Storage Resources

Overview

ARC offers several different storage options for users’ data:

Persistent Storage

Name	Intent	File System	Environment Variable	Per User Maximum	Data Lifespan	Available On
Home	Long-term storage of files	Qumulo	$HOME	640 GB 1 million files	As long as the user account is active	Login and Compute Nodes
Project	Long-term storage of shared, group files	GPFS (replaced a BeeGFS system)	- n/a -	50 TB, 5 million files per faculty researcher (Expandable via investment)	As long as the project account is active	Login and Compute Nodes
Archive	Long-term storage for infrequently-accessed files	GPFS	$ARCHIVE	-	to be negotiated in accordance with demonstrated need	Login Nodes

Scratch (temporary) storage

Name	Intent	Per User Maximum	Data Lifespan	File System	Environment Variable	Available On
Global Scratch	Short-term access to working files. Automatic deletion.	No size limits enforced	90 days	Vast	- n/a -	Login and compute nodes
Fast Scratch (deprecated)	(deprecated) Short-term access to working files	No size limits enforced	90 days	Vast	- n/a -	Login and compute nodes
Local Scratch (TMPDIR)	Fast, temporary storage. Auto-deleted when job ends	Size of node hard drive	Length of Job	Local disk hard drives, usually spinning disk or SSD	$TMPDIR	Compute Nodes
Local Scratch (TMPNVME)	Fast, temporary storage. Auto-deleted when job ends	Size of node hard drive	Length of Job	Local disk hard drives, usually spinning disk or SSD	$TMPDIR	Compute Nodes
Memory (TMPFS)	Very fast I/O	Size of node memory allocated to job	Length of Job	Memory (RAM)	$TMPFS	Compute Nodes

Centralized repositories

Name	Intent	File System	Environment Variable	Per User Maximum	Data Lifespan	Available On
Global	Central repo of large datasets and databases	VAST	- n/a -	-	-	Login and compute nodes, Tinkercliffs only.

Each is described in the sections that follow.

Home

Home provides long-term storage for system-specific data or files, such as installed programs or compiled executables. Home can be reached the variable $HOME, so if a user wishes to navigate to their Home directory, they can simply type cd $HOME. Each user is provided a maximum of 640 GB in their Home directories (across all systems). Home directories are not allowed to exceed this limit. Note that running jobs fail if they try to write to a Home directory when the hard limit is reached.

Note

Avoid reading/writing data to/from HOME in a job or using it as a working directory. Stage files into a “scratch” location to keep unnecessary I/O off of the HOME filesystem and improve performance. /fastscratch and Local Scratch

Project

Project provide long-term storage for files shared among a research project or group, facilitating collaboration and data exchange within the group. Each Virginia Tech faculty member can request group storage up to the prescribed limit at no cost by requesting a storage allocation via ColdFront. Additional storage may be purchased through the investment computing or cost center programs.

Data ownership passes to the shared directory creator/owner

A project PI requests a shared storage directory and gives access to others. When given access to the shared directory, they will have the ability to add, modify, and delete files from the directory according to the mode (set of permissions) of the directory.

Modes get set and changed in lots of different ways, and this sometimes results in group members, even the group owner, not having access to some files or subdirectories in their shared directory. The owner(s) of such files can fix this on their own with some chmod and/or chown commands. ARC encourages shared directory owners to work with their group members to establish best practices and to make a point to ensure their files are properly culled, organized, and manageble by the group before leaving the group. ARC personnel can consult on the commands to use and best practices for implementing such a transfer.

When a project owner removes a user from their shared directory via ColdFront, that user will no longer be able to access the directory to make such changes.

We have recently (March 2022) amended the removal process so that it executes a script which will ensure the group id (gid) and mode (permissions) of every file that user owned in the shared directory is set to allow allow all group members access.

Archive

Note

As of Fall 2023, the current storage system which hosts the VTARCHIVE storage has reached its end-of-life. We are working with individual groups with the largest footprint on how to manage data currently in place there.

