UB-SPEBT / pyMatcal

Python implementation of the system response matrix analytical calculation

pyMatcal

Python implementation of the system response matrix analytical calculation

pair-calc.py

Dependency

• Python version 3
• Numpy
• MPI can be Open MPI or Intel MPI

Running on UB CCR HPC

On interactive node

1. Ask for an interactive node and login

salloc --qos=nih --partition=general-compute --job-name "interactive-job" --nodes=1 --ntasks=16 --mem=32G  --time=03:00:00;srun --pty /bin/bash --login

2. Setup the environment with module load, we need OpenMPI.

module load ucx/1.13.1 is suggested by the ccr support team to suppress the error message but not working for now. However the error message will not prevent us from getting the result.

module load gcc/11.2.0 openmpi/4.1.1
module load scipy-bundle/2021.10
module load ucx/1.13.1

3. Install the python package dependency: mpi4py, numpy and pyyaml. This step only needs to be done once. But it won't hurt to put it in the sbatch script.

python3 -m pip install -r requirements.txt

4. Running pair-calc.py to produce the system response matrix file

mpirun python pair-calc.py

Running on local desktops

Tested Enviornment:

• Ubuntu 22.04.1, Linux kernel 6.5.0-21-generic
• Python 3.10.12 with GCC 11.4.0
• Open MPI 4.1.2
• Numpy 1.26.3

readSysmat.py

This script can be used to plot the calculated system response matrix

Dependency

• Python version 3
• Numpy
• Matplotlib

Running the script

Simply do:

python readSysmat.py

The script will read configs/config.yml and find the produced matrix. If the matrix file .npz is moved, you will need to modify the readSysmat.py