Merge branch 'elmerice' into glads_gl

ElmerCSC · Oct 16, 2024 · 1bd4a7b · 1bd4a7b
2 parents 85ff151 + b1e79a0
commit 1bd4a7b
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diff --git a/.github/workflows/build-macos-homebrew.yaml b/.github/workflows/build-macos-homebrew.yaml
@@ -98,9 +98,9 @@ jobs:
         run: |
           cd ${GITHUB_WORKSPACE}/build
           ctest . \
-            -L "quick|elmerice-fast" \
+            -LE slow \
             -j$(sysctl -n hw.logicalcpu) \
-            --timeout 180
+            --timeout 300
 
       - name: re-run tests
         if: always() && (steps.run-ctest.outcome == 'failure')

diff --git a/.github/workflows/build-windows-mingw.yaml b/.github/workflows/build-windows-mingw.yaml
@@ -18,7 +18,7 @@ jobs:
 
     runs-on: windows-latest
 
-    name: MSYS2 (${{ matrix.umfpack }} UMFPACK, ${{ matrix.msystem }})
+    name: MSYS2 (${{ matrix.dependencies }} dependencies, ${{ matrix.msystem }})
 
     defaults:
       run:
@@ -31,10 +31,11 @@ jobs:
       matrix:
         # msystem: [MINGW64, CLANG64]
         msystem: [MINGW64]
-        umfpack: [internal, external]
+        dependencies: [bundled, external]
         include:
-          - umfpack: external
-            umfpack-cmake-flags: "-DEXTERNAL_UMFPACK=ON"
+          - dependencies: external
+            external-packages: parpack:p
+            external-cmake-flags: -DEXTERNAL_UMFPACK=ON -DEXTERNAL_ARPACK=ON -DEXTERNAL_PARPACK=ON
 
     steps:
       - name: get CPU name
@@ -83,6 +84,7 @@ jobs:
             unixodbc:p
             utf8cpp:p
             opencascade:p
+            ${{ matrix.external-packages }}
 
       - name: install MSMPI
         uses: mpi4py/setup-mpi@v1
@@ -121,7 +123,7 @@ jobs:
             -DWITH_MATC=ON \
             -DWITH_PARAVIEW=ON \
             -DCREATE_PKGCONFIG_FILE=ON \
-            ${{ matrix.umfpack-cmake-flags }} \
+            ${{ matrix.external-cmake-flags }} \
             ..
 
       - name: build
@@ -142,9 +144,9 @@ jobs:
         run: |
           cd ${GITHUB_WORKSPACE}/build
           ctest . \
-            -L "quick|elmerice-fast" \
+            -LE slow \
             -j$(nproc) \
-            --timeout 180
+            --timeout 300
 
       - name: re-run tests
         if: always() && (steps.run-ctest.outcome == 'failure')

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -86,14 +86,19 @@ jobs:
             $([ "${{ matrix.mpi }}" == "with" ] && echo "libhypre-dev") \
             $([ "${{ matrix.mpi }}" == "with" ] && echo "libopenmpi-dev libmumps-dev libparmetis-dev") \
             $([ "${{ matrix.compiler }}" == "gcc" ] && echo "libsuitesparse-dev") \
+            $([ "${{ matrix.compiler }}" == "gcc" ] && [ "${{ matrix.mpi }}" == "with" ] && echo "librocalution-dev") \
             libqwt-qt5-dev qtscript5-dev libqt5svg5-dev \
             libvtk9-qt-dev libglvnd-dev \
             occt-misc libocct-data-exchange-dev libocct-draw-dev \
             $([ "${{ matrix.mpi }}" == "with" ] && echo "trilinos-all-dev libptscotch-dev")
 
