Merge branch 'main' into simlapointe/complex-pc

awslabs · Dec 30, 2024 · 0dbaaec · 0dbaaec
2 parents f8eda5a + 7383601
commit 0dbaaec
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diff --git a/.github/workflows/build-and-test-linux.yml b/.github/workflows/build-and-test-linux.yml
@@ -93,12 +93,15 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: 'recursive'
-
+      - name: Configure GNU Compilers
+        run: |
+          sudo update-alternatives --install $(which gcc) gcc $(which gcc-12) 999 \
+            --slave $(which g++) g++ $(which g++-12) \
+            --slave $(which gfortran) gfortran $(which gfortran-12)
       - name: Configure Open MPI
         if: matrix.mpi == 'openmpi'
         run: |
           sudo apt-get install -y openmpi-bin libopenmpi-dev
-
       - name: Configure MPICH
         if: matrix.mpi == 'mpich'
         run: |
@@ -160,12 +163,12 @@ jobs:
           elif [[ "${{ matrix.compiler }}" == 'clang' ]]; then
             export CC=clang
             export CXX=clang++
-            export FC=gfortran-12
+            export FC=gfortran
             export LDFLAGS='-fuse-ld=lld'
           elif [[ "${{ matrix.compiler }}" == 'gcc' ]]; then
-            export CC=gcc-12
-            export CXX=g++-12
-            export FC=gfortran-12
+            export CC=gcc
+            export CXX=g++
+            export FC=gfortran
           fi
           if [[ "${{ matrix.math-libs }}" == 'aocl' ]]; then
             export AOCLROOT=/opt/AMD/aocl/aocl-linux-gcc-4.1.0/gcc

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -168,10 +168,10 @@ test-build-aocl:
   script:
     # Install AMD Optimizing CPU Libraries (AOCL)
     - apt-get install -y libmpich-dev
-    - wget https://download.amd.com/developer/eula/aocl/aocl-4-1/aocl-linux-gcc-4.1.0_1_amd64.deb
-    - apt-get install -y ./aocl-linux-gcc-4.1.0_1_amd64.deb
+    - wget https://download.amd.com/developer/eula/aocl/aocl-5-0/aocl-linux-gcc-5.0.0_1_amd64.deb
+    - apt-get install -y ./aocl-linux-gcc-5.0.0_1_amd64.deb
     - rm aocl-linux-gcc-*.deb
-    - export AOCLROOT=/opt/AMD/aocl/aocl-linux-gcc-4.1.0/gcc
+    - export AOCLROOT=/opt/AMD/aocl/aocl-linux-gcc-5.0.0/gcc
     - export LD_LIBRARY_PATH=$AOCLROOT/lib:$LD_LIBRARY_PATH
     - mkdir build && cd build
     - cmake ..

diff --git a/cmake/ExternalGitTags.cmake b/cmake/ExternalGitTags.cmake
@@ -34,7 +34,7 @@ set(EXTERN_BUTTERFLYPACK_GIT_BRANCH
   "Git branch for external ButterflyPACK build"
 )
 set(EXTERN_BUTTERFLYPACK_GIT_TAG
-  "cbde1bb675a5bd74b778eb29f6b9dacc0607542c" CACHE STRING
+  "3ea057d9c00b319c854361e8d38b18f80b35d09c" CACHE STRING
   "Git tag for external ButterflyPACK build"
 )
 
@@ -48,7 +48,7 @@ set(EXTERN_GSLIB_GIT_BRANCH
   "Git branch for external GSLIB build"
 )
 set(EXTERN_GSLIB_GIT_TAG
-  "d5d4ee04ad4d32bebfef730a3608cbe988223dbd" CACHE STRING
+  "95acf5b42301d6cb48fda88d662f1d784b863089" CACHE STRING
   "Git tag for external GSLIB build"
 )
 
