Home Directories (/home/...)

A home directory is established for each new user when his or her account is created, as a subdirectory of /home, with an initial disk quota of 500 megabytes. Home directories are shared between the SGI systems. That is, the same files and directories appear in your home directory on helix and nimbus. 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.

Charge

Disk storage in home directories is charged at the rate $0.0033/megabyte/day.

Technical notes

• Home directories actually reside on disks attached to specialized file servers. They are made accessible to the other systems via the Network File System (NFS).

A user may simply need more permanent disk storage in his or her home directory. Users who require higher quotas should send email to staff@helix.nih.gov to make their request.

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 shared across all of the SGI systems and Biowulf in the same way as /home. 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.

Extra Storage

Network Disk Storage (/scratch/export)

/scratch/export, a subdirectory of /scratch, has the same characteristics as /scratch, but in addition is exported as part of the Network File System (NFS). This space is accessible from workstations which can act as NFS clients. Data in this directory should not be considered secure since it is accessible from the network. The /scratch/export filesystem is shared between all SGI systems that are part of the Helix Systems. To mount /scratch/export using NFS, use the following mount command:

mount helixscratch.nih.gov:/vol/scratch/export /mnt

where /mnt is a directory present on your workstation.

Storage Shared with the Biowulf Linux Cluster (/data/...)

In addition to its SGI systems, the Helix Systems also include a Linux cluster named Biowulf. All of these systems, SGI and the cluster, also have access to additional permanent storage on 4 Network Appliance filers, which are specialized high-performance NFS fileservers using RAID-4 disk arrays. This storage is accessible as the /data directory and is used for very large datasets. Filesystems accessible through /data are the only ones shared across SGI systems and the Linux cluster.

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.Z

Note that compressed files are renamed by the gzip command to have an extension of .z. 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.Z | lpr

See the gzip man page for more information.