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Merge pull request #3233 from Crivella/feature-MetalWalls
[testlib] Added MetalWalls scalability test for `mw`
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‎docs/hpctestlib.rst

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@@ -106,6 +106,10 @@ Scientific Applications
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:members:
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:show-inheritance:
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.. automodule:: hpctestlib.sciapps.metalwalls.benchmarks
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:members:
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:show-inheritance:
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System
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=======================
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‎hpctestlib/sciapps/metalwalls/benchmarks.py

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"""ReFrame benchmark for MetalWalls"""
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import re
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import reframe as rfm
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import reframe.utility.sanity as sn
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from reframe.core.builtins import (performance_function, run_after, run_before,
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sanity_function)
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from reframe.core.parameters import TestParam as parameter
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from reframe.core.variables import TestVar as variable
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address_tpl = (
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'https://gitlab.com/ampere2/metalwalls/-/raw/{version}/{bench}/{file}'
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'?ref_type=tags&inline=false'
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)
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extract_fields = [
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#######
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('Ions->Atoms Coulomb potential', 'long range', 'I->A Cpot'),
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('Ions->Atoms Coulomb potential', 'k==0', 'I->A Cpot'),
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('Ions->Atoms Coulomb potential', 'short range', 'I->A Cpot'),
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#######
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('Atoms->Atoms Coulomb potential', 'long range', 'A->A Cpot'),
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('Atoms->Atoms Coulomb potential', 'k==0', 'A->A Cpot'),
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('Atoms->Atoms Coulomb potential', 'short range', 'A->A Cpot'),
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('Atoms->Atoms Coulomb potential', 'self', 'A->A Cpot'),
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#######
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('Atoms->Atoms Coulomb grad Q', 'long range', 'A->A gradQ'),
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('Atoms->Atoms Coulomb grad Q', 'k==0', 'A->A gradQ'),
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('Atoms->Atoms Coulomb grad Q', 'short range', 'A->A gradQ'),
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('Atoms->Atoms Coulomb grad Q', 'self', 'A->A gradQ'),
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#######
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('Ions Coulomb forces', 'long range', 'Ions Cfrc'),
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('Ions Coulomb forces', 'k==0', 'Ions Cfrc'),
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('Ions Coulomb forces', 'short range', 'Ions Cfrc'),
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('Ions Coulomb forces', 'intramolecular', 'Ions Cfrc'),
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#######
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('Ions Coulomb potential', 'long range', 'Ions Cpot'),
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('Ions Coulomb potential', 'k==0', 'Ions Cpot'),
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('Ions Coulomb potential', 'short range', 'Ions Cpot'),
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('Ions Coulomb potential', 'intramolecular', 'Ions Cpot'),
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('Ions Coulomb potential', 'self', 'Ions Cpot'),
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#######
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(
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'Ions Coulomb electric field (due to charges)',
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'long range',
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'Ions Cfield(charges)'
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),
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(
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'Ions Coulomb electric field (due to charges)',
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'k==0',
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'Ions Cfield(charges)'
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),
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(
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'Ions Coulomb electric field (due to charges)',
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'short range',
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'Ions Cfield(charges)'
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),
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(
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'Ions Coulomb electric field (due to charges)',
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'intramolecular',
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'Ions Cfield(charges)'
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),
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#######
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(
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'Ions Coulomb electric field (due to dipoles)',
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'long range',
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'Ions Cfield(dipoles)'
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),
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(
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'Ions Coulomb electric field (due to dipoles)',
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'k==0',
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'Ions Cfield(dipoles)'
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),
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(
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'Ions Coulomb electric field (due to dipoles)',
