you are applying for a grant and need to reference these resources, you can use the link below. This is to help researchers copy and paste general, high-level, descriptions of infrastructure into their grants, IRB proposals, contracts, etc.
http://rc.partners.org/boilerplates
It would be very much appreciated if the Enterprise Research IS group and/or individual Research Computing members receive acknowledgement in publications if you feel our service and facilities have helped your projects. You can find a guideline for such acknowledgement at:
https://rc.partners.org/research-apps-and-services/boilerplates-templates/it-infrastructure#citing-eris
Please let us know how ERIS helped your research!
https://rc.partners.org/research-apps-services/boilerplates-templates/research-thumbs