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Accepting request 1175904 from home:jngrad:branches:devel:languages:python:numeric

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ESPResSo 4.2.2

OBS-URL: https://build.opensuse.org/request/show/1175904
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python3-espressomd?expand=0&rev=53
This commit is contained in:
Christoph Junghans 2024-05-22 19:37:29 +00:00 committed by Git OBS Bridge
parent 7ab71284ad
commit ba0c2e9378
8 changed files with 114 additions and 542 deletions
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19
array-bounds.patch
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@ -1,19 +0,0 @@
diff --git a/src/core/p3m/interpolation.hpp b/src/core/p3m/interpolation.hpp
index a25b0d8f66..0573648938 100644
--- a/src/core/p3m/interpolation.hpp
+++ b/src/core/p3m/interpolation.hpp
@@ -109,10 +109,10 @@ class p3m_interpolation_cache {
InterpolationWeights<cao> ret;
ret.ind = ca_fmp[i];
- auto const offset = ca_frac.data() + 3 * i * m_cao;
- boost::copy(make_const_span(offset + 0 * m_cao, m_cao), ret.w_x.begin());
- boost::copy(make_const_span(offset + 1 * m_cao, m_cao), ret.w_y.begin());
- boost::copy(make_const_span(offset + 2 * m_cao, m_cao), ret.w_z.begin());
+ auto const offset = ca_frac.data() + 3 * i * cao;
+ boost::copy(make_const_span(offset + 0 * cao, cao), ret.w_x.begin());
+ boost::copy(make_const_span(offset + 1 * cao, cao), ret.w_y.begin());
+ boost::copy(make_const_span(offset + 2 * cao, cao), ret.w_z.begin());
return ret;
}

3
espresso-4.2.1.tar.gz
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:d74b46438b0d013cac35602e28f3530686446a3a307f6771baf15395066bdad5
size 13458982

3
espresso-4.2.2.tar.gz Normal file
View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:2bc02f91632b0030f1203759768bd718bd8a0005f72696980b12331b4bfa0d76
size 13463564

479
mpi.patch
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@ -1,479 +0,0 @@
diff --git a/src/core/EspressoSystemStandAlone.cpp b/src/core/EspressoSystemStandAlone.cpp
index 90788c3c0..900fc5cdf 100644
--- a/src/core/EspressoSystemStandAlone.cpp
+++ b/src/core/EspressoSystemStandAlone.cpp
@@ -31,2 +31,3 @@
#include <boost/mpi.hpp>
+#include <boost/mpi/environment.hpp>
@@ -35,3 +36,3 @@
EspressoSystemStandAlone::EspressoSystemStandAlone(int argc, char **argv) {
- auto mpi_env = mpi_init(argc, argv);
+ m_mpi_env = mpi_init(argc, argv);
@@ -41,3 +42,3 @@ EspressoSystemStandAlone::EspressoSystemStandAlone(int argc, char **argv) {
// initialize the MpiCallbacks framework
- Communication::init(mpi_env);
+ Communication::init(m_mpi_env);
@@ -52,2 +53,6 @@ EspressoSystemStandAlone::EspressoSystemStandAlone(int argc, char **argv) {
+EspressoSystemStandAlone::~EspressoSystemStandAlone() {
+ Communication::deinit();
+}
+
void EspressoSystemStandAlone::set_box_l(Utils::Vector3d const &box_l) const {
diff --git a/src/core/EspressoSystemStandAlone.hpp b/src/core/EspressoSystemStandAlone.hpp
index d11838356..198b235c2 100644
--- a/src/core/EspressoSystemStandAlone.hpp
+++ b/src/core/EspressoSystemStandAlone.hpp
@@ -23,2 +23,10 @@
+#include <memory>
+
+namespace boost {
+namespace mpi {
+class environment;
+}
+} // namespace boost
+
/** Manager for a stand-alone ESPResSo system.
