All use of Scientific Computing and Data resources in publications and presentations must acknowledge Mount Sinai’s CTSA funding award. Click here

Scientific Computing and Data / High Performance Computing / Documentation / CMS Data

CMS (Centers for Medicare & Medicaid Services)
Controlled Data Access Guide

The Minerva CMS cluster is restricted to RIF (Research Identifiable File) and LDS (Limited Data Set) data.

You will need to provide an approved and active RIF or LDS DUA with Mount Sinai GCO that are paired to Minerva HPC DMP SAQ, in order to access this cluster.

1. Get Minerva account

2. Connecting to Minerva CMS cluster

Minerva CMS cluster currently has a set of login nodes which are used to access the compute cluster and data. The login nodes are connected to the campus network allowing access only on campus or via tunneling over Mount Sinai’s VPN if off campus.

The address of the login nodes is:

  • minerva-res.hpc.mssm.edu – round-robin redirect

For security, Minerva CMS cluster requires the Secure Shell (ssh) protocol and Microsoft Azure Multi-Factor Authentication (MFA).

Connection Steps

  1. VPN: If you are off-campus, you must first connect to the Mount Sinai School VPN.
  2. SSH Command: Open your terminal in Mac or an SSH client like PuTTY or MobaXterm for Windows
  3. Authentication:
    • Username: Use your standard Sinai credentials.
    • Password: Enter your Sinai password.
    • MFA Challenge: Complete the second-step verification using your chosen Azure MFA method.

SSH command:

ssh yourUserID@minerva-res.hpc.mssm.edu
(yourUserID@minerva-res.hpc.mssm.edu) Password: <Enter your Sinai School Password Only>
Enter Your Microsoft verification code<609017>

!!!For detailed instructions, please refer to the full Logging In documentation on general Minerva system. Please note to change the login address to minerva-res.hpc.mssm.edu !!!

3. Logging Into the Minerva Open Ondemand Web Portal

You can also access the Minerva CMS cluster via Open OnDemand web interface for GUI and interactive applications such as Rstudio and Jupyter Notebook.

Please note that new user home directories are not created until the first login using standard SSH. If you are new Minerva users be sure to connect via SSH before attempting to access Open OnDemand. Failing to do so will produce an error from Open OnDemand regarding the lack of home directory.

  • Point your browser to https://ondemand-res.hpc.mssm.edu.
  • Login with your Mount Sinai username/password and multi-factor authentication device.

4. File system

Home directory

  • User home directories are located at /arionencrypt/users/.
  • Previous home directories remain available in read-only mode until June 20 for data retrieval and reference.
  • User HOME directories. 30 GB quota. It is NOT purged and is backed up. Generally used for all the ‘rc’ and configuration files for various programs.

CMS project directory

  • CMS project data is located at /arionencrypt/cmsdata/.
  • PIs can request project storage. Click here to submit an CMS allocation request and renew annually. Then please complete Minerva Storage – Information Collection Form by PI or project manager/delegate for fund information for chargeback.
  • A directory for each approved project. The quota is set to the approved allocation for the project. It is NOT purged but it is NOT backed up.

How to transfer your controlled CMS data into the Cluster?

Please contact hpchelp@hpc.mssm.edu for data transfer

SAS and STATA License Cost and Standard Minerva Chargeback

  • License fee for running the SAS software on Minerva: $150 per activation (SAS License Request Form)
    • If you already have an active SAS license on a local machine, no need to purchase a separate one to run on Minerva.
  • License fee for running the STATA software on Minerva: users responsible for obtaining a valid STATA license and installation, and the HPC team provides technical assistance if there is any issue encountered by users
  • Standard Minerva chargeback: $155 per TB per year (Minerva Fee and Schedule Policy)

Actions required after maintenance

  • Log in using the dedicated login node at Minerva-res.hpc.mssm.edu
  • Update workflows, scripts, or job submissions referencing previous login nodes or paths.
  • Retrieve required files from previous home directories before June 20 while read-only access is available.