       - name: configure
-        # CHOLMOD requires a working OpenMP package. So, disable it for clang.
+        # CHOLMOD and rocALUTION require a working OpenMP package. So, disable them for clang.
         run: |
+          # work around error in the rocALUTION CMake config file distributed by Ubuntu
+          if [ "${{ matrix.compiler }}" == "gcc" ] && [ "${{ matrix.mpi }}" == "with" ]; then
+            sudo sed -i '/find_dependency(HIP)/d' /usr/lib/x86_64-linux-gnu/cmake/rocalution/rocalution-config.cmake
+          fi
           mkdir ${GITHUB_WORKSPACE}/build
           cd ${GITHUB_WORKSPACE}/build
           cmake \
@@ -106,6 +111,7 @@ jobs:
             $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Mumps=ON" || echo "-DWITH_Mumps=OFF") \
             $([ "${{ matrix.compiler }}" == "gcc" ] && echo "-DWITH_CHOLMOD=ON" || echo "-DWITH_CHOLMOD=OFF") \
             $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Hypre=ON -DHYPRE_INCLUDE_DIR=/usr/include/hypre" || echo "-DWITH_Hypre=OFF") \
+            $([ "${{ matrix.compiler }}" == "gcc" ] && [ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_ROCALUTION=ON" || echo "-DWITH_ROCALUTION=OFF") \
             $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_ElmerIce=ON" || echo "-DWITH_ElmerIce=OFF") \
             -DWITH_ELMERGUI=ON \
             -DWITH_VTK=ON \
@@ -135,9 +141,9 @@ jobs:
         run: |
           cd ${GITHUB_WORKSPACE}/build
           ctest . \
-            -L "quick|elmerice-fast" \
+            -LE slow \
             -j$(nproc) \
-            --timeout 180
+            --timeout 300
 
       - name: Re-run tests
         if: always() && (steps.run-ctest.outcome == 'failure')

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -81,6 +81,7 @@ SET(WITH_MKL FALSE CACHE BOOL "Use Intel Math Kernel library")
 SET(WITH_Mumps FALSE CACHE BOOL "Use Mumps sparse direct solver")
 SET(WITH_Hypre FALSE CACHE BOOL "Use Hypre linear algebra library")
 SET(WITH_CHOLMOD FALSE CACHE BOOL "Use CHOLMOD linear algebra library")
+SET(WITH_UMFPACK TRUE CACHE BOOL "Use UMFPACK for LU factorization")
 SET(WITH_ELMERGUI FALSE CACHE BOOL "Include ElmerGUI")
 SET(WITH_ElmerIce FALSE CACHE BOOL "Include ElmerIce")
 SET(WITH_XIOS FALSE CACHE BOOL "Include XIOS")
@@ -227,6 +228,10 @@ ENDIF(WITH_MPI)
 
 IF (WITH_ROCALUTION)
 
+  IF(NOT WITH_MPI)
+    MESSAGE(FATAL_ERROR "Building with rocALUTION requires MPI")
+  ENDIF()
+
   MESSAGE(STATUS "------------------------------------------------")
   MESSAGE(STATUS "Looking for rocALUTION installation")
 
@@ -238,12 +243,6 @@ IF (WITH_ROCALUTION)
 
   SET(HAVE_ROCALUTION TRUE CACHE BOOL "")
   MARK_AS_ADVANCED(HAVE_ROCALUTION)
-  INCLUDE_DIRECTORIES("${ROCALUTION_INCLUDE_DIR}")
-  MESSAGE(STATUS "  ---------------------------------")
-  MESSAGE(STATUS "  ROCALTUION:           " "${HAVE_ROCALUTION}")
-  MESSAGE(STATUS "  ROCALTUON_INCLUDE_DIR:       " "${ROCALUTION_INCLUDE_DIR}")
-  MESSAGE(STATUS "  ROCALTUON_LIBRARY:           " "${ROCALUTION_LIBRARY}")
-#  LINK_DIRECTORIES("${ROCALUTION_LINK_DIRECTORIES}")
 ENDIF()
 
