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Improve benchmark scripts (espressomd#4753)
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Follow up to our work with HPC Vega and the EESSI project.

Description of changes:
- add GPU support in P3M and LB
- remove MASS dependency in P3M
- adjust steepest descent for large particle numbers
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kodiakhq[bot] authored and jngrad committed Jul 18, 2023
1 parent a3547e2 commit 278e818
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Showing 8 changed files with 50 additions and 36 deletions.
20 changes: 8 additions & 12 deletions maintainer/benchmarks/lb.py
Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,8 @@
type=float, default=0.03, required=False,
help="Fraction of the simulation box volume occupied by "
"particles (range: [0.01-0.74], default: 0.50)")
parser.add_argument("--gpu", default=False, action="store_true")
parser.add_argument("--no-gpu", dest="gpu", action="store_false")
parser.add_argument("--output", metavar="FILEPATH", action="store",
type=str, required=False, default="benchmarks.csv",
help="Output file (default: benchmarks.csv)")
Expand All @@ -51,6 +53,8 @@
"volume_fraction exceeds the physical limit of sphere packing (~0.74)"

required_features = ["LENNARD_JONES"]
if args.gpu:
required_features.append("CUDA")
espressomd.assert_features(required_features)

# System
Expand All @@ -66,8 +70,7 @@

# System parameters
#############################################################

n_proc = system.cell_system.get_state()['n_nodes']
n_proc = system.cell_system.get_state()["n_nodes"]
n_part = n_proc * args.particles_per_core
# volume of N spheres with radius r: N * (4/3*pi*r^3)
box_l = (n_part * 4. / 3. * np.pi * (lj_sig / 2.)**3
Expand All @@ -84,7 +87,6 @@
#############################################################
system.time_step = 0.01
system.cell_system.skin = 0.5
system.thermostat.turn_off()

# Interaction setup
#############################################################
Expand Down Expand Up @@ -119,15 +121,9 @@


system.thermostat.turn_off()
print(f"LB shape: [{lb_grid}, {lb_grid}, {lb_grid}]")
print(f"LB agrid: {agrid:.3f}")
if hasattr(espressomd.lb, "LBFluid"):
LBClass = espressomd.lb.LBFluid
elif hasattr(espressomd.lb, "LBFluidWalberla"):
LBClass = espressomd.lb.LBFluidWalberla
else:
raise Exception("LB not built in")

LBClass = espressomd.lb.LBFluid
if args.gpu:
LBClass = espressomd.lb.LBFluidGPU
lbf = LBClass(agrid=agrid, dens=1, visc=1, tau=system.time_step, kT=1, seed=1)
system.actors.add(lbf)
system.thermostat.set_lb(gamma=10, LB_fluid=lbf, seed=2)
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4 changes: 1 addition & 3 deletions maintainer/benchmarks/lj.py
Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,7 @@

# System parameters
#############################################################

n_proc = system.cell_system.get_state()['n_nodes']
n_proc = system.cell_system.get_state()["n_nodes"]
n_part = n_proc * args.particles_per_core
# volume of N spheres with radius r: N * (4/3*pi*r^3)
box_l = (n_part * 4. / 3. * np.pi * (lj_sig / 2.)**3
Expand All @@ -88,7 +87,6 @@
#############################################################
system.time_step = 0.01
system.cell_system.skin = 0.5
system.thermostat.turn_off()

# Interaction setup
#############################################################
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34 changes: 19 additions & 15 deletions maintainer/benchmarks/p3m.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,10 @@
help="Fraction of the simulation box volume occupied by "
"particles (range: [0.01-0.74], default: 0.25)")
parser.add_argument("--prefactor", metavar="PREFACTOR", action="store",
type=float, default=4., required=False,
type=float, default=1., required=False,
help="P3M prefactor (default: 4)")
parser.add_argument("--gpu", default=False, action="store_true")
parser.add_argument("--no-gpu", dest="gpu", action="store_false")
group = parser.add_mutually_exclusive_group()
group.add_argument("--output", metavar="FILEPATH", action="store",
type=str, required=False, default="benchmarks.csv",
Expand All @@ -55,7 +57,9 @@
assert measurement_steps >= 50, \
f"{measurement_steps} steps per tick are too short"

required_features = ["P3M", "LENNARD_JONES", "MASS"]
required_features = ["P3M", "LENNARD_JONES"]
if args.gpu:
required_features.append("CUDA")
espressomd.assert_features(required_features)

# make simulation deterministic
Expand All @@ -67,7 +71,6 @@

# Interaction parameters (Lennard-Jones, Coulomb)
#############################################################

species = ["anion", "cation"]
types = {"anion": 0, "cation": 0}
charges = {"anion": -1.0, "cation": 1.0}
Expand All @@ -76,12 +79,10 @@
WCA_cut = 2.**(1. / 6.)
lj_cuts = {"anion": WCA_cut * lj_sigmas["anion"],
"cation": WCA_cut * lj_sigmas["cation"]}
masses = {"anion": 1.0, "cation": 1.0}

# System parameters
#############################################################

n_proc = system.cell_system.get_state()['n_nodes']
n_proc = system.cell_system.get_state()["n_nodes"]
n_part = n_proc * args.particles_per_core
# volume of N spheres with radius r: N * (4/3*pi*r^3)
lj_sig = (lj_sigmas["cation"] + lj_sigmas["anion"]) / 2
Expand All @@ -96,12 +97,10 @@
# Integration parameters
#############################################################
system.time_step = 0.01
system.cell_system.skin = .4
system.thermostat.turn_off()
system.cell_system.skin = 0.5

