Jacquard Linux Environment

The version of Linux installed on Jacquard is based on the SUSE distribution. Third-party and public domain software installed and managed by NERSC's User Services Group (USG) is accessible through the module system. Most third-party software is not in the default command search path; the corresponding module must be loaded to use the software.

User Environment

Environment initialization files ("dot-files") in home directories have been configured for maximum flexibility and ease of maintenance, both for the user and for NERSC staff. A long listing of a newly-created home directory (for user elvis) should look similar to this:

% ls -al
total 152
drwx------    3 elvis   elvis   8192 Jul  6 13:22 .
drwxr-xr-x  112 root    root    8192 Jul  6 13:22 ..
-rw-------    1 elvis   elvis     53 Jul  6 13:22 .Xauthority
lrwxrwxrwx    1 elvis   elvis     38 Jul  6 13:22 .bash_profile -> /usr
/common/usg/etc/skel/.bash_profile
lrwxrwxrwx    1 elvis   elvis     32 Jul  6 13:22 .bashrc -> /usr/commo
n/usg/etc/skel/.bashrc
-rwx------    1 elvis   elvis    147 Jul  6 13:22 .bashrc.ext
lrwxrwxrwx    1 elvis   elvis     31 Jul  6 13:22 .cshrc -> /usr/common
/usg/etc/skel/.cshrc
-rwx------    1 elvis   elvis    146 Jul  6 13:22 .cshrc.ext
lrwxrwxrwx    1 elvis   elvis     32 Jul  6 13:22 .kshenv -> /usr/commo
n/usg/etc/skel/.kshenv
-rwx------    1 elvis   elvis    147 Jul  6 13:22 .kshenv.ext
lrwxrwxrwx    1 elvis   elvis     31 Jul  6 13:22 .login -> /usr/common
/usg/etc/skel/.login
-rwx------    1 elvis   elvis    146 Jul  6 13:22 .login.ext
-rwx------    1 elvis   elvis     17 Jul  6 13:22 .modules
-rw-r--r--    1 elvis   elvis   2153 Jul  6 13:22 .modulesbeginenv
lrwxrwxrwx    1 elvis   elvis     33 Jul  6 13:22 .profile -> /usr/comm
on/usg/etc/skel/.profile
-rwx------    1 elvis   elvis    148 Jul  6 13:22 .profile.ext
drwx------    2 elvis   elvis   8192 Jul  6 13:22 .ssh
lrwxrwxrwx    1 elvis   elvis     32 Jul  6 13:22 .tcshrc -> /usr/commo
n/usg/etc/skel/.tcshrc
-rwx------    1 elvis   elvis    147 Jul  6 13:22 .tcshrc.ext

The files .bash_profile, .bashrc, .cshrc, .kshenv, .login, .profile, and .tcshrc are links to read-only files, and should not be deleted. All individual customizations (aliases, environment variables, etc.) should be made in the files named .bashrc.ext, .cshrc.ext, .kshenv.ext, .login.ext, .profile.ext, and .tcshrc.ext. These .ext files are sourced by the corresponding dot-files.

To have a module automatically loaded upon every login, the following command should be issued once:

% module initadd module_name

If your home directory does not contain these links and .ext files, run the following command to re-create them, then log out and log in again. Please note that this command will completely replace all of the above dot-files; any user-defined customizations will be lost.

% /usr/common/usg/bin/fixdots

Note: If you had already made personal settings in your dot files which you wish to save, first save your personal settings. For example, in your home directory:

% mkdir Savedots
% cp .[a-z]* Savedots

This will make copies of all your dot files in the directory $HOME/Savedots. After running the fixdots tool, you can then modify the appropriate .ext files for your login shell, using the settings you saved in Savedots. For example, if your login shell is tcsh, you would put your aliases, environment variables, etc into .tcshrc.ext.

Shells

Process Limits

On the interactive nodes, user processes are limited to 131072 kbytes of memory and 1 hour of CPU time.

On the compute nodes, user processes are limited to 2621440 kbytes of virtual memory. This can be increased to a maximum of 5242880 kbytes. In the bash shell it is done in this way:

%  ulimit -v  5242880 

%  limit vmemoryuse 5242880 

By default, corefiles from jobs that crash on the compute nodes are not written out. To have corefiles written out do the following in the bash shell:

% ulimit -c unlimited

% limit coredumpsize unlimited