radical.synapse Experiments

run experiments:

• install gromacs 5.0.4

• make sure that 'perf stat' can be executed by user

• make sure 'perf stat' reports CPU cycles etc.

• create Python virtualenv

• install Synapse v0.10

  • pip install radical.synapse==0.10

• edit 'run.sh'

  • adjust parameter space to scan (steps, smapling rates etc)
  • adjust path for storing data files (DBURL)

• run 'run.sh pro' for profiling runs

• run 'run.sh exe' for execution timings (w/o profiling)

• run 'run.sh emu' for emulation runs

• to add data from other hosts,

  • first run profiling mode above
  • perform the same steps as above, but
    • no 'perf stat' support is needed
    • no profiling run is needed
    • before running the emulation, copy the data files from the original profiling host to the same (relative) location on the target host (or use a mongodb url which is accessible by noth hosts)

create plots:

• cd plots
• run 'ipython notebook'
• open the 'Synapse_WRAP.ipynb' notebook
• make sure the first cell loads the required modules and shows the expected synapse version
• asjust the path to the data files in cell two
• run all cells
• plots will be stored in '/plots/'