 
@@ -626,29 +625,35 @@ IF(WITH_ElmerIce)
   ADD_SUBDIRECTORY(elmerice)
 ENDIF(WITH_ElmerIce)
 
-IF (EXTERNAL_UMFPACK)
-  MESSAGE(STATUS "Using external UMFPACK instead of built-in")
-  FIND_PACKAGE(UMFPACK REQUIRED)
-
-  # Check for size of "SuiteSparse_long"
-  INCLUDE(CheckTypeSize)
-  SET(old_CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES})
-  SET(old_CMAKE_EXTRA_INCLUDE_FILES ${CMAKE_EXTRA_INCLUDE_FILES})
-  LIST(APPEND CMAKE_REQUIRED_INCLUDES "${UMFPACK_INCLUDE_DIR}")
-  LIST(APPEND CMAKE_EXTRA_INCLUDE_FILES "umfpack.h")
-  CHECK_TYPE_SIZE("SuiteSparse_long" SIZEOF_SUITESPARSE_LONG LANGUAGE C)
-  SET(CMAKE_REQUIRED_INCLUDES ${old_CMAKE_REQUIRED_INCLUDES})
-  SET(CMAKE_EXTRA_INCLUDE_FILES ${old_CMAKE_EXTRA_INCLUDE_FILES})
-  IF (HAVE_SIZEOF_SUITESPARSE_LONG)
-    IF (SIZEOF_SUITESPARSE_LONG EQUAL 4)
-      SET(UMFPACK_LONG_FORTRAN_TYPE "C_INT32_T")
-    ELSE()
-      SET(UMFPACK_LONG_FORTRAN_TYPE "C_INT64_T")
+IF (WITH_UMFPACK)
+  IF (EXTERNAL_UMFPACK)
+    MESSAGE(STATUS "Using external UMFPACK instead of built-in")
+    FIND_PACKAGE(UMFPACK REQUIRED)
+
+    # Check for size of "SuiteSparse_long"
+    INCLUDE(CheckTypeSize)
+    SET(old_CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES})
+    SET(old_CMAKE_EXTRA_INCLUDE_FILES ${CMAKE_EXTRA_INCLUDE_FILES})
+    LIST(APPEND CMAKE_REQUIRED_INCLUDES "${UMFPACK_INCLUDE_DIR}")
+    LIST(APPEND CMAKE_EXTRA_INCLUDE_FILES "umfpack.h")
+    CHECK_TYPE_SIZE("SuiteSparse_long" SIZEOF_SUITESPARSE_LONG LANGUAGE C)
+    SET(CMAKE_REQUIRED_INCLUDES ${old_CMAKE_REQUIRED_INCLUDES})
+    SET(CMAKE_EXTRA_INCLUDE_FILES ${old_CMAKE_EXTRA_INCLUDE_FILES})
+    IF (HAVE_SIZEOF_SUITESPARSE_LONG)
+      IF (SIZEOF_SUITESPARSE_LONG EQUAL 4)
+        SET(UMFPACK_LONG_FORTRAN_TYPE "C_INT32_T")
+      ELSE()
+        SET(UMFPACK_LONG_FORTRAN_TYPE "C_INT64_T")
+      ENDIF()
     ENDIF()
+  ELSE()
+    MESSAGE(STATUS "Using built-in UMFPACK")
+    ADD_SUBDIRECTORY(umfpack)
   ENDIF()
+  SET(HAVE_UMFPACK ON)
+  MARK_AS_ADVANCED(HAVE_UMFPACK)
 ELSE()
-  MESSAGE(STATUS "Using built-in UMFPACK")
-  ADD_SUBDIRECTORY(umfpack)
+  MESSAGE(STATUS "Building without UMFPACK")
 ENDIF()
 IF(NOT DEFINED UMFPACK_LONG_FORTRAN_TYPE)
   # Old versions of UMFPACK before "SuiteSparse_long" was defined used "long"
@@ -708,13 +713,16 @@ MESSAGE(STATUS "------------------------------------------------")
 MESSAGE(STATUS "  BLAS library:   " "${BLAS_LIBRARIES}")
 MESSAGE(STATUS "  LAPACK library: " "${LAPACK_LIBRARIES}")
 MESSAGE(STATUS "------------------------------------------------")
-IF(UMFPACK_FOUND)
-  MESSAGE(STATUS " UMFPACK library: " "${UMFPACK_LIBRARIES}")
-  MESSAGE(STATUS " UMFPACK headers: " "${UMFPACK_INCLUDE_DIR}")
-  MARK_AS_ADVANCED(HAVE_UMFPACK)
-  MESSAGE(STATUS "------------------------------------------------")
+IF(WITH_UMFPACK)
+  IF(UMFPACK_FOUND)
+    MESSAGE(STATUS " UMFPACK library: " "${UMFPACK_LIBRARIES}")
+    MESSAGE(STATUS " UMFPACK headers: " "${UMFPACK_INCLUDE_DIR}")
+    MESSAGE(STATUS "------------------------------------------------")
+  ELSE()
+    MESSAGE(STATUS " UMFPACK library: Using internal Elmer library")
+  ENDIF()
 ELSE()
-  MESSAGE(STATUS " UMFPACK library: Using internal Elmer library")
+  MESSAGE(STATUS " UMFPACK library: Building without UMFPACK")
 ENDIF()
 IF(CHOLMOD_FOUND AND SPQR_FOUND)
   MESSAGE(STATUS " CHOLMOD library: " "${CHOLMOD_LIBRARIES}")
@@ -825,6 +833,10 @@ IF(HAVE_EXTOPTIM)
   MESSAGE(STATUS "------------------------------------------------")
 ENDIF(HAVE_EXTOPTIM)
 