The term “Archive” is meant to convey the idea of a thoughtful, curated collection whose members are discrete, well packaged and labeled. In this sense “scratch” and “work” are conceptual opposites of “archive”. VT’s ARCHIVE storage is also different in concept from a “backup”.

Archive provides users with long-term storage for data that does not need to be frequently accessed i.e. storing important/historical results. Archive is accessible from all ARC’s systems. Archive is not mounted on compute nodes, so running jobs cannot access files on it. Archive can be reached the shell variable $ARCHIVE, so if a user wishes to navigate to their Archive directory, they can simply type cd $ARCHIVE.

Since “Archival” is a long-term concept and students are generally expected to be users for a few years, they should not have or use a personal archive directory. A more appropriate arrangement would be to package and transfer data to their advisor or PI who maintains an archive of curated and packaged datasets.

Best Practices for archival storage

Because the ARCHIVE filesystem is backed by tape (a high capacity but very high latency medium), it is very inefficient and disruptive to do file operations (especially on lots of small files) on the archive filesystem itself. Archival systems are designed to move and replicate very large files; ideally users will tar all related files into singular, large files. Procedures are below:

To place data in $ARCHIVE:

create a tarball containing the files in your $HOME (or $WORK) directory
copy the tarball to the $ARCHIVE filesystem (use rsync in case the transfer were to fail)

To retrieve data from $ARCHIVE:

copy the tarball back to your $HOME (or $WORK) directory (use rsync in case the transfer were to fail).
untar the file on the login node in your $HOME (or $WORK) directory. Directories can be tarred up in parallel with, for example, gnu parallel (available via the parallel module). This line will create a tarball for each directory more than 180 days old:

find . -maxdepth 1 -type d -mtime +180 | parallel [[ -e {}.tar.gz ]] || tar -czf {}.tar.gz {}

The resulting tarballs can then be moved to Archive and directories can then be removed. (Directories can also be removed automatically by providing the --remove-files flag to tar, but this flag should of course be used with caution.)

Scratch Filesystems

VAST - Global Scratch (Tinkercliffs only)

Note

Files and directories stored here are subject to automatic deletion. Do not use it for long term storage.

Local scratch storage options (see below) generally provide the best performance, but are constrained to the duration of a job and are strictly local to the compute node(s) allocated to a job. In constrast, we also have a VAST storage system which provides storage for temporary staging and working space with better performance characteristics than HOME or PROJECTS. It is “global” in the sense that it is accessible from any node on the Tinkercliffs cluster.

It is a shared resource and has limited capacity (364TB), but individual use at any point in time is unlimited provided it the space is available. A strict automatical deletion policy is in place wherein any file will be automatically deleted when it has reached an age of 90 days on /globalscratch.

Best practices

create a directory for yourself mkdir /globalscratch/<username>
stage files for a job or set of jobs
keep the number of files and directories relatively small (ie. less than 10,000). It is a network-attached filesystem and incurs the same performance overhead for file operations that you would get with /home or /projects.
immediately copy any files you want to keep to a permanent location to avoid accidental deletion
always remember the 90-day automatic deletion policy

Automatic Deletion Details

As mentioned above, files and directories in /globalscratch will be automatically deleted based on aging policies. Here is how that works:

The storage system runs an hourly job to identify files which have exceeding the aging policy (90 days) and adds these to the deletion queue.
The storage system runs an automated job at 12:00am UTC (7:00PM EST) every day to process the deletion queue.
Additionally, the storage system will detect and delete all empty directories regardless of age.

Restoring files

In some situations, deleted files and directories may be restored from “snapshots”. Snapshots are an efficient way to keep several instances of the status of a file system at regular points in time.