@@ -29,2 +37,3 @@ class EspressoSystemStandAlone {
EspressoSystemStandAlone(int argc, char **argv);
+ ~EspressoSystemStandAlone();
void set_box_l(Utils::Vector3d const &box_l) const;
@@ -36,2 +45,3 @@ class EspressoSystemStandAlone {
bool head_node;
+ std::shared_ptr<boost::mpi::environment> m_mpi_env;
};
diff --git a/src/core/MpiCallbacks.hpp b/src/core/MpiCallbacks.hpp
index 2f58f460d..153c410f6 100644
--- a/src/core/MpiCallbacks.hpp
+++ b/src/core/MpiCallbacks.hpp
@@ -50,2 +50,3 @@
#include <boost/mpi/communicator.hpp>
+#include <boost/mpi/environment.hpp>
#include <boost/optional.hpp>
@@ -366,3 +367,3 @@ class MpiCallbacks {
std::tuple<Args...>>::value>>
- CallbackHandle(MpiCallbacks *cb, F &&f)
+ CallbackHandle(std::shared_ptr<MpiCallbacks> cb, F &&f)
: m_id(cb->add(std::forward<F>(f))), m_cb(cb) {}
@@ -376,3 +377,3 @@ class MpiCallbacks {
int m_id;
- MpiCallbacks *m_cb;
+ std::shared_ptr<MpiCallbacks> m_cb;
@@ -402,3 +403,2 @@ class MpiCallbacks {
- MpiCallbacks *cb() const { return m_cb; }
int id() const { return m_id; }
@@ -421,4 +421,6 @@ class MpiCallbacks {
explicit MpiCallbacks(boost::mpi::communicator comm,
+ std::shared_ptr<boost::mpi::environment> mpi_env,
bool abort_on_exit = true)
- : m_abort_on_exit(abort_on_exit), m_comm(std::move(comm)) {
+ : m_abort_on_exit(abort_on_exit), m_comm(std::move(comm)),
+ m_mpi_env(std::move(mpi_env)) {
/* Add a dummy at id 0 for loop abort. */
@@ -740,2 +742,7 @@ class MpiCallbacks {
+ /**
+ * The MPI environment used for the callbacks.
+ */
+ std::shared_ptr<boost::mpi::environment> m_mpi_env;
+
/**
diff --git a/src/core/communication.cpp b/src/core/communication.cpp
index 20b7d0526..d8b26cb38 100644
--- a/src/core/communication.cpp
+++ b/src/core/communication.cpp
@@ -30,2 +30,4 @@
#include <boost/mpi.hpp>
+#include <boost/mpi/communicator.hpp>
+#include <boost/mpi/environment.hpp>
@@ -41,7 +43,2 @@
-namespace Communication {
-auto const &mpi_datatype_cache = boost::mpi::detail::mpi_datatype_cache();
-std::shared_ptr<boost::mpi::environment> mpi_env;
-} // namespace Communication
-
boost::mpi::communicator comm_cart;
@@ -49,3 +46,3 @@ boost::mpi::communicator comm_cart;
namespace Communication {
-std::unique_ptr<MpiCallbacks> m_callbacks;
+static std::shared_ptr<MpiCallbacks> m_callbacks;
@@ -57,2 +54,8 @@ MpiCallbacks &mpiCallbacks() {
}
+
+std::shared_ptr<MpiCallbacks> mpiCallbacksHandle() {
+ assert(m_callbacks && "Mpi not initialized!");
+
+ return m_callbacks;
+}
} // namespace Communication
@@ -122,4 +125,2 @@ namespace Communication {
void init(std::shared_ptr<boost::mpi::environment> mpi_env) {
- Communication::mpi_env = std::move(mpi_env);
-
MPI_Comm_size(MPI_COMM_WORLD, &n_nodes);
@@ -133,3 +134,3 @@ void init(std::shared_ptr<boost::mpi::environment> mpi_env) {
Communication::m_callbacks =
- std::make_unique<Communication::MpiCallbacks>(comm_cart);
+ std::make_shared<Communication::MpiCallbacks>(comm_cart, mpi_env);
@@ -139,2 +140,4 @@ void init(std::shared_ptr<boost::mpi::environment> mpi_env) {
}
+
+void deinit() { Communication::m_callbacks.reset(); }
} // namespace Communication
diff --git a/src/core/communication.hpp b/src/core/communication.hpp
index cab2d8507..243bf8d05 100644
--- a/src/core/communication.hpp
+++ b/src/core/communication.hpp
@@ -65,2 +65,3 @@ namespace Communication {
MpiCallbacks &mpiCallbacks();
+std::shared_ptr<MpiCallbacks> mpiCallbacksHandle();
} // namespace Communication
@@ -138,6 +139,2 @@ namespace Communication {
*
- * and calls @ref on_program_start. Keeps a copy of
- * the pointer to the mpi environment to keep it alive
- * while the program is loaded.
