High Performance Computing on Kong

General
Modules
Applications
Compilers
Disk Quotas
Job Queuing
Manual Pages
Mailing List

General

  • Cluster specifications

  • Researchers who wish access to Kong should send mail to that effect to ARCS@njit.edu

  • Researchers who purchase nodes have exclusive use of those nodes. Contact ARCS@njit.edu for details.

  • The cluster management software used is Warewulf, which provides a framework for managing clusters. A single image is created with only the essential components needed for operation. This image is stored on the master node and each slave node pulls a copy of this image at boot time. After each node boots, a RAM disk stores an image of the OS, which is kept as small as possible.

  • Logins to Kong are via UCID and AFS password. However, users who log into Kong will be placed into their local Kong home directory, /home/X/<UCID>, in which X is first letter of the UCID, rather than their AFS home directory.

  • Logins to the head node are automatically authenticated to AFS via Kerberos, and thus can access anything in AFS for which they have the proper permission.

  • Users may choose to work in an AFS directory in which they have write access - e.g., their AFS home directory, or a research directory assigned to them - rather than in their home directory that is local to Kong.

  • Files in /scratch, /tmp, /nscratch, and /bscratch are not backed up. Output files in /tmp or /scratch that users wish to save should be copied from Kong to an AFS directory in which the user has write access.

  • Direct connections to Kong are made using ssh only, and must be done from within the NJIT network. If a connection to Kong must be made from outside of the NJIT network, then a VPN client must be used, or a connection to one of the AFS systems open to the Internet, afs<N>.njit.edu, must be used as a jump-in point to Kong. Information on obtaining and using the VPN client can be found at : http://ist.njit.edu/vpn/.

  • All local software applications that are installed by ARCS are placed in /export/apps and associated wrapper scripts are placed in /export/site/bin . Specialized libraries used in computational runs are installed in /opt .

  • Detailed Documentation

Modules

The user's environment is set by using the module program. Use module to set your environment for the particular computations you intend to do. See Modules

Applications

A broad range of opensource and commercial applications is available. A dynamic listing of such applications is under development, but not yet implemented. To enquire about particular applications contact ARCS at ARCS@njit.edu

Compilers

GNU, Intel, Sun and Java compilers are available, as well as python, perl, ruby, and other interpreters. To enquire about particular compilers or interpreters, contact ARCS at ARCS@njit.edu

Libraries

Local libraries are located in /opt . In addition, many libraries are located in AFS. To enquire about particular libraries, contact ARCS at ARCS@njit.edu

Disk Quotas

All user accounts on Kong are assigned a default disk quota of 5 GB.

The quota command (/usr/bin/quota) can be used to check the user's available disk quota.

   /usr/bin/quota

    Disk quotas for user yourucid (uid 7102):
     Filesystem  blocks   quota   limit   grace   files   quota   limit grace
/dev/mapper/home_vg-home_lv
                1741116  5000000 5000000           19874       0       0

The above shows quota details. The blocks column shows the amount of disk space in use (approximately 1.74GB). The first quota column shows the total quota available for the user. The files column shows the number of files in the user's home directory.

Faculty and staff who require quotas larger than the default 5GB should send email to ARCS@njit.edu requesting the amount of disk space that is needed. Students who require a quota increase should contact their faculty advisor and have them make the request on their behalf.

Job Queuing

All jobs, both serial and parallel, must be submitted to a job queue. The queuing system in use on Kong is Grid Engine (GE, or SGE). 

Manual Pages

All packages have man pages. The availability of man pages is dependent on the corresponding module having being loaded.

To access man pages of packages not loaded by default:

module load <package>

Mailing List

The kong-users mailing list, kong-users@listserver.njit.edu, is used for communication amongst Kong users and administrators.

List archives are available. To access them, you must log into the kong-users list, at http://listserver.njit.edu/mailman/options/kong-users. To do this, you need your list password. To get that, at the URL above, enter your email address, then scroll to "Remind" at the bottom of the page and select that. Your list password will then be mailed to you. Use that password at http://listserver.njit.edu/mailman/options/kong-users, then go to http://listserver.njit.edu/mailman/listinfo/kong-users to access the archives.

 

 

Last Updated: August 24, 2017