Storage

Sensitive Data

Important

Personal information and other sensitive data, including statutory, regulatory, and contractually protected data - for example, human subjects research, restricted research, student and educational data, and personal health information (PHI) — are prohibited on the Hoffman2 Cluster.

Storage Overview

The Hoffman2 Cluster network exported storage for users data is subdivided into three file systems (for users’ home directories, users’ scratch, and group purchased project directories) which relay on a multi-node NetApp storage system. Current HPC storage capacity is 2.5 petabytes, augmented by 250TB of flash-based storage for home and scratch directories. Research groups whose members need to share data or applications and who need storage beyond the 20GB of their home directories, can purchase additional HPC storage in increments of 1TB per year.

A fourth filesystem, locally mounted to each of the compute nodes (and not exported between them), is also available as local scratch via the scheduler set $TMPDIR variable.

Filesystems available for user data

Name

Path

Type

Quota (disk/file)

Backups

Temporary

$HOME

/u/home/

NFS

20 GB / 200,000

Yes

No

project

/u/project/

NFS

varies

Yes

No

$TMPDIR

/work

local disk

circa 200 GB

No

Yes

$SCRATCH

/u/scratch/

NFS

2 TB / 5,000,000

No

Yes

Table description
Name - the general storage name, or the environmental variable that points to it
Path - the path to the storage directory
Type - remote or local file system
Quota - limits placed on your data, both in terms of disk usage and number of files
Backups - your data is backed up for disaster recovery purposes
Temporary - indicates whether the space is routinely reclaimed or not

Your home directory

Each user account is given a 20 GB home directory ($HOME), which is physically located on our fast, highly responsive NetApp storage. Files in your home directory have no expiration date. The name of your home directory follows the patters:

/u/scratch/${USER:0:1}/$USER

where ${USER:0:1} is the first character of your username and $USER is the environmental variable corresponding to you account name. For example, if your username is joebruin, your home directory would be: /u/home/j/joebruin.

Your home directories, mounted on every node in the cluster, is a place to store and manage your scripts and source code. The $HOME environment variable refers to your home directory. It is better to use $HOME than to hardcode its path in your scripts and source code.

To check the path of your home directory you can use the following command:

echo $HOME

Your home directory is periodically backed up. In case of catastrophic hardware failure, files in home directories will be restored from the last backup that was taken. The purpose of the backup is not to be able to restore files that you accidentally delete or overwrite. See Protecting from accidental loss.

Your project directory

Tip

If members of your research group require more than 20GB of storage, need to share data or need a common application area, backed-up project storage space is available for purchase in 1TB increments. Please talk to your faculty sponsor to see Purchasing additional resources.

If your resource group has purchased additional storage, you may have a directory on that filesystem. If that is the case, in your home directory there will be convenient symlinks to your project subdirectory(s). To see what project storage space is available for your user account, issue the command:

$ ls -l $HOME | grep project-

For example, user joebruin, part of the bruins group but also part of the bears group, with a project directory in /u/project/bruins/joebruin and a project directory in /u/project/bears/joebruin, would see the following symlinks in the $HOME directory:

$HOME/project-bruins

is the same as:

/u/project/bruins/joebruin

Note

Data written to a project directory do not count over the 20GB quota of you $HOME as they are written under the /u/project filesystem and not the /u/home one.

therefore for user joebruin the directories:

lrwxrwxrwx. 1 joebruin bruins 27 May 21  2019 /u/home/j/joebruin/project-bruins -> /u/project/bruins/joebruin
lrwxrwxrwx. 1 joebruin bruins 27 May 21  2019 /u/home/j/joebruin/project-bears -> /u/project/bears/joebruin

Your scratch directory

Each user has a scratch directory ($SCRATCH), with an individual quota of 2TB that is physically located on flash-based, NetApp storage. The name of your scratch directory is like:

/u/scratch/${USER:0:1}/$USER

where ${USER:0:1} is the first character of your username. For example, if your user name is joebruin, your scratch directory is /u/scratch/j/joebruin. On the Hoffman2 Cluster the $SCRATCH environment variable refers to your scratch directory.

To check the path of your scratch directory you can use the following command:

echo $SCRATCH

Note

Your scratch directory is a temporary space that is accessible from any node in the cluster and is intended to support your output from large jobs for later retrieval and analysis. Any important file should not be stored there, as files in your scratch directory are eligible for removal after 14 days. This retention policy guarantees that enough space exists for the creation of new files.