- *
* @param mpi_env MPI environment that should be used
@@ -145,3 +142,13 @@ namespace Communication {
void init(std::shared_ptr<boost::mpi::environment> mpi_env);
+void deinit();
} // namespace Communication
+
+struct MpiContainerUnitTest {
+ std::shared_ptr<boost::mpi::environment> m_mpi_env;
+ MpiContainerUnitTest(int argc, char **argv) {
+ m_mpi_env = mpi_init(argc, argv);
+ Communication::init(m_mpi_env);
+ }
+ ~MpiContainerUnitTest() { Communication::deinit(); }
+};
#endif
diff --git a/src/core/unit_tests/EspressoSystemStandAlone_test.cpp b/src/core/unit_tests/EspressoSystemStandAlone_test.cpp
index aec1c71d5..d1fbe0cca 100644
--- a/src/core/unit_tests/EspressoSystemStandAlone_test.cpp
+++ b/src/core/unit_tests/EspressoSystemStandAlone_test.cpp
@@ -359,3 +359,5 @@ int main(int argc, char **argv) {
- return boost::unit_test::unit_test_main(init_unit_test, argc, argv);
+ int retval = boost::unit_test::unit_test_main(init_unit_test, argc, argv);
+ espresso::system.reset();
+ return retval;
}
diff --git a/src/core/unit_tests/MpiCallbacks_test.cpp b/src/core/unit_tests/MpiCallbacks_test.cpp
index 3afbe3f2a..7ae484aa8 100644
--- a/src/core/unit_tests/MpiCallbacks_test.cpp
+++ b/src/core/unit_tests/MpiCallbacks_test.cpp
@@ -31,2 +31,3 @@
#include <boost/mpi.hpp>
+#include <boost/mpi/environment.hpp>
#include <boost/optional.hpp>
@@ -38,2 +39,3 @@
+static std::weak_ptr<boost::mpi::environment> mpi_env;
static bool called = false;
@@ -113,3 +115,3 @@ BOOST_AUTO_TEST_CASE(adding_function_ptr_cb) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cb(world);
+ Communication::MpiCallbacks cb(world, ::mpi_env.lock());
@@ -145,3 +147,3 @@ BOOST_AUTO_TEST_CASE(RegisterCallback) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cb(world);
+ Communication::MpiCallbacks cb(world, ::mpi_env.lock());
@@ -159,3 +161,4 @@ BOOST_AUTO_TEST_CASE(CallbackHandle) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cbs(world);
+ auto const cbs =
+ std::make_shared<Communication::MpiCallbacks>(world, ::mpi_env.lock());
@@ -163,3 +166,3 @@ BOOST_AUTO_TEST_CASE(CallbackHandle) {
Communication::CallbackHandle<std::string> cb(
- &cbs, [&m_called](std::string s) {
+ cbs, [&m_called](std::string s) {
BOOST_CHECK_EQUAL("CallbackHandle", s);
@@ -172,3 +175,3 @@ BOOST_AUTO_TEST_CASE(CallbackHandle) {
} else {
- cbs.loop();
+ cbs->loop();
BOOST_CHECK(called);
@@ -184,3 +187,3 @@ BOOST_AUTO_TEST_CASE(reduce_callback) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cbs(world);
+ Communication::MpiCallbacks cbs(world, ::mpi_env.lock());
@@ -205,3 +208,3 @@ BOOST_AUTO_TEST_CASE(ignore_callback) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cbs(world);
+ Communication::MpiCallbacks cbs(world, ::mpi_env.lock());
@@ -231,3 +234,3 @@ BOOST_AUTO_TEST_CASE(one_rank_callback) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cbs(world);
+ Communication::MpiCallbacks cbs(world, ::mpi_env.lock());
@@ -256,3 +259,3 @@ BOOST_AUTO_TEST_CASE(main_rank_callback) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cbs(world);
+ Communication::MpiCallbacks cbs(world, ::mpi_env.lock());
@@ -275,3 +278,3 @@ BOOST_AUTO_TEST_CASE(call_all) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cbs(world);
+ Communication::MpiCallbacks cbs(world, ::mpi_env.lock());
