What is the KPMP HPC Enclave?
The KPMP High Performance Computing (HPC) Enclave is a secure, computational space that houses high-dimensional biomedical datasets produced by KPMP technologies such as electronic health records (EHR), whole genome sequencing (WGS), or other omics data. It is hosted on the Minerva supercomputer at Mount Sinai’s Icahn School of Medicine and maintained by High Performance Computing (HPC).
Minerva specifications:
- Over 20 petaflops of computing power
- 25,584 Intel Platinum processors in different generations including 2.1 GHz, 2.3 GHz, 2.6 GHz, and 2.9 GHz computing cores (112 cores or 96 cores or 64 cores or 48 cores per node with two sockets in each node) with 1.5 terabytes (TB) or 2 terabytes (TB) of memory per node
- 408 graphical processing units (GPUs) including 48 Nvidia B200s, 236 Nvidia H100s, 32 Nvidia L40S, 44 Nvidia A100s, 48 Nvidia V100s, 452 TB of total memory
- 32 petabytes of spinning storage accessed via IBM’s Spectrum Scale/General Parallel File System (GPFS)
- Minerva has contributed to over 2,100 peer-reviewed publications since its creation in 2012
Who should use it?
Researchers, clinicians, and data scientists seeking a place to analyze KPMP data using substantial computational resources for advanced bioinformatics analysis, machine learning, or statistical modeling but may not have the required resources for their desired computational work are the types of users we expect to need access to the KPMP HPC Enclave.
- NOTE: Users cannot download data, only their computational results.
This space is not well-suited for users that would prefer to access the data directly and have the necessary resources for the computational work they will be performing.
How to request access
Please follow these steps for successful access to the HPC Enclave and compliance.
Step 1: Submit a Controlled Access Data Request
- Complete and submit a KPMP HPC Enclave controlled access request form to initiate your request.
Step 2: Submit a Data Use Agreement
- Once Step 1 has been completed, a KPMP Data Use Agreement (DUA) will be emailed to the email address you provided in the request form.
- Work with your institution to execute the necessary review of the DUA for completion between your institution and KPMP. The agreement is only valid for data specifically outlined in your request.
- You must have an approved DUA before moving forward.
Step 3: Request a Minerva User Account
- Sponsorship and approval from the KPMP Principal Investigator (PI) at Mount Sinai is required for all Minerva user accounts and the PI will request a user account on your behalf.
- Once your DUA is approved and completed, the process of requesting your user account will begin.
- Your request will be cross-referenced with your signed DUA.
Step 4: Access Is Assigned
- The KPMP HPC Enclave team will grant access to the requested data based on the approved DUA and account access information from KPMP’s Central Hub.
Step 5: Begin Using your Minerva Compute Space
- Once your account is active, you will have access to Data2Evidence tools set up specifically for use with KPMP data within the Minerva compute space.
- For more information, see: connecting to Minerva, or how to log in
- PLEASE NOTE:
- Compute usage over 1TB will be charged at $149 per TB per year.
- Accounts will be deactivated by June 30, 2027 or according to the terms of the DUA, whichever is earlier.
Frequently Asked Questions
Do I need sponsorship to request a Minerva account?
- Yes, all account requests require sponsorship and approval from a KPMP Principal Investigator at Mount Sinai.
Who should I contact for help or questions?
- General data questions: contact KPMP Atlas Support
- Minerva support:
- Minerva help documentation
- Questions can be directed to hpchelp@hpc.mssm.edu
- Data Use Agreement: Contact Ashveena Dighe at ashveena.dighe@mssm.edu.
How do I download data from the KPMP HPC Enclave?
- Users cannot download data from Minerva but only their computational results.
What happens when my DUA expires?
- Account and data access will be revoked, and your Minerva account will be deactivated according to the DUA terms.
What is the KPMP HPC Enclave?
The KPMP High Performance Computing (HPC) Enclave is a secure, computational space that houses high-dimensional biomedical datasets produced by KPMP technologies such as electronic health records (EHR), whole genome sequencing (WGS), or other omics data. It is hosted on the Minerva supercomputer at Mount Sinai’s Icahn School of Medicine and maintained by High Performance Computing (HPC).
Minerva specifications:
- Over 20 petaflops of computing power
- 25,584 Intel Platinum processors in different generations including 2.1 GHz, 2.3 GHz, 2.6 GHz, and 2.9 GHz computing cores (112 cores or 96 cores or 64 cores or 48 cores per node with two sockets in each node) with 1.5 terabytes (TB) or 2 terabytes (TB) of memory per node
- 408 graphical processing units (GPUs) including 48 Nvidia B200s, 236 Nvidia H100s, 32 Nvidia L40S, 44 Nvidia A100s, 48 Nvidia V100s, 452 TB of total memory
- 32 petabytes of spinning storage accessed via IBM’s Spectrum Scale/General Parallel File System (GPFS)
- Minerva has contributed to over 2,100 peer-reviewed publications since its creation in 2012
Who should use it?
Researchers, clinicians, and data scientists seeking a place to analyze KPMP data using substantial computational resources for advanced bioinformatics analysis, machine learning, or statistical modeling but may not have the required resources for their desired computational work are the types of users we expect to need access to the KPMP HPC Enclave.
- NOTE: Users cannot download data, only their computational results.
This space is not well-suited for users that would prefer to access the data directly and have the necessary resources for the computational work they will be performing.
How to request access
Please follow these steps for successful access to the HPC Enclave and compliance.
Step 1: Submit a Controlled Access Data Request
- Complete and submit a KPMP HPC Enclave controlled access request form to initiate your request.
Step 2: Submit a Data Use Agreement
- Once Step 1 has been completed, a KPMP Data Use Agreement (DUA) will be emailed to the email address you provided in the request form.
- Work with your institution to execute the necessary review of the DUA for completion between your institution and KPMP. The agreement is only valid for data specifically outlined in your request.
- You must have an approved DUA before moving forward.
Step 3: Request a Minerva User Account
- Sponsorship and approval from the KPMP Principal Investigator (PI) at Mount Sinai is required for all Minerva user accounts and the PI will request a user account on your behalf.
- Once your DUA is approved and completed, the process of requesting your user account will begin.
- Your request will be cross-referenced with your signed DUA.
Step 4: Access Is Assigned
- The KPMP HPC Enclave team will grant access to the requested data based on the approved DUA and account access information from KPMP’s Central Hub.
Step 5: Begin Using your Minerva Compute Space
- Once your account is active, you will have access to Data2Evidence tools set up specifically for use with KPMP data within the Minerva compute space.
- For more information, see: connecting to Minerva, or how to log in
- PLEASE NOTE:
- Compute usage over 1TB will be charged at $149 per TB per year.
- Accounts will be deactivated by June 30, 2027 or according to the terms of the DUA, whichever is earlier.
Frequently Asked Questions
Do I need sponsorship to request a Minerva account?
- Yes, all account requests require sponsorship and approval from a KPMP Principal Investigator at Mount Sinai.
Who should I contact for help or questions?
- General data questions: contact KPMP Atlas Support
- Minerva support:
- Minerva help documentation
- Questions can be directed to hpchelp@hpc.mssm.edu
- Data Use Agreement: Contact Ashveena Dighe at ashveena.dighe@mssm.edu.
How do I download data from the KPMP HPC Enclave?
- Users cannot download data from Minerva but only their computational results.
What happens when my DUA expires?
- Account and data access will be revoked, and your Minerva account will be deactivated according to the DUA terms.
