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High Performance Computing on Kong

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General Information
Applications
Disk Quotas
Job Queuing
Libraries
Manual Pages
Mailing List

Commercial Software
ganglia (Accessible within NJIT only)

Notice on SGE 5.3 -> 6.1 Upgrade

General Information

  1. Specifications
  2. Researchers who wish access to kong should send mail to that effect to ucssys@njit.edu
  3. Nodes on kong can be purchased by researchers. Researchers who purchase nodes have exclusive use of those nodes. Contact ucssys@njit.edu for details.
  4. The cluster management software in use 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, making each slave node essentially diskless. After each node boots up, a RAM disk stores an image of the OS, which is a small 45MB.
  5. Logins to kong are via AFS username and 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 ucid), rather than their AFS home directory.
  6. Users can use klog to authenticate to AFS, and thus access anything in AFS for which they have the proper permission.
  7. Users may choose to work in an AFS directory in which they have write access - e.g., their AFS home directory, or a project or research directory assigned to them - rather than in their home directory that is local to kong.
  8. User files in AFS are backed up frequently, whereas user files on kong are not backed up. Output files that users wish to save should be copied from kong to an AFS directory in which the user has write access.
  9. 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 public AFS systems 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/.
  10. All local software applications that installed by UCS 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 .
  11. Detailed Documentation

Applications

The following applications are available :

The following compilers are available :

  • GNU C, C++, F77; Version : 3.4.6-3.1; Located in /usr/bin
  • gcc4-gfortran (Fortran 90 compliant); /usr/bin/gfortran
  • Sun Studio 12 C, C++, F77, F90, F95; Located in /afs/cad/linux/compilers.12/sunstudio12

    To place the Sun Studio compilers in your path the sun12 module must be loaded :

    module load sun12

Disk Quotas

All user accounts on kong are assigned a 5GB disk quota.

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

    Disk quotas for user andym (uid 43407): 
     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 for user andym. The blocks column shows the amount of disk space in use (approximately 1.74GB). The first quota column shows the total quota available for user andym. The files column shows the number of files in andym's home directory.

Faculty who require quotas larger than the default 5GB should send email to ucssys@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 send email to ucssys@njit.edu on their behalf to request the needed quota.

Job Queuing

All jobs, both serial and parallel, must be submitted to a job queue. The queuing system in use on kong is Sun Grid Engine (SGE). For detailed information on how to submit jobs and interact with SGE, see the Sun Grid Engine page : http://ist.njit.edu/cyberinfrastructure/sge.php

Libraries

All package libraries are under /opt.

/opt/ATLAS/gnu3/lib
/opt/goto/lib

/opt/fftpack/5.0/gnu3/lib

/opt/fftw/2.1.5/gnu3/lib
/opt/fftw/3.1.2/gnu3/lib

/opt/local/lib

/opt/local/lib/matlab/lib64

/opt/mpi/tcp/lam-gnu3-7.1.2/lib

/opt/mpi/tcp/mpich-gnu3-1.2.7/lib

/opt/mpi/tcp/mpich2-gnu3-1.0.3/lib64
/opt/mpi/tcp/mpich2-gnu3-1.0.5p2/lib64
/opt/mpi/tcp/openmpi-gnu3-1.1.1/lib64
/opt/mpi/tcp/openmpi-gnu3-1.1.4/lib64

/opt/namd/tcl-8.3.3/lib

/opt/sge/lib

Manual Pages

All packages have man pages. The availability of man pages is dependent on the corresponding module having being loaded. Modules loaded by default are:

  • mpi/mpich-gnu3
  • sge
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.