@@ -296,3 +299,3 @@ BOOST_AUTO_TEST_CASE(check_exceptions) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cbs(world);
+ Communication::MpiCallbacks cbs(world, ::mpi_env.lock());
@@ -308,3 +311,4 @@ BOOST_AUTO_TEST_CASE(check_exceptions) {
int main(int argc, char **argv) {
- boost::mpi::environment mpi_env(argc, argv);
+ auto const mpi_env = std::make_shared<boost::mpi::environment>(argc, argv);
+ ::mpi_env = mpi_env;
diff --git a/src/core/unit_tests/Verlet_list_test.cpp b/src/core/unit_tests/Verlet_list_test.cpp
index 433683965..43947c50c 100644
--- a/src/core/unit_tests/Verlet_list_test.cpp
+++ b/src/core/unit_tests/Verlet_list_test.cpp
@@ -243,2 +243,3 @@ int main(int argc, char **argv) {
}
+ espresso::system.reset();
return error_code;
diff --git a/src/python/espressomd/_init.pyx b/src/python/espressomd/_init.pyx
index 0ef6ee52f..0b9699914 100644
--- a/src/python/espressomd/_init.pyx
+++ b/src/python/espressomd/_init.pyx
@@ -19,2 +19,3 @@
import sys
+import atexit
from . cimport script_interface
@@ -30,3 +31,13 @@ communication.init(mpi_env)
# Has to be _after_ mpi_init
-script_interface.init(communication.mpiCallbacks())
+script_interface.init(communication.mpiCallbacksHandle())
+
+
+def session_shutdown():
+ mpi_env.reset()
+ communication.deinit()
+ script_interface.deinit()
+
+
+atexit.register(session_shutdown)
+
diff --git a/src/python/espressomd/communication.pxd b/src/python/espressomd/communication.pxd
index aeb4f43ad..7065f96a9 100644
--- a/src/python/espressomd/communication.pxd
+++ b/src/python/espressomd/communication.pxd
@@ -32,2 +32,4 @@ cdef extern from "communication.hpp" namespace "Communication":
MpiCallbacks & mpiCallbacks()
+ shared_ptr[MpiCallbacks] mpiCallbacksHandle()
void init(shared_ptr[environment])
+ void deinit()
diff --git a/src/python/espressomd/script_interface.pxd b/src/python/espressomd/script_interface.pxd
index bd2b0c286..5e9bd38dd 100644
--- a/src/python/espressomd/script_interface.pxd
+++ b/src/python/espressomd/script_interface.pxd
@@ -60,3 +60,3 @@ cdef extern from "script_interface/ContextManager.hpp" namespace "ScriptInterfac
cdef cppclass ContextManager:
- ContextManager(MpiCallbacks & , const Factory[ObjectHandle] & )
+ ContextManager(const shared_ptr[MpiCallbacks] & , const Factory[ObjectHandle] & )
shared_ptr[ObjectHandle] make_shared(CreationPolicy, const string &, const VariantMap) except +
@@ -71,2 +71,3 @@ cdef extern from "script_interface/get_value.hpp" namespace "ScriptInterface":
-cdef void init(MpiCallbacks &)
+cdef void init(const shared_ptr[MpiCallbacks] &)
+cdef void deinit()
diff --git a/src/python/espressomd/script_interface.pyx b/src/python/espressomd/script_interface.pyx
index d6fff6879..01922140d 100644
--- a/src/python/espressomd/script_interface.pyx
+++ b/src/python/espressomd/script_interface.pyx
@@ -486,3 +486,3 @@ def script_interface_register(c):
-cdef void init(MpiCallbacks & cb):
+cdef void init(const shared_ptr[MpiCallbacks] &cb):
cdef Factory[ObjectHandle] f
@@ -493 +493,6 @@ cdef void init(MpiCallbacks & cb):
_om = make_shared[ContextManager](cb, f)
+
+
+cdef void deinit():
+ global _om
+ _om.reset()
diff --git a/src/python/espressomd/system.pyx b/src/python/espressomd/system.pyx
index 3bb08f381..3003f66c9 100644
--- a/src/python/espressomd/system.pyx
+++ b/src/python/espressomd/system.pyx
