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Accepting request 1003846 from devel:languages:python:numeric

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OBS-URL: https://build.opensuse.org/request/show/1003846
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=15
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Dominique Leuenberger 2022-09-15 21:00:00 +00:00 committed by Git OBS Bridge
commit bce20dafdc
3 changed files with 268 additions and 0 deletions
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fix-broken-fft-check.patch Normal file
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@ -0,0 +1,260 @@
From 12b1c3a77060a0d402984ce88b230744fa31c79d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= <jgrad@icp.uni-stuttgart.de>
Date: Thu, 1 Sep 2022 13:37:40 +0200
Subject: [PATCH] core: Fix broken FFT check
Properly check the magnitude of complex residuals. Add a parameter
to disable the check for debugging purposes.
---
src/core/electrostatics/p3m.cpp | 8 +++++---
src/core/electrostatics/p3m.hpp | 3 ++-
src/core/p3m/fft.cpp | 2 +-
.../unit_tests/EspressoSystemStandAlone_test.cpp | 2 +-
src/python/espressomd/electrostatics.py | 7 +++++++
src/script_interface/electrostatics/CoulombP3M.hpp | 6 ++++--
.../electrostatics/CoulombP3MGPU.hpp | 6 ++++--
testsuite/python/coulomb_interface.py | 6 ++++--
testsuite/python/icc_interface.py | 14 ++++++++++----
testsuite/python/save_checkpoint.py | 1 +
testsuite/python/test_checkpoint.py | 2 ++
11 files changed, 41 insertions(+), 16 deletions(-)
diff --git a/src/core/electrostatics/p3m.cpp b/src/core/electrostatics/p3m.cpp
index d0d059157f1..b06300fed9e 100644
--- a/src/core/electrostatics/p3m.cpp
+++ b/src/core/electrostatics/p3m.cpp
@@ -270,9 +270,11 @@ void CoulombP3M::init() {
}
CoulombP3M::CoulombP3M(P3MParameters &&parameters, double prefactor,
- int tune_timings, bool tune_verbose)
+ int tune_timings, bool tune_verbose,
+ bool check_complex_residuals)
: p3m{std::move(parameters)}, tune_timings{tune_timings},
- tune_verbose{tune_verbose} {
+ tune_verbose{tune_verbose}, check_complex_residuals{
+ check_complex_residuals} {
m_is_tuned = !p3m.params.tuning;
p3m.params.tuning = false;
@@ -490,7 +492,7 @@ double CoulombP3M::long_range_kernel(bool force_flag, bool energy_flag,
}
/* Back FFT force component mesh */
- auto const check_complex = !p3m.params.tuning;
+ auto const check_complex = !p3m.params.tuning and check_complex_residuals;
for (int d = 0; d < 3; d++) {
fft_perform_back(p3m.E_mesh[d].data(), check_complex, p3m.fft, comm_cart);
}
diff --git a/src/core/electrostatics/p3m.hpp b/src/core/electrostatics/p3m.hpp
index 4f682bf7fa8..a8d02b055b4 100644
--- a/src/core/electrostatics/p3m.hpp
+++ b/src/core/electrostatics/p3m.hpp
@@ -89,13 +89,14 @@ struct CoulombP3M : public Coulomb::Actor<CoulombP3M> {
int tune_timings;
bool tune_verbose;
+ bool check_complex_residuals;
private:
bool m_is_tuned;
public:
CoulombP3M(P3MParameters &&parameters, double prefactor, int tune_timings,
- bool tune_verbose);
+ bool tune_verbose, bool check_complex_residuals);
bool is_tuned() const { return m_is_tuned; }
diff --git a/src/core/p3m/fft.cpp b/src/core/p3m/fft.cpp
index 55ff03c66d3..2c1d193155c 100644
--- a/src/core/p3m/fft.cpp
+++ b/src/core/p3m/fft.cpp
@@ -738,7 +738,7 @@ void fft_perform_back(double *data, bool check_complex, fft_data_struct &fft,
for (int i = 0; i < fft.plan[1].new_size; i++) {
fft.data_buf[i] = data[2 * i]; /* real value */
// Vincent:
- if (check_complex && (data[2 * i + 1] > 1e-5)) {
+ if (check_complex and std::abs(data[2 * i + 1]) > 1e-5) {
printf("Complex value is not zero (i=%d,data=%g)!!!\n", i,
data[2 * i + 1]);
if (i > 100)
diff --git a/src/core/unit_tests/EspressoSystemStandAlone_test.cpp b/src/core/unit_tests/EspressoSystemStandAlone_test.cpp
index 94cbc51a24d..ddf19a283ed 100644
--- a/src/core/unit_tests/EspressoSystemStandAlone_test.cpp
+++ b/src/core/unit_tests/EspressoSystemStandAlone_test.cpp
@@ -115,7 +115,7 @@ static void mpi_set_tuned_p3m_local(double prefactor) {
0.654,
1e-3};
auto solver =
- std::make_shared<CoulombP3M>(std::move(p3m), prefactor, 1, false);
+ std::make_shared<CoulombP3M>(std::move(p3m), prefactor, 1, false, true);
::Coulomb::add_actor(solver);
}
diff --git a/src/python/espressomd/electrostatics.py b/src/python/espressomd/electrostatics.py
index 6b91ec6d355..60a12cc4483 100644
--- a/src/python/espressomd/electrostatics.py
+++ b/src/python/espressomd/electrostatics.py
@@ -155,6 +155,7 @@ def default_params(self):
"mesh_off": [-1., -1., -1.],
"prefactor": 0.,
"check_neutrality": True,
+ "check_complex_residuals": True,
"tune": True,
"timings": 10,
"verbose": True}
@@ -231,6 +232,9 @@ class P3M(_P3MBase):
check_neutrality : :obj:`bool`, optional
Raise a warning if the system is not electrically neutral when
set to ``True`` (default).
