BeamBeam3DPlus

Extending BeamBeam3D code with I/O options

PREREQUEST: module load cmake

================== For using with ADIOS2 =============

PREREQUEST: adios2

=> if you need to build adios2, first get from repo:

  git clone https://github.com/ornladios/ADIOS2

  build and install adios2 (use python3 as the python library)

=> How to build with adios2:

  export ADIOS2_DIR=<YOUR/ADIOS2/INSTALL/>

  mkdir build-adios2

  cd build-adios2


  cmake  ../source/adios2

  make 

=> To Test:

  cd ../test/adios2 

It contains a sample input files: beam1.in beam2.in + adios2-config.xml

• Important:

  make sure ADIOS is in your library path:
  
  export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/global/cscratch1/sd/junmin/software/adios2/master/install-release/lib64/
  

• Simulation:

  mpirun -n 4 ../../build-adios2/bin/adios2.xmain 
  

• Analysis:

  ../../build-adios2/bin/adios2.mod_tunefoot
  

without argument, if looks for file tunefoot.in. which shall look like this:

more tunefoot.in

0                       #bunch <0 or 1>

0 1000                  #particleStart & count

0 4096                  #turnStart & count

1 0 1 0 1 0             #x #px #y #py #z #pz

=> To plot with tunePlot.py

PREREQUEST:

- Have ffmeg in your file path (to save to movie) 

- Point pythonpath to ADIOS python library, e.g.      

  	  export PYTHONPATH=/Users/junmin/software/adios2/master/install/lib/python3.7/site-packages/

- Command to use the python script to visualize: (using default args) images will refresh and outputs saved to figs/ a movie is also generated from all files in figs/

  	  python3 tunePlot.py -i tunefoot.bp

  "Note: tunefoot.bp is the filename hardcoded in the analysis code to store every tunefoot created in the file"

   	- Command to plot for attrs x y with resonance lines at (0.3, 0.3) with refresh rate at 1 sec 

  	  python3 tunePlot.py -i tunefoot.bp/ -a x y  -p 0.3 0.3  -s 1 

- Command to plot for attrs x y with resonance lines at (0.3, 0.3) with no figures on screen, outputs directly to figs/:
  python3 tunePlot.py -i tunefoot.bp/ -a x y  -p 0.3 0.3  -s 0
          
- Command to plot for attrs x y with all episodes (timelines): (resonance lines ignored)
  viewing up to 8 episodes in the display. By default it is colored by histogram. (add "-3dtype delta" to be colored by delta. delta = sqrt(deltaAtX **2 + deltaAtY ** 2) for each particle's tunefoot)

  python3 tunePlot.py -i tunefoot.bp/ -a x y  -3d -m 8 

- Alternative is to list all the inputs in a config file, example contents see: plot.in 
  and pass as -c:
  python3 tunePlot.py -c plot.in

Workflow can be

  Simulation --- SST/BPFile --- Analysis ---- SST/BPFile --- Python 

where SST or BPFile mode are specified in the adios2_config.xml

• Simulation -- Analysis uses "SimulationOutput" I/O
• Analysis -- Python uses "TuneFoot" I/O