@@ -204,2 +204,4 @@ cdef class System:
+ self._setup_atexit()
+
# lock class
@@ -208,2 +210,10 @@ cdef class System:
+ def _setup_atexit(self):
+ import atexit
+
+ def session_shutdown():
+ self.actors.clear()
+
+ atexit.register(session_shutdown)
+
# __getstate__ and __setstate__ define the pickle interaction
@@ -232,2 +242,3 @@ cdef class System:
System.__setattr__(self, property_name, params[property_name])
+ self._setup_atexit()
diff --git a/src/script_interface/ContextManager.cpp b/src/script_interface/ContextManager.cpp
index 7bb3dfd37..e7f20c347 100644
--- a/src/script_interface/ContextManager.cpp
+++ b/src/script_interface/ContextManager.cpp
@@ -55,6 +55,7 @@ std::string ContextManager::serialize(const ObjectHandle *o) const {
-ContextManager::ContextManager(Communication::MpiCallbacks &callbacks,
- const Utils::Factory<ObjectHandle> &factory) {
+ContextManager::ContextManager(
+ std::shared_ptr<Communication::MpiCallbacks> const &callbacks,
+ const Utils::Factory<ObjectHandle> &factory) {
auto local_context =
- std::make_shared<LocalContext>(factory, callbacks.comm());
+ std::make_shared<LocalContext>(factory, callbacks->comm());
@@ -63,3 +64,3 @@ ContextManager::ContextManager(Communication::MpiCallbacks &callbacks,
m_global_context =
- (callbacks.comm().size() > 1)
+ (callbacks->comm().size() > 1)
? std::make_shared<GlobalContext>(callbacks, local_context)
diff --git a/src/script_interface/ContextManager.hpp b/src/script_interface/ContextManager.hpp
index 7f5a098a5..47fa10a73 100644
--- a/src/script_interface/ContextManager.hpp
+++ b/src/script_interface/ContextManager.hpp
@@ -69,3 +69,3 @@ class ContextManager {
- ContextManager(Communication::MpiCallbacks &callbacks,
+ ContextManager(std::shared_ptr<Communication::MpiCallbacks> const &callbacks,
const Utils::Factory<ObjectHandle> &factory);
diff --git a/src/script_interface/GlobalContext.hpp b/src/script_interface/GlobalContext.hpp
index d4de6ebbc..ede913359 100644
--- a/src/script_interface/GlobalContext.hpp
+++ b/src/script_interface/GlobalContext.hpp
@@ -88,9 +88,9 @@ class GlobalContext : public Context {
public:
- GlobalContext(Communication::MpiCallbacks &callbacks,
+ GlobalContext(std::shared_ptr<Communication::MpiCallbacks> const &callbacks,
std::shared_ptr<LocalContext> node_local_context)
: m_local_objects(), m_node_local_context(std::move(node_local_context)),
- m_is_head_node(callbacks.comm().rank() == 0),
+ m_is_head_node(callbacks->comm().rank() == 0),
// NOLINTNEXTLINE(bugprone-throw-keyword-missing)
- m_parallel_exception_handler(callbacks.comm()),
- cb_make_handle(&callbacks,
+ m_parallel_exception_handler(callbacks->comm()),
+ cb_make_handle(callbacks,
[this](ObjectId id, const std::string &name,
@@ -99,3 +99,3 @@ class GlobalContext : public Context {
}),
- cb_set_parameter(&callbacks,
+ cb_set_parameter(callbacks,
[this](ObjectId id, std::string const &name,
@@ -104,3 +104,3 @@ class GlobalContext : public Context {
}),
- cb_call_method(&callbacks,
+ cb_call_method(callbacks,
[this](ObjectId id, std::string const &name,
@@ -109,3 +109,3 @@ class GlobalContext : public Context {
}),
- cb_delete_handle(&callbacks,
+ cb_delete_handle(callbacks,
[this](ObjectId id) { delete_handle(id); }) {}
diff --git a/src/script_interface/tests/GlobalContext_test.cpp b/src/script_interface/tests/GlobalContext_test.cpp
