Merge pull request #127 from OpenSEMBA/debugging-movies

Debugging MPI problem with movies and mapvtk

.github/workflows/ubuntu.yml

@@ -88,6 +88,7 @@ jobs:
 
     - name: Run python tests
       env:
+        SEMBA_FDTD_ENABLE_MPI: ${{ matrix.mpi }}
         SEMBA_FDTD_ENABLE_MTLN: ${{ matrix.mtln }}
         SEMBA_FDTD_ENABLE_HDF: ${{ matrix.hdf }}
       run: python -m pytest test/

.github/workflows/windows.yml

@@ -69,6 +69,7 @@ jobs:
 
     - name: Run python tests (except codemodel)
       env:
+        SEMBA_FDTD_ENABLE_MPI: ${{ matrix.mpi }}
         SEMBA_FDTD_ENABLE_MTLN: ${{ matrix.mtln }}
         SEMBA_FDTD_ENABLE_HDF: ${{ matrix.hdf }}
       run: python -m pytest -m 'not codemodel' test/

src_main_pub/timestepping.F90

@@ -1,3 +1,44 @@
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+! MIT License
+! 
+! Copyright (c) 2023 University of Granada
+! 
+! Permission is hereby granted, free of charge, to any person obtaining a copy
+! of this software and associated documentation files (the "Software"), to deal
+! in the Software without restriction, including without limitation the rights
+! to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+! copies of the Software, and to permit persons to whom the Software is
+! furnished to do so, subject to the following conditions:
+! 
+! The above copyright notice and this permission notice shall be included in all
+! copies or substantial portions of the Software.
+! 
+! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+! IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+! FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+! AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+! LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+! OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+! SOFTWARE.
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!  SEMBA_FDTD sOLVER MODULE
+!  Creation date Date :  April, 8, 2010
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+!__________________________________________________________________________________________________
+!******************************** REVISAR PARA PGI (CRAY) *****************************************
+!---> AdvanceMultiportE
+!---> AdvanceAnisMultiportE
+!---> AdvanceMultiportH
+!---> AdvanceAnisMultiportH
+!---> dfUpdateE
+!---> dfUpdateH
+!---> MinusCloneMagneticPMC
+!________________________________________________________________________________________
+
 module Solver
 