+IF(NOT HAVE_UMFPACK AND NOT HAVE_MUMPS)
+  MESSAGE(WARNING "Elmer is configured without backend for direct solvers (UMFPACK or MUMPS).\n"
+                  "Are you sure this is intended?")
+ENDIF()
 
 
 # Packaging

diff --git a/ElmerGUI/Application/plugins/egconvert.cpp b/ElmerGUI/Application/plugins/egconvert.cpp
@@ -4969,8 +4969,10 @@ static int LoadGmshInput41(struct FemType *data,struct BoundaryType *bound,
 	printf("Physical tag offset for %dD is %d\n",tagdim,phystagoffset[tagdim]);
       }
 
-      tagoffset[meshdim] = maxphystag[meshdim];
-      tagoffset[meshdim-1] = phystagoffset[0];
+      if(meshdim>0) {
+        tagoffset[meshdim] = maxphystag[meshdim];
+        tagoffset[meshdim-1] = phystagoffset[0];
+      }
       for(tagdim=meshdim-2;tagdim>=0;tagdim--) {
 	tagoffset[tagdim] = tagoffset[tagdim+1]+MAX(0,maxtag[tagdim+1]);
 	printf("Geometric tag offset for %dD is %d\n",tagdim,tagoffset[tagdim]);

diff --git a/ElmerGUI/Application/plugins/egmesh.cpp b/ElmerGUI/Application/plugins/egmesh.cpp
@@ -924,7 +924,8 @@ void InitializeKnots(struct FemType *data)
   data->nodalexists = FALSE;
   /* data->invtopoexists = FALSE; */
   data->partitiontableexists = FALSE;
-
+  data->maxpartitiontable = 0;
+
   data->invtopo.created = FALSE;
   data->nodalgraph2.created = FALSE;
   data->dualgraph.created = FALSE;
@@ -2457,19 +2458,19 @@ int FindCorners(struct GridType *grid,struct CellType *cell,
 	continue;
 
