Turbomole

The HEC hosts serial and SMP parallel versions of the Turbomole ab initio Electronic Structure Calculations package. The package is licensed to Andrew Kerridge in the Chemistry Department. Please contact him to authorise access to the software. Further information can be found on the Turbomole website.

Further information can be found on the Turbomole website

Viewing available verisons of turobmole

To view the currently available turbomole modules, run the command module av turbomole. It will produce output similar to this:

--------- /usr/shared_apps/Nmodules/apps ----------
turbomole/6.6  turbomole/6.6-smp  turbomole/7.3-mpi

The default is the serial version.

Serial turbomole batch jobs may be run by creating a batch job script (for instance, called jobex.com) like the following:

#!/bin/bash

#SBATCH -p parallel
#SBATCH -C node_type=10GethAny
#SBATCH --nodes=1
#SBATCH --exclusive

source /etc/profile
module add turbomole/6.6

jobex

The final line in the script is a call to the relevant turbomole script (in this case jobex). Note that no additional environment variables need to be set up - this is all handled by the turbomole module file. The script is then submitted for running by running the following from the directory containing your job’s data files: qsub jobex.com

The job submission template above follows the same template as a general serial batch job. You can read more about this on the Submitting jobs on the HEC page under the Batch jobs section.

A sample batch job script for SMP parallel jobex

For job types which support SMP parallel versions of Turbomole applications, the following template job script can be used:

#!/bin/bash

#SBATCH -p parallel
#SBATCH --cpus-per-task=8
#SBATCH --mem=10G

source /etc/profile
module add turbomole/6.6-smp

export TM_PAR_FORK=ON

jobex

A sample batch job script for serial NumForce

#!/bin/bash

#SBATCH -p serial
#SBATCH --mem=10G

source /etc/profile
module add turbomole/6.6

NumForce

A sample batch job script for SMP parallel NumForce

#!/bin/bash

#SBATCH -p parallel
#SBATCH --cpus-per-task=8
#SBATCH --mem=10G

source /etc/profile
module add turbomole/6.6-smp

NumForce -mfile $TMPDIR/sparfile

SMP Turbomole Guidelines

Not all Turbomole tools are multi-core, and not all multi-core tools may be efficient with large numbers of cores - please refer to the Turbomole guide for details. To prevent wasting resource on the HEC, SMP Turbomole should only be used for workloads that can efficiently use the number of requested cores.

The template above is intended as an example. The template can be modified in the same way as an OpenMP parallel job. Please refer to the Using OpenMP on the HEC page for an explanation of the job directives contained in the above templates.