ITC

Quantum Chemistry
Columbus
 
Batch system
Documentation
   

Batch systems for the
Vienna Quantum Chemistry Group


 

Instructions for using the batch systems:

At ITC:

  1. To submit a job, you must be logged in adler machine.

  2. You can submit your job from the home directory. 

  3. You should not have more than 7 simultaneous jobs running and/or submitted.

  4. Long jobs (> 10 min) or several sequential short jobs must run only via batch system. Occasional short jobs can run directly without to be submitted to the batch system.

  5. The system contains three types of machines (see description below). Each type can be specified in the submission script, by changing the lines 
    #PB -l nodes=PIV-3GHz-2GB
    #PB -l nodes=AMD-1.7GHz-0.8GB
    #PB -l nodes=EM64T
    Change PB to PBS to select one particular type of machine.

  6. Very long jobs (> 1 week) should be submitted to Schroedinger clusters. 

At Schrödinger:

  1. To submit a job, you must be logged in at Schrödinger cluster:
    ssh username@erwin.univie.ac.at

  2. At Schrödinger you can use the general cluster or our exclusive sub-cluster. You can access the exclusive sub-cluster by typing:
    . /usr/local/bin/switch_to_fs1
    You return to the general Schrödinger cluster by typing:
    . /usr/local/bin/switch_to_fs2

  3. At the exclusive sub-cluster, you should not have more than 4 simultaneous jobs running and/or submitted.

  4. Long jobs (> 10 min) or several sequential short jobs must run only via batch system. Occasional short jobs can run directly without to be submitted to the batch system.

  5. You can transfer your files from or to Schrödinger by secure FTP:
    sftp username@erwin.univie.ac.at

 

Useful commands:

To submit the job: qsub <script>
To see the status of the jobs (at ITC): qstat -n 
To see the status of the jobs (at Schrödinger): qstat -u <username> 
To delete the job: qdel ID
To see the available nodes (at ITC): pbsnodes -a  

See Complete documentation.

 

Shell scripts:

Scripts: Specific information:
Columbus (ITC) www.univie.ac.at/columbus/ 
Columbus (Schrödinger)
Columbus: Potential energy curve (ITC)
Columbus: Force constant (ITC)
Turbomole (ITC) www.turbomole.com/ 
Turbomole (Schrödinger)
EF.X (ITC)
ACES2 (ITC) www.aces2.de
Mopac (ITC) perseo.dcci.unipi.it/software/mopac.html 
Gamess (ITC) wwwmsg.fi.ameslab.gov/GAMESS/ 
Gaussian 03 (Schrödinger) www.gaussian.com 
Test PBS: AMD or PIV (ITC) www.openpbs.org/ 
Newton-X (ITC) www.univie.ac.at/newtonx 
Newton-X (Schroedinger)  

 

Description of the node-machines:

At ITC:

Machine CPU Memory

#PBS -l nodes=EM64T

condor1 PIV-3.2 GHz 2GB
...
...
...
condor7 PIV-3.2 GHz 2GB
fox1
PIV-3.2 GHz 2GB
...
...
...
fox10
PIV-3.2 GHz 2GB

#PBS -l nodes=PIV-3GHz-2GB

ronja

PIV-3 GHz

2 GB

ronja2

PIV-3 GHz

2 GB

ronja3

PIV-3 GHz

2 GB

ronja4

PIV-3 GHz

2 GB

ronja5

PIV-3 GHz

2 GB

lama1

PIV-3 GHz

2 GB

lama2

PIV-3 GHz

2 GB

lama3

PIV-3 GHz

2 GB

lama4

PIV-3 GHz

2 GB

panda1

PIV-3 GHz

2 GB

panda2

PIV-3 GHz

2 GB

#PBS -l nodes=AMD-1.7GHz-0.8GB

paria1

AMD-1.7 GHz

0.8 GB

paria2

AMD-1.7 GHz

0.8 GB

paria3

AMD-1.7 GHz

0.8 GB

At Schrödinger:

Exclusive sub-cluster: 16 PIV 3 GHz nodes. 

 

Contact:

Daniel Tunega: daniel.tunega@itc.univie.ac.at

About this homepage: mario.barbatti@univie.ac.at

 

Last update: June 2006.