Storage Resources

Overview

ARC offers several different storage options for users’ data:

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	Unlimited	Login and Compute Nodes
Group (Cascades, DragonsTooth, Huckleberry)	Long-term storage of shared, group files	GPFS	- n/a -	10 TB, 5 million files per faculty researcher (Expandable via investment)	Unlimited	Login and Compute Nodes
Project (TinkerCliffs, Infer)	Long-term storage of shared, group files	BeeGFS	- n/a -	25 TB, 5 million files per faculty researcher (Expandable via investment)	Unlimited	Login and Compute Nodes
Work (Cascades, DragonsTooth, Huckleberry)	Fast I/O, Temporary storage	GPFS	$WORK	14 TB, 3 million files	120 days	Login and Compute Nodes
Work (TinkerCliffs, Infer)	Fast I/O, Temporary storage	BeeGFS	$WORK	1 TB, 1 million files	Unlimited	Login and Compute Nodes
Archive	Long-term storage for infrequently-accessed files	GPFS	$ARCHIVE	-	Unlimited	Login Nodes
Local Scratch	Local disk (hard drives)		$TMPDIR	Size of node hard drive	Length of Job	Compute Nodes
Memory (tmpfs)	Very fast I/O	Memory (RAM)	$TMPFS	Size of node memory allocated to job	Length of Job	Compute Nodes

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). When a user exceeds the soft limit, they are given a grace period after which they can no longer add any files to their Home directory until they are below the soft limit. Home directories are also subject to a 690 GB hard limit; users Home directories are not allowed to exceed this limit. Note that running jobs fail if they try to write to a Home directory after the soft limit grace period is expired or when the hard limit is reached.

Group and Project

Project (on TinkerCliffs and Infer) and Group (on Cascades, DragonsTooth, and Huckleberry) 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.

Quotas on Project

The file system that provides Project and Work directories on TinkerCliffs and Infer does quotas based on the group ID (GID) associated with files. This means that:

Files in your Work directory can count against your Project quota if they have that project’s GID
Files in your Project directory can count against your Work quota if they have your personal GID

You can check your Project and Work quotas with the quota command. You can check the GID associated with your files with ll (the same as ls -l) and can change the group with chgrp (chgrp -R for recursive on a directory). You can find files in a more automated fashion with find – see the example below. As an example, here we find some files in /projects/myproject that are owned by mypid:

[mypid@tinkercliffs2 ~]$ find /projects/myproject/test -group mypid
/projects/myproject/test
/projects/myproject/test/datafile
/projects/myproject/test/test.txt
[mypid@tinkercliffs2 ~]$ ls -ld /projects/myproject/test/
drwxrwxr-x 2 mypid mypid 2 Oct  4 08:43 /projects/myproject/test/
[mypid@tinkercliffs2 ~]$ ls -lh /projects/myproject/test/
total 1.1G
-rw-rw-r-- 1 mypid mypid 1.0G Oct  4 08:43 datafile
-rw-rw-r-- 1 mypid mypid    5 Jun  8 10:51 test.txt

These files will count against mypid’s Work quota. We change their ownership to the associated group with chgrp -R:

[mypid@tinkercliffs2 ~]$ chgrp -R arc.myproject /projects/myproject/test
[mypid@tinkercliffs2 ~]$ ls -ld /projects/myproject/test/
drwxrwxr-x 2 mypid arc.myproject 2 Oct  4 08:43 /projects/myproject/test/
[mypid@tinkercliffs2 ~]$ ls -lh /projects/myproject/test/
total 1.1G
-rw-rw-r-- 1 mypid arc.myproject 1.0G Oct  4 08:43 datafile
-rw-rw-r-- 1 mypid arc.myproject    5 Jun  8 10:51 test.txt

The files will now count against the Project quota.

A more automated example would be to have find both locate and change ownership of the files:

[mypid@tinkercliffs2 ~]$ ls -lh /projects/myproject/test/
total 1.1G
-rw-rw-r-- 1 mypid mypid 1.0G Oct  4 08:43 datafile
-rw-rw-r-- 1 mypid mypid    5 Jun  8 10:51 test.txt
[mypid@tinkercliffs2 ~]$ find /projects/myproject/test -group mypid -exec chgrp arc.myproject {} +
[mypid@tinkercliffs2 ~]$ ls -lh /projects/myproject/test/
total 1.1G
-rw-rw-r-- 1 mypid arc.myproject 1.0G Oct  4 08:43 datafile
-rw-rw-r-- 1 mypid arc.myproject    5 Jun  8 10:51 test.txt

Work

Work provides users with fast, user-focused storage for use during simulations or other research computing applications. However, it encompasses two paradigms depending on the cluster where it is being used:

On TinkerCliffs and Infer, it provides 1 TB of user-focused storage that is not subject to a time limit. Note that this quota is enforced by the GID associated with files and not by directory, so files in Project storage can wind up being counted against your Work quota; see here for details and fixes.
On Cascades, DragonsTooth, and Huckleberry, it provides up to 14 TB of space. However, ARC reserves the right to purge files older than 120 days from this file system. It is therefore aimed at temporary files, checkpoint files, and other scratch files that might be created during a run but are not needed long-term. Work for a given system can be reached via the variable $WORK. So if a user wishes to navigate to Work directory, they can simply type cd $WORK.

Archive

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 variable $ARCHIVE, so if a user wishes to navigate to their Archive directory, they can simply type cd $ARCHIVE.

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.)

Local Scratch

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

Memory

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.

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         -          -           

           BEEGFS                                                                              
mypid      /projects/myproject1                109.3        931                                
mypid      /projects/myproject2                2648.4       25600                              
mypid      /work/mypid                         2.7          931                                