    use fdetypes
@@ -2782,8 +2823,11 @@ subroutine fillMtag(sgg,sggMiEx, sggMiEy, sggMiEz, sggMiHx, sggMiHy, sggMiHz,sgg
          integer(kind = 4)  ::  i, j, k
          integer(kind = INTEGERSIZEOFMEDIAMATRICES)  ::  medio1,medio2,medio3,medio4,medio5
          logical  ::  mediois1,mediois2,mediois3,mediois4
-
-
+         integer, dimension(3) :: lbx, lby, lbz
+         lbx = lbound(tag_numbers%face%x)
+         lby = lbound(tag_numbers%face%y)   
+         lbz = lbound(tag_numbers%face%z)
+
          mediois3=.true.; mediois4=.true.
 #ifdef CompileWithOpenMP
 !$OMP  PARALLEL DO  DEFAULT(SHARED) private (i,j,k,medio1,medio2,medio3,medio4,medio5,mediois1,mediois2,mediois3,mediois4)
@@ -2801,7 +2845,7 @@ subroutine fillMtag(sgg,sggMiEx, sggMiEy, sggMiEz, sggMiHx, sggMiHy, sggMiHz,sgg
                   mediois3= .true. !.not.((medio5==1).and.(((sggMiHx(i-1,j,k)/=1).or.(sggMiHx(i+1,j,k)/=1)))) !esta condicion en realidad no detecta alabeos de una celda que siendo slots son acoples de un agujerito solo en el peor de los casos
                   if ((mediois1.or.mediois2).and.(mediois3))  then
                       !solo lo hace con celdas de vacio porque en particular el mismo medio sgbc con diferentes orientaciones tiene distintos indices de medio y lo activaria erroneamente si lo hago para todos los medios
-                      tag_numbers%face%x(i,j,k)=-ibset(iabs(tag_numbers%face%x(i,j,k)),3) 
+                      tag_numbers%face%x(i+lbx(1)-1,j+lbx(2)-1,k+lbx(3)-1)=-ibset(iabs(tag_numbers%face%x(i+lbx(1)-1,j+lbx(2)-1,k+lbx(3)-1)),3) 
                       !ojo no cambiar: interacciona con observation tags 141020 !151020 a efectos de mapvtk el signo importa
                   endif
                End do
@@ -2823,7 +2867,7 @@ subroutine fillMtag(sgg,sggMiEx, sggMiEy, sggMiEz, sggMiHx, sggMiHy, sggMiHz,sgg
                   mediois2= (medio5==1).and.(medio3/=1).and.(medio4/=1).and.(medio1==1).and.(medio2==1)
                   mediois3= .true. !.not.((medio5==1).and.(((sggMiHy(i,j-1,k)/=1).or.(sggMiHy(i,j+1,k)/=1))))
                   if ((mediois1.or.mediois2).and.(mediois3))  then
-                     tag_numbers%face%y(i,j,k)=-ibset(iabs(tag_numbers%face%y(i,j,k)),4) 
+                     tag_numbers%face%y(i+lby(1)-1,j+lby(2)-1,k+lby(3)-1)=-ibset(iabs(tag_numbers%face%y(i+lby(1)-1,j+lby(2)-1,k+lby(3)-1)),4) 
                   endif
                End do
             End do
@@ -2844,7 +2888,7 @@ subroutine fillMtag(sgg,sggMiEx, sggMiEy, sggMiEz, sggMiHx, sggMiHy, sggMiHz,sgg
                   mediois2= (medio5==1).and.(medio3/=1).and.(medio4/=1).and.(medio1==1).and.(medio2==1)
                   mediois3= .true. !.not.((medio5==1).and.(((sggMiHz(i,j,k-1)/=1).or.(sggMiHz(i,j,k+1)/=1))))
                   if ((mediois1.or.mediois2).and.(mediois3))  then
-                     tag_numbers%face%z(i,j,k)=-ibset(iabs(tag_numbers%face%z(i,j,k)),5) 
+                     tag_numbers%face%z(i+lbz(1)-1,j+lbz(2)-1,k+lbz(3)-1)=-ibset(iabs(tag_numbers%face%z(i+lbz(1)-1,j+lbz(2)-1,k+lbz(3)-1)),5) 
                   endif
                End do
             End do

src_pyWrapper/pyWrapper.py

@@ -24,7 +24,8 @@ class Probe():
         + BULK_CURRENT_PROBE_TAGS \
         + POINT_PROBE_TAGS \
         + FAR_FIELD_TAG \
-        + MOVIE_TAGS 
+        + MOVIE_TAGS
+
     def __init__(self, probe_filename):
         if isinstance(probe_filename, os.PathLike):
             self.filename = probe_filename.as_posix()
@@ -92,7 +93,7 @@ def __init__(self, probe_filename):
             self.field, self.direction = Probe._getFieldAndDirection(tag)
             self.cell_init, self.cell_end = \
                 Probe._positionStrToTwoCells(position_str)
-            
+
             if self.domainType == 'time':
                 self.data = self.data.rename(columns={
                     't': 'time',
@@ -179,17 +180,32 @@ def _getFieldAndDirection(tag: str):
 
 
 class FDTD():
-    def __init__(self, input_filename, path_to_exe=None, flags=[], run_in_folder=None):
+    def __init__(self, input_filename, path_to_exe=None,
+                 flags=None, run_in_folder=None, mpi_command=None):
+
         self._setFilename(input_filename)
 
         if path_to_exe is None:
-            self.path_to_exe = os.path.join(
-                os.getcwd(), DEFAULT_SEMBA_FDTD_PATH)
+            semba_exe = \
+                os.path.join(os.getcwd(), DEFAULT_SEMBA_FDTD_PATH)
+        else:
+            semba_exe = path_to_exe
+        assert os.path.isfile(semba_exe)
+
+        if mpi_command is None:
+            mpi_command_parts = []
         else:
-            self.path_to_exe = path_to_exe
-        assert os.path.isfile(self.path_to_exe)
+            mpi_command_parts = mpi_command.split()
+
+        if flags is None:
+            flags = []
+        elif isinstance(flags, str):
+            flags = flags.split()
+
+        case_name = self.getCaseName() + ".json"
+        self.run_command = \
+            mpi_command_parts + [semba_exe] + ["-i", case_name] + flags
 