Storage quotas

To see your quota and current disk space usage for your home, storage and any project directories, at the shell prompt, enter:

myquota

Backups

The home and project file systems are backed up, with a target backup window that runs once per 24 hours to disk-based storage.

  • The criteria for backing up a file is a change in UNIX ctime, mtime or file size. Once a version of a file has been successfully backed up, its contents will be retained for 30 days upon being removed or changed on the file system.

The purpose of the backups is to protect against catastrophic hardware failures, not accidental deletions or overwrites. See Protecting from accidental loss.

File systems for temporary use

There are two kinds of file systems for temporary files that you may use:

  • $TMPDIR - local to each compute node, deleted at the end of a job

  • $SCRATCH - mounted everywhere on each node on the cluster, files within it are deleted after 14 days

The purpose of these file systems is to accommodate data used by jobs while they are executing.

Warning

Do not write files in any /tmp directory.

$TMPDIR

The scheduler sets up for each interactive session or batch job a temporary directory, which can be referenced to with the $TMPDIR environmental variable. This directory is created on the local disk of the master node where the job/interactive session is running. Each node has a hard disk with approximately 200 GB of space, your job can use up to that much only if you request exclusive access to any node assigned to it. Access to this directory may be faster than to access your home, project and scratch directories. The files in this directory are not visible from all nodes in a parallel job; each node has its own directory (therefore the use of this temporary directory is not compatible with parallel I/O).

Note

The batch system creates this directory when your job starts and deletes it when your job ends.

Tip

Files in $TMPDIR will be deleted by the job scheduler at the end of your job or interactive session. If you want to keep files written to $TMPDIR, tell your submission script to copy them to permanent space (e.g., $HOME) before the end of your job or session. Files written to $TMPDIR are not backed up.

For example, in your job script, you could have something like:

# enter the temporary directory:
cd $TMPDIR
# ... execute your code
# ... write some files to $TMPDIR
# copy files from $TMPDIR to home directory:
cp -r $TMPDIR/*  $HOME/
# job exits; $TMPDIR and its files are deleted automatically

Use $TMPDIR for life-of-the-job and high-activity files to avoid the overhead of network traffic associated with the network file systems and improve your job’s throughput. For your convenience examples of how to modify you C/Fortan/Java/Perl/Python code to perform I/O on $TMPDIR are given here:

Using $TMPDIR may not be suitable for MPI-style jobs because it is not visible by other compute nodes within the same MPI run.

Warning

Files stored on a compute node’s local file system, which are not related to a job running on that node will be deleted without notice.

$SCRATCH

$SCRATCH

The global scratch file system is mounted on all nodes of the Hoffman2 Cluster. There is a 2TB per user limit. The system provides an environment variable $SCRATCH which corresponds to a unique directory for your login ID.

Tip

To submit a job that will write large and frequent output to $SCRATCH you could try any of the following:

  1. make sure that any variable for temporary files storage that your software may use is pointed to $SCRATCH

  2. make sure that your job submission script copies relevant files to $SCRATCH and starts the computation there, for example:

# create a variable with the local directory name:
RUN_DIR=`pwd`
# create a directory in $SCRATCH after the unique $JOB_ID:
mkdir $SCRATCH/$JOB_ID
# copy files needed for the run:
cp -rp ./* $SCRATCH/$JOB_ID
cd $SCRATCH/$JOB_ID
# enter the temporary directory:
# ... do some computations
# ... write some files to $SCRATCH
# copy files from $TMPDIR to home directory:
cp $SCRATCH/$JOB_ID/*  $HOME/
# job exits; $SCRATCH/$JOB_ID files will be deleted in 14 days
  1. modify your code so that it will perform the intensive part of the I/O on $SCRATCH

As the $SCRATCH file system resides on fast flash-based storage, writing to $SCRATCH is especially recommended, for performance reasons, to parallel jobs, especially those with high I/O requirements.

Under normal circumstances, files you store in $SCRATCH are allowed to remain there for 14 days. Any files older than 14 days may be automatically deleted by the system to guarantee that enough space exists for the creation of new files. However, there may be occasions when even after all files older than 14 days have been deleted, there is still insufficient free space remaining. Under that circumstance, files belonging to those users who are using the preponderance of the disk space in $SCRATCH will be deleted even though they have not been there for 14 days. Files written to $SCRATCH are not backed up.

Warning

Files on the global scratch file system which are outside of $SCRATCH directories will be deleted without further notice.