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Merged
merged 25 commits into from
Nov 29, 2021
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[testlib] Add GROMACS benchmark tests #2186

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4bd71ed
add redesigned gromacs tests
hurricane642 Sep 9, 2021
189916f
fix problems with blank line and white space
hurricane642 Sep 9, 2021
9bc222e
fix problems with blank line and white space
hurricane642 Sep 9, 2021
b72545d
delete unused import
hurricane642 Sep 15, 2021
6faeb2d
Merge branch 'master' into gromacs_test
Nov 10, 2021
d3e81b6
WIP: Gromacs benchmarks as library tests
Nov 11, 2021
3629c0e
Merge branch 'master' into gromacs_test
Nov 12, 2021
aaf83ca
Rewrite Gromacs CSCS checks
Nov 15, 2021
22362a8
Fix PEP8 complaints
Nov 15, 2021
a423280
Merge branch 'master' of https://github.com/eth-cscs/reframe into gro…
victorusu Nov 15, 2021
b4f7299
Update the GROMACS reference numbers
victorusu Nov 16, 2021
ad5f7d1
Merge branch 'gromacs_test' of https://github.com/hurricane642/refram…
victorusu Nov 16, 2021
963275f
Address PR comments
Nov 16, 2021
cc098a7
Fix PEP8 issues
Nov 16, 2021
17682cb
Merge branch 'master' into gromacs_test
Nov 16, 2021
7a231b6
Add additional test and update perf numbers
victorusu Nov 25, 2021
43e702f
Merge branch 'gromacs_test' of https://github.com/hurricane642/refram…
victorusu Nov 25, 2021
8d47325
Address PR comments
Nov 26, 2021
abcc7c1
Merge branch 'master' into gromacs_test
Nov 26, 2021
1a723b6
Adapt tags and remove modes
Nov 26, 2021
7ffec82
Make PEP8 happy again
Nov 26, 2021
c3ce674
Add documentation to the gromacs lib tests
victorusu Nov 29, 2021
22d1b88
Fix the documentation
Nov 29, 2021
4e91bb6
Merge branch 'master' into gromacs_test
Nov 29, 2021
bc46db7
Merge branch 'master' into gromacs_test
Nov 29, 2021
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353 changes: 227 additions & 126 deletions cscs-checks/apps/gromacs/gromacs_check.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,139 +3,240 @@
#
# SPDX-License-Identifier: BSD-3-Clause

import contextlib
import os

import reframe as rfm
import reframe.utility.sanity as sn


class GromacsBaseCheck(rfm.RunOnlyRegressionTest):
def __init__(self, output_file):
if self.current_system.name in ['eiger', 'pilatus']:
self.valid_prog_environs = ['cpeGNU']
else:
self.valid_prog_environs = ['builtin']

self.executable = 'gmx_mpi'
from hpctestlib.sciapps.gromacs.benchmarks import gromacs_check

# Reset sources dir relative to the SCS apps prefix
self.sourcesdir = os.path.join(self.current_system.resourcesdir,
'Gromacs', 'herflat')
self.keep_files = [output_file]

energy = sn.extractsingle(r'\s+Potential\s+Kinetic En\.\s+Total Energy'
r'\s+Conserved En\.\s+Temperature\n'
r'(\s+\S+){2}\s+(?P<energy>\S+)(\s+\S+){2}\n'
r'\s+Pressure \(bar\)\s+Constr\. rmsd',
output_file, 'energy', float, item=-1)
energy_reference = -3270799.9

self.sanity_patterns = sn.all([
sn.assert_found('Finished mdrun', output_file),
sn.assert_reference(energy, energy_reference, -0.001, 0.001)
])

self.perf_patterns = {
'perf': sn.extractsingle(r'Performance:\s+(?P<perf>\S+)',
output_file, 'perf', float)
@rfm.simple_test
class cscs_gromacs_check(gromacs_check):
modules = ['GROMACS']
maintainers = ['VH', 'VK']
use_multithreading = False
extra_resources = {
'switches': {
'num_switches': 1
}

self.modules = ['GROMACS']
self.maintainers = ['VH', 'SO']
self.strict_check = False
self.use_multithreading = False
self.extra_resources = {
'switches': {
'num_switches': 1
}
}
executable_opts += ['-dlb yes', '-ntomp 1', '-npme -1']
valid_prog_environs = ['builtin']