index b5556b2d1..da0401ad4 100644
--- a/src/script_interface/tests/GlobalContext_test.cpp
+++ b/src/script_interface/tests/GlobalContext_test.cpp
@@ -28,2 +28,3 @@
#include <boost/mpi/communicator.hpp>
+#include <boost/mpi/environment.hpp>
@@ -34,2 +35,4 @@
+static std::weak_ptr<boost::mpi::environment> mpi_env;
+
namespace si = ScriptInterface;
@@ -56,9 +59,8 @@ struct Dummy : si::ObjectHandle {
-auto make_global_context(Communication::MpiCallbacks &cb) {
+auto make_global_context(std::shared_ptr<Communication::MpiCallbacks> &cb) {
Utils::Factory<si::ObjectHandle> factory;
factory.register_new<Dummy>("Dummy");
- boost::mpi::communicator comm;
return std::make_shared<si::GlobalContext>(
- cb, std::make_shared<si::LocalContext>(factory, comm));
+ cb, std::make_shared<si::LocalContext>(factory, cb->comm()));
}
@@ -67,3 +69,4 @@ BOOST_AUTO_TEST_CASE(GlobalContext_make_shared) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cb{world};
+ auto cb =
+ std::make_shared<Communication::MpiCallbacks>(world, ::mpi_env.lock());
auto ctx = make_global_context(cb);
@@ -76,3 +79,3 @@ BOOST_AUTO_TEST_CASE(GlobalContext_make_shared) {
} else {
- cb.loop();
+ cb->loop();
}
@@ -82,3 +85,4 @@ BOOST_AUTO_TEST_CASE(GlobalContext_serialization) {
boost::mpi::communicator world;
- Communication::MpiCallbacks cb{world};
+ auto cb =
+ std::make_shared<Communication::MpiCallbacks>(world, ::mpi_env.lock());
auto ctx = make_global_context(cb);
@@ -110,3 +114,3 @@ BOOST_AUTO_TEST_CASE(GlobalContext_serialization) {
} else {
- cb.loop();
+ cb->loop();
}
@@ -115,3 +119,4 @@ BOOST_AUTO_TEST_CASE(GlobalContext_serialization) {
int main(int argc, char **argv) {
- boost::mpi::environment mpi_env(argc, argv);
+ auto const mpi_env = std::make_shared<boost::mpi::environment>(argc, argv);
+ ::mpi_env = mpi_env;
diff --git a/src/script_interface/tests/ParallelExceptionHandler_test.cpp b/src/script_interface/tests/ParallelExceptionHandler_test.cpp
index c78c11c0c..30f0bb7dc 100644
--- a/src/script_interface/tests/ParallelExceptionHandler_test.cpp
+++ b/src/script_interface/tests/ParallelExceptionHandler_test.cpp
@@ -47,2 +47,3 @@
#include <boost/mpi/communicator.hpp>
+#include <boost/mpi/environment.hpp>
@@ -54,2 +55,4 @@ namespace utf = boost::unit_test;
+static std::weak_ptr<boost::mpi::environment> mpi_env;
+
namespace Testing {
@@ -70,3 +73,3 @@ BOOST_AUTO_TEST_CASE(parallel_exceptions) {
boost::mpi::communicator world;
- Communication::MpiCallbacks callbacks{world};
+ Communication::MpiCallbacks callbacks{world, ::mpi_env.lock()};
ErrorHandling::init_error_handling(callbacks);
@@ -135,3 +138,4 @@ BOOST_AUTO_TEST_CASE(parallel_exceptions) {
int main(int argc, char **argv) {
- boost::mpi::environment mpi_env(argc, argv);
+ auto const mpi_env = std::make_shared<boost::mpi::environment>(argc, argv);
+ ::mpi_env = mpi_env;

109
python3-espressomd.changes
View File

@ -1,4 +1,113 @@
-------------------------------------------------------------------
Wed May 22 16:08:22 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Exclude 32bit architectures
-------------------------------------------------------------------
Wed May 22 14:36:04 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Update to 4.2.2:
This release provides a number of corrections for the ESPResSo 4.2 line.