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'short range',
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'Ions Cfield(dipoles)'
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),
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(
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'Ions Coulomb electric field (due to dipoles)',
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'intramolecular',
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'Ions Cfield(dipoles)'
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),
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(
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'Ions Coulomb electric field (due to dipoles)',
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'self',
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'Ions Cfield(dipoles)'
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),
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#######
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('Ions Coulomb electric field gradient', 'long range', 'Ions Cfield grad'),
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(
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'Ions Coulomb electric field gradient',
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'short range',
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'Ions Cfield grad'
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),
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('Ions Coulomb electric field gradient', 'self', 'Ions Cfield grad'),
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#######
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('Ions Coulomb gradient mu', 'long range', 'Ions C mu_grad'),
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('Ions Coulomb gradient mu', 'k==0', 'Ions C mu_grad'),
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('Ions Coulomb gradient mu', 'short range', 'Ions C mu_grad'),
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('Ions Coulomb gradient mu', 'self', 'Ions C mu_grad'),
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#######
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('Rattle', 'positions', 'Rattle'),
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('Rattle', 'velocities', 'Rattle'),
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#######
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('van der Waals', 'vdW forces', 'van der Waals'),
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('van der Waals', 'vdW potential', 'van der Waals'),
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#######
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('Intramolecular', 'Intramolecular forces', 'Intramolecular'),
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('Intramolecular', 'Intramolecular potential', 'Intramolecular'),
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#######
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('Additional degrees', 'Electrode charge computation', 'Deg of freedom'),
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('Additional degrees', 'Inversion of the matrix', 'Deg of freedom'),
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('Additional degrees', 'One matrix-vector product', 'Deg of freedom'),
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('Additional degrees', 'Melt dipoles computation', 'Deg of freedom'),
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('Additional degrees', 'Inversion of the matrix', 'Deg of freedom'),
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('Additional degrees', 'One matrix-vector product', 'Deg of freedom'),
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('Additional degrees', 'AIM DOFs computation', 'Deg of freedom'),
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#######
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('Diagnostics', 'diagnostics computations', 'Diagnostics'),
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('Diagnostics', 'IO', 'Diagnostics'),
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]
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@rfm.simple_test
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class MetalWallsCheck(rfm.RunOnlyRegressionTest):
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"""MetalWalls benchmark test.
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`MetalWalls <https://gitlab.com/ampere2/metalwalls>`__ is a molecular
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dynamics code dedicated to the modelling of electrochemical systems.
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Its main originality is the inclusion of a series of methods allowing to
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apply a constant potential within the electrode materials.
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The benchmarks consist of a set of different inputs files that vary in the
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number of atoms and the type of simulation performed.
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They can be found in the following repository, which is also versioned:
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https://gitlab.com/ampere2/metalwalls/.
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"""
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#: The name of the output files to keep.
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#:
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#: :type: :class:`List[str]`
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#: :default: ``'run.out'``
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keep_files = ['run.out', ]
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#: The version of the benchmark suite to use.
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#:
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#: :type: :class:`str`
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#: :default: ``'21.06.1'``
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benchmark_version = variable(str, value='21.06.1', loggable=True)
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executable = 'mw'
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tags = {'sciapp', 'chemistry'}
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descr = 'MetalWalls `mw` benchmark'
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#: Collect and report detailed performance metrics.
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#:
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#: :type: :class:`bool`
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#: :default: ``False``
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debug_metrics = variable(bool, value=False, loggable=True)
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#: Parameter pack encoding the benchmark information.
