AIMall
Overview
AIMall is a program for performing quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems – starting from molecular wavefunction data.
Version 17.11.14 is installed on the CSF.
Restrictions on use
This software is restricted to members of Prof. Nik kaltsoyannis’ group. All requests to be added to the aimall-nk unix group which controls access must be approved by him.
Set up procedure
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.
Load one of the following modulefiles:
module load apps/binapps/aimall/19.02.13-nk module load apps/binapps/aimall/17.11.14-nk
Running the application
Please do not run AIMall on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Ensure that your input files are in the directory from which you wish to run your job.
Create a batch submission script (which will load the modulefile in the jobscript) in the same directory, for example:
#!/bin/bash --login #SBATCH -p serial # Job will run in the serial partition #SBATCH -t 1-0 # Wallclock limit 1 day, Max permitted 7 days (7-0) module purge module load apps/binapps/aimall/17.11.14 aimqb.ish -nogui 111propellane.wfn
#!/bin/bash --login #$ -cwd # Job will run from the current directory # NO -V line - we load modulefiles in the jobscript module load apps/binapps/aimall/17.11.14 aimqb.ish -nogui 111propellane.wfn
Submit the jobscript using:
sbatch scriptname
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Ensure that your input files are in the directory from which you wish to run your job.
Create a batch submission script (which will load the modulefile in the jobscript) in the same directory, for example:
#!/bin/bash --login #SBATCH -p multicore #SBATCH -n 8 # $SLURM_NTASKS below automatically sets to the number requested here #SBATCH -t 1-0 # Wallclock limit 1 day, Max permitted 7 days (7-0 module purge module load apps/binapps/aimall/17.11.14 aimqb.ish -nogui -nproc=$SLURM_NTASKS 111propellane.wfn
#!/bin/bash --login #$ -cwd #$ -pe smp.pe 8 ## $NSLOTS below automatially sets to the number requested here module load apps/binapps/aimall/17.11.14 aimqb.ish -nogui -nproc=$NSLOTS 111propellane.wfn
Submit the jobscript using:
sbatch scriptname
qsub scriptname
where scriptname is the name of your jobscript.
Interactive use
In order to use the GUI element to view files, users should use one of the interactive nodes.
# log on to interactive node srun -p interactive -t 0-1 --pty bash module load apps/binapps/aimall/17.11.14 aimstudio.ish nameOffile
# log on to interactive node qrsh -l short module load apps/binapps/aimall/17.11.14 aimstudio.ish nameOffile
Further info
Updates
None.