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.