/ptycho

Primary LanguageJupyter Notebook

ptycho

Personal repo for electron ptychography related scripts

-- Chia-Hao Lee @ UIUC

Contents

  • BatchSubmit.sh: Shell script that submit multiple sbatch jobs to the camplus cluster through Slurm
  • 4hr_2task_V100_runPtycho_template.sbatch: Template sbatch file used to submit jobs concurrently to cluster GPU node
  • eng_2task_V100_runPtycho_template.sbatch: Template sbatch file used to submit jobs concurrently to cluster GPU node
  • runPtycho_cc_Themis_${DATE}_${SAMPLE}_{ExpTime}.m: Template Matlab script used to execute ptycho reconstruction
  • GeneratePtychoScripts.ipynb: Jupyter notebook that generates all the .sh, .sbatch, and .m in batch to make our life easier

Dependencies

  1. fold_slice github repo
  2. Matlab with Parallel Computing Toolbox license (either local or remote)
  3. Python 3 with jupyter notebook if you want to generate script files in batch

How to start

  • Run runPtycho_cc_Themis_${DATE}_${SAMPLE}_{ExpTime}.m script file locally if you have a licensed Matlab installation
  • Use the .sbatch and .m to submit jobs to the campus cluster nodes to run remotely
  • For batch processing, run GeneratePtychoScripts.ipynb with jupyter notebook to generate all the needed scripts in one go
    • Type in sh BatchSubmit.sh to run the shell script for batch job submission