       /* point (i,j) must now be a corner */
-      if(cellno = grid->numbered[j][i]) {
+      if((cellno = grid->numbered[j][i])) {
 	elem = GetElementIndex(&(cell)[cellno],1,1);
 	ind  = BOTLEFT;
       } 
-      else if(cellno = grid->numbered[j][i-1]) {
+      else if((cellno = grid->numbered[j][i-1])) {
 	elem = GetElementIndex(&(cell)[cellno],cell[cellno].xelem,1);
 	ind  = BOTRIGHT;
       } 
-      else if(cellno = grid->numbered[j-1][i]) {
+      else if((cellno = grid->numbered[j-1][i])) {
 	elem = GetElementIndex(&(cell)[cellno],1,cell[cellno].yelem);
 	ind  = TOPLEFT;
       } 
-      else if(cellno = grid->numbered[j-1][i-1]) {
+      else if((cellno = grid->numbered[j-1][i-1])) {
 	elem = GetElementIndex(&(cell)[cellno],cell[cellno].xelem,cell[cellno].yelem);
 	ind  = TOPRIGHT;
       }
@@ -9906,7 +9907,7 @@ int CreateDualGraph(struct FemType *data,int unconnected,int info)
   int *invrow,*invcol;
   struct CRSType *dualgraph;
 
-  printf("Creating a dual graph of the finite element mesh\n");  
+  if(info) printf("Creating a dual graph of the finite element mesh\n");  
 
   dualgraph = &data->dualgraph;
   if(dualgraph->created) {
@@ -9924,7 +9925,7 @@ int CreateDualGraph(struct FemType *data,int unconnected,int info)
   /* If a dual graph only for the unconnected nodes is requested do that.
      Basically the connected nodes are omitted in the graph. */
   if( unconnected ) {
-    printf("Removing connected nodes from the dual graph\n");
+    if(info) printf("Removing connected nodes from the dual graph\n");
     if( data->nodeconnectexist ) {
       if(info) printf("Creating connected elements list from the connected nodes\n");
       SetConnectedElements(data,info);
@@ -10034,6 +10035,7 @@ int CreateDualGraph(struct FemType *data,int unconnected,int info)
   }
   else {
     dualsize = freeelements;
+    if(info) printf("Allocating for the dual graph for %d with %d connections\n",dualsize,totcon);
     dualrow = Ivector(0,dualsize);
     for(i=1;i<=dualsize;i++) 
       dualrow[i] = 0;
@@ -10053,7 +10055,7 @@ int CreateDualGraph(struct FemType *data,int unconnected,int info)
     goto omstart;
   } 
 
-  if( orphanelements ) {
+  if( orphanelements && info ) {
     printf("There are %d elements in the dual mesh that are not connected!\n",orphanelements);
     if(unconnected) printf("The orphan elements are likely caused by the hybrid partitioning\n");
   }
@@ -10160,3 +10162,51 @@ int MeshTypeStatistics(struct FemType *data,int info)
   return(0);
 }
 
