Software and Packages
- Software and Applications
- Schrodinger Suite
- MATLAB, Simulink and MATLAB Distributed Compute Server
- Jupyter Notebook
Queues and Resources
- LSF Queues And Policies
- GPU Etiquette
- Access TSM with GUI
- Access TSM with Command Line
- Checkpoint Restart
- Disaster Recovery Plan
The scratch space on Minerva resources utilizes GPFS, the General Parallel File System, a massively parallel distributed file system. This space is intended for temporary production work and not long term storage. Files in scratch directories are not backed up and are subject to being purged after 14 days. It is the user’s responsibility to back up all important data to archival storage or other storage resources.
The scratch space is accessible from Minerva as:
The scratch file system cannot be used for long term storage and files on scratch are not backed up or guaranteed by Minerva. In the event of a file system crash or purge, files in scratch directories cannot be recovered. It is the user’s responsibility to back up all important data to archival storage or other storage resources.
Files are exempt from purge if they have been written to or read within the last 14 days. To see the list of files that will be purged you can use:
find /sc/arion/scratch/$USER -atime +14
Scratch usage on Hydra (/sc/hydra/scratch) frequently reaches its maximum. This causes unnecessary errors for users who rely on it to pull large data temporarily. To ameliorate the issue, a per-user quota (15T) is implemented in the scratch folders in Hydra. This policy is to avoid any one user from consuming all off the scratch space and reduce related job failures.
Special Note: Modifying file access times (using touch or any other method) for the purpose of circumventing purge policies may result in the loss of access to the scratch file systems. Under special circumstances, users may request a purge exemption by submitting a request in a timely manner that includes detailed justification to email@example.com. Please include file system (e.g. Hydra), PI of the project, user requesting exemption, Account #, time requested (e.g. two weeks), and detailed justification.
How to check your GFPS quota
To check your GPFS quotas, you can run the following script, either per user or per project is listed:
# showquota -h usage: showquota [-h] [-u USER | -p PROJECT] optional arguments: -h, --help Show this help message and exit -u USER, --user USER Show quota for user in groups -p PROJECT, --project PROJECT Show quota for a project
You can find your quota on scratch by
# showquota -p scratch
Please also understand that the quota is based on GPFS’s quota report that is queried every 15 mins and might have a fudge factor (including some -ve numbers that you should ignore for small set of files) to account for files being created or deleted.