Home and Lab directories

Please see the Data Storage on our main website information on other storage options and for clarification on any unfamiliar terms.

This page describes the resources which are available to each user account and lab, and is a guide for day-to-day usage.

See also our Introduction to FASRC Cluster Storage video

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Home Directories

Every user whose account has cluster access receives a 100 GB home directory. Your initial working directory upon login is your home directory. This location is for your use in storing everyday data for analysis, scripts, documentation, etc. This is also where files such as  you .bashrc reside. Home directories paths look like /n/homeNN/XXXX where homeNN is home01–home15 and XXXX is your login. For example, user jharvard’s home directory might be /n/home12/jharvard. You can also reach your home directory using the Unix shortcut ~, as in: cd ~

• Size Limit: 100GB (hard limit)
• Availability: All cluster nodes. Can be mounted on desktops and laptops
• Backup: Daily snapshots. Retained for 2 weeks
• Retention policy: indefinite
• Performance: Moderate. Not appropriate for I/O intensive or large numbers of jobs
• Cost: Provided with each user account

Your home volume has good performance for most simple tasks. However, I/O intensive or large numbers of jobs should not be processed in home directories. Widespread computation against home directories would result in poor performance for all users. For these types of tasks, the scratch filesystem is better suited.

Home directories are private to your account and will follow you no matter should you change labs, but are not suitable for storing HRCI/level 3 or above data. This is a violation of Harvard security policies.

Your home directory is exported from the disk arrays using CIFS/SMB file protocols and so can be mounted as a ‘shared drive’ on your desktop or laptop. Please see this help document for step-by-step instructions.

Home directories are backed up into a directory called .snapshot in your home. This directory will not appear in directory listings. You can cd or ls this directory specifically to make it visible. Contained herein are copies of your home directory in date specific subdirectories. Hourly, daily, weekly snapshots can be found. To restore older files, simply copy them from the correct .snapshot subdirectory. NOTE: If you delete your entire home directory, you will also delete the snapshots. This is not recoverable.

The 100 GB quota is enforced with a combination of a soft quota warning at 95GB and a hard quota stop at 100 GB. Hitting quota during processing of large data sets can result in file write/read failures or segmentation faults. You can check your usage using the df command: df -h ~ (where ~ is the unix shortcut for ‘home’)

TIP: If you are trying to determine usage, you might try using du -h -d 1 ~ to see the usage by sub-directory, or du -ax . | sort -n -r | head -n 20 to get a sorted list of the top 20 largest.

When attempting to log in when your home directory is over quota, you will often see an error in the .Xauthority file:
/usr/bin/xauth: error in locking authority file .Xauthority Logging into an NX or other virtual service will fail as the service cannot write to your home directory.

When at or over quota, you will need to remove unneeded files. Home directory quotas are global and cannot be increased for individuals. You may be able to use lab or scratch space to assist with copying or moving files from your home directory to free up space.

 

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Lab Directories

Each lab which uses the cluster receives a 4 TB lab directory (as of 2022 – these will reside in /n/holylabs/LABS). This location is for each lab group’s use in storing everyday data for analysis, scripts, documentation, etc. Each such lab will have a directory on our high-performance scratch filesystem (see below).

• Size Limit: 4TB (hard limit), 1 million files
• Availability: All cluster nodes. Cannot be mounted on desktops and laptops
• Backup: Highly redundant, no backups
• Retention policy: Duration of the lab group
• Performance: Moderate. Not appropriate for I/O intensive or large numbers of jobs
• Cost: Provided with each lab group

Lab directories have good performance for most simple tasks. However, I/O intensive or large numbers of jobs should not be processed in lab directories. Widespread computation against lab directories would result in poor performance for all users. For these types of tasks, the scratch filesystem is better suited.

This lab directory is owned by the lab’s PI and is intended only to be used for research data on the cluster. research storage should not be used for administrative files and data.

Lab directories are not suitable for storing HRCI/level 3 or above data. This is a violation of Harvard security policies.

The 4 TB quota is enforced with a combination of a soft quota warning and a hard quota stop at 4 TB. Hitting quota during processing of large data sets can result in file write/read failures or segmentation faults. If your lab requires additional storage, see our Data Storage page for a list of available storage options.