SCOREC · jacobmerson · Jun 20, 2025 · May 26, 2025 · Jun 2, 2025 · Jun 10, 2025
diff --git a/.github/workflows/python-api-test.yml b/.github/workflows/python-api-test.yml
@@ -0,0 +1,103 @@
+name: Build and Test PUMI Python Interface
+
+on:
+  push:
+    branches: [develop]
+  pull_request:
+    branches: [develop]
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+
+    env:
+      PYTHONPATH: ${{ github.workspace }}/build/python_wrappers
+      LD_LIBRARY_PATH: ${{ github.workspace }}/libs/install/lib:${LD_LIBRARY_PATH}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cmake mpich build-essential libbz2-dev
+          pip3 install mpi4py
+
+      - name: Build SWIG
+        run: |
+          git clone https://github.com/swig/swig.git
+          cd swig
+          ./autogen.sh
+          ./configure --prefix=${{ github.workspace }}/libs/install
+          make
+          make install
+
+      - name: Build GKlib
+        run: |
+          git clone https://github.com/KarypisLab/GKlib.git
+          cd GKlib
+          make config prefix=${{ github.workspace }}/libs/install
+          make install
+
+      - name: Build METIS
+        run: |
+          git clone https://github.com/KarypisLab/METIS.git
+          cd METIS
+          make config prefix=${{ github.workspace }}/libs/install
+          make install
+
+      - name: Build ParMETIS
+        run: |
+          git clone https://github.com/KarypisLab/ParMETIS.git
+          cd ParMETIS
+          make config prefix=${{ github.workspace }}/libs/install
+          make install
+
+      - name: Build Zoltan from Trilinos (minimal)
+        run: |
+          git clone https://github.com/trilinos/Trilinos.git
+          mkdir build-zoltan
+          cd build-zoltan
+          cmake ../Trilinos \
+            -DCMAKE_INSTALL_PREFIX=${{ github.workspace }}/libs/install \
+            -DTPL_ENABLE_MPI:BOOL=ON \
+            -DCMAKE_C_FLAGS="-O3 -fPIC" \
+            -DCMAKE_CXX_FLAGS="-O3 -fPIC" \
+            -DTrilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
+            -DTrilinos_ENABLE_Zoltan:BOOL=ON \
+            -DZoltan_ENABLE_EXAMPLES:BOOL=OFF \
+            -DZoltan_ENABLE_TESTS:BOOL=OFF \
+            -DZoltan_ENABLE_ParMETIS:BOOL=ON \
+            -DParMETIS_INCLUDE_DIRS=${{ github.workspace }}/libs/install \
+            -DParMETIS_LIBRARY_DIRS=${{ github.workspace }}/libs/install
+          make
+          make install
+
+      - name: Configure PUMI
+        run: |
+          cmake -S . -B build \
+            -DCMAKE_INSTALL_PREFIX=${{ github.workspace }}/build/install \
+            -DCMAKE_C_COMPILER=mpicc \
+            -DCMAKE_CXX_COMPILER=mpicxx \
+            -DSCOREC_CXX_OPTIMIZE=ON \
+            -DMDS_ID_TYPE=int \
+            -DPCU_COMPRESS=ON \
+            -DENABLE_ZOLTAN=ON \
+            -DZOLTAN_PREFIX=${{ github.workspace }}/libs/install \
+            -DPUMI_PYTHON_INTERFACE=ON \
+            -DBUILD_SHARED_LIBS=ON \
+            -DBUILD_EXES=OFF \
+            -DIS_TESTING=OFF \
+            -DENABLE_OMEGA_H=OFF \
+            -DPARMETIS_PREFIX=${{ github.workspace }}/libs/install \
+            -DENABLE_SIMMETRIX=OFF
+
+      - name: Build and install
+        run: |
+          cmake --build build -j 4 --target install
+
+      - name: Run Python test
+        working-directory: ${{github.workspace}}/python_wrappers
+        run: |
+          python3 test_pyCore.py -g input/cube.dmg -m input/cube.smb
diff --git a/pcu/PCU.h b/pcu/PCU.h
@@ -110,8 +110,15 @@ class PCU {
   int Received(size_t *size) noexcept;
   void *Extract(size_t size) noexcept;
 
+  /*
+   * Debug print function with printf-style formatting
+   * This function is excluded from SWIG parsing due to complex macro usage
+   * with variadic argument. Also, such functionalities is not needed for the Python API.
+   */
+  #ifndef SWIG
   void DebugPrint(const char* format, ...) noexcept PCU_FORMAT_ATTRIBUTE(2, 3)
   void DebugPrint(const char* format, va_list args) noexcept;
+  #endif // SWIG
   /* Debug functions */
   void DebugOpen() noexcept;
 
@@ -141,7 +148,12 @@ void Init(int *argc, char ***argv);
  */
 void Finalize();
 