-        self.flags = flags
         self._hasRun = False
 
         if run_in_folder != None:
@@ -263,9 +279,7 @@ def run(self):
             json.dump(self._input, open(self._filename, 'w'))
 
         os.chdir(self.getFolder())
-        case_name = self.getCaseName() + ".json"
-        self.output = subprocess.run(
-            [self.path_to_exe, "-i", case_name]+self.flags)
+        self.output = subprocess.run(self.run_command)
 
         self._hasRun = True
         assert self.hasFinishedSuccessfully()

test/pyWrapper/test_integration.py

@@ -39,6 +39,19 @@ def test_towel_hanger_case_creates_output_probes(tmp_path):
     assert countLinesInFile(probe_mid[0]) == 3
     assert countLinesInFile(probe_end[0]) == 3
 
+@no_mpi_skip
+def test_airplane_case_with_mpi(tmp_path):
+    fn = CASES_FOLDER + 'airplane/airplane.fdtd.json'
+    solver = FDTD(fn, 
+                  path_to_exe=SEMBA_EXE,
+                  run_in_folder=tmp_path, 
+                  flags=['-mapvtk'],
+                  mpi_command='mpirun -np 2')
+    solver.run()
+
+    vtkmapfile = solver.getVTKMap()
+    assert os.path.isfile(vtkmapfile)
+
 
 def test_sphere_case_with_far_field_probe_launches(tmp_path):
     fn = CASES_FOLDER + 'sphere/sphere.fdtd.json'
@@ -66,29 +79,34 @@ def test_tagnumbers_3_surfaces(tmp_path):
     solver['general']['numberOfSteps'] = 1
 
     solver.run()
-    
+
     vtkmapfile = solver.getVTKMap()
     assert os.path.isfile(vtkmapfile)
 
-    face_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'tagnumber')
+    face_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='tagnumber')
     assert face_tag_dict[64] == 4
     assert face_tag_dict[128] == 4
     assert face_tag_dict[192] == 4
 
-    line_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'tagnumber')
+    line_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='tagnumber')
     assert line_tag_dict[64] == 8
     assert line_tag_dict[128] == 4
     assert line_tag_dict[192] == 4
-
-    face_media_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'mediatype')
-    assert face_media_dict[0] == 4 #PEC surface
-    assert face_media_dict[304] == 4 #SGBC surface
-    assert face_media_dict[305] == 4 #SGBC surface
-
-    line_media_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'mediatype')
-    assert line_media_dict[0.5] == 8 #PEC line
-    assert line_media_dict[3.5] == 8 #SGBC line
-
+
+    face_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='mediatype')
+    assert face_media_dict[0] == 4  # PEC surface
+    assert face_media_dict[304] == 4  # SGBC surface
+    assert face_media_dict[305] == 4  # SGBC surface
+
+    line_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='mediatype')
+    assert line_media_dict[0.5] == 8  # PEC line
+    assert line_media_dict[3.5] == 8  # SGBC line
+
+
 def test_tagnumbers_1_volume(tmp_path):
     fn = CASES_FOLDER + 'tagNumber_mediaType/pec_volume.fdtd.json'
     solver = FDTD(input_filename=fn, path_to_exe=SEMBA_EXE,
@@ -100,18 +118,23 @@ def test_tagnumbers_1_volume(tmp_path):
     vtkmapfile = solver.getVTKMap()
     assert os.path.isfile(vtkmapfile)
 
-    face_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'tagnumber')
+    face_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='tagnumber')
     assert face_tag_dict[64] == 36
-
-    line_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'tagnumber')
+
+    line_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='tagnumber')
     assert len(line_tag_dict) == 0
-
-    face_media_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'mediatype')
-    assert face_media_dict[0] == 36 #PEC surface
-
-    line_media_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'mediatype')
+
+    face_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='mediatype')
+    assert face_media_dict[0] == 36  # PEC surface
+
+    line_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='mediatype')
     assert len(line_media_dict) == 0
 
+
 def test_tagnumbers_2_volumes(tmp_path):
     fn = CASES_FOLDER + 'tagNumber_mediaType/pec_volumes.fdtd.json'
     solver = FDTD(input_filename=fn, path_to_exe=SEMBA_EXE,
@@ -123,19 +146,24 @@ def test_tagnumbers_2_volumes(tmp_path):
     vtkmapfile = solver.getVTKMap()
     assert os.path.isfile(vtkmapfile)
 
