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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.
Due to the nature of the funding, the NIH HPC systems are not available to extramural scientists with NIH grants. The NIH Strides program can enable cloud resources for NIH extramural projects; please contact strides@nih.gov for more information.
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 HHS Policy for Rules of Behavior for Use of Information and IT Resources (Appendix D, section 1.3.G), a separate HPC account must be established for each user:
Not use another person’s account, identity, password/passcode/PIN, or PIV card or allow others to use my GFE and/or other HHS/OpDiv information resources provided to me to perform my official work duties and tasks. This includes not sharing passwords or provide passwords to anyone, including system administrators.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.
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.
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.
Additional information is available at:
PII data at toolkit.ncats.nih.gov.
De-identifying PHI data under the Privacy Rule at privacyruleandresearch.nih.gov.
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 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.
Users are welcomed and encouraged to send email to staff@hpc.nih.gov if they have problems or concerns relating to Biowulf. The HPC staff will respond during normal weekday business hours. If an email is sent late in the evening or on a weekend, there is no guarantee of an immediate staff response unless there is a system problem affecting a large number of HPC users, but the staff will respond on the next business day.
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]
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 8 pm on the first Sunday of every month unless Monday is a holiday, in which case they are rebooted the following Sunday evening at 8 pm. Downtime during a reboot will typically be 15-30 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 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 (staff@hpc.nih.gov, 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.
The NIH Data Management and Sharing Policy comes into effect on Jan 25, 2023. Published scientific data that is currently on Biowulf will need to be moved to an appropriate repository to fulfill the requirements of this policy. Biowulf disk storage is intended for active data and cannot be used for longterm archiving; therefore Biowulf disk storage is not appropriate for the NIH Data Management Policy requirements.
Sharing via Globus will not fulfill the requirements of the NIH Data Sharing policy, since no accession number or DOI can be obtained for data shared this way. Globus sharing should be utilized only for sharing data with collaborators during a project.
Users and PIs who have published scientific data on Biowulf that needs to be shared for 3 years to fulfill the NIH policies should contact their Scientific Director's office to discuss possible repositories. Details of the NIH Data Management/Sharing Policy can be found at https://sharing.nih.gov/. A list of NIH-supported Data Sharing Repositories can be found at https://www.nlm.nih.gov/NIHbmic/nih_data_sharing_repositories.html.
It may be possible to upload data directly from Biowulf to a repository (e.g. to NCBI's SRA repository, or to OpenNeuro.org): check the Biowulf data transfer page for details.