thesis

Ph. D. thesis work

How to install inversion infrastructure

Create a new Conda yenvironment

conda create --name "asi" python=3.10

Install ASI Spectral Inversion

conda activate asi
pip install numpy~=1.0 scipy apexpy glob2 scikit-image matplotlib h5py
git clone https://github.com/almule12/asispectralinversion.git
pip install asispectralinversion/src/

How to install GEMINI on HEC

1. Clone code

git clone https://github.com/gemini3d/gemini3d.git

2. Load modules

module use /nasa/modulefiles/testing
module load gcc/13.2
module load openmpi/4.1.6-toss4-gnu
module load comp-intel/2023.2.1

3. Configure build directory and compile code

cmake -B build
cmake --build build --parallel

4. Run Ctests

ctest --test-dir build

How to install GEMINI on WSL

Install WSL distribution

1. From Windows Powershell:

wsl --install Ubuntu

2. Generate a username, <firstnamelastname>, and password.

Install standard packages

3. In WSL:

sudo apt update && sudo apt upgrade
sudo apt install build-essential # for c and c++ compiler: gcc and g++
sudo apt install gcc gfortran # for fortran compiler: gfortran
sudo apt install cmake # for cmake
sudo apt install libopenmpi-dev openmpi-bin # for mpi commands: e.g. mpiexec
sudo apt install libhdf5-dev # for h5c++, h5cc, and h5fc
sudo apt-get install liblapack-dev # for lapack
which gcc g++ gfortran cmake mpiexec h5c++ h5cc h5fc # make sure all of these commands exists

Install external packages

4. In WSL's /home/username:

mkdir gemini
cd gemini
git clone https://github.com/gemini3d/external.git
cmake -B external/build -S external -DCMAKE_INSTALL_PREFIX=~/gemini/libgem
cmake --build external/build

5. At the end of ~/.bashrc add

export CMAKE_PREFIX_PATH=~/gemini/libgem

6. Restart WSL.

echo $CMAKE_PREFIX_PATH

Install GEMINI and run self tests

7. In WSL's /home/username/gemini:

git clone https://github.com/gemini3d/gemini3d.git
cd gemini3d
cmake -B build -DCMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH
cmake --build build --parallel
ctest --test-dir build

Install MATLAB packages

8. In WSL's /home/username/gemini:

git clone --recurse-submodules https://github.com/gemini3d/mat_gemini
git clone --recurse-submodules https://github.com/gemini3d/mat_gemini-scripts

Mount LynchK to WSL (Ubuntu)

sudo apt install cifs-utils
sudo mount -t cifs -o username=f123451,domain=KIEWIT.DARTMOUTH.EDU -o vers=3.0,file_mode=0660,dir_mode=0770,uid=julesvanirsel //dartfs-hpc.dartmouth.edu/rc/lab/L/LynchK /mnt/lynchk

How to run a Gemini simulation on Andes:

1. "mkdir LynchK/public_html/Gemini3D/<SIMULATION NAME>"
   • Try and stick to a sensible simulation name such as <function>_<type>_<descriptor>_<version>, e.g. aurora_sharc_wide_02
2. "cp LynchK/public_html/Gemini3D/<PREVIOUS SIMULATION NAME>/config.nml LynchK/public_html/Gemini3D/<SIMULATION NAME>"
   • If you're building on an old simulation, copy that simulation's config.nml
3. Edit config.nml in <SIMULATION NAME> to your liking.
   • See below for details on config.nml entries
4. If not already done so, open a MATLAB screen with "screen -S mat"
5. In MATLAB screen, run "matlab -nodisplay"
6. In MATLAB, navigate to <SIMULATION NAME> and run "gemini3d.model.setup('.','.')"
7. If not already done so, open a Gemini screen with "screen -S gem"
8. In Gemini screen, navigate to LynchK directory
9. In Gemini screen, run "mpiexec -np 36 gemini/gemini3d/build/gemini.bin public_html/Gemini3D/<SIMULATION NAME>"
   • Make sure that -np even divides nx2 x nx3, e.g. 144 x 216 / 36 = 864 cells per processor
10. In MATLAB screen, navigate to LynchK/Jules/thesis
11. In MATLAB screen, run "process('../../public_html/Gemini3D/<SIMULATION NAME>',<OPTIONS>)". Options include
    • plot=1 for plotting
    • video=1 for making videos
    • vtk=0 for making paraview files