# CSCS-specific parameterization
num_nodes = parameter([1, 2, 4, 6, 8, 16])
allref = {
1: {
'sm_60': {
'HECBioSim/Crambin': (195.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (78.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (8.5, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (9.2, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (3.0, None, None, 'ns/day'),
},
'broadwell': {
'HECBioSim/Crambin': (116.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (38.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (4.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (8.0, None, None, 'ns/day'),
},
'zen2': {
'HECBioSim/Crambin': (320.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (120.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (16.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (31.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (7.0, None, None, 'ns/day'),
},
},
2: {
'sm_60': {
'HECBioSim/Crambin': (202.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (111.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (15.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (18.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (6.0, None, None, 'ns/day'),
},
'broadwell': {
'HECBioSim/Crambin': (200.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (65.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (8.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (13.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (4.0, None, None, 'ns/day'),
},
'zen2': {
'HECBioSim/Crambin': (355.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (210.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (31.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (53.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (13.0, None, None, 'ns/day'),
},
},
4: {
'sm_60': {
'HECBioSim/Crambin': (200.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (133.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (22.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (28.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (10.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (5.0, None, None, 'ns/day'),
},
'broadwell': {
'HECBioSim/Crambin': (260.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (111.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (15.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (23.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (7.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (3.0, None, None, 'ns/day'),
},
'zen2': {
'HECBioSim/Crambin': (340.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (230.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (56.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (80.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (25.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (11.0, None, None, 'ns/day'),
},
},
6: {
'sm_60': {
'HECBioSim/Crambin': (213.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (142.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (28.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (35.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (13.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (8.0, None, None, 'ns/day'),
},
'broadwell': {
'HECBioSim/Crambin': (308.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (127.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (22.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (29.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (9.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (5.0, None, None, 'ns/day'),
},
'zen2': {
'HECBioSim/Glutamine-Binding-Protein': (240.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (75.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (110.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (33.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (13.0, None, None, 'ns/day'),
},
},
8: {
'sm_60': {
'HECBioSim/Crambin': (206.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (149.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (37.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (39.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (16.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (9.0, None, None, 'ns/day'),
},
'broadwell': {
'HECBioSim/Crambin': (356.0, None, None, 'ns/day'),
'HECBioSim/Glutamine-Binding-Protein': (158.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (28.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (39.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (11.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (6.0, None, None, 'ns/day'),
},
'zen2': {
'HECBioSim/Glutamine-Binding-Protein': (250.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (80.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (104.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (43.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (20.0, None, None, 'ns/day'),
},
},
16: {
'sm_60': {
'HECBioSim/Glutamine-Binding-Protein': (154.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (43.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (54.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (21.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (14.0, None, None, 'ns/day'),
},
'broadwell': {
'HECBioSim/Glutamine-Binding-Protein': (200.0, None, None, 'ns/day'), # noqa: E501
'HECBioSim/hEGFRDimer': (44.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (54.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (19.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (10.0, None, None, 'ns/day'),
},
'zen2': {
'HECBioSim/hEGFRDimer': (82.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerSmallerPL': (70.0, None, None, 'ns/day'),
'HECBioSim/hEGFRDimerPair': (49.0, None, None, 'ns/day'),
'HECBioSim/hEGFRtetramerPair': (25.0, None, None, 'ns/day'),
},
}
self.tags = {'scs', 'external-resources'}


@rfm.parameterized_test(*([s, v]
for s in ['small', 'large']
for v in ['prod', 'maint']))
class GromacsGPUCheck(GromacsBaseCheck):
def __init__(self, scale, variant):
super().__init__('md.log')
self.valid_systems = ['daint:gpu']
self.descr = 'GROMACS GPU check'
self.executable_opts = ['mdrun', '-dlb yes', '-ntomp 1', '-npme 0',
'-s herflat.tpr']
self.variables = {'CRAY_CUDA_MPS': '1'}
self.num_gpus_per_node = 1
if scale == 'small':
self.valid_systems += ['dom:gpu']
self.num_tasks = 72
self.num_tasks_per_node = 12
else:
self.num_tasks = 192
self.num_tasks_per_node = 12

references = {
'maint': {
'large': {
'daint:gpu': {'perf': (63.0, -0.10, None, 'ns/day')}
}
},
'prod': {
'small': {
'dom:gpu': {'perf': (37.0, -0.05, None, 'ns/day')},
'daint:gpu': {'perf': (35.0, -0.10, None, 'ns/day')}
},
'large': {
'daint:gpu': {'perf': (63.0, -0.20, None, 'ns/day')}
}
}

@run_after('init')
def setup_filtering_criteria(self):
# Update test's description
self.descr += f' ({self.num_nodes} node(s))'

