Systems Biology User FAQ

New users can request an account by emailing Rebecca Yohannes, HPC liaison, at ry111@cumc.columbia.edu. Please include the following information:

- Full Name
- UNI                        
- Phone number
- Name of department
- Job title     
- Project title
- A brief description of your project
- Anticipated software, hardware, and storage requirements
- Faculty manager/PI (include only if you are a student researcher)

Once your request is approved and your account is created, you will receive an email with login instructions, along with your ARCS domain login and password.

You can access the cluster through the pool of 5 login nodes. You’ll need to Secure Shell (SSH) to login.c2b2.columbia.edu and use your ARCS domain login and password. 

MacOS users can use the built-in Terminal application. Windows users will need to use a third-party program like PuTTY or Cygwin.

No. Absolutely no computation should take place on the login nodes. The login nodes are ONLY to access compute and storage resources. 

Please contact Rebecca Yohannes, HPC liaison, at ry111@cumc.columbia.edu for password resets.

Applications can be found in /nfs/apps. Please review the Cluster Documentation for more information on how to run programs, along with sample scripts. 

Some project support is provided free of charge to MSPH users. The HPC liaison works closely with users to determine their project's ideal configuration and design a custom solution that encompasses storage requirement, software environment, and automation of tasks. 

Users can send an email to Rebecca Yohannes, HPC liaison, at ry111@cumc.columbia.edu with the full description of the issue, including the submitted script and any errors that may appear. The liaison will review the error to identify the cause and work with System Biology staff to develop a solution for the user to execute.

You may use the following HPC text in your grant proposal:

The Mailman School of Public Health (MSPH) provides faculty with secure High Performance Computing (HPC) capabilities for research use. The multiple high-performance compute clusters, as well as high-memory systems, are housed in two data centers totaling more than 3,000 sq. ft. of floor space. The facility has redundant air conditioning, state-of-the-art networking, a 1MW universal power supply (UPS), and 24/7/365 security.

The clusters includes 6,336 CPU cores and 73,728 CUDA-cores (GPU), which will have a maximum performance of 212 TFlops, 10 Gbps Ethernet fabric throughout, 40 Gbps QDR InfiniBand, GPU-enhanced computing, and lower-power hardware architecture. The cluster maintains two high-memory systems with 1TB of system memory each and a pool of computational servers for compilation, debugging, and job control. In total, the cluster provides over 1.4PB of high-speed redundant storage for the compute clusters and user data. A secondary Isilon clustered file system provides daily replication of valuable data to a secondary site as well as additional iSCSI Ethernet SAN storage. 

MSPH has designed a variety of best-practices data-storage protocols to ensure that all data remains secure, including Columbia University Information Technology (CUIT) and HIPAA-compliant security measures as well as regular data snapshots, replication, and offsite backup. 

All of the clusters run current variants of the Linux operating systems and are managed by Univa Grid Engine. The cluster supports Java, Perl, Matlab, and R languages but can support other program sets as needed.