Biowulf High Performance Computing at the NIH
NIH HPC Systems Policies

Who May Use the NIH HPC Systems

Accounts on the NIH HPC systems are for the use of researchers in the NIH intramural research programs.

NIH Guest Researchers and Volunteers can maintain HPC accounts for the duration of their NIH status.

NIH HPC users must be listed in the NIH NED. When a user is removed from the NED, the associated Helix and Biowulf accounts become inactive. If the user remains out of the NED for more than 14 days, the associated Helix and Biowulf accounts are deleted. Any data associated with those accounts will be deleted six months after that unless arrangements are made by the user or PI to transfer the data to another account or move it off the system.

User Responsibilities

The NIH HPC Systems are for appropriate government use only

System resources are for the work-related use of authorized users only.

Account Sharing

Account sharing among multiple users is strictly prohibited. By NIH Account Lifecycle and Password Policy, a separate HPC account must be established for each user.

Access to data and applications is restricted

Even if a user has inadvertently allowed access to their files, do not access files or directories belonging to another user without explicit permission.

Data Recovery

User data directories and shared data directories are NOT backed up to tape (with the exception of directories that are part of a storage buy-in agreement). If you accidentally delete files you can often recover them from daily or weekly snapshots maintained on the system. HOWEVER, any data that you consider irreplaceable should be saved to your local disk storage in case of a catastrophic event on a Biowulf file system. We have more information on our Backups/snapshots web page.

PII & PHI data

NIH HPC users are forbidden from transmitting or storing any Personally Identifiable Information (PII, e.g. patient data containing names or social security numbers) or Protected Health Information (PHI) data anywhere on the NIH HPC systems, including their /home, /data, and any group (shared) /data directories.

Controlled Access Data (CAD)

Controlled access data such as dbGaP data may be stored on the systems, but it is the responsibility of the user to fulfill all requirements of the agreement with the data provider. (See here and here for dbGaP requirements, for example).
Amongs other things this means that
  • Users may not move or copy CAD to our anonymous ftp space or a datashare directory nor make CAD available to the outside in any other way.
  • Users must maintain permissions on all CAD such that only authorized users can read the data.
  • If CAD is housed in shared data directory, all members of the unix group set up for the shared directory must be authorized to access the data. If the Unix group membership changes over time, again, it is the group owner's responsibility to ensure that all members are authorized to access the data.

Read the announcements!

Users are responsible for reading the system messages and announcements. These will appear as messages during login, and will also be sent to all Helix users by email. [Archive of NIH HPC messages]

Monthly Reboots

To improve system security and availability, a monthly maintenance cycle has been instituted. This cycle will generally involve a reboot of both Helix and the Biowulf login node (not the entire cluster). The reboots are scheduled at 7 am on the first Monday of every month, or the following Tuesday if that Monday is a holiday. Downtime during a reboot will typically be 10-15 minutes.

Scheduled maintenance that requires a longer downtime and emergency maintenance will be announced separately. Every effort will be made to minimize disruptions.

See the System Status Calendar for the reboot and downtime schedule.

Helix Usage

Helix is a single shared system with 48 Intel(R) Xeon(R) Gold 6136 (3.00GHz) CPUs and 1.5 TB of memory. It is intended for interactive file transfers, such as Aspera transfers which are not easily performed on Biowulf compute nodes. All compute-intensive jobs should be performed on the Biowulf cluster, which is intended for large-scale computing.

Scientific applications are not available, and should not be run on Helix.

Please contact the NIH HPC staff (, or 301-496-4825) if you have questions about the appropriateness of your job for a particular platform, or need more information about how to run your job.