# Setup system filtering
valid_systems = {
'cpu': {
1: ['daint:mc', 'dom:mc', 'eiger:mc', 'pilatus:mc'],
2: ['daint:mc', 'dom:mc', 'eiger:mc', 'pilatus:mc'],
4: ['daint:mc', 'dom:mc', 'eiger:mc', 'pilatus:mc'],
6: ['daint:mc', 'dom:mc', 'eiger:mc', 'pilatus:mc'],
8: ['daint:mc', 'eiger:mc'],
16: ['daint:mc', 'eiger:mc']
},
'gpu': {
1: ['daint:gpu', 'dom:gpu', 'eiger:gpu', 'pilatus:gpu'],
2: ['daint:gpu', 'dom:gpu', 'eiger:gpu', 'pilatus:gpu'],
4: ['daint:gpu', 'dom:gpu', 'eiger:gpu', 'pilatus:gpu'],
6: ['daint:gpu', 'dom:gpu', 'eiger:gpu', 'pilatus:gpu'],
8: ['daint:gpu', 'eiger:gpu'],
16: ['daint:gpu', 'eiger:gpu']
}
}
with contextlib.suppress(KeyError):
self.reference = references[variant][scale]

self.tags |= {'maintenance' if variant == 'maint' else 'production'}


@rfm.parameterized_test(*([s, v]
for s in ['small', 'large']
for v in ['prod']))
class GromacsCPUCheck(GromacsBaseCheck):
def __init__(self, scale, variant):
super().__init__('md.log')
self.valid_systems = ['daint:mc', 'eiger:mc', 'pilatus:mc']
self.descr = 'GROMACS CPU check'
self.executable_opts = ['mdrun', '-dlb yes', '-ntomp 1', '-npme -1',
'-nb cpu', '-s herflat.tpr']
try:
self.valid_systems = valid_systems[self.nb_impl][self.num_nodes]
except KeyError:
self.valid_systems = []

if scale == 'small':
self.valid_systems += ['dom:mc']
if (self.current_system.name in ['daint', 'dom']):
self.num_tasks = 216
self.num_tasks_per_node = 36
elif (self.current_system.name in ['eiger', 'pilatus']):
self.num_tasks = 768
self.num_tasks_per_node = 128
else:
if (self.current_system.name in ['daint', 'dom']):
self.num_tasks = 576
self.num_tasks_per_node = 36
elif (self.current_system.name in ['eiger', 'pilatus']):
self.num_tasks = 2048
self.num_tasks_per_node = 128
# Setup prog env. filtering
if self.current_system.name in ('eiger', 'pilatus'):
self.valid_prog_environs = ['cpeGNU']

references = {
'prod': {
'small': {
'dom:mc': {'perf': (40.0, -0.05, None, 'ns/day')},
'daint:mc': {'perf': (38.8, -0.10, None, 'ns/day')},
'eiger:mc': {'perf': (103.00, -0.10, None, 'ns/day')},
'pilatus:mc': {'perf': (103.00, -0.10, None, 'ns/day')}
},
'large': {
'daint:mc': {'perf': (68.0, -0.20, None, 'ns/day')},
'eiger:mc': {'perf': (146.00, -0.20, None, 'ns/day')},
'pilatus:mc': {'perf': (146.00, -0.20, None, 'ns/day')}
}
},
if self.num_nodes in (6, 16):
self.tags |= {'production'}
if (self.nb_impl == 'gpu' and
self.bench_name == 'HECBioSim/hEGFRDimerSmallerPL'):
self.tags |= {'maintenance'}

@run_before('run')
def setup_run(self):
self.skip_if_no_procinfo()

# Setup GPU run
if self.nb_impl == 'gpu':
self.num_gpus_per_node = 1
self.variables = {'CRAY_CUDA_MPS': '1'}

proc = self.current_partition.processor

# Choose arch; we set explicitly the GPU arch, since there is no
# auto-detection
arch = proc.arch
if self.current_partition.fullname in ('daint:gpu', 'dom:gpu'):
arch = 'sm_60'

try:
found = self.allref[self.num_nodes][arch][self.bench_name]
except KeyError:
self.skip(f'Configuration with {self.num_nodes} node(s) of '
f'{self.bench_name!r} is not supported on {arch!r}')

# Setup performance references
self.reference = {
'*': {
'perf': self.allref[self.num_nodes][arch][self.bench_name]
}
}
self.reference = references[variant][scale]
self.tags |= {'maintenance' if variant == 'maint' else 'production'}

# Setup parallel run
self.num_tasks_per_node = proc.num_cores
self.num_tasks = self.num_nodes * self.num_tasks_per_node
3 changes: 3 additions & 0 deletions docs/hpctestlib.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,9 @@ Scientific Applications
:members:
:show-inheritance:

.. automodule:: hpctestlib.sciapps.gromacs.benchmarks
:members:
:show-inheritance:

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