User guid

Contents

  1. Connecting to the grid cluster of IRE NAS of Ukraine
  2. Software cluster resources
  3. Local resource management system Torque
  4. IRE NASU grid cluster

Connecting to the grid cluster of IRE NAS of Ukraine

Linux client

ssh user@gdeveloper.ire.kharkov.ua

Windows client

You can use PuTTY as a ssh-client for OS Windows. Do not forget to specify the settings to use UTF-8:


PuTTY
PuTTY

 

 

 

Data exchange with a cluster

You can use scp (details – man scp) for a Linux client, as well as more convenient utilities such as Midnight Commander (details – man mc):

Midnight Commander
Midnight Commander

WinSCP client you can use for Windows :

 

 

 

WinSCP

 

 

 

 

Software cluster resources

ORCA

http://www.mpibac.mpg.de/bac/logins/neese/description.php
To start the job via the Grid is recommended to use a script / opt / orca / grid-orca.sh. To place a job on the local queue, use the script / opt / orca / qsub-orca.sh

CPMD

http://www.cpmd.org

GAMESS

http://www.msg.chem.iastate.edu/gamess

NAMD

http://www.ks.uiuc.edu/Research/namd

Library Intel MKL

http://software.intel.com/en-us/intel-mkl

Library GSL

http://www.gnu.org/software/gsl

 

Local resource management system Torque

Job control

In order to put the program be considered in the queue, you must make the appropriate reference in the form of a script. Full documentation on its development and use of management tasks can be found here: (http://www.clusterresources.com/torquedocs21/usersmanual.shtml). In the script: you must make the transition into the working directory (where your program) or use an absolute path (this also applies to the output files). Ready script queued command qsub :

qsub task.sh
9694.cluster

The indication of the job, you can command qstat :

qstat -a

console:

Job ID                Name       User         Time           Use S Queue
-------------------- -------- -------- ---------------- --------------------
9694.cluster         task.sh     user       00:08:15            R batch

To delete the job from the queue, use the command qdel :

qdel 9694

IRE NASU grid cluster

IRE NASU grid cluster operates as a part of the Ukrainian NATIONAL Grid (UNG) infrastructure. To use the computing resources of Grid user must have a valid personal digital certificate. To obtain permission appeal to the National Certification center.

Our grid cluster is running middleware Nordugrid ARC. To work effectively in this environment, be sure to check the documentation (here) on the developer’s site, especially the user’s manual (put file arc-ui.pdf).

Links: