EMSES-tutorials

Initial Tutorial (Running EMSES)

Follow the steps below to set up and run EMSES on Kyoto University’s supercomputer camphor.

1. Development Environment Setup

Goal: Connect to the supercomputer remotely from VSCode.

Launch VSCode and install the Remote-SSH extension
Log in to Kyoto University’s supercomputer camphor
Open a TERMINAL

2. Environment Configuration and EMSES Installation

Goal: Secure storage space, install dependencies, and set up EMSES.

# Secure storage space
mkdir /LARGE0/gr20001/$USER
ln -s /LARGE0/gr20001/$USER ~/large0

# Add environment variables to .bashrc
grep -qxF 'module load intel-python' ~/.bashrc || echo 'module load intel-python' >> ~/.bashrc
grep -qxF 'export PATH="$PATH:$HOME/.local/bin"' ~/.bashrc || echo 'export PATH="$PATH:$HOME/.local/bin"' >> ~/.bashrc

exec $SHELL -l

# Install tutorial repository
mkdir ~/large0/Github
cd ~/large0/Github
git clone https://github.com/CS12-Laboratory/EMSES-tutorials.git
cd EMSES-tutorials
pip install -r requirements.txt # includes: git+https://github.com/CS12-Laboratory/MPIEMSES3D.git

# Open in VSCode
code --reuse-window ~/large0/Github/EMSES-tutorials

Details: Installing EMSES (MPIEMSES3D)

**For end-users (non-developers)** Already included when running `pip install -r requirements.txt`: ```bash pip install git+https://github.com/CS12-Laboratory/MPIEMSES3D.git ``` **For developers** ```bash cd ~/large0/Github git clone https://github.com/CS12-Laboratory/MPIEMSES3D.git cd MPIEMSES3D pip install -e . # runs make ```

3. Preparing Execution

Goal: Set up executable files and submit jobs.

Copy executables:

emses-cp dshield0/ # = cpem dshield0/
emses-cp dshield1/
emses-cp dshield2/

Test run in dshield0 directory:

cd ~/large0/Github/EMSES-tutorials/dshield0
mysbatch job.sh

※ mysbatch: A custom command (from camptools) that reads nodes(:) from plasma.inp, sets the process count in job.sh, and then runs sbatch.

4. Job Monitoring and Management

Check job status:

qs        # job status
squeue    # job list
qgroup    # available resources
latestjob # tail the latest job log

Cancel job: scancel <job-id>
Standard output: stdout.****.log
Standard error: stderr.****.log

5. Checking Job Completion

If it does not appear in squeue, the job is finished.
Check stdout/stderr logs.
Verify visualization results.

6. Visualization

Method 1: Generate PNG/GIF with .mypython/plot.py Example: phisp_2d_xy.png plot

Method 2: Use Jupyter Notebook (dshield0/plot_example.ipynb)

Python interpreter setup

Example using venv:

cd ~/large0
/usr/bin/python3.11 -m venv .venv
# reinstall
~/large0/.venv/bin/python -m pip install -r ~/large0/Github/EMSES-tutorials/requirements.txt
~/large0/.venv/bin/python -m pip install -U emout

Then select ~/large0/.venv/bin/python in VSCode.

Or specify camphor’s Intel-Python: /opt/system/app/intelpython/2024.2.0/bin/python

select-interpreter

References
- emout visualization library
- Sample code

7. Simulation Extensions

Extend runtime: Change nstep=100 in dshield0/plasma.inp to a larger value.
Run other setups: Check plasma.inp in dshield1 / dshield2 and compare results.
Visualization and discussion: Analyze outputs as with dshield0.

8. Predicting Results

ds0: Negative charge in vacuum
ds1: Plasma with density 107/cm³ and temperature 3 eV
ds2: Same as ds1 but with 1/16 density

Q1. What does the potential distribution look like in ds0? Q2. What changes occur in ds1? Q3. How do electrons and ions behave in ds1? Q4. How does ds2 differ? Q5. What is the effect of changing temperature?

9. Practice Tasks

Run and visualize dshield0–2.
Compare predictions with results and analyze differences.
Note: When visualizing ds0, emout does not work if wp=0.0d0. Set wp=1.0d0 (or similar) in plasma.inp.

10. How to Study

If execution fails, consult M1 seniors first.
When asking your professor, include:
1. What you asked seniors
2. Their answers
3. What you tried based on those answers
4. What remains unresolved
Minimum outputs to check: electron density (nd1p), ion density (nd2p), potential distribution (phisp).
Discuss results among B4 members and share insights in the next tutorial.

References

Kyoto Univ. Supercomputer User Manual (restricted)
Kobe Univ. Supercomputer User Manual
Miyake & Usui (2009), Phys. Plasmas, 16, 062904. https://doi.org/10.1063/1.3147922
Miyake et al. (2019), Multiphase Flow, 33(3), 258–266. https://doi.org/10.3811/jjmf.2019.T011
Lapenta, PIC Methods for Space Weather, PSC Project. http://fishercat.sr.unh.edu/psc/_downloads/lapenta.pdf
Matsumoto, pCANS Documentation, Chiba Univ. CANS Project. http://www.astro.phys.s.chiba-u.ac.jp/pcans/
Past master’s and bachelor’s theses

Do you want me to also polish this into a shorter “quick start” handout (like one page with only the essential steps), or keep it as a full manual style?

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