GENAREAL RULES
No interactive jobs on beo01.
There is no backup of /home diectory but data are safe on RAID 5 array of disks. Deleted data can't be restored
Use qsub command or sbmit jobs on the nodes directly (including code compilation or testing). People submiting jobs on beo01 will be banned from using cluster.
If you have interactive job ssh to any of the free nodes and run it there. If you want to submit interactive job through queuing system, copy /apps/bin/interactive to your home directory and modify DISPLAY settings inside.
Afterwards submit it through queiong system, it will display new interactive window on your computer (remember to allow connection: xhost + beo01 and add beo01 as trusted machine to your firewall).
CPU time limit is one month. Jobs longer than that are automatically killed. If you need more time please contact me.
Use qsub command with proper script. Scripts are located in directory /apps/bin. If you need your own script modify default script or ask for help.
Genaral example of job submition:
qsub /apps/bin/script name_of_your_job
Than job is automatically dispatch to the free node or waits for execution in two cases:
1. You have already more than max. job running which is 9 at the moment. Your job will wait till one of your running jobs is over.
2. Whole cluster is occupied and you have to wait till one of the jobs is finished
qsub -q nodeXX /apps/bin/script name_of_your_job
Interactive jobs:
Copy /apps/bin/interactive to your home directory and add following line:
export DISPLAY=name_of_you_pc:0.0
qsub /home/$USER/interactive
Wait few seconds and gnome-terminal should appear on your screen. Than you can do your interactiv work. Be sure that your PC accepts X connection (on Linux machine do: xhost +)
KILLING SUBMITTED JOB
To kill the submitted job first type: qstat |sort
to obtain ID of the job and than type: qdel ID_of_the_job
SPECIFIC EXAMPLES
Gaussian jobs:
qsub /apps/bin/gauss03 name_of_the_job (without .inp extension)
ADF 2004 01
qsub /apps/bin/runadf name_of_the_job (without .inp extension)
Dalton job:
qsub -q node14.q /apps/bin/dalton -D -W name -S name dyn name (choose the node with you need, remember to put full name like node23.q)
DeMon:
qsub /apps/bin/run_deMon input_file
Molcas job:
ssh nodeXX
cd your_directory
submit ./your_submit_script
Mathematica 5.0
type: mathematica
MATLAB 7.1
Matlab is only running on node5,6,7,8 at the moment due to the problems with RHEL 3. Please don't use beo01 for interactive jobs.
type: matlab7
Molden
type: molden
Molekel:
type molekel
Moplot:
type: moplot
PGI compliers:
use one of the programs: pgf77, pgf90, pgcc, pgc, pgCC
Intel Fortran 8.1:
usage: ifort
GaussView:
type: gview
You need Exceed 3D as well on Windows machines