Gaussian on Jazz
From Java CoG Kit
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Information on JAZZ
Here is specific information about the resource LCRC Jazz Cluster: For more information please see the 'Getting Started' document located at:
http://www.lcrc.anl.gov/jazz/Documentation/NewUserGuide/index.php
Security: Only ssh key access and globus access is allowed. Please read the
http://www.lcrc.anl.gov/jazz/Documentation/General/sshkey.php and http://www.lcrc.anl.gov/jazz/Documentation/Policies/sshpolicy.php
web pages. You must have ssh keys installed on Jazz before you will be able to log onto the cluster. Once you have generated them, as explained in the URLs above, please email them to systems@lcrc.anl.gov.
Jazz New User Welcome
Access: Use jazz.lcrc.anl.gov as the login host. That should put you (round-robin) on one of the jlogin machines.
Filesystems: Your home directory, /home/<username>, is on a GFS filesystem that is mounted across all nodes in the cluster. You should use this path in all scripts and jobs. In general, there is no need to manually copy files out to the nodes. In addition, there is a /pvfs/scratch/<username> directory on a PVFS filesystem that is also mounted across the entire cluster. Please do not use /pvfs/scratch/<username> as a permanent storage location. It is a scratch area and as such, all data in it may be destroyed without prior notice at any time. For a complete discussion of the different filesystems available on Jazz, please see: http://www.lcrc.anl.gov/jazz/Documentation/General/filesystems.php.
Environment: SoftEnv is used to manage software access. SoftEnv man pages are available in the default environment (use 'man softenv'). You can use the command 'softenv' to see what packages are available.
Running jobs: Please use PBS to submit your jobs. To view job status you may use the standard PBS commands: 'qstat -a','qstat -f <jobid>', etc.
Help: Mail to systems@lcrc.anl.gov will generate a trouble ticket that will be handled by the first available administrator.
Mail Lists: All users on Jazz are members of the jazz-users@lcrc.anl.gov mailing list. This list is used by administrators for long term information such as cluster policies. The notify@lcrc.anl.gov mailing list is used by the administrators to communicate operational status that would be of interest to the active user community (for example, short emergency outages). New users are automatically subscribed to notify at account creation time. After that, membership on that maillist is managed by the users using the 'notifyme' command located on all Jazz systems. To receive notifications, type 'notifyme -y' on any Jazz machine, to stop receiving notifications, type 'notifyme -n' on any Jazz machine. The discuss@lcrc.anl.gov mailing list is provided for users to discussion questions and issues regarding the use of the LCRC Jazz cluster. New users are automatically added to this mailing list and you may subscribe or unsubscribe at any time.
Information on Gaussian
Gaussian is a chemistry application that we wanted to use as a substitute for Active Tables. Mike Dvorak, said they have Gaussian '98(and also a newer version they are not sure which) running on Jazz. I checked the gaussian website earlier and their latest application is a '03 release. So, we already have it up and running. Here's the link to the documentation on using it.
http://www.lcrc.anl.gov/jazz/Documentation/ApplicationDocumentation/g98/index.php
I have applied for an account on Jazz. The above link gave the information on how I can run jobs on Jazz and there is a link to documentation for Gaussian '98 too.
TBD
Run a simple Gaussian. Co-ordinate with Mike how to create a karajan workflow of it. Ideally create an example including timers, the gaussian. This info is needed for NCSA work.
