Tmole.sub HowTo

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HowTo modify the script

In the tmole.sub script there are 3 key lines where you define exactly what and where you want the job to be...

1.) In the SGE environment setup... 2 lines

#$ -pe cq4m4_mpi 8

Defines both the version of MPI for the queue that you are using... namely cq4m4 (p4-quad-core with 4GB ram), and the number of processes that you will be given by SGE (here 8)

#$ -masterq cq4m4.q

Defines precicely which queue is being asked for... the options are...

cq4m4.q (as shown above)

kimik2.q (the Xeon-quad cores with 8GB of ram)

FG_c8m24.q (the new octa-core nodes with 24GB ram)

The queue you ask for must be the same in each of the above lines, or the job will not work.

2.) In the Turbomole environment setup...

export PARNODES=8

Defines the number of processors that Turbomole expects to use. It lets the queue system define where it goes and how the processes are to be split over the nodes. The number of processors you ask for here must be the same as in the first line, above.

Generally, ask for multiples of 4 processors for the quad-core machines, and multiples of 8 for the octa-core machines.

Calling the correct module/link in tmole.sub

Turbomole can run individual parts of the calculations separately, like running just one link to do the SCF in Gaussian, but the most common usage is to use a script to combine all of the links (or modules, as they are called in Turbomole) together to run an optimization.

In the script, this is done in the final line, using the command jobex

This is called generally using...

jobex > jobex.out

However, there are many options on how to run the optimization (see the manuals for more info), and in the sample tmole.sub script, you see how to call the jobex script for running a RI-DFT job with a maximum of 100 SCF steps, using the command...

jobex -ri -c 100 > jobex.out

you can name the output anything you like, so, for example, jobex.out could be called water_test.out