|Purpose||home directory||temporary files||large files|
|Accessible from||Helix, Biowulf head node, Biowulf computational nodes||Helix, Biowulf head node||Helix, Biowulf head node, Biowulf computational nodes|
|Quotas||8 GB default quota||no
Note that this 500 GB space is shared by all users
|100 GB default quota|
|Creation||with Helix account||created by user||with Biowulf account|
|Snapshots||hourly, nightly, weekly||nightly||nightly, weekly|
|Time Limits||none||deleted after 14 days||none|
Home, data and scratch directories actually reside on disks attached to specialized file servers. They are made accessible to the other systems via the Network File System (NFS).
To determine how much disk space you are using, use the checkquota command:[user@helix ~]$checkquota Mount Used Quota Percent Files /data7: 6.7 GB 100.0 GB 6.70% 2838 /home: 330.0 MB 8.0 GB 4.13% 3563 mailbox: 64.5 MB 200.0 MB 32.23%
Users who require higher quotas in their /data directories should complete the online request form.
Home Directories (/home/...)
A home directory is established for each new user when his or her Helix account is created, with the pathname /home/username. The initial quota is 8 GB. Files in home directories may be considered permanent in the sense that they remain on the system as long as the user wishes. Snapshots are made of home directories every three hours. Users who are over quota at the time of login will receive a warning message at that time.
The charge for disk storage in home directories is given on our Accounts page.
Temporary Storage (/scratch/...)
Instead of /tmp or /usr/tmp, the /scratch directory should be used for the temporary storage of relatively large amounts of data. We recommend that a user create a directory in /scratch and place files there. The /scratch directory is accessible from Helix and the Biowulf head node. While /tmp and /usr/tmp are the traditional temporary directories on UNIX systems, users are discouraged from making use of them on the NIH Helix Systems since they are often used by system utilities, compilers, and application programs. Files in /tmp and /usr/tmp are subject to removal at any time.
Files in /scratch which have not been accessed for 14 days are automatically deleted. The usefulness of /scratch depends on users' cooperation. It is inappropriate to regularly 'touch' files in /scratch as a means for extending the 14 day time limit. Users who require more permanent disk space should request it.
Files on /scratch are not backed up to tape, but snapshots are taken nightly. Disk storage on /scratch is not charged.
Large Volume Storage (/data/...)
Users who require very large datasets (typically Biowulf cluster users) have additional storage in the directory /data/username. This area is accessible from Helix, the Biowulf head node and the Biowulf computational nodes.
/data directories can be created to allow shared access by a group of users to a command storage area. Users can request a shared data directory by filling out the online form at https://helix.nih.gov/nih/shared_data_request.html. Please contact email@example.com for more information.
Mapped Network Drives and Desktop File Access
/home, /data, and /scratch can be mounted on desktop machines via the Samba server Helixdrive. This allows simple drag/drop access to files. See here for more information.
Using Disk Space Efficiently
Use the gzip program to reduce the amount of disk space used by infrequently accessed files. Depending on the file, this can significantly reduce space requirements. For example, the disk space required for the text file below was reduced by more than 50%:helix% ls -l -rw------- 1 quux 925594 Apr 20 12:48 TDATA helix% gzip TDATA helix% ls -l -rw------- 1 quux 334198 Apr 20 12:50 TDATA.gz
Note that compressed files are renamed by the gzip command to have an extension of .gz. The gunzip command is used to return a compressed file to an uncompressed form. The zcat command is used to produce an uncompressed byte stream from a file without uncompressing it, for example:zcat huge-postscript-file.gz | lpr
See the gzip man page for more information.