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#:
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#: The first element of the tuple refers to the benchmark name,
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#: the second is the final kinetic energy the third is the related
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#: tolerance, the fourth is the absolute temperature and the fifth is
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#: the related tolerance
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#:
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#: :type: `Tuple[str, float, float, float, float]`
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#: :values:
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benchmark_info = parameter([
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('hackathonGPU/benchmark', 14.00, 0.05, 301.74, 0.5),
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('hackathonGPU/benchmark2', 14.00, 0.05, 301.74, 0.5),
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('hackathonGPU/benchmark3', 16.08, 0.05, 293.42, 0.5),
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('hackathonGPU/benchmark4', 16.08, 0.05, 293.42, 0.5),
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('hackathonGPU/benchmark5', 25.72, 0.05, 297.47, 0.5),
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('hackathonGPU/benchmark6', 25.72, 0.05, 297.47, 0.5),
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], fmt=lambda x: x[0], loggable=True)
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@run_after('init')
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def prepare_test(self):
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"""Hook to the set the downloading of the pseudo-potentials"""
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self.__bench, _, _, _, _ = self.benchmark_info
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self.descr = f'MetalWalls {self.__bench} benchmark'
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files_addresses = [
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address_tpl.format(
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version=self.benchmark_version,
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bench=self.__bench,
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file=_
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) for _ in ['data.inpt', 'runtime.inpt']
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]
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self.prerun_cmds += [
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f"curl -LJO '{_}'" for _ in files_addresses
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]
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@performance_function('s')
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def total_elapsed_time(self):
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"""Extract the total elapsed time from the output file"""
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return sn.extractsingle(
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r'Total elapsed time:\s+(?P<time>\S+)', 'run.out', 'time', float
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)
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@sn.deferrable
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def extract_kinetic_energy(self):
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"""Extract the final kinetic energy from the output file"""
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rgx = r'\|step\| +kinetic energy: +(?P<flag>\S+)'
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app = sn.extractall(rgx, 'run.out', 'flag', float)
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return app[-1]
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@sn.deferrable
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def extract_temperature(self):
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"""Extract the final temperature from the output file"""
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rgx = r'\|step\| +temperature: +(?P<flag>\S+)'
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app = sn.extractall(rgx, 'run.out', 'flag', float)
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return app[-1]
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def extract_time(
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self, name: str = None, parent: str = None, kind: str = None
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) -> float:
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"""Extract the time from a specific report section of the output file
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Args:
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name (str): The name of the report to extract
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parent (str): The parent section of the report
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kind (str): The kind of time to extract (avg or cumul)
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"""
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if kind is None:
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return 0
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kind = kind.lower()
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if kind == 'avg':
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tag = 1
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elif kind == 'cumul':
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tag = 2
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else:
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raise ValueError(f'Unknown kind: {kind}')
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# Example Fromat:
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# Ions->Atoms Coulomb potential
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# -----------------------------
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# long range 9.55040E-03 9.64590E-01 0.71
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# k==0 2.48271E-02 2.50754E+00 1.84
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# short range 8.72464E-02 8.81189E+00 6.46
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#
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# NEXT SECTION
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res = -1
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rgx = re.compile(rf'^ +{name}\s+(\S+) +(\S+)')
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flag = False
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with open('run.out', 'r') as file:
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for line in file:
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if flag:
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if rgx.match(line):
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res = float(rgx.match(line).group(tag))
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break
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elif not line.strip():
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break
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else:
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if parent in line:
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flag = True
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return res
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@run_before('performance')
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def set_perf_variables(self):
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"""Build a dictionary of performance variables"""
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self.perf_variables['total_elapsed_time'] = self.total_elapsed_time()
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if self.debug_metrics:
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for parent, name, short in extract_fields:
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name2 = name.replace(' ', '_')
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for kind in ['avg', 'cumul']:
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app = self.extract_time(name, parent, kind)
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self.perf_variables[f'{short}__{name2}__{kind}'] = app
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@sanity_function
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def assert_job_finished(self):
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"""Check if the job finished successfully"""
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energy = self.extract_kinetic_energy()
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temp = self.extract_temperature()
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_, energy_ref, energy_tol, temp_ref, temp_tol = self.benchmark_info
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en_rtol = energy_tol / energy_ref
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t_rtol = temp_tol / temp_ref
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return sn.all([
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sn.assert_found(r'Total elapsed time', 'run.out'),
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sn.assert_reference(energy, energy_ref, -en_rtol, en_rtol),
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sn.assert_reference(temp, temp_ref, -t_rtol, t_rtol)
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])

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