We recommend that this release be used for all production simulations.
The interface has not been changed between ESPResSo 4.2.1 and 4.2.2.
However, some bugs were discovered which can affect simulation results.
Please find the list of changes below. The numbers in brackets refer to
ticket numbers on https://github.com/espressomd/espresso
Improved documentation
----------------------
* Installation instructions now mention the FFTW3 MPI dependency
of long-range solvers and provide recommended version numbers
for Jupyter Notebook dependencies (#4790).
* Installation instructions now mention Python environments (#4922).
* Observables not properly document return values, array shapes,
and use a more consistent mathematical notation (#4898).
Bug fixes
---------
* Fatal runtime errors due to MPI global variables lifetime
were addressed (#4858). Older ESPResSo releases built with
Boost 1.84 or later might randomly crash when exiting
the Python interpreter.
* Virtual sites no longer contribute to the kinetic energy
of the system (#4839). The regression was introduced
in April 2021 and affected the 4.2 branch of ESPResSo.
* Inertialess tracers are now integrated along the z-axis (#4714).
The regression was introduced in February 2022 and affected
the 4.2 branch of ESPResSo.
* Inertialess tracers now throw an exception when attempting to use
LB GPU with 2 or more MPI ranks (#4714). Before, tracers on non-root
MPI ranks would be silently ignored by the CUDA kernels,
and would have a constant velocity, either 0 if the particle never
visited the fluid domain on the root rank, or the last known velocity
if the particle was once on the root rank. This bug affected all
ESPResSo versions.
* Particles close to the faces of the simulation box are now properly
coupled to the LB fluid (#4827). Due to numerical instability, it was
previously possible for particles to be outside the box simulation by
a tiny amount and skip LB particle coupling. The probability of this
bug occurring was low, but could be enhanced in simulations that
purposefully placed particle near the faces of the simulation box:
polymers sheared by Lees-Edwards boundary conditions, raspberry
particles (colloids, bacteria, etc.) when crossing a periodic
boundary, or cell membranes placed close to a periodic boundary.
* Resizing the box now throws a runtime error if there are constraints
present (#4778), since constraint preconditions might no longer be
fulfilled. For example, a wall constraint might end up outside the
box boundaries when the box shrinks.
* Resizing the box via `system.box_l = new_box_l` now throws
a runtime error if there are particles present, because particle
position folding cannot be guaranteed to be correct (#4901);
use `system.change_volume_and_rescale_particles()` instead,
which properly rescales particle positions.
* The velocity Verlet NpT propagator doesn't apply friction and noise
on angular velocities. ESPResSo now throws an error when NpT
encounters a rotating particle (#4843). This bug affected all
ESPResSo versions.
* The Brownian thermostat can no longer be configured with
`act_on_virtual=True` due to an unresolved bug (#4295)
that will be addressed in the next minor release.
* Restrictions on the number of MPI ranks have been lifted from the
checkpointing mechanism (#4724). It is now possible to use
checkpointing again in MPI-parallel simulations when the system
contains LB boundaries or `Union` shape-based constraints.
These restrictions had been introduced in 4.2.0 for technical
reasons that have since been resolved.
* When passing an invalid value to a function that expects an input
parameter of type `list` of size 3, an exception is now raised (#4911).
Previously, some functions would print an error message and continue
their execution with uninitialized data.
* The per-`type` and per-`mol_id` contributions from
`system.analysis.energy()`, `system.analysis.pressure()`
and `system.analysis.pressure_tensor()` now return the correct
values (#4788). Older version of ESPResSo were confusing the
particle `mol_id` with the particle `type`. The total pressure
was unreliable when `mol_id` properties were set to non-zero values.
