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python3-espressomd
mpi.patch
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File mpi.patch of Package python3-espressomd
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;
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