ADF/AMS

Overview

Amterdam Modelling Suite.

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

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 the relevant PI.

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/2023.104-nk # Nik Kaltsoyannis Group
module load apps/binapps/adf/2023.101-nk # Nik Kaltsoyannis Group

module load apps/binapps/adf/2022.103-mb # Michael Baker Group . Max no. of license tokens available = 32
module load apps/binapps/adf/2023.101-cg # Conrad Goodwin. 30th May 2023 - evaluation license.

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. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

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
#$ -cwd             # Job will run from the current directory    
        
#$ -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.

module load apps/binapps/adf/2022.103-nk # Or the appropriate modulefile for your PI/group

adf -n $NSLOTS < run.in > run.out

## OR for versions 2020 and above, use the ams command as below.

ams -n $NSLOTS < 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.

Note 2: The variable $NSLOTS will automatically be set to 1 core.

To submit the job use this command

qsub scriptname

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
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript
#$ -pe smp.pe 4     # REQUEST CORES. SET A NUMBER BETWEEN 2 and 32.
#$ -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 smp.pe line.

module load apps/binapps/adf/2022.103-nk

adf -n $NSLOTS < run.in > run.out

## OR for versions 2020 and higher use the ams command as below.

ams -n $NSLOTS < run.in > run.out

Submit the jobscript using:

qsub 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 mroe information.

Note 2: The variable $NSLOTS will automatically be set to the number of cores you have specified against #$ -l smp.pe

To submit the job use this command

qsub 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:

module load apps/binapps/adf/2022.103-nk
qrsh -l short -V -cwd adf2aim

Further info

• AMS Website & ADF Website

Updates

None.