Getting Started

Before beginning your research project, you should do the following:

Unix/Linux skills

You’ll be using supercomputing resources which means you need to get good at using the unix command line. Here are a few tutorials to help you get familiar with that:

Get a supercomputing account

Request a supercomputing account at BYU’s office of research computing. If you don’t have BYU credentials, you’ll be asked to register for them. During the application process, you’ll be asked some questions about your research and how you will use their resources. When asked about your research project:

We construct atomic-scale models of alloy systems that are suspected to outperform current materials used in our society. These models are then used to simulate the material at finite temperature to determine their stability and viability as an improvement over current materials

When you are asked to describe the computing resources you will use:

We use mostly single-processor jobs with 10-20 GB of memory. Occasionally we’ll use a multi-processor job but that will not be the norm. We like to use job arrays to submit many single-processor jobs at once.

Logging In

Once your account is approved, you can login via the command line:

ssh <username>@ssh.fsl.byu.edu

(insert your username in place of <username>)

You’ll then be asked to enter your password and the two-factor authentication code. (You’ll need the Google Authenticator App)

Setting up your filesystem

The first time you login there are some things you should setup and that you’ll only have to do once.

Setup your `bin` folder

Traditionally, people create a folder named bin and put all of their executable files in there. Then they set the environment variable named PATH to look in that folder. This allows you to execute anything that is in the bin folder from anywhere in your filesystem.

Make the bin folder
```
mkdir ~/bin
```

Now that you have a bin folder, copy some commonly used executables there.

cp ~/fsl_groups/fslg_byui_materials/vasp6_serial ~/bin/.
cp ~/fsl_groups/fslg_byui_materials/vasp6 ~/bin/.
cp ~/fsl_groups/fslg_byui_materials/mlp ~/bin/.
cp ~/fsl_groups/fslg_byui_materials/makestr.x ~/bin/.
cp ~/fsl_groups/fslg_byui_materials/kpoints.x ~/bin/.
cp ~/fsl_groups/fslg_byui_materials/getKPoints ~/bin/.

Setup important system variables

Now that you have a bin folder you need to tell the system to look there when searching for available executables. This is done with a system variable named PATH. We’ll assign a value to this variable in a file name .bash_profile, which gets executed every time you login.

Make a file named .bash_profile.
```
emacs ~/.bash_profile
```

Add the following lines to this file

module purge
module load intel-compilers/2019 intel-mpi/2019 intel-mkl/2019
module load makedepf90
module load libfabric
module load python/3.7
export HISTSIZE=100000
export ENUMX=~/bin/enum.x
export PATH=$PATH:~/bin
export MAKESTRX=~/bin/makestr.x
alias workon='workon'
function workon
{
source ~/environments/$1/bin/activate
}
alias workon='workon'

(Notice the PATH variable in there)

Save the file:
```
ctrl-x ctrl-c y
```
source the file: (This is done automatically at login)
```
source ~/.bash_profile
```