+ check_complex_residuals: :obj:`bool`, optional
+ Raise a warning if the backward Fourier transform has non-zero
+ complex residuals when set to ``True`` (default).
"""
_so_name = "Coulomb::CoulombP3M"
@@ -281,6 +285,9 @@ class P3MGPU(_P3MBase):
check_neutrality : :obj:`bool`, optional
Raise a warning if the system is not electrically neutral when
set to ``True`` (default).
+ check_complex_residuals: :obj:`bool`, optional
+ Raise a warning if the backward Fourier transform has non-zero
+ complex residuals when set to ``True`` (default).
"""
_so_name = "Coulomb::CoulombP3MGPU"
diff --git a/src/script_interface/electrostatics/CoulombP3M.hpp b/src/script_interface/electrostatics/CoulombP3M.hpp
index 147ee7d0af7..0f167cfa442 100644
--- a/src/script_interface/electrostatics/CoulombP3M.hpp
+++ b/src/script_interface/electrostatics/CoulombP3M.hpp
@@ -69,6 +69,8 @@ class CoulombP3M : public Actor<CoulombP3M, ::CoulombP3M> {
{"timings", AutoParameter::read_only,
[this]() { return actor()->tune_timings; }},
{"tune", AutoParameter::read_only, [this]() { return m_tune; }},
+ {"check_complex_residuals", AutoParameter::read_only,
+ [this]() { return actor()->check_complex_residuals; }},
});
}
@@ -85,8 +87,8 @@ class CoulombP3M : public Actor<CoulombP3M, ::CoulombP3M> {
get_value<double>(params, "accuracy")};
m_actor = std::make_shared<CoreActorClass>(
std::move(p3m), get_value<double>(params, "prefactor"),
- get_value<int>(params, "timings"),
- get_value<bool>(params, "verbose"));
+ get_value<int>(params, "timings"), get_value<bool>(params, "verbose"),
+ get_value<bool>(params, "check_complex_residuals"));
});
set_charge_neutrality_tolerance(params);
}
diff --git a/src/script_interface/electrostatics/CoulombP3MGPU.hpp b/src/script_interface/electrostatics/CoulombP3MGPU.hpp
index d212a5e671f..3fe11a9de85 100644
--- a/src/script_interface/electrostatics/CoulombP3MGPU.hpp
+++ b/src/script_interface/electrostatics/CoulombP3MGPU.hpp
@@ -70,6 +70,8 @@ class CoulombP3MGPU : public Actor<CoulombP3MGPU, ::CoulombP3MGPU> {
{"timings", AutoParameter::read_only,
[this]() { return actor()->tune_timings; }},
{"tune", AutoParameter::read_only, [this]() { return m_tune; }},
+ {"check_complex_residuals", AutoParameter::read_only,
+ [this]() { return actor()->check_complex_residuals; }},
});
}
@@ -86,8 +88,8 @@ class CoulombP3MGPU : public Actor<CoulombP3MGPU, ::CoulombP3MGPU> {
get_value<double>(params, "accuracy")};
m_actor = std::make_shared<CoreActorClass>(
std::move(p3m), get_value<double>(params, "prefactor"),
- get_value<int>(params, "timings"),
- get_value<bool>(params, "verbose"));
+ get_value<int>(params, "timings"), get_value<bool>(params, "verbose"),
+ get_value<bool>(params, "check_complex_residuals"));
});
m_actor->request_gpu();
set_charge_neutrality_tolerance(params);
diff --git a/testsuite/python/coulomb_interface.py b/testsuite/python/coulomb_interface.py
index eff174e6e08..a5a1dc6b828 100644
--- a/testsuite/python/coulomb_interface.py
+++ b/testsuite/python/coulomb_interface.py
@@ -59,7 +59,8 @@ def tearDown(self):
system, espressomd.electrostatics.P3M,
dict(prefactor=2., epsilon=0., mesh_off=[0.6, 0.7, 0.8], r_cut=1.5,
cao=2, mesh=[8, 10, 8], alpha=12., accuracy=0.01, tune=False,
- check_neutrality=True, charge_neutrality_tolerance=7e-12))
+ check_neutrality=True, charge_neutrality_tolerance=7e-12,
+ check_complex_residuals=False))
test_p3m_cpu_non_metallic = tests_common.generate_test_for_actor_class(
system, espressomd.electrostatics.P3M,
dict(prefactor=2., epsilon=3., mesh_off=[0.6, 0.7, 0.8], r_cut=1.5,
@@ -78,7 +79,8 @@ def tearDown(self):
system, espressomd.electrostatics.P3MGPU,
dict(prefactor=2., epsilon=0., mesh_off=[0.6, 0.7, 0.8], r_cut=1.5,
