Historical: Seaborg File Systems
Seaborg decommissioned January 2008
All user-accessible file storage
is provided by the General Parallel File System (GPFS),
which provides a large
amount of fast data storage and is available from all nodes.
User home directories and a large
amount of scratch space are both provided by GPFS.
Your $HOME Directory
When you log in, you are put into your
home directory by default.
Home directories are available from all nodes.
Your home directory can (and should)
always be referred to by the environment variable
$HOME. The absolute path to your home directory
(e.g., /u4/joe/) may change,
but the value of $HOME will always be correct.
Home directories are not backed up
(except for file system recovery purposes).
Please save all your
important files to HPSS
on a regular basis.
For security reasons, you should never allow "world write" access
to your $HOME directory or your $HOME/.ssh directory.
NERSC scans for such security weakness, and, if detected, will change
the permissions on your directories.
In your home directory are various login control files (e.g.
".login", ".cshrc", ".profile"). These are symbolic links to common
files that contain definitions shared by all users. Please do not
remove the links in your home directory.
If you wish to customize your login behavior, please
place all your personal customizations in extension files with
names such as .login.ext, .cshrc.ext, and .profile.ext.
The home
directories are part of the General Parallel File System
(GPFS).
Each user has a quota of allowed disk space usage in $HOME and
a separate quota for the number of inodes.
Each file or directory that you own counts as one inode against
your quota.
The myquota command (with no options) will
give you information on the limits in your $HOME directory. For example:
% myquota
------- Block (MB) ------ --------- Inode ---------
FileSystem Usage Quota InDoubt Usage Quota InDoubt
---------- ------- ------- ------- ------- ------- -------
/u4 4525 15360 75 6038 22500 175
/scratch 388 256000 0 143 50000 0
The output shows the limit on file space (Block Quota) and inodes (Inode Quota), as
well as the current usage.
If you reach the "Quota" value, you will not be able to save anything
else to disk in that file system.
In this example the home directory is in /u4. The "InDoubt" columns
tells you that the reported "Usage" may be off by that amount. This occurs
because GPFS does not update this information immediately upon change.
Your $SCRATCH Directory
NERSC provides a scratch
directory referred to by the
environment variable $SCRATCH.
For temporary storage you should always use $SCRATCH and never
/tmp.
- $SCRATCH
-
The environment variable $SCRATCH refers to a user's directory
space in the /scratch GPFS file system.
$SCRATCH is available from all nodes and is tuned to be
higher performing than $HOME.
The contents of
$SCRATCH may be deleted at any time after the job finishes
if the system's disks are near capacity. In general, files in $SCRATCH
will persist for at least 7 days, but users are "taking chances" by using
$SCRATCH to store after the job finishes and should not rely on
it to be "semi-permanent" file storage space.
NOTE: In order to provide sufficient disc space for running batch
jobs, NERSC purges /scratch several times per year.
Files are removed strictly based on age (access time), oldest files first,
until utilization drops to a predetermined level (typically 85%).
Users who are found to be accessing their files solely to avoid having
them purged are subject to having their accounts suspended. Please use
HPSS to store files that are not being used on a daily basis.
There is a (large) quota for users on the /scratch file system.
Use the myquota command to check your usage and quota.
- /tmp
-
The /tmp file system is local to each node and
is small. DO NOT USE /tmp; it may crash your node!
Some software, such as the compilers and editors, will try to use /tmp
unless the user has specified a value for the environment variable
TMPDIR. NERSC has set TMPDIR to be SCRATCH.
If TMPDIR is not defined, user Fortran codes which open files
with status="scratch" will write those files into /tmp.
The project Directory
The NERSC Global Filesystem (NGF) provides a large-capacity file storage
resource that is shared between all the major compute platforms. Usage
is organized by "projects", which will usually (but not always) be the
same as repositories. File space in NGF is not automatically allocated
to individual users; it must be requested by project administrators.
Complete information may be found here.
Quota Summary
| Machine | File system | Space quota |
Inode quota |
|---|
| Seaborg | $HOME | 15GB | 22,500 |
| $SCRATCH | 250GB | 50,000 |
| NGF | /project | 1TB | 250,000 |
NERSC sometimes grants temporary quota increases for legitimate purposes. To apply for such an increase, please see Disk Quota Change Request Form.
| 