-    face_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'tagnumber')
+    face_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='tagnumber')
     assert face_tag_dict[64] == 36
     assert face_tag_dict[128] == 36
-
-    line_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'tagnumber')
+
+    line_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='tagnumber')
     assert len(line_tag_dict) == 0
-
-    face_media_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'mediatype')
-    assert face_media_dict[0] == 72 #PEC surface
-
-    line_media_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'mediatype')
+
+    face_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='mediatype')
+    assert face_media_dict[0] == 72  # PEC surface
+
+    line_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='mediatype')
     assert len(line_media_dict) == 0
 
+
 def test_tagnumbers_1_line(tmp_path):
     fn = CASES_FOLDER + 'tagNumber_mediaType/pec_line.fdtd.json'
     solver = FDTD(input_filename=fn, path_to_exe=SEMBA_EXE,
@@ -147,18 +175,23 @@ def test_tagnumbers_1_line(tmp_path):
     vtkmapfile = solver.getVTKMap()
     assert os.path.isfile(vtkmapfile)
 
-    face_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'tagnumber')
+    face_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='tagnumber')
     assert len(face_tag_dict) == 0
-
-    line_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'tagnumber')
+
+    line_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='tagnumber')
     assert line_tag_dict[64] == 2
-
-    face_media_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'mediatype')
+
+    face_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='mediatype')
     assert len(face_media_dict) == 0
-
-    line_media_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'mediatype')
-    assert line_media_dict[0.5] == 2 #PEC line
-
+
+    line_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='mediatype')
+    assert line_media_dict[0.5] == 2  # PEC line
+
+
 def test_tagnumbers_volume_and_surfaces(tmp_path):
     fn = CASES_FOLDER + 'tagNumber_mediaType/volume_and_surfaces.fdtd.json'
     solver = FDTD(input_filename=fn, path_to_exe=SEMBA_EXE,
@@ -170,26 +203,31 @@ def test_tagnumbers_volume_and_surfaces(tmp_path):
     vtkmapfile = solver.getVTKMap()
     assert os.path.isfile(vtkmapfile)
 
-    face_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'tagnumber')
+    face_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='tagnumber')
     assert face_tag_dict[64] == 6
     assert face_tag_dict[128] == 1
     assert face_tag_dict[192] == 1
-
-    line_tag_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'tagnumber')
+
+    line_tag_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='tagnumber')
     assert line_tag_dict[64] == 1
     assert line_tag_dict[128] == 4
     assert line_tag_dict[192] == 3
-
-    face_media_dict = createPropertyDictionary(vtkmapfile, celltype = 9, property = 'mediatype')
-    assert face_media_dict[-1] == 1 #PEC surface
-    assert face_media_dict[0] == 6 #PEC surface
-    assert face_media_dict[305] == 1 #SGBC surface
-
-    line_media_dict = createPropertyDictionary(vtkmapfile, celltype = 3, property = 'mediatype')
-    assert line_media_dict[-0.5] == 4 #PMC line
-    assert line_media_dict[0.5] == 1 #PEC line
-    assert line_media_dict[3.5] == 3 #SGBC line
-
+
+    face_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=9, property='mediatype')
+    assert face_media_dict[-1] == 1  # PEC surface
+    assert face_media_dict[0] == 6  # PEC surface
+    assert face_media_dict[305] == 1  # SGBC surface
+
+    line_media_dict = createPropertyDictionary(
+        vtkmapfile, celltype=3, property='mediatype')
+    assert line_media_dict[-0.5] == 4  # PMC line
+    assert line_media_dict[0.5] == 1  # PEC line
+    assert line_media_dict[3.5] == 3  # SGBC line
+
+
 def test_tagnumbers_count_bug(tmp_path):
     fn = CASES_FOLDER + 'tagNumber_mediaType/count_bug.fdtd.json'
     solver = FDTD(input_filename=fn, path_to_exe=SEMBA_EXE,
@@ -201,10 +239,10 @@ def test_tagnumbers_count_bug(tmp_path):
     solver["materialAssociations"][1]["materialId"] = 1
     solver["materialAssociations"][2]["materialId"] = 3
     solver.cleanUp()
-    solver.run()    
-    
+    solver.run()
+
     solver["materialAssociations"][0]["materialId"] = 3
     solver["materialAssociations"][1]["materialId"] = 3
     solver["materialAssociations"][2]["materialId"] = 1
     solver.cleanUp()
-    solver.run()
+    solver.run()