# Interaction setup
#############################################################

for i in range(len(species)):
ion1 = species[i]
for j in range(i, len(species)):
Expand All @@ -115,34 +114,39 @@

# Particle setup
#############################################################

pid = 0
for i in range(0, n_part, len(species)):
for t in species:
system.part.add(pos=np.random.random(3) * system.box_l,
q=charges[t], type=types[t], mass=masses[t])
id=pid, q=charges[t], type=types[t])
pid += 1

# Warmup Integration
#############################################################

# warmup
benchmarks.minimize(system, n_part / 10.)
benchmarks.minimize(system, n_part / 2.)

system.integrator.set_vv()
system.thermostat.set_langevin(kT=1.0, gamma=1.0, seed=42)

p3m_class = espressomd.electrostatics.P3M
if args.gpu:
p3m_class = espressomd.electrostatics.P3MGPU

# tuning and equilibration
min_skin = 0.2
max_skin = 1.6
p3m_params = {'prefactor': args.prefactor, 'accuracy': 1e-4}
print("Equilibration")
p3m_params = {"prefactor": args.prefactor, "accuracy": 1e-3}
p3m = p3m_class(**p3m_params)
print("Quick equilibration")
system.integrator.run(min(3 * measurement_steps, 1000))
print("Tune skin: {:.3f}".format(system.cell_system.tune_skin(
min_skin=min_skin, max_skin=max_skin, tol=0.05, int_steps=100,
adjust_max_skin=True)))
print("Equilibration")
system.integrator.run(min(3 * measurement_steps, 3000))
print("Tune p3m")
p3m = espressomd.electrostatics.P3M(**p3m_params)
system.actors.add(p3m)
print("Equilibration")
system.integrator.run(min(3 * measurement_steps, 3000))
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6 changes: 4 additions & 2 deletions testsuite/scripts/benchmarks/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,10 @@ add_custom_target(
${CMAKE_SOURCE_DIR}/maintainer/benchmarks ${BENCHMARKS_DIR})

benchmark_test(FILE test_lj.py)
benchmark_test(FILE test_lb.py)
benchmark_test(FILE test_p3m.py)
benchmark_test(FILE test_lb.py SUFFIX cpu)
benchmark_test(FILE test_lb.py SUFFIX gpu LABELS "gpu")
benchmark_test(FILE test_p3m.py SUFFIX cpu)
benchmark_test(FILE test_p3m.py SUFFIX gpu LABELS "gpu")
benchmark_test(FILE test_ferrofluid.py)
benchmark_test(FILE test_mc_acid_base_reservoir.py)

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2 changes: 2 additions & 0 deletions testsuite/scripts/benchmarks/test_ferrofluid.py
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
#
# Copyright (C) 2019-2022 The ESPResSo project
#
# This file is part of ESPResSo.
Expand All @@ -14,6 +15,7 @@
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

import unittest as ut
import importlib_wrapper
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9 changes: 7 additions & 2 deletions testsuite/scripts/benchmarks/test_lb.py
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
#
# Copyright (C) 2019-2022 The ESPResSo project
#
# This file is part of ESPResSo.
Expand All @@ -14,6 +15,7 @@
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

import unittest as ut
import importlib_wrapper
Expand All @@ -22,9 +24,12 @@
# make simulation deterministic
np.random.seed(42)

gpu = "gpu" in "@TEST_LABELS@".split(";")
cmd_arguments = ["--particles_per_core", "80", "--gpu" if gpu else "--no-gpu"]
benchmark, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@BENCHMARKS_DIR@/lb.py", cmd_arguments=["--particles_per_core", "80"],
measurement_steps=200, n_iterations=2, min_skin=0.688, max_skin=0.688)
"@BENCHMARKS_DIR@/lb.py", gpu=gpu, measurement_steps=200, n_iterations=2,
min_skin=0.688, max_skin=0.688,
cmd_arguments=cmd_arguments, script_suffix="@TEST_SUFFIX@")


@skipIfMissingFeatures
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2 changes: 2 additions & 0 deletions testsuite/scripts/benchmarks/test_lj.py
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
#
# Copyright (C) 2019-2022 The ESPResSo project
#
# This file is part of ESPResSo.
Expand All @@ -14,6 +15,7 @@
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

import unittest as ut
import importlib_wrapper
Expand Down
9 changes: 7 additions & 2 deletions testsuite/scripts/benchmarks/test_p3m.py
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
#
# Copyright (C) 2019-2022 The ESPResSo project
#
# This file is part of ESPResSo.
Expand All @@ -14,6 +15,7 @@
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

import unittest as ut
import importlib_wrapper
Expand All @@ -22,9 +24,12 @@
# make simulation deterministic
np.random.seed(42)

gpu = "gpu" in "@TEST_LABELS@".split(";")
cmd_arguments = ["--particles_per_core", "400", "--gpu" if gpu else "--no-gpu"]
benchmark, skipIfMissingFeatures = importlib_wrapper.configure_and_import(
"@BENCHMARKS_DIR@/p3m.py", cmd_arguments=["--particles_per_core", "400"],
measurement_steps=100, n_iterations=2, min_skin=0.262, max_skin=0.262,
"@BENCHMARKS_DIR@/p3m.py", gpu=gpu, measurement_steps=100, n_iterations=2,
cmd_arguments=cmd_arguments, script_suffix="@TEST_SUFFIX@",
min_skin=0.262, max_skin=0.262,
p3m_params={'prefactor': 4, 'accuracy': 1e-4, 'cao': 7, 'r_cut': 3.182,
'mesh': [24, 24, 24], 'alpha': 1.02742, 'tune': False})

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