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gromacs: add adh_dodec, change nsteps to variable #356

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merged 5 commits into from
Dec 20, 2023
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gromacs: add adh_dodec, change nsteps to variable #356

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cf0757f
gromacs: add adh_dodec, change nsteps to variable
danielahlin Dec 18, 2023
d24b6ff
gromacs: make most of command parameters variables
danielahlin Dec 19, 2023
2a70a21
Minor cleanups
danielahlin Dec 19, 2023
1fcd787
gromacs: fix style issues
danielahlin Dec 19, 2023
efccda1
gromacs: add valid values on relevant variables
danielahlin Dec 20, 2023
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59 changes: 54 additions & 5 deletions var/ramble/repos/builtin/applications/gromacs/application.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,16 +23,16 @@ class Gromacs(SpackApplication):
software_spec('impi2018', spack_spec='[email protected]')
software_spec('gromacs', spack_spec='[email protected]', compiler='gcc9')

executable('pre-process', 'gmx_mpi grompp ' +
executable('pre-process', '{grompp} ' +
'-f {input_path}/{type}.mdp ' +
'-c {input_path}/conf.gro ' +
'-p {input_path}/topol.top ' +
'-o exp_input.tpr', use_mpi=False, output_capture=OUTPUT_CAPTURE.ALL)
executable('execute-gen', 'gmx_mpi mdrun -notunepme -dlb yes ' +
'-v -resethway -noconfout -nsteps 4000 ' +
executable('execute-gen', '{mdrun} {notunepme} -dlb {dlb} ' +
'{verbose} -resetstep {resetstep} -noconfout -nsteps {nsteps} ' +
'-s exp_input.tpr', use_mpi=True, output_capture=OUTPUT_CAPTURE.ALL)
executable('execute', 'gmx_mpi mdrun -notunepme -dlb yes ' +
'-v -resethway -noconfout -nsteps 4000 ' +
executable('execute', '{mdrun} {notunepme} -dlb ${dlb} ' +
'{verbose} -resetstep {resetstep} -noconfout -nsteps {nsteps} ' +
'-s {input_path}', use_mpi=True, output_capture=OUTPUT_CAPTURE.ALL)

input_file('water_gmx50_bare', url='https://ftp.gromacs.org/pub/benchmarks/water_GMX50_bare.tar.gz',
Expand Down Expand Up @@ -98,6 +98,49 @@ class Gromacs(SpackApplication):
input='JCP_benchmarks')
workload('ion_channel', executables=['pre-process', 'execute-gen'],
input='JCP_benchmarks')
workload('adh_dodec', executables=['pre-process', 'execute-gen'],
input='JCP_benchmarks')

all_workloads = [
'water_gmx50',
'water_bare',
'lignocellulose',
'hecbiosim',
'benchpep',
'benchpep_h',
'benchmem',
'benchrib',
'stmv_rf',
'stmv_pme',
'rnase_cubic',
'ion_channel',
'adh_dodec',
]

workload_variable('gmx', default='gmx_mpi',
description='Name of the gromacs binary',
workloads=all_workloads)
workload_variable('grompp', default='{gmx} grompp',
description='How to run grompp',
workloads=all_workloads)
workload_variable('mdrun', default='{gmx} mdrun',
description='How to run mdrun',
workloads=all_workloads)
workload_variable('nsteps', default=str(20000),
description='Simulation steps',
workloads=all_workloads)
workload_variable('resetstep', default='{str(int(0.9*{nsteps}))}',
description='Reset performance counters at this step',
workloads=all_workloads)
workload_variable('verbose', default="", values=['', '-v'],
description='Set to empty string to run without verbose mode',
workloads=all_workloads)
workload_variable('notunepme', default='-notunepme', values=['', '-notunepme'],
description='Whether to set -notunepme for mdrun',
workloads=all_workloads)
workload_variable('dlb', default='yes', values=['yes', 'no'],
description='Whether to use dynamic load balancing for mdrun',
workloads=all_workloads)

workload_variable('size', default='1536',
values=['0000.65', '0000.96', '0001.5',
Expand Down Expand Up @@ -152,6 +195,12 @@ class Gromacs(SpackApplication):
workload_variable('input_path', default='{JCP_benchmarks}/{workload_name}',
description='Input path for JCP_benchmark {workload_name}',
workloads=['ion_channel', 'rnase_cubic'])
workload_variable('input_path', default='{JCP_benchmarks}/{workload_name}',
description='Input path for JCP_benchmark {workload_name}',
workloads=['adh_dodec'])
workload_variable('type', default='pme_verlet',
description='Workload type for JCP_benchmarks',
workloads=['adh_dodec'])

log_str = os.path.join(Expander.expansion_str('experiment_run_dir'),
'md.log')
Expand Down