-/* explicit instantiations of template functions */
+/*
+ * Explicit instantiations of template functions,
+ * ignored by SWIG to avoid difficulties when parsing macros involving
+ * template functions. Templates are initialized manually in the interface file.
+ */
+#ifndef SWIG
 #define PCU_EXPL_INST_DECL(T)                                                  \
   extern template void PCU::Add<T>(T * p, size_t n) noexcept;                  \
   extern template T PCU::Add<T>(T p) noexcept;                                 \
@@ -158,6 +170,7 @@ PCU_EXPL_INST_DECL(size_t)
 PCU_EXPL_INST_DECL(long)
 PCU_EXPL_INST_DECL(double)
 #undef PCU_EXPL_INST_DECL
+#endif // SWIG
 
 } // namespace pcu
 

diff --git a/python_wrappers/apf.i b/python_wrappers/apf.i
@@ -2,6 +2,8 @@
 %{
 #include <mpi.h>
 #include <vector>
+#include <pcu_defines.h>
+#include <PCU.h>
 #include <PCU_C.h>
 #include <pcu_util.h>
 #include <gmi.h>
@@ -40,14 +42,35 @@
 
 /* PCU RELATED WRAPPERS */
 /* ==== FROM PCU.h ====*/
-MPI_Comm PCU_Get_Comm(void);
-int PCU_Comm_Init(void);
-int PCU_Comm_Free(void);
+int PCU_Comm_Init(PCU_t* h);
+int PCU_Comm_Free(PCU_t* h);
 
-int PCU_Comm_Self(void);
-int PCU_Comm_Peers(void);
+int PCU_Comm_Self(PCU_t h);
+int PCU_Comm_Peers(PCU_t h);
 double PCU_Time(void);
-bool PCU_Comm_Initialized(void);
+bool PCU_Comm_Initialized(PCU_t h);
+%include<pcu_defines.h>
+%include<PCU.h>
+%template(Add_int) pcu::PCU::Add<int>;
+%template(Min_int) pcu::PCU::Min<int>;
+%template(Max_int) pcu::PCU::Max<int>;
+%template(Exscan_int) pcu::PCU::Exscan<int>;
+%template(ALLgather_int) pcu::PCU::Allgather<int>;
+%template(Add_size_t) pcu::PCU::Add<size_t>;
+%template(Min_size_t) pcu::PCU::Min<size_t>;
+%template(Max_size_t) pcu::PCU::Max<size_t>;
+%template(Exscan_size_t) pcu::PCU::Exscan<size_t>;
+%template(ALLgather_size_t) pcu::PCU::Allgather<size_t>;
+%template(Add_long) pcu::PCU::Add<long>;
+%template(Min_long) pcu::PCU::Min<long>;
+%template(Max_long) pcu::PCU::Max<long>;
+%template(Exscan_long) pcu::PCU::Exscan<long>;
+%template(ALLgather_long) pcu::PCU::Allgather<long>;
+%template(Add_double) pcu::PCU::Add<double>;
+%template(Min_double) pcu::PCU::Min<double>;
+%template(Max_double) pcu::PCU::Max<double>;
+%template(Exscan_double) pcu::PCU::Exscan<double>;
+%template(ALLgather_double) pcu::PCU::Allgather<double>;
 
 /* ==== FROM pcu_util.h ====*/
 void PCU_Assert_Fail(const char* msg);
@@ -221,7 +244,7 @@ void lion_set_verbosity(int lvl);
         local_min = val;
     }
     self->end(it);
-    PCU_Min_Doubles(&local_min, 1);
+    self->getPCU()->Min(&local_min, 1);
     return local_min;
   }
   double getMaxOfScalarField(apf::Field* field)
@@ -238,7 +261,7 @@ void lion_set_verbosity(int lvl);
         local_max = val;
     }
     self->end(it);
-    PCU_Max_Doubles(&local_max, 1);
+    self->getPCU()->Max(&local_max, 1);
     return local_max;
   }
   bool isBoundingModelRegion(int rtag, int dim, int tag)
@@ -262,16 +285,17 @@ void lion_set_verbosity(int lvl);
 
 #define __attribute__(x)
 %ignore apf::fail;
+%ignore apf::writeCGNS;
 %include<apf.h>
 %include<apfNumbering.h>
 %include<apfShape.h>
 
 
 
 namespace apf {
-  apf::Mesh2* makeEmptyMdsMesh(gmi_model* model, int dim, bool isMatched);
-  apf::Mesh2* loadMdsMesh(const char* modelfile, const char* meshfile);
-  apf::Mesh2* loadMdsMesh(gmi_model* model, const char* meshfile);
+  apf::Mesh2* makeEmptyMdsMesh(gmi_model* model, int dim, bool isMatched, pcu::PCU *PCUObj);
+  apf::Mesh2* loadMdsMesh(const char* modelfile, const char* meshfile, pcu::PCU *PCUObj);
+  apf::Mesh2* loadMdsMesh(gmi_model* model, const char* meshfile, pcu::PCU *PCUObj);
   void writeASCIIVtkFiles(const char* prefix, apf::Mesh2* m);
   /* void writeVtkFiles(const char* prefix, apf::Mesh* m, int cellDim = -1); */
   /* void writeVtkFiles(const char* prefix, apf::Mesh* m, */

