TURBOMOLE

Overview

TURBOMOLE is a quantum chemical program used in homogeneous and heterogeneous catalysis, inorganic and organic chemistry, various types of spectroscopy and biochemistry. It claims to be one of the fastest and most stable codes available for standard quantum chemical applications. The main focus is to provide a fast and stable code to treat molecules of industrial relevance within reasonable time and memory constraints.

Versions 7.2.1, 7.2, 7.1.1, 7.1 and 6.3.1 have been installed on the CSF.

Restrictions on use

The license agreement, a copy of which is available in

/opt/gridware/apps/binapps/turbomole/TURBOMOLE_license_2015.pdf

must be strictly adhered to by users. Important points to note are:

Who may use TURBOMOLE?

The software is only available to users from EPS and they must be a member of Staff or a Student of the University of Manchester or visiting scientists who are collaborating with a member of Staff and who have been given an official University of Manchester IT username.

Users are reminded that they must not share their password with anyone, or allow anyone else to utilise their account.

Access to the software cannot be granted to users whose primary location is not the main University campus.

What may TURBOMOLE be used for?

The software may be used for academic research and educational purposes only.

No commercial work must be undertaken using the software.

Further details are available in clause 3 of the license.

What may TURBOMOLE not be used for?

TUBOMOLE may not be used for any commercial work or calculations for third parties. See clause 3 of the license agreement for further detail of how this is defined.

You must not:

• Copy or distribute the software,
• decompile, disassemble, or reverse engineer the software,
• share the data generated with the software with third parties for purposes other than academic research or publication in a scientific journal,
• use the data generated in a patent application,

Further details are available in clause 3 of the license.

How should the program be cited?

Data generated may be published in scientific journals and presentations. You must correctly cite the software using this format:

“TURBOMOLE , TURBOMOLE GmbH, Karlsruhe, , http://www.turbomole.com”
All COSMOxxx products should be cited clearly by name and version number.

See clause 5 of the license agreement and the TURBOMOLE manual/website for further guidance.

Getting access to the software

Anyone wishing to use TURBOMOLE must request access to the turbomole unix group via its-ri-team@manchester.ac.uk.

Set up procedure

You must load the appropriate modulefile:

module load modulefile

replacing modulefile with one of the modules listed in the table below

Version	Modulefile	Notes
Serial	apps/binapps/turbomole/7.1/serial	Single core jobs only.
Shared Memory	apps/binapps/turbomole/7.1/smp	Single compute node only. Maximum job size 24 cores.
MPI	apps/binapps/turbomole/7.1/mpi	Distributed memory (MPI) jobs using more than one node.
MPI plus global arrays	apps/binapps/turbomole/7.1/ga

If you wish to use 7.2.1 then please replace ‘7.2’ in the modulefile name with ‘7.2.1’
If you wish to use 7.2 then please replace ‘7.2’ in the modulefile name
If you wish to use 7.1.1 then please replace ‘7.1’ in the modulefile name with ‘7.1.1
If you wish to use 6.3.1 then please replace ‘7.1’ in the modulefile name with ‘6.3.1’ e.g.

apps/binapps/turbomole/7.1/serial becomes apps/binapps/turbomole/7.1.1/serial
apps/binapps/turbomole/7.1/serial becomes apps/binapps/turbomole/6.3.1/serial

If you require a different TURBOMOLE configuration please contact the helpdesk.

Running the application

Please do not run turbomole on the login nodes. All work must be submitted to the batch system.
Many of the environment settings needed for the different job types are set by default in the relevant modulefile so you do not need to set everything specified in the turbomole manual. The examples below contain all the key information for running a job.

All the input files required for running your job must be in the same directory from which you submit.

Serial (1 core) batch job submission

Load a serial modulefile (see table above).

This script can be used to submit serial jobs, replacing TURBOMOLE_COMMAND with the instructions that define your job:

#!/bin/bash
### SGE script to submit a serial TURBOMOLE computation
#$ -cwd
#$ -V

TURBOMOLE_COMMAND

To submit the job: qsub scriptname

Jobs of 2 to 24 cores

• Known as shared memory jobs.
• Must use smp.pe .
• Load an smp turbomole version modulefile (see table above).
• Must set export PARNODES=$NSLOTS before the TURBOMOLE commands.
• These jobs use a single compute node and thus avoid inter node communication, Note: it is likely any shared memory implementation will be more efficient and run quicker than an MPI version./li>

The following script defines a 4 core job. Ensure you replace TURBOMOLE_COMMAND with the instructions that define your job.

#!/bin/bash
### SGE script to submit a 4 core shared memory job
#$ -cwd
#$ -V
#$ -pe smp.pe 4

export PARNODES=$NSLOTS
TURBOMOLE_COMMAND

Jobs of 48 cores or more in multiples of 24

• For distributed memory (MPI) and global array jobs
• Must use hp-mpi-24.pe (a pe specific to turbomole needs) .
• Must be 48 cores or more and a multiple of 24.
• Load an mpi version of turbomole modulefile (see table above)
• Uses two or more compute nodes.
• Must set export PARNODES=$NSLOTS and export HOSTS_FILE=machinefile.$JOB_ID before the TURBOMOLE commands.

The following script defines a 48 core job. Ensure you replace TURBOMOLE_COMMAND with the instructions that define your job.

#!/bin/bash
### SGE script to submit a 48 core job
#$ -cwd
#$ -V
#$ -pe hp-mpi-24.pe 48

export PARNODES=$NSLOTS
export HOSTS_FILE=machinefile.$JOB_ID
TURBOMOLE_COMMAND

To submit your job:

qsub jobscript

Where job script is the name of the job submission script.

Further info

Further information can be found on the TURBOMOLE or COSMOlogic websites including Turbomole news, FAQs, the latest basis sets, documentation, and tutorials. There is also a user mailing list to announce news, bugs and fixes, and a TURBOMOLE User Forum.

Updates

None at present.