Directory for getting started with fission calculations in HFBTHOv3.
First, you need to be able to ssh into the HPCC, this means having access to some sort of Un*x style terminal. If you want to see visualisations from the python scripts you also need to be X11 forwarding enabled. My favorite method of doing this is Cygwin. There are instuctions for downloading and installing it here. There listed required files should be enough to get started with.
After you have Cygwin installed, you can ssh into the hpcc. First make sure that Xming is running, this is your local X11 server that is needed to open graphical windows over SSH.
To connect, run the command
ssh -XY nedID@hpcc.msu.edu
You should be prompted for your HPCC password and brought to the gateway. From here you can ssh into other development nodes. If you need to test if X11 forwarding is working run xclock. This should pop up a simple clock. ICER maintains some of their own documentation for connecting here.
You should also set up ssh keys between the HPCC, your desktop, and the NSCL's fishtank so you're not constantly prompted for a password. You should also consider adding ssh keys to your github account, instructions here. There is some documentation on how to do that for the HPCC here and the NSCL here
Once on the HPCC, checkout this repo into your home directory using the commands
cd ~/
git clone git@github.com:nscl-hira/FissionHFBTHO.git
If you don't have ssh keys in github you'll have to replace that last command with
https://github.com/nscl-hira/FissionHFBTHO.git
If you ls in your home directory, you should see a new folder names FissionHFBTHO
The most important linux command is man. For nearly any command you can type man command and get the manual page wich has all of the information on what the command does. Going through a linux quickstart guide or something is probably beneficial.
Once on the HPCC, and before doing anything with the code, make sure the enviroment variables are set correctly. From within the folder, this is done with the command
source ~/bin/env.sh
This also loads all of the required modules to run HFBTHO as complied in my (Adam's) directory. In addition this adds the directory /bin to the PATH variable so scripts can easily be called.
Git is a a version control system. Basically, it allows you to save a record of the changes to a directory or code base, and allows you to revert to old versions as needed. It is also useful for tracking changes made by multiple people and merging everything together. GitHub has a page that describes some of the philisophy around git and diestributed version control systems here.
- See the changes made since the last commit
git status
- Add the changes made to some file
dir/test.pyto the next commit
git add dir/test.py
- Add all of the changes since the last commit to the next commit
git add .
- Create a new commit
git commit -m "This is the message for this commit"
- Push the status of your local repository to the remote repository (what is on github)
git push
- Pull any changes from the remote repository
git pull
Setting up the ability to plot stuff on the HPCC is a pain. The easiest way to just build a local installation of Conda, a package/enviroment manager for python. There are installation instructions here. You will need to either use wget or curl to download the file to the HPCC, or download it locally and scp it over. The first option (wget) is probably the easiest.
HFBTHO, which stands for Hartree-Fock-Bogoliubov (HFB) Transformed Harmonic Oscillator (THO) does what the name says. It's a program that iterativley "solves the nuclear Skyrme-Hartree–Fock (HF) or Skyrme-Hartree–Fock–Bogoliubov (HFB) problem by using the cylindrical transformed deformed harmonic oscillator basis." It iterates, trying to find the lowest energy state given the constraints put on the system. The energy is found by integrating over the space of some phenomenological energy density functional (EDF), which is a functional of the proton and neutron densities. It's these EDF models that are the main physics input to the code.