Materials Studio is a versatile modelling suite for building and quantum and classical simulation of molecules, materials and nanostructures.
CSC has obtained a reduced Materials Studio license for 2021 (heavy usage is recommended to be done with Maestro). Decision to continue beyond 2021 will be made by autumn 2021.
Materials Studio is a commercial program by Biovia Inc. CSC has purchased a national academic license for the year 2020 that allows non-profit usage in Finnish institutes proviging higher education (for example universities). If you're new to Materials Studio, consider also Maestro, and AMS.
Puhti: Version 2020
Materials Studio version 2020 can be downloaded and installed on your local computer. The graphical user interface runs only on Windows, but the back end server components can also be run on Linux.
Look here for installation files and instructions to configure licensing (requires Haka authentication)
The way to use Materials Studio is to install it locally and:
- Prepare jobs (build systems, set simulation parameters) locally
- Either run them locally or write the input files on disk
- Copy them to Puhti, prepare a batch script to run the files
- Copy the results back for analysis
See above for instructions for download, local installation and license configuration. Usage on Puhti does not require any installation steps.
Detailed workflow and tips for running standalone jobs on Puhti
- Once you've set up your simulation, instead of running it, click the "Files" button next to the "Run" button, and save the files on your local disk. You can find the location of the files, by right clicking one of them in the "project" view.
Note, that by default Windows file manager does not show all files, so you may need to edit the preferences.
Use some graphical file transfer tool to copy all files in the subdirectory created by the Materials Studio GUI to a subdirectory in Puhti in your /scratch area.
Open an ssh-connection to Puhti, and copy/paste the template batch script from below to that directory.
Change the "seedname" to match yours (name of the local folder and preceded by
.paramfile names), make sure you have the right binary set (
RunCASTEP.sh, RunDMol3.sh, ...), the right
--account=<project>, number of tasks, etc.
Submit the batch job with
Once it has completed, copy back all the files to the same folder in your local computer (you can overwrite all existing files).
Refresh the "project" view in the Materials Studio GUI.
Different Materials Studio "modules" require a little bit different batch scripts to run as standalone jobs on Puhti. A simple example for DMol3:
#!/bin/bash #SBATCH --time=00:10:00 #SBATCH --ntasks=2 #SBATCH --mem-per-cpu=1G #SBATCH --account=<project> #SBATCH --partition=test # select which Materials Studio server you want to run #RunMS="/appl/soft/chem/MS/MaterialsStudio20.1/etc/CASTEP/bin/RunCASTEP.sh" #RunMS="/appl/soft/chem/MS/MaterialsStudio20.1/etc/MesoDyn/bin/RunMesoDyn.sh" RunMS="/appl/soft/chem/MS/MaterialsStudio20.1/etc/DMol3/bin/RunDMol3.sh" # set the seedname for the input files seedname=TiO2 # no need to edit below here $RunMS -np $SLURM_NTASKS $seedname
And a multistep example for CASTEP, which first runs an energy calculation and then two property calculations using the optimized wavefunction (you need to have input files for all of them).
#!/bin/bash #SBATCH --time=00:10:00 #SBATCH --ntasks=8 #SBATCH --mem-per-cpu=1G #SBATCH --account=<project> #SBATCH --partition=test # select which Materials Studio server you want to run RunMS="/appl/soft/chem/MS/MaterialsStudio20.1/etc/CASTEP/bin/RunCASTEP.sh" #RunMS="/appl/soft/chem/MS/MaterialsStudio20.1/etc/DMol3/bin/RunDMol3.sh" #RunMS="/appl/soft/chem/MS/MaterialsStudio20.1/etc/MesoDyn/bin/RunMesoDyn.sh" # set the seedname for the input files seedname=TiO2 $RunMS -np $SLURM_NTASKS $seedname # if you have specified property calculations # run them after the energy or geometry optimization job # you should have a $seedname.param file for each of these seedname=TiO2_BandStr $RunMS -np $SLURM_NTASKS $seedname seedname=TiO2_DOS $RunMS -np $SLURM_NTASKS $seedname
Some modules, like Forcite, require a different way (MaterialsScript) to run them on Puhti. Instructions on using this will provided later. You can find the details from the Materials Studio help under "Running MaterialsScript in standalone mode".
Please see method descriptions and log files in Materials Studio for details.
The Biovia website has useful material for self study, and the documentation which comes with the Suite has several very useful tutorials.
Last edited Mon Nov 9 2020