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

HPC Documentation

CMS Controlled Data Access

OverviewThe Minerva CMS environment operates as a distinct subset of the Minerva-Res cluster, strictly restricted to Research Identifiable File (RIF) and Limited Data Set (LDS) data from the Centers for Medicare & Medicaid Services (CMS).

To access this environment, researchers must provide an approved and active RIF or LDS Data Use Agreement (DUA) registered with the Mount Sinai Grants and Contracts Office (GCO), paired with a Minerva HPC Data Management Plan (DMP) Security Assessment Questionnaire (SAQ).

Note: All fundamental connections—including VPN requirements, SSH commands, MFA protocols, and Open OnDemand usage—are identical to the standard Minerva-Res environment. Please reference the main Minerva Restricted Cluster documentation for complete access instructions.
1 Projects & Accounts

Before utilizing CMS resources, you must have an approved CMS project and an active Minerva-Res account.

Inactivity Lock: CMS user accounts are strictly audited and will be automatically locked after 60 days of inactivity on Minerva. To reactivate a locked account, you must contact hpchelp@hpc.mssm.edu.
2 Logging In

Access to the CMS environment is routed through the main Minerva-Res entry points. Connections require the Mount Sinai campus network or VPN.

1. SSH Terminal Access

For command-line access, connect to the Minerva-Res login nodes using your standard Mount Sinai credentials and Microsoft Azure MFA.

Shell
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>

2. Open OnDemand Web Portal

For GUI and interactive applications (such as RStudio and Jupyter Notebook), access the web interface.

3 CMS Storage & Filesystem

The CMS environment utilizes specific designated directories within the encrypted filesystem.

CMS Project Directory

  • Path: /arionencrypt/cmsdata/
  • Allocation: A dedicated directory is provisioned for each approved project based on requested allocations.
  • Data Retention: Data in this path is NOT purged, but it is NOT backed up.
  • Chargeback: Following project approval, the PI or project delegate must complete the Minerva Storage Information Collection Form to provide fund information for chargebacks.

User Home Directory

  • Path: /arionencrypt/users/
  • Quota: 30 GB standard quota.
  • Data Retention: Data in the home directory is not purged and is backed up. It should be used for configuration files and standard scripts.
4 Data Transfer

Because of strict CMS compliance requirements, standard self-service transfers are restricted.

Data Management Responsibilities

As outlined in Minerva Restricted Supercomputer Policies and Procedures, which all CMS users must agree to:

  • Principal Investigators (PIs) are responsible for the management and oversight of all project data, ensuring full compliance with Data Use Agreements (DUAs) and institutional policies.
  • Users must execute all controlled data transfers strictly in accordance with the applicable DUA, approved institutional procedures, and official user documentation.
  • The HPC Team provisions and maintains the Minerva-Res computational environment but does not conduct or manage controlled data transfers on behalf of users.

Transfer Procedures

  • Non-Controlled Data (Inbound / Outbound): Please follow the standard non-controlled data transfer procedure documented in the Minerva Restricted Cluster documentation.
  • Controlled Data (Inbound): Direct download from approved repositories only.
    • Requires the External Connectivity Request Form (justification + source IP/subnet).
    • Security review: 2–3 weeks. Approved IPs are allow-listed for the transfer window only, then removed. Access is one-time only.
    • Once approved, log in to OnDemand-Res and launch the Desktop app.
    • Open a terminal session within the Desktop, run ml firefox res_proxies, and visit the approved data source website to complete the download.
  • Controlled Data (Outbound): Users must document the exact transfer destination prior to movement. RIF and LDS data may only be transferred to another strictly vetted CMS-compliant environment. Contact hpchelp@hpc.mssm.edu with justification to initiate a transfer.
Note for CMS Data: If you are downloading Centers for Medicare & Medicaid Services (CMS) Research Identifiable Files (RIF) or Limited Data Sets (LDS), please ensure you follow all procedures outlined in the CMS Minerva-Res Download Checklist.
5 Software Licenses & Chargebacks

Use of the CMS environment and specific statistical packages are subject to standard licensing and chargeback models.

Resource / Software Cost & Details
Standard Minerva Chargeback $155 per TB per year. Review the Fee and Schedule Policy.
SAS Software License $150 per activation. Requires the SAS License Request Form. (If you hold an active local SAS license, a separate purchase is not required).
STATA Software License User-provided. Users are responsible for obtaining their own valid STATA license. HPC provides technical installation assistance if needed.