Many of these notes were developed while I was at the University of Florida and worked with undergraduates doing computational materials science research as their senior project. Some of these notes were updated when I was doing my postdoc at Ohio State University, I am updating these notes to reflect the new environment. My current position is now at Johns Hopkins University Applied Physics Laboratory. I will not really be updating HPC notes except as it pertains to my personal cluster.
However, some of these notes also often function as notes to myself. I AM OFTEN LEARNING NEW PORTIONS OF THE SOFTWARE, SO I OFTEN DOCUMENT THESE OPTIONS FOR MYSELF. So some portions of this guide might not be entirely appropriate for an undergraduate for self-study. However, I am always trying to improve it. I consider the notes provided within to be mostly self-contained.
Windows 10. The setup for a Windows 10 is more intensive because you need both a functional UNIX-like environment as well as the native Windows environment. Since Windows does not have many Unix tools, you will need to setup these tools. In general, the tools you will need are access to an MD simulation package (which will most likely be LAMMPS), a density functional theory simulation package (which used to be VASP for me, but since VASP isn't available without an expensive license, I am currently evaluating on whether Quantum Espresso/Abinit is a better a way to go, and python for general scripting and analysis.
1.1 Logging in to your environment.
1.2 Setting up your environment.
1.6 Setting up git for version control
1.8 Setting up MongoDB
When you are getting started you should print out these cheat sheets
2.1 SLURM
2.2 TORQUE
A tutorial for developing in python probably isn't applicable in a tutorial in computational materials science.