* The OpenGL visualizer now extracts the correct non-bonded potential
parameter `sigma` when feature `WCA` is compiled in but `LENNARD_JONES`
isn't (#4720). The regression was introduced in 4.2.1.
* Method `OifCell.elastic_forces()` no longer throws a `TypeError` (#4813).
* Benchmark scripts were adjusted to support large particle numbers (#4753).
Under the hood changes
----------------------
* Several Clang 16 and GCC 13 compiler diagnostics have been addressed
(#4715).
* A non-critical GCC C++20 deprecation warning in Cython-generated code
was disabled (#4725).
* Several deprecation warnings emitted by CMake 3.27 have been silenced
(#4792).
* Add support for setuptools version 67.3.0 and above (#4709).
* Add support for Python 3.12 in testsuites run by CTest (#4852).
* Python requirements have been updated (#4924).
* CI pipeline URLs have been fixed (#4736).
- Removed upstreamed patches:
- array-bounds.patch
- mpi.patch
- setuptools.patch
- tracers.patch
-------------------------------------------------------------------
Fri Feb 2 16:23:08 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
- Fix undefined behavior due to improper handling of MPI static globals

12
python3-espressomd.spec
View File

@ -22,22 +22,14 @@
%define pkgname espresso
%define modname %{pkgname}md
Name: python3-%{modname}
Version: 4.2.1
Version: 4.2.2
Release: 0
Summary: Parallel simulation software for soft matter research
License: GPL-3.0-or-later
URL: http://espressomd.org
Source: https://github.com/%{modname}/%{pkgname}/releases/download/%{version}/%{pkgname}-%{version}.tar.gz
# PATCH-FIX-UPSTREAM setuptools.patch gh#espressomd/espresso#4709
Patch0: setuptools.patch
# PATCH-FIX-UPSTREAM tracers.patch gh#espressomd/espresso#4714
Patch1: tracers.patch
# PATCH-FIX-UPSTREAM array-bounds.patch gh#espressomd/espresso#4715
Patch2: array-bounds.patch
# PATCH-FIX-UPSTREAM mpi.patch gh#espressomd/espresso#4858
Patch3: mpi.patch
# According to gh#espressomd/espresso#4537 32bit architectures are not supported any more
ExcludeArch: %{ix86}
ExcludeArch: %{ix86} armv7l
BuildRequires: cmake
BuildRequires: fftw3-devel
BuildRequires: gcc-c++

18
setuptools.patch
View File

@ -1,18 +0,0 @@
diff --git a/testsuite/python/unittest_decorators.py b/testsuite/python/unittest_decorators.py
index 109f89cc8..a9a0e5200 100644
--- a/testsuite/python/unittest_decorators.py
+++ b/testsuite/python/unittest_decorators.py
@@ -20,5 +20,5 @@
import sys
import importlib
-import setuptools
+import pkg_resources
import unittest
@@ -75,5 +75,5 @@ def skipIfUnmetModuleVersionRequirement(module, version_requirement):
except ImportError:
return skipIfMissingModules(module)
- if not setuptools.version.pkg_resources.packaging.specifiers.SpecifierSet(
+ if not pkg_resources.packaging.specifiers.SpecifierSet(
version_requirement).contains(_module.__version__):
return unittest.skip(

13
tracers.patch
View File

@ -1,13 +0,0 @@
diff --git a/src/core/virtual_sites/lb_inertialess_tracers.cpp b/src/core/virtual_sites/lb_inertialess_tracers.cpp
index 5aae5af66c..b87b2d4232 100644
--- a/src/core/virtual_sites/lb_inertialess_tracers.cpp
+++ b/src/core/virtual_sites/lb_inertialess_tracers.cpp
@@ -92,7 +92,7 @@ void IBM_UpdateParticlePositions(ParticleRange const &particles,
// Euler integrator
for (auto &p : particles) {
if (p.is_virtual()) {
- for (int axis = 0; axis < 2; axis++) {
+ for (int axis = 0; axis < 3; axis++) {
#ifdef EXTERNAL_FORCES
if (not p.is_fixed_along(axis))
#endif