For the /globalscratch file system, these are kept in the “hidden directory” /globalscratch/.snapshots which contains a set of snapshots named according to the type (daily, weekly, or monthly) and the date-time when they were recorded. For example:

/globalscratch/.snapshot/week_2023-11-13_12_00_00_UTC

is an instance of a weekly snapshot which was recorded on 2023-11-13 at 12:00:00PM UTC.

Snapshots may be recorded in daily, weekly, and monthly cycles, but ARC reserves the right to adjust the frequencies and quantities of snapshots which are retained. Changes in the frequencies and quantities may occasionally be needed to adjust how much of the storage system capacity is dedicated to snapshot retentions.

Note

While snapshots provide some level of protection against data loss, they should not be viewed as a “backup” or as part of a data retention plan.

VAST - Fast Scratch (deprecated - do not use)

Warning

2024-03-08: The /fastscratch filesystem on Tinkercliffs is being replaced by /globalscratch and will be removed from Tinkercliffs at the end of the 2024 Spring semester. Recover any files you need from that system before then.

While the use of scratch storage options below are constrained to the duration of a job, the VAST storage system provides a temporary staging and working space with better performance characteristics than HOME or PROJECT. It is a shared resource and has limited capacity (200TB), but individual use is unlimited provided it

Local Scratch

Running jobs are given a workspace on the local drives on each compute node which are allocated to the job. The path to this space is specified in the $TMPDIR environment variable. This provides a higher performing option for I/O which is a bottleneck for some tasks that involve either handling a large volume of data or a large number of file operations.

Note

Any files in local scratch are removed at the end of a job, so any results or files to be kept after the job ends must be copied to another location as part of the job. /globalscratch is a good choice for most people.

Local Drives

Running jobs are given a workspace on the local drives on each compute node. The path to this space is specified in the $TMPDIR environment variable

Solid State Drives (SSDs)

Solid state drives do not use rotational media (spinning disks/platters) but memory-like flash storage which gives it better performance characteristics. The environment variable $TMPSSD is set to a directory on an SSD accessible to the owner of a job when SSD is available on compute nodes allocated to a job.

Memory as storage

Running jobs have access to an in-memory mount on compute nodes via the $TMPFS environment variable. This should provide very fast read/write speeds for jobs doing I/O to files that fit in memory (see the system documentation for the amount of memory per node on each system). Please note that these files are removed at the end of a job, so any results or files to be kept after the job ends must be copied to Work or Home.

NVMe Drives

Same idea as Local Scratch, but on NVMe media which “has been designed to capitalize on the low latency and internal parallelism of solid-state storage devices.” Running jobs are given a workspace on the local NVMe drive on each compute node if it is so equipped. The path to this space is specified in the $TMPNVME environment variable. This provides another option for users who would prefer to do I/O to local disk (such as for some kinds of big data tasks). Please note that any files in local scratch are automatically removed at the end of a job, so any results or files to be kept after the job ends must be copied to Work or Home.

NVMe local scratch storage is available on nodes in the following nodes and capacities:

Cascades
- largemem_q nodes, 1.8TB
- k80_q nodes, 1.8TB
Tinkercliffs
- a100_normal_q nodes, 11.7TB
- intel_q nodes, 3.2TB

Global

On Tinkercliffs, the /global/ directory has been set up to provide centralized access to some commonly used databases and datasets which are large and/or have many files. All users can read these files, but for stability purposes, write permissions are only available to ARC personnel.

Some example datasets are the imagenet dataset and some biodatabases such as those neede by AlphaFold or other genomics applications. If you know of a dataset you think we should add to this repository, please let us know by submitted an ARC helpdesk request.

Checking Usage

You can check your current storage usage (in addition to your compute allocation usage) with the quota command:

[mypid@tinkercliffs2 ~]$ quota
USER       FILESYS/SET                         DATA (GiB)   QUOTA (GiB) FILES      QUOTA      NOTE 
mypid      /home                               584.2        596         -          -           

           GPFS                                                                              
mypid      /projects/myproject1                109.3        931                                
mypid      /projects/myproject2                2648.4       25600                              