diff --git a/python_wrappers/input/sphere.smd b/python_wrappers/input/sphere.smd
@@ -0,0 +1,110 @@
+smi 5 0
+<part> smd 33
+simple 33 1
+*
+-1
+-0.00050000000000000001 -0.00050000000000000001 -0.00050000000000000001
+0.00050000000000000001 0.00050000000000000001 0.00029999999999999997
+1 1007 9 0
+0 0 0 0
+-0.00050000000000000001 -0.00050000000000000001 -0.00050000000000000001
+0.00050000000000000001 0.00050000000000000001 0.00029999999999999997
+_sim_empty
+-1
+0 0 0 0
+
+0
+1 2 1 0
+0 0 0 0
+0 0 0 0
+0 0 0 0
+2
+1 5 65 -1 -1 
+2 5 65 -1 -1 
+65 1 9 0 210 0 2 -1 -1
+1 2 
+_sim_empty
+-1
+1 3.1415926535897931 -0.00040000000000000002 4.8985871965894131e-20 0.00029999999999999997
+1e-08
+1 3
+0 6.2831853071795862
+0 0 0.00029999999999999997
+0.00040000000000000002 6.2831853071795862
+0 0 1
+1 0 0
+1 6 11 1 0 2
+1 65 1 0 2 6 11 0 0 1
+1 65 2 1 11 2 9 0 203 0
+1 1 
+0
+
+  1 2 
+0
+
+0
+_sim_empty
+-1
+0 0 0 0 0 0
+0
+1 3
+0 0 0
+0 1 0
+1 -0 0
+0 0 -1
+0.00050000000000000001 0 0 6.2831853071795862
+3 6 100 1 0 4
+1 65 1 1 4 6 100 0 0 3
+1 65 2 0 100 2 9 0 203 0
+1 3 
+0
+
+  1 4 
+0
+
+0
+_sim_empty
+-1
+0 0 0 0 0 0
+0
+1 0
+0 0 0.00029999999999999997
+1 0 0
+0 1 0
+1 1 1
+1 8 1 2
+11 0 100 0 1 3 9 0 205 0 1 
+1 
+0
+0
+_sim_empty
+-1
+0 -1
+3 8 2 2
+11 1 100 1 2 3 8 0 303 0 1 
+3 
+0
+0
+_sim_empty
+-1
+0
+0 -1
+0 -1
+0 -1
+0 -1
+0 -1
+<part> auxmm 3
+0
+0
+<index>
+2
+smd 8
+auxmm 1160
+</index>
+<header>
+4
+71 file:///lore/yus9/scorec_software/core/python_wrappers/input/sphere.smd24 model.nonmanifold.simple6 # 1 0 0 
+0
+0
+</header>
+1179 1215                                                                                                                      
diff --git a/python_wrappers/test_pyCore.py b/python_wrappers/test_pyCore.py
@@ -23,13 +23,13 @@ def main(argv):
    print('Mesh  file is "', mesh)
 
    # PCU initialization
-   pyCore.PCU_Comm_Init()
+   PCUObj = pyCore.PCU(MPI.COMM_WORLD)
 
    # gmi initialization
    pyCore.gmi_register_mesh()
 
    # load the mesh and model and write the initial mesh to vtk
-   mesh = pyCore.loadMdsMesh(model, mesh)
+   mesh = pyCore.loadMdsMesh(model, mesh, PCUObj)
    pyCore.writeASCIIVtkFiles('before', mesh);
 
    # setup uniform refiner and call mesh adapt
@@ -40,7 +40,7 @@ def main(argv):
    pyCore.writeASCIIVtkFiles('after', mesh);
 
    # gmi finalization
-   pyCore.PCU_Comm_Free()
+   del PCUObj
 
 if __name__ == "__main__":
    main(sys.argv[1:])

diff --git a/python_wrappers/test_pyCore_with_simx.py b/python_wrappers/test_pyCore_with_simx.py
@@ -25,7 +25,7 @@ def main(argv):
    pyCore.lion_set_verbosity(1)
 
    # PCU initialization
-   pyCore.PCU_Comm_Init()
+   PCUObj = pyCore.PCU(MPI.COMM_WORLD)
 
    # SIMX initialization
    pyCore.start_sim('simlog.txt')
@@ -38,7 +38,7 @@ def main(argv):
    pyCore.gmi_register_sim()
 
    # load the mesh and model and write the initial mesh to vtk
-   mesh = pyCore.loadMdsMesh(model, mesh)
+   mesh = pyCore.loadMdsMesh(model, mesh, PCUObj)
    print("num verts in the mesh is ", mesh.count(0))
 
    it = mesh.begin(0)
@@ -85,7 +85,7 @@ def main(argv):
    pyCore.stop_sim()
 
    # gmi finalization
-   pyCore.PCU_Comm_Free()
+   del PCUObj
 
 if __name__ == "__main__":
    main(sys.argv[1:])