ADF/AMS

Overview

Amterdam Modelling Suite provides ADF, Amsterdam Density Functional (ADF), which is a premium DFT code that predicts properties & reactivity of molecules with quantum precision.

We have a number of installs of ADF and AMS on the CSF. Details below.

Restrictions on use

Three PIs/research groups are licensed to use this software on the CSF:

• Steve Liddle
• Nikolas Kaltsoyannis
• Michael Baker

Only members of the above groups may use the software and only the versions for which they are licensed.

To get access please email its-ri-team@manchester.ac.uk copying (CC) the relevant PI on your request.

License restrictions

The license may limit how many cores/tokens can be in use at any one time. If you or other colleagues have jobs running that mean this limit has been reached, then your jobs will queue until enough licenses (and other resources, e.g. cores) become available.

Set up procedure

Load one of the following modulefiles appropriate to your group:

module load apps/binapps/adf/2017.114-sl # Steve Liddle Group.

module load apps/binapps/adf/2024.106-nk # Nik Kaltsoyannis Group.
module load apps/binapps/adf/2023.105-nk # Nik Kaltsoyannis Group.
    # Max no. of license tokens available between all versions = 32

module load apps/binapps/adf/2023.104-mb # Michael Baker Group . 
    # Max no. of license tokens available = 32

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this.

Running the application

Please do not run ADF on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

To run a job create a directory with the relevant input files in it.

In the same directory create a batch submission script (which will load the modulefile in the jobscript) using gedit , for example:

#!/bin/bash --login
#SBATCH -p serial        # Use nodes dedicated to 1-core jobs
#SBATCH -n 1             # Use 1 core
#SBATCH -t 2-0           # A wallclock limit to 2 day (of a maximum of 7 days).
#SBATCH -L adflic_nk:1   # This line is essential. 
                         # If necessary replace nk with the appropriate PI initials (sl, nk, mb). 
                         # The no. must be 1.

# Load the appropriate modulefile for your PI/group
module purge
module load apps/binapps/adf/2022.103-nk 
ams < run.in > run.out

Note 1: You can replace in the above command with another component if you wish, for example gennbo6, adfnbo. Make sure that if specific parameters are required you also specify these.

To submit the job use this command

sbatchscriptname

where scriptname is the name of your jobscript.

Parallel batch job submission

To run a job create a directory with the relevant input files in it.

In the same directory create a batch submission script (which will load the modulefile in the jobscript) using gedit , for example:

#!/bin/bash --login
#SBATCH -p multicore     # Use the AMD 168-core nodes
#SBATCH -n 4             # Number of cores
#SBATCH -t 2-0           # A wallclock limit to 2 days (of a maximum of 7 days).
#SBATCH -L adflic_nk:4   # This line is essential. 
                         # If necessary replace nk with the appropriate PI initials (sl, nk, mb). 
                         # The no. must match the no. you ask for on the -n line.

# Load the appropriate modulefile for your PI/group
module purge
module load apps/binapps/adf/2022.103-nk
ams < run.in > run.out

Submit the jobscript using:

sbatch scriptname

where scriptname is the name of your jobscript.

Note 1: You can replace in the above command with another component if you wish, for example gennbo6 adfnbo. Make sure that if specific parameters are required you also specify these. Not all components will be able to use more than one core, check the official ADF documentation for more information.

Note 2: When using the Amsterdam Modelling Suite (AMS) driver, the command will detect the number of available tasks and start as many processes. To limit this count, pass a value between 1 and $SLURM_NTASKS using ams -n NUM.

To submit the job use this command

sbatch jobscript

where jobscript is the name of the file that contains your jobscript.

Interactive jobs

Sometimes you may wish to run some short steps without resorting to a batch job. For that try an interactive job – this requests some resources on a compute node and runs commands there for you. For example the following uses adf2aim to process the relevant file in your current directory:

salloc -p interactive -t 60 -L adflic_nk:1
module purge
module load apps/binapps/adf/2022.103-nk
srun adf2aim

Further info

• AMS Website & ADF Website

Updates

None.