+int BoundingBox(struct FemType *data,int nomesh,int nomeshes,int info)
+{
+  int i;
+  Real xmin, xmax, ymin, ymax, zmin, zmax, sidemax;
+
+  xmin = xmax = data->x[1];
+  ymin = ymax = data->y[1];
+  zmin = zmax = data->z[1];
+
+  for(i=1; i<=data->noknots; i++){
+    xmax = MAX( xmax, data->x[i] );
+    xmin = MIN( xmin, data->x[i] );
+    ymax = MAX( ymax, data->y[i] );
+    ymin = MIN( ymin, data->y[i] );
+    zmax = MAX( zmax, data->z[i] );
+    zmin = MIN( zmin, data->z[i] );
+  }
+  sidemax = MAX(xmax-xmin,ymax-ymin);
+  sidemax = MAX(sidemax,zmax-zmin);
+
+  if(nomeshes > 1)  {
+    printf("Bounding box of all nodes in mesh[%d] of [%d] meshes:\n",nomesh,nomeshes);
+  }
+  else  {
+    printf("Bounding box of all nodes in mesh:\n");
+  }
+
+  printf("X:[%g,%g] ",xmin,xmax);
+  printf("Y:[%g,%g] ",ymin,ymax);
+  printf("Z:[%g,%g]\n",zmin,zmax);
+
+  if(sidemax > 49.9)  {
+    printf("\nNotice: the longest bounding box side length of [%g] is greater than 50.\n",sidemax);
+    printf("ElmerGUI includes a library of material properties, defined in SI units.  If using ElmerGUI, \n");
+    printf("then the geometry is expected to have meters as length.  Geometry that exceeds 50 meters \n");
+    printf("in length or width or height may not be intended.  Many Geometry generators assume \n");
+    printf("millimeters as the basic unit of length.  Scaling the geometry from millimeters to meters \n");
+    printf("may be the desired action.  For more help, search the Elmer users forum for posts \n");
+    printf("about SI units, or for posts about Coordinate Scaling.\n");
+    printf("Scaling can be accomplished in at least three ways, as follows:\n");
+    printf(" 1. Define the original geometry in meters, not millimeters.\n");
+    printf(" 2. Call ElmerGrid with -scale 0.001 0.001 0.001 as an option.\n");
+    printf(" 3. Add Coordinate Scaling = 0.001 to the simulation section of the sif file.\n");
+    printf("If using Elmer to analyze large geometry, such as a glacier, then ignore this notice.\n\n");
+  }
+
+  return(0);
+}
diff --git a/ElmerGUI/Application/plugins/egmesh.h b/ElmerGUI/Application/plugins/egmesh.h
@@ -112,3 +112,4 @@ int DestroyDualGraph(struct FemType *data,int info);
 int CreateInverseTopology(struct FemType *data,int info);
 int DestroyInverseTopology(struct FemType *data,int info);
 int MeshTypeStatistics(struct FemType *data,int info);
+int BoundingBox(struct FemType *data,int nomesh,int nomeshes,int info);
diff --git a/ElmerGUI/Application/plugins/egnative.cpp b/ElmerGUI/Application/plugins/egnative.cpp
@@ -1169,7 +1169,7 @@ void SetCellData(struct GridType *grid,struct CellType *cell,int info)
 
   for(j=1;j<= grid->ycells ;j++)                   /* cells direction up    */
     for(i=1;i<= grid->xcells; i++)                 /* cells direction right */      
-      if( cnew = grid->numbered[j][i] ) {          /* if cell is occupied   */
+      if( (cnew = grid->numbered[j][i]) ) {          /* if cell is occupied   */
 
         /* Initialize the numbering to zero  */
         cell[cnew].left1st = 0;

diff --git a/elmergrid/src/egmesh.c b/elmergrid/src/egmesh.c
@@ -2458,19 +2458,19 @@ int FindCorners(struct GridType *grid,struct CellType *cell,
 	continue;
 
       /* point (i,j) must now be a corner */
-      if(cellno = grid->numbered[j][i]) {
+      if((cellno = grid->numbered[j][i])) {
 	elem = GetElementIndex(&(cell)[cellno],1,1);
 	ind  = BOTLEFT;
       } 
-      else if(cellno = grid->numbered[j][i-1]) {
+      else if((cellno = grid->numbered[j][i-1])) {
 	elem = GetElementIndex(&(cell)[cellno],cell[cellno].xelem,1);
 	ind  = BOTRIGHT;
       } 
-      else if(cellno = grid->numbered[j-1][i]) {
+      else if((cellno = grid->numbered[j-1][i])) {
 	elem = GetElementIndex(&(cell)[cellno],1,cell[cellno].yelem);
 	ind  = TOPLEFT;
       } 
-      else if(cellno = grid->numbered[j-1][i-1]) {
+      else if((cellno = grid->numbered[j-1][i-1])) {
 	elem = GetElementIndex(&(cell)[cellno],cell[cellno].xelem,cell[cellno].yelem);
 	ind  = TOPRIGHT;
       }