Hi, I’m new using Haddock and I’m trying to run the local installation using a queuing system (Grid Engine). I’m not that familiar with queuing systems either. From what I understand, I have to modify the configuration file (QUEUE_CMD) and the run.cns file (queue_1), but I don’t know what to write there and if I need to write something specific on the job submission script. I am able to run Haddock using interactive sessions, but it doesn’t generate the models when using qsub. Thank you for the help.
You will have to talk to local people to see how to submit to the grid engine.
In the batch-tools directory there is an example of a wrapper script to submit to slurm.
Also check this example of running haddock using a queuing system
Thank you for the quick response. Once I have the wrapper script, I’ll have to change the run.cns file to provide the path to the wrapper script (queue_1=‘path/to/wrapper/script’), right?
How should I modify the configuration file? What should I write for the QUEUE_CMD?
Thanks for the help.
You can indeed change it in the configuration file and reconfigure.
Or edit the run.cns file in the protocols directory of your current installation and change the queue command.