QuickStart "for impatient"

1. Log on the CERIT-SC frontend:

$ ssh <username>@zuphux.cerit-sc.cz

Password: <Enter META password>

The details about available frontends as well as available log-in methods can be found in the section Infrastructure access.

2. Create job's startup script:

The following lines present the creation of a startup script running the Gaussian version 03. Refer to the Examples section for further details on creating the startup scripts in the CERIT-SC environment.

zuphux$ cat - >myjob.sh <<EOF

#!/bin/sh

# init the modular system

. /packages/run/modules-2.0/init/sh

# init the Gaussian's module

module add g03

# prepare job's input data

mkdir /scratch/$USER/$PBS_JOBID

cd /scratch/$USER/$PBS_JOBID

wget http://www.cerit-sc.cz/en/docs/quickstart/gaussian_test.com

# start the Gaussian application

g03 <gaussian_test.com >results.out

# move the produced (output) data to user's home directory

cp results.out /home/$USER

# clean the /scratch volume

rm -rf /scratch/$USER/$PBS_JOBID

EOF

3. Specify job's parameters/properties and submit the job:

The following lines present the above job's submission, requesting 1 node having 4 processors, and specifying its maximum run time in the length of 1 hour:

zuphux$ qsub -l walltime=1:00:00 -l nodes=1:ppn=4 myjob.sh

12345.wagap.cerit-sc.cz # = jobID

Further details about jobs' parameters specification, and especially about the usage of the optional walltime parameter (specifying the maximum job's run time), can be found in the section Job's/Node's property specification. (The default walltime value restricts jobs' run time to 24 hours.)

4. Check/Monitor the job's state:

zuphux$ qstat 12345.wagap.cerit-sc.cz

Note: The above job's run time is about 20 minutes.

5. Examine job's standard output and standard error output (as soon as the job finishes):

zuphux$ less ~/results.out # job's output data

zuphux$ less ~/myjob.sh.o12345   # job's standard output

                                 # empty for now (forwarded to results.out)

zuphux$ less ~/myjob.sh.e12345 # job's standard error output