cao=2, mesh=[8, 10, 8], alpha=12., accuracy=0.01, tune=False,
- check_neutrality=True, charge_neutrality_tolerance=7e-12))
+ check_neutrality=True, charge_neutrality_tolerance=7e-12,
+ check_complex_residuals=False))
test_p3m_gpu_non_metallic = tests_common.generate_test_for_actor_class(
system, espressomd.electrostatics.P3MGPU,
dict(prefactor=2., epsilon=3., mesh_off=[0.6, 0.7, 0.8], r_cut=1.5,
diff --git a/testsuite/python/icc_interface.py b/testsuite/python/icc_interface.py
index 2b968d2432b..6eadca2d0e7 100644
--- a/testsuite/python/icc_interface.py
+++ b/testsuite/python/icc_interface.py
@@ -121,15 +121,21 @@ def test_exceptions_small_r_cut(self):
@utx.skipIfMissingFeatures(["P3M"])
def test_exceptions_large_r_cut(self):
- icc, (_, p) = self.setup_icc_particles_and_solver(max_iterations=1)
- p3m = espressomd.electrostatics.P3M(**self.valid_p3m_parameters())
+ icc, (_, p) = self.setup_icc_particles_and_solver(
+ max_iterations=1, convergence=10.)
+ p3m = espressomd.electrostatics.P3M(
+ check_complex_residuals=False, **self.valid_p3m_parameters())
self.system.actors.add(p3m)
self.system.actors.add(icc)
-
with self.assertRaisesRegex(Exception, f"Particle with id {p.id} has a charge .+ that is too large for the ICC algorithm"):
- p.q = 1e9
+ p.q = 1e8
self.system.integrator.run(0)
+
+ self.system.actors.remove(icc)
+ self.system.part.clear()
+ icc, (_, p) = self.setup_icc_particles_and_solver(max_iterations=1)
+ self.system.actors.add(icc)
with self.assertRaisesRegex(Exception, "ICC failed to converge in the given number of maximal steps"):
p.q = 0.
self.system.integrator.run(0)
diff --git a/testsuite/python/save_checkpoint.py b/testsuite/python/save_checkpoint.py
index 09ebda6f002..55ab1b37b82 100644
--- a/testsuite/python/save_checkpoint.py
+++ b/testsuite/python/save_checkpoint.py
@@ -125,6 +125,7 @@
cao=1,
alpha=1.0,
r_cut=1.0,
+ check_complex_residuals=False,
timings=15,
tune=False)
if 'ELC' in modes:
diff --git a/testsuite/python/test_checkpoint.py b/testsuite/python/test_checkpoint.py
index 17363085c3f..98f9959f68f 100644
--- a/testsuite/python/test_checkpoint.py
+++ b/testsuite/python/test_checkpoint.py
@@ -504,6 +504,7 @@ def test_p3m(self):
reference = {'prefactor': 1.0, 'accuracy': 0.1, 'mesh': 3 * [10],
'cao': 1, 'alpha': 1.0, 'r_cut': 1.0, 'tune': False,
'timings': 15, 'check_neutrality': True,
+ 'check_complex_residuals': False,
'charge_neutrality_tolerance': 1e-12}
for key in reference:
self.assertIn(key, state)
@@ -519,6 +520,7 @@ def test_elc(self):
p3m_reference = {'prefactor': 1.0, 'accuracy': 0.1, 'mesh': 3 * [10],
'cao': 1, 'alpha': 1.0, 'r_cut': 1.0, 'tune': False,
'timings': 15, 'check_neutrality': True,
+ 'check_complex_residuals': False,
'charge_neutrality_tolerance': 7e-12}
elc_reference = {'gap_size': 6.0, 'maxPWerror': 0.1,
'delta_mid_top': 0.9, 'delta_mid_bot': 0.1,

6
python3-espressomd.changes
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@ -1,3 +1,9 @@
-------------------------------------------------------------------
Thu Sep 15 07:47:38 UTC 2022 - Guillaume GARDET <guillaume.gardet@opensuse.org>
- Add upstream patch to fix test on aarch64:
* fix-broken-fft-check.patch
-------------------------------------------------------------------
Tue Jul 19 19:40:59 UTC 2022 - Matej Cepl <mcepl@suse.com>

2
python3-espressomd.spec
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@ -50,6 +50,8 @@ Patch1: missing_size_t.patch
Patch2: hdf5.patch
# PATCH-FIX-OPENSUSE rpath.patch boo#1198352
Patch3: rpath.patch
# PATCH-FIX-UPSTREAM fix-broken-fft-check.patch gh#espressomd/espresso#4567
Patch4: fix-broken-fft-check.patch
# According to gh#espressomd/espresso#4537 32bit architectures are not supported any more
ExcludeArch: %{ix86}
BuildRequires: cmake