Tinker-HP on Sulis
Tinker-HP a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Polarizable Force Fields.
Accessing Tinker-HP
First, check the list of existing Tinker-HP modules
[user@login01(sulis) ~]$ module spider Tinker-HP
The following
[user@login01(sulis) ~]$ module spider Tinker-HP/1.2
Will printout its dependencies to be loaded prior the chosen Tinker-HP module. Currently (Jan 2022) there is no GPU version installed on Sulis. Do please request a GPU build via the appropriate support mechanism should one be required.
Running Tinker-HP
To run one of the proposed Tinker-HP examples, copy the corresponding files with help of the loaded Tinker-HP module
module purge
module load iccifort/2019.5.281 impi/2019.7.217
module load Tinker-HP/1.2
# copy the example files
cp ${EBROOTTINKERMINHP}/example/{puddle.dyn,puddle.key,puddle.xyz} .
# copy the parameter file
cp ${EBROOTTINKERMINHP}/params/water.prm .
# also point to the copied parameter file in puddle.key
sed -i "s/parameters ..\/params\/water/parameters .\/water/" puddle.key
Loaded Tinker-HP module is required for defining the $EBROOTTINKERMINHP variable, the root directory of the installation. Finally, the following batch script template can be used to submit a job.
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=12
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=3850
#SBATCH --time=15:00:00
#SBATCH --account=suXXX-somebudget
ulimit -s unlimited
module purge
module load iccifort/2019.5.281 impi/2019.7.217
module load Tinker-HP/1.2
srun dynamic puddle 10 2.0 1.0 2 300.0