Configuration file details:

base

• ymd = 2015,2,1 -------- year,month,day
• UTsec0 = 35850 -------- initial second of day
• tdur = 300 -------- run duration in seconds
• dtout = 10 -------- output cadance in seconds
• activ = 137.6,143.7,20 -------- F10.7 3-month avg, F10.7 daily, Ap daily
• tcfl = 0.9 -------- Courant number
• Teinf = 1500 -------- exospheric electron temperature

setup

• glat = 65.8 -------- geographic center latitude
• glon = 207.7 -------- geographic center longitude
• xdist = 3400e3 -------- rough east-west span in meters
• ydist = 1200e3 -------- rough north-south span in meters
• alt_min = 80e3 -------- minimum altitude in meters
• alt_max = 950e3 -------- maximum altitude in meters
• alt_scale = 10e3, 8e3, 500e3, 150e3 -------- d1 + d2*tanh((alt - d3)/d4)
• x2parms = 400e3, 18.8e3, 50e3, 100e3 -------- d2 + d3*(1 + tanh((x - xdist/2 + d1)/d4))/2 mirrored
• x3parms = 400e3, 1.625e3, 18.5e3, 50e3 -------- d2 + d3*(1 + tanh((y - ydist/2 + d1)/d4))/2 mirrored
• lxp = 1 -------- number of east-west cells if uniform
• lyp = 1 -------- number of north-south cells if uniform
• Bincl = 90 -------- geomagnetic inclination in degrees
• eq_dir = '/dartfs-hpc/rc/lab/L/LynchK/Jules/initial_conditions/null_02' -------- directory to equalibrium run
• setup_functions = 'gemscr.functions.aurora' -------- callable matlab input function

flags

• potsolve = 1 -------- 0 - no; 1 - electrostatic; 2 - inductive
• flagperiodic = 0 -------- 0 - not periodic in x3; 1 - periodic in x3
• flagoutput = 1 -------- what info in output: 1 - all; 2 - avg plasma parameters; 3 - ne only

files

• file_format = 'h5' -------- data filename extensions
• indat_size = 'inputs/simsize.h5' -------- location of grid size file
• indat_grid = 'inputs/simgrid.h5' -------- location of grid file
• indat_file = 'inputs/initial_conditions.h5' -------- location of intial conditions file

precip

• dtprec = 1 -------- precip input cadance
• prec_dir = 'inputs/particles' -------- location of precip files

precip_BG

• PhiWBG = 1e-5 -------- total energy flux (mW/m^2)
• W0BG = 3e3 -------- characteristic energy (eV)

efield

• dtE0 = 10 -------- current/potential input cadance
• E0_dir = 'inputs/fields' -------- location of current/potential files

aurora_parameters

• driftE = 0 -------- TBD
• driftN = 0
• ctr_spn = 1e5
• ctr_slp = 0
• ctr_pos = 0
• bar_frc = 0
• bar_pos = 4.5e5
• bar_vel = 0
• bar_gsl = 1e5
• dim_frc = 0
• dim_tim = 100
• dim_del = 100
• Q_amp_h = 3
• Q_amp_l = 3
• Q_wth_h = 2e4
• Q_wth_l = 2e5
• Q_gsl_h = 0.4
• Q_gsl_l = 0.1
• Q_off_h = -0.6
• Q_off_l = 5e4
• Q_floor = 0.3
• E_amp_h = 3e3
• E_amp_l = 3e3
• E_wth_h = 2e4
• E_wth_l = 2.2e5
• E_gsl_h = 0.4
• E_gsl_l = 0.1
• E_floor = 1.5e3
• K_amp = 0.3
• J_wth = 3e5
• J_gsl = 0.1
• F_amp = 2e3
• F_wth = 5e4
• F_gsl = 0.3
• flagdirich = 1
• ap_ExBg = 0
• ap_EyBg = 0
• ap_np = 16
• ap_cad2 = 4
• ap_cad3 = 1

How to make an ssh key on andes

ssh-keygen -t ed25519 -C "your_email@example.com"
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519
clip < ~/.ssh/id_ed25519.pub

in github.com/julesvanirsel go to

• settings
• SSH and GPG keys
• New SSH key enter a Title and paste the key

git remote set-url origin git@github.com:julesvanirsel/thesis.git
git config --global user.name "your_username"
git config --global user.email "your_email_address@example.com"