Available File Systems

Home Directory Service

Each user ID has a home directory on the NetApp WAFL service. You have the same home directory regardless of what system you’re on, including all login nodes and all compute nodes, so your files are accessible everywhere. Most of your work in the login environment will be done in your home directory.

OSC currently has a high performance NetApp applicance to provide home directories. The absolute path to the home directory for user ID usr1234 will have the form /users/project/usr1234 , where project is the default project for the account (for example, PAS1234 ). The environment variable $HOME is the absolute path to your home directory. You should use $HOME or ~/ instead of absolute paths to refer to your home directory wherever possible.

The default permissions on home directories for academic projects allow anyone with an OSC HPC account to read your files, although only you have write permission. You can change the permissions if you want to restrict access. Home directories for accounts on commercial projects are slightly more restrictive, and only allow the owning account and the project group to see the files by default.

Each user has a quota of 500 gigabytes (GB) of storage and 1,000,000 files. This quota cannot be increased. If you have many small files, you may reach the file limit before you reach the storage limit. In this case we encourage you to “ tar ” or “ zip ” your files or directories, creating an archive. If you approach your storage limit, you should delete any unneeded files and consider compressing your files using bzip or gzip . You can archive/unarchive/compress/uncompress your files inside a batch script, using scratch storage that is not subject to quotas, so your files are still conveniently usable. As always, contact OSC Help if you need assistance.

Home directories are considered permanent storage. Accounts that have been inactive for 18 months may be archived, but otherwise there is no automatic deletion of files.

All files in the home directories are backed up daily. Two copies of files in the home directories are written to tape in the tape library.

Access to home directories is relatively slow compared to local or parallel file systems. Batch jobs should not perform heavy I/O in the home directory tree because it will slow down your job. Instead you should copy your files to fast local storage and run your program there.

Project Storage Service

For projects that require more than 500GB storage and/or more than 1,000,000 files, additional storage space is available. Principal Investigators should contact OSC Help to request additional storage on this service, outside the home directory. Allocations of one to five terabytes are typical; these small allocations can be granted by OSC staff; for large allocations you will have to submit a proposal to the Allocations Committee of the Statewide Users’ Group (SUG). Here is the required information:

  1. How much space your project will need and what will be the file limit (i.e. what kind of file count do you expect)
  2. What measures you are and will continue to take to optimize the space usage (deleting unneeded data, compression of data, moving infrequently used data to archive, etc.)
  3. Why you need the project storage space
  4. How long you will need the space

Fill out this form and follow the instructions.

Small storage request 

Example 1

Large storage request 

Example 1

Example 2

Project directories are created on the Project filesystem. The absolute path to the project directory for project PRJ0123 will have the following form:  /fs/project/PRJ0123 .

Default permissions on a project directory allow read and write access by all members of the group, with deletion restricted to the file owner. (OSC projects correspond to Linux groups.)

The quota on the project space is shared by all members of the project and corresponds to the allocation that was granted.  It is typically 1-5TB with a limit of 1,000,000 files.

Project space is allocated for a specific period of time, usually one to three years. At the end of that time you may apply for an extension.

All files in the project directories are backed up daily, with a single copy written to tape.

The recommendations for archiving and compressing files are the same for project directories as for home directories.

Filesystem performance is better than home directories, but for certain workloads scratch space local to the compute nodes will be a better choice.

Local Disk

Each compute node has a local disk used for scratch storage. This space is not shared with any other system or node.

The batch system creates a temporary directory for each job on each node assigned to the job. The absolute path to this directory is in the environment variable $TMPDIR. The directory exists only for the duration of the job; it is automatically deleted by the batch system when the job ends. Temporary directories are not backed up.

$TMPDIR is a large area where users may execute codes that produce large intermediate files. Local storage has the highest performance of any of the file systems because data does not have to be sent across the network and handled by a file server. Typical usage is to copy input files, and possibly executable files, to $TMPDIR at the beginning of the job and copy output files to permanent storage at the end of the job. See the batch processing documentation for more information.

The size of the temporary file space on each Owens node is 1500GB; on Ruby it is 857GB; on Oakley it is 812GB. There are 8 data analytics nodes on Owens with 24x 2TB scratch drives. This area is used for spool space for stdout and stderr from batch jobs as well as for $TMPDIR.  If your job requests less than the entire node, you will be sharing this space with other jobs, although each job has a unique directory in $TMPDIR.

Please use $TMPDIRand not /tmp on the compute nodes to ensure proper cleanup.

The login nodes have local scratch space in /tmp. This area is not backed up, and the system removes files last accessed more than 24 hours previously.

Scratch Service

OSC provides a parallel file system for use as high-performance, high-capacity, shared temporary space. The current capacity of the parallel file system is about 1,000TB.

The scratch service is visible from all OSC HPC systems and all compute nodes at /fs/scratch. It can be used as either batch-managed scratch space or as user-managed temporary space. There is no quota on this system.

In batch job, users add the node attribute " pfsdir" in the request ( nodes=XX:ppn=XX:pfsdir), which allows the batch system to create a scratch directory for each job on the scratch service. The absolute path to this directory is in the environment variable $PFSDIR, which is located at  /fs/scratch/userID/jobIDjobID inlcudes the job number and batch server name for Oakley and Owens job, and only the job number for Ruby job). This directory is shared across nodes. It exists only for the duration of the job and is automatically deleted by the batch system when the job ends.

Users may also create their own directories; see 'How to Create Directories on Scratch'. This is a good place to store large amounts of temporary data that you need to keep for a modest amount of time. Files that have not been accessed for some period of time may be deleted. This service should be used only for data that you can regenerate or that you have another copy of. It is not backed up.

The scratch service is a high performance file system that can handle high loads. It should be used by parallel jobs that perform heavy I/O and require a directory that is shared across all nodes. It is also suitable for jobs that require more scratch space than what is available locally. It should be noted that local disk access is faster than any shared file system, so it should be used whenever possible.

You should not store executables on the parallel file system. Keep program executables in your home or project directory or in $TMPDIR .

See this page for Scratch Storage Policy. 

How To Create Directories on Scratch

Users do not have the ability to directly create directories under /fs/scratch. Please create your own directories under /fs/scratch/project, where project is the project account (for example,  PAS1234 ). The directory /fs/scratch/project is owned by root, in the group project, with permission of drwxrwx--T

All data stored on scratch service follows the Scratch Storage Policy on this page

File Deletion Policy

The scratch service is temporary storage, and it is not backed up. Data stored on this service is not recoverable if it is lost for any reason, including user error or hardware failure. Data that have not been accessed for more than or equal to 120 days will be removed from the system every Wednesday. It is a policy violation to use scripts (like touch command) to change the file access time to avoid being purged.  Any user found to be violating this policy will be contacted; further violations may result in the HPC account being locked.

If you need an exemption to the deletion policy, please contact OSC Help including the following information in a timely manner:

  1. Your OSC HPC username
  2. Path of directories/files that need exemption to file deletion
  3. Duration: from requested date till MM/DD/YY (The max exemption duration is 120 days)
  4. Detailed justification

Any exemption request needs approval by OSC managers. We will discuss alternatives if your request can't be fulfilled.