Working with Spaces, Folders, and Files

Intended use, organization, & considerations

We wish to bring to your attention a number of items that will help you work efficiently and prevent you from having future problems:

  • Remember that home folders are not sharable, and typically contain files that pertain to your work only. This also includes the default location for configuration or preference files, work that is considered 'in development'.

  • Project folders are shared locations, and ideally used for collaborative project spaces. Please see our recommendation below on organizing project spaces. NOTE: Only those persons who are listed on the data usage agreement or IRB proposal should have access to these directories. This is the responsibility of the primary HBS faculty member.

  • Do not dump the contents of your laptop or desktop in your home or project spaces as a backup. Please consider solutions like Dropbox, CrashPlan, or BackBlaze; or the free Connect Backup service from HBS IT if the functionality of a backup is needed (HBS members only).

  • HBS IT regularly scans the research storage areas for viruses as a part of the Harvard University security policy. Normally viruses are quarantined or removed via antivirus software on HBS-issued laptops and desktops, preventing them from reaching the research storage. But personal devices may not have similar protections. If you should receive a message from HBS IT or RCS about virus-containing files in your home or project spaces, please remove these as soon as possible to ensure the safety and integrity of research data across the entire computing grid and research storage.

Disk quotas and notifications

The default size for project directories on the Research Grid is 50GB, with increases granted upon request. When a project directory is full, the system may not save files properly, which could result in a loss of data. As you work, please regularly check your space usage. To check the amount of space you are currently using in a project directory enter this command in an SSH (or ‘terminal’) session:

researchgrid$ df -h /export/projects/projectname

When your project directory is 99% or 100% full, you will receive an email from RCS with the following subject line:

IMPORTANT: Project directory on the Research Grid is 99/100% full

Please first see if you are able to archive any data using the instructions here. If you are unable to clear a significant amount of space, please send an email to RCS to request a space increase.

NOTE: These notices only go out once a day. They are not a substitute for regularly checking your space usage.

If you are working in an especially large project space you may receive an email at the 99% or 100% full mark, but still have significant amount space to work with. There is no way to turn off these notices, but if you would like to ignore them, you can create a rule in Outlook to send these emails to a single folder. See our Project Directory Space Notifications HOWTO document.

Access controls and permissions

On the Research Grid, directories and files have a set of permissions indicating that the User, Group and World has permission to Read, Write and/or Execute. A file listing shows the combination of permissions. This shows read/write/execute for User and Group, with no permissions for World.

drwxrwx--- UserGroupWorld (‘d’ indicates listing is a directory)

In directory /export/projects/generic_project, enter this command line to get the directory listing. (These are lower case 'L's; there is a space between 'ls' and '-la'.)
Here is an example:

researchgrid$ ls –la
-rw-r----- 1 jharvard rcs_project_generic 241215 Jul 30 2015 Article_d1.pdf

The permissions on this file saved to the space are read/write (user rw-) and read only (group r--). ‘jharvard’ is the file owner and ‘rcs_project_generic’ is the group name. The permissions can change when a file is transferred from a desktop to a drive mapped to the drive in grid storage. The person listed as 'owner' of a file (eg. ‘jharvard’) is the only person who can change the permissions. To change the permissions on files, please refer to the document ‘Changing Permissions on the Research Grid’.

Organization and other Best Practices

Organizing one's work has shifted from filing cabinets to disks filled with hundreds, if not thousands of files. And as with paper files, it is easy to become overwhelmed or lose things. To that end, we offer the following advices on storage Organization and other Best Practices:

  • Two well written papers, Gentzkow & Shapiro (2014) and Noble (2009), discuss strategies for organizing research project involving computational components and are Must Reads! (The latter paper is geared towards biologists, but all the content is relevant nonetheless.)

  • Data files should be in a directory accessible to all. If data has been cleaned and organized for analysis, consider making the foundational files ‘read only’ for the group to prevent accidental overwrites.

  • Descriptive README files in subdirectories can be useful in a space shared by multiple researchers.

  • Do not keep multiple copies of large data files in separate project directories. Move such files into a 'Reference Data' folder and mark it as 'read only'.

  • Consider having a directory for each group member to keep programs and other files they are working on organized.

  • Group members should periodically check permissions on files to ensure that members have the desired combination of  read, write and execute functionality. See the previous section on "Access controls and permissions".