Add genesis experiment

[slabasan]

Description

To test on Fugaku:

cd benchpark
. setup-env.sh
benchpark system init --dest fugaku-system fugaku 
benchpark experiment init --dest genesis-openmp genesis +openmp
benchpark setup genesis-openmp ./fugaku-system workspace/

Then follow the output steps.

Please validate the runtime parameters in the ramble.yaml (workspace/genesis-openmp/ramble.yaml)
Please validate the output when the job completes

Experiment.py for genesis.

Dependencies: None

Fixes issue(s): Part of #460.

Type of Change

• {X} Adding a system, benchmark, or experiment
• { } Modifying an existing system, benchmark, or experiment
• { } Documentation update
• { } Build/CI update
• { } Benchpark core functionality

Checklist:

If adding/modifying a system:

• { } Create a new directory for the system and a new system.py file
• { } Add a new dry run unit test in .github/workflows
• { } System appears in System Specifications table in docs catalogue section

If adding/modifying a benchpark:

• { } Add a new application.py and (maybe) package.py under a new directory
  for this benchmark
• { } Configure an experiment
• { } Benchmark appears in Benchmarks and Experiments table in docs catalogue
  section

If adding/modifying a experiment:

• { x } Extend experiment.py under existing directory for specific benchmark
• { } Define a single node and multi-node experiments

If adding/modifying core functionality:

• { } Update docs
• { } Update .github/workflows and .gitlab/ci unit tests (if needed)

[dyokelson]

Tested on Ruby, currently fails during job execution with the following error:

srun: error: ruby50: task 0: Exited with exit code 1
 Open_file> File /usr/WS2/yokelson/benchpark/workspace/genesis-openmp/Cts-6d48f81/workspace/inputs/genesis/DHFR/benchmark-2020/npt/genesis2.0beta/jac_amber/p1.inp does not exist  rank_no =     0

Steps to reproduce:

benchpark experiment init --dest=genesis-openmp genesis +openmp
benchpark setup genesis-openmp ./ruby-system workspace/

Then follow the rest of the prompts, ramble on successfully submits the batch job but the job fails.

It looks like it can't find an input file but input files do exist there but they have different names (p16.inp, p32.inp, p64.inp, p8.inp). Maybe we need to increase the number of processes so it grabs the right one?

[dyokelson]

Ok increasing the MPI ranks seems to have fixed it but I am not sure if it ran all the way through, we should have Riken folks validate the parameters and test on Fugaku

[pearce8]

@jdomke can you or your team please review this PR to validate the parameters and test on Fugaku?

[slabasan]

Confirmed this works on ruby with the most recent changes from @jdomke, last part of output is:

[STEP6] Deallocate Arrays
 
Output_Time> Averaged timer profile (Min, Max)
  total time      =      36.228
    setup         =       1.175
    dynamics      =      35.053
      energy      =      24.199
      integrator  =       7.526
      pairlist    =       2.155 (       2.071,       2.243)
... 
  integrator       
    constraint    =       0.466 (       0.437,       0.494)
    update        =       1.060 (       1.045,       1.073)
    comm_coord    =       1.213 (       1.126,       1.311)
    comm_force    =       1.367 (       1.152,       1.509)
    comm_migrate  =       0.062 (       0.060,       0.064)

[slabasan]

@pearce8 @jdomke This is ready for final review before merge.