Merge branch 'python' into scafacos-split

.gitlab-ci.yml

@@ -224,7 +224,7 @@ clang-sanitizer:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
 
 cuda11-maxset:
   <<: *global_job_definition
@@ -271,7 +271,7 @@ cuda10-maxset:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
 
 tutorials-samples-maxset:
   <<: *global_job_definition
@@ -295,7 +295,7 @@ tutorials-samples-maxset:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
 
 tutorials-samples-default:
   <<: *global_job_definition
@@ -318,7 +318,7 @@ tutorials-samples-default:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
   only:
     - schedules
 
@@ -344,7 +344,7 @@ tutorials-samples-empty:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
   only:
     - schedules
 
@@ -405,7 +405,7 @@ installation:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
   when: manual
 
 empty:
@@ -425,7 +425,7 @@ empty:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
 
 check_sphinx:
   <<: *global_job_definition
@@ -448,7 +448,7 @@ check_sphinx:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
 
 run_tutorials:
   <<: *global_job_definition
@@ -468,7 +468,7 @@ run_tutorials:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
   only:
     - schedules
 
@@ -519,7 +519,7 @@ check_with_odd_no_of_processors:
   tags:
     - docker
     - linux
-    - cuda-kepler
+    - cuda
 
 
 .deploy_base:

maintainer/CI/build_cmake.sh

@@ -76,7 +76,6 @@ set_default_value() {
 # handle environment variables
 set_default_value srcdir "$(pwd)"
 set_default_value cmake_params ""
-set_default_value with_fftw true
 set_default_value with_coverage false
 set_default_value with_coverage_python ${with_coverage}
 set_default_value with_ubsan false
@@ -133,12 +132,6 @@ else
     cmake_params="${cmake_params} -DWITH_STOKESIAN_DYNAMICS=OFF"
 fi
 
-if [ "${with_fftw}" = true ]; then
-    :
-else
-    cmake_params="-DCMAKE_DISABLE_FIND_PACKAGE_FFTW3=ON ${cmake_params}"
-fi
-
 if [ "${with_coverage}" = true ]; then
     cmake_params="-DWITH_COVERAGE=ON ${cmake_params}"
 fi
@@ -175,7 +168,7 @@ builddir="${srcdir}/build"
 
 outp srcdir builddir \
     make_check_unit_tests make_check_python make_check_tutorials make_check_samples make_check_benchmarks \
-    cmake_params with_fftw \
+    cmake_params \
     with_coverage with_coverage_python \
     with_ubsan with_asan \
     check_odd_only \
@@ -285,13 +278,11 @@ if [ "${run_checks}" = true ]; then
 else
     start "TEST"
 
-    if [ "${HIP_PLATFORM}" != "hcc" ]; then
-      check_proc_particle_test=${check_procs}
-      if [ "${check_proc_particle_test}" -gt 4 ]; then
-        check_proc_particle_test=4
-      fi
-      mpiexec -n ${check_proc_particle_test} ./pypresso "${srcdir}/testsuite/python/particle.py" || exit 1
+    check_proc_particle_test=${check_procs}
+    if [ "${check_proc_particle_test}" -gt 4 ]; then
+      check_proc_particle_test=4
     fi
+    mpiexec -n ${check_proc_particle_test} ./pypresso "${srcdir}/testsuite/python/particle.py" || exit 1
 
     end "TEST"
 fi

maintainer/files_with_header.sh

@@ -23,10 +23,11 @@
 git ls-files --exclude-standard |
 grep -vE '\.(blk|gz|npz|data|dat|tab|chk|jpg|png|pdf|fig|gif|xcf|css|bib|vtf|vtk|svg|ico|eps|rst|ipynb)$' |
 grep -vE '^testsuite/configs/|^old/|^cmake/|^libs/' |
-grep -vE '(ChangeLog|AUTHORS|COPYING|NEWS|README|INSTALL)' |
-grep -vE '(\.gitmodules|\.github|\.gitignore|\.codecov\.yml|\.gitlab-ci\.yml|\.travis\.yml|bors\.toml)' |
-grep -vE '(\.clang-format|\.clang-tidy|\.pylintrc|tools/ubsan-suppressions\.txt)' |
-grep -vE '(Doxyfile|latexmk\.1|latexmkrc|assemble_quickref\.awk|doc/misc/homepage/palette\.html)' |
+grep -vE '(ChangeLog|AUTHORS|COPYING|NEWS|README|INSTALL|README\.md|CONTRIBUTING\.md)' |
+grep -vE '(\.gitmodules|\.github|\.gitignore|\.codecov\.yml|\.gitlab-ci\.yml|kodiak\.toml)' |
+grep -vE '(\.clang-format|\.cmake-format|\.clang-tidy|\.coveragerc|\.pylintrc|ubsan\.supp)' |
+grep -vE '(\.lgtm\.yml|\.pre-commit-config\.yaml|requirements\.txt)' |
+grep -vE '(Doxyfile|latexmk\.1|latexmkrc|assemble_quickref\.awk)' |
 grep -vE '(src/config/features\.def)' |
 grep -vE '(featurelist)' |
 grep -vE '(\.cproject|\.project|\.settings)'

src/python/espressomd/visualization_opengl.py

@@ -426,11 +426,10 @@ def __init__(self, system, **kwargs):
         self.system = system
         self.system_info = {}
 
-        self.last_T = -1
         self.last_box_l = self.system.box_l
         self.fps_last = 0
         self.fps = 0
-        self.fps_count = 0
+        self.fps_count = 1
 
         self.glut_main_loop_started = False
         self.screenshot_initialized = False
@@ -447,10 +446,9 @@ def __init__(self, system, **kwargs):
         self.timers = []
         self.particles = {}
 
-        self.update_elapsed = 0
-        self.update_timer = 0
-        self.draw_elapsed = 0
-        self.draw_timer = 0
+        # times of last call of update(), redraw_on_idle()
+        self.last_update = time.time()
+        self.last_draw = time.time()
 
         self.trigger_set_particle_drag = False
         self.trigger_reset_particle_drag = False
@@ -594,18 +592,19 @@ def run(self, integration_steps=1):
 
         def main():
             while True:
-
                 self.update()
-
-                if self.paused:
-                    time.sleep(0.0001)  # sleep(0) is worse
-                else:
+                if not self.paused:
                     try:
                         self.system.integrator.run(integration_steps)
                     except Exception as e:
                         print(e)
                         os._exit(1)
 
+                # Necessary to regularly drop the Global Interpreter Lock (GIL)
+                # which prevents freezing of the visualizer under certain
+                # circumstances (see Issue #3764).
+                time.sleep(1e-12)
+
         t = Thread(target=main)
         t.daemon = True
         t.start()
@@ -639,32 +638,28 @@ def update(self):
                 self.hasParticleData = True
 
             # UPDATES
-            self.update_elapsed += (time.time() - self.update_timer)
-            if self.update_elapsed > 1.0 / self.specs['update_fps']:
-                self.update_elapsed = 0
-
+            if (time.time() - self.last_update) > 1.0 / \
+                    self.specs['update_fps']:
                 # ES UPDATES WHEN SYSTEM HAS PROPAGATED. ALSO UPDATE ON PAUSE
                 # FOR PARTICLE INFO
-                if self.paused or not self.last_T == self.system.time:
-                    self.last_T = self.system.time
-                    self._update_particles()
+                self._update_particles()
 
-                    # LB UPDATE
-                    if self.specs['LB_draw_velocity_plane']:
-                        self._update_lb_velocity_plane()
+                # LB UPDATE
+                if self.specs['LB_draw_velocity_plane']:
+                    self._update_lb_velocity_plane()
 
-                    # BOX_L CHANGED
-                    if not (self.last_box_l == self.system.box_l).all():
-                        self.last_box_l = np.copy(self.system.box_l)
-                        self._box_size_dependence()
+                # BOX_L CHANGED
+                if not (self.last_box_l == self.system.box_l).all():
+                    self.last_box_l = np.copy(self.system.box_l)
+                    self._box_size_dependence()
 
                 # KEYBOARD CALLBACKS MAY CHANGE ESPRESSO SYSTEM PROPERTIES,
                 # ONLY SAVE TO CHANGE HERE
                 for c in self.keyboard_manager.userCallbackStack:
                     c()
                 self.keyboard_manager.userCallbackStack = []
 
-            self.update_timer = time.time()
+                self.last_update = time.time()
 
             # DRAG PARTICLES
             if self.specs['drag_enabled']:
@@ -1400,11 +1395,9 @@ def motion(x, y):
 
         def redraw_on_idle():
             # DON'T REPOST FASTER THAN 60 FPS
-            self.draw_elapsed += (time.time() - self.draw_timer)
-            if self.draw_elapsed > 1.0 / 60.0:
-                self.draw_elapsed = 0
+            if (time.time() - self.last_draw) > 1.0 / 60.0:
                 OpenGL.GLUT.glutPostRedisplay()
-            self.draw_timer = time.time()
+                self.last_draw = time.time()
             return
 
         def reshape_callback(w, h):
@@ -1426,6 +1419,19 @@ def close_window():
         OpenGL.GLUT.glutIdleFunc(redraw_on_idle)
 
     def _init_timers(self):
+        """
+        Starts infinite loops of timed function callbacks.
+
+        Using `OpenGL.GLUT.glutTimerFunc()` a timed function callback is
+        registered that after (at least) the specified time calls a
+        specific function, which re-registers a timed callback to itself
+        plus does some other stuff.
+        Per callback registered in `self.timers`, one such infinite
+        callback loop is started.
+        In addition, potential keyboard input is handled every (at least)
+        17 ms, corresponding to a rate of ~60 1/s.
+
+        """
 
         # TIMERS FOR register_callback
         def dummy_timer(index):
@@ -1435,10 +1441,8 @@ def dummy_timer(index):
                 dummy_timer,
                 index)
 
-        index = 0
-        for t in self.timers:
-            OpenGL.GLUT.glutTimerFunc(t[0], dummy_timer, index)
-            index += 1
+        for index, timer in enumerate(self.timers):
+            OpenGL.GLUT.glutTimerFunc(timer[0], dummy_timer, index)
 
         # HANDLE INPUT WITH 60FPS
         # pylint: disable=unused-argument
@@ -1530,7 +1534,7 @@ def _reset_particle_drag(self, pos, pos_old):
         if self.drag_id != -1:
             self.trigger_reset_particle_drag = True
 
-    def _get_particle_info(self, pos):
+    def _get_particle_info(self, pos, pos_old):
         part_id, _ = self._get_particle_id(pos)
         if self.show_system_info:
             self.show_system_info = False