@@ -62,7 +62,7 @@ set(EXTERN_HYPRE_GIT_BRANCH
   "Git branch for external HYPRE build"
 )
 set(EXTERN_HYPRE_GIT_TAG
-  "aa1f66d633b144eae83edf89937d2316d2d63268" CACHE STRING
+  "e5f4984ea0cceb897d3d29516988f38996d7d07d" CACHE STRING
   "Git tag for external HYPRE build"
 )
 
@@ -76,7 +76,7 @@ set(EXTERN_LIBCEED_GIT_BRANCH
   "Git branch for external libCEED build"
 )
 set(EXTERN_LIBCEED_GIT_TAG
-  "be8d6f551b0f7f956d1f45b9192fb65aa4e4d3da" CACHE STRING
+  "5a7f61ca9ae98f99006c9d3babed48bcc256dfea" CACHE STRING
   "Git tag for external libCEED build"
 )
 
@@ -90,21 +90,21 @@ set(EXTERN_LIBXSMM_GIT_BRANCH
   "Git branch for external LIBXSMM build"
 )
 set(EXTERN_LIBXSMM_GIT_TAG
-  "bbc71343595f9b71664d0985b02e87e0654c8cdc" CACHE STRING
+  "b4514e4c52b6c735c30700992b1966e7c9dcdcae" CACHE STRING
   "Git tag for external LIBXSMM build"
 )
 
 # MAGMA
 set(EXTERN_MAGMA_URL
-  "https://bitbucket.org/icl/magma.git" CACHE STRING
+  "https://github.com/icl-utk-edu/magma.git" CACHE STRING
   "URL for external MAGMA build"
 )
 set(EXTERN_MAGMA_GIT_BRANCH
   "master" CACHE STRING
   "Git branch for external MAGMA build"
 )
 set(EXTERN_MAGMA_GIT_TAG
-  "4917e80ca559d0e0d4fdb56abfca381639f9b821" CACHE STRING
+  "95903129f839bb401d9d9c53bd3d8e1b5e14c238" CACHE STRING
   "Git tag for external MAGMA build"
 )
 
@@ -132,7 +132,7 @@ set(EXTERN_MFEM_GIT_BRANCH
   "Git branch for external MFEM build"
 )
 set(EXTERN_MFEM_GIT_TAG
-  "7c1a0eb5e3f70ff9d161c9d6e3f228ba2513acca" CACHE STRING
+  "e2a20d381c3e180d77cd2ad32df30580f42c261b" CACHE STRING
   "Git tag for external MFEM build"
 )
 
@@ -146,7 +146,7 @@ set(EXTERN_MUMPS_GIT_BRANCH
   "Git branch for external MUMPS build"
 )
 set(EXTERN_MUMPS_GIT_TAG
-  "1324a3358aae44279b6af4630609956f06131d6f" CACHE STRING
+  "0f50568b2fbd88413774d2ce1c88ab3851b24abe" CACHE STRING
   "Git tag for external MUMPS build"
 )
 
@@ -174,7 +174,7 @@ set(EXTERN_PETSC_GIT_BRANCH
   "Git branch for external PETSc build"
 )
 set(EXTERN_PETSC_GIT_TAG
-  "2ad7182b1093845a8c26c56c2f6611a55c3328ce" CACHE STRING
+  "ba43b2edcffc84c955e282b517bbd116334b0005" CACHE STRING
   "Git tag for external PETSc build"
 )
 
@@ -202,7 +202,7 @@ set(EXTERN_SLEPC_GIT_BRANCH
   "Git branch for external SLEPc build"
 )
 set(EXTERN_SLEPC_GIT_TAG
-  "89b995ba7ee626d15a64b368ee92d6d4a4f6d6fb" CACHE STRING
+  "616e8b6ac8dbb41a1dc314e5c099b8af246c688d" CACHE STRING
   "Git tag for external SLEPc build"
 )
 
@@ -216,7 +216,7 @@ set(EXTERN_STRUMPACK_GIT_BRANCH
   "Git branch for external STRUMPACK build"
 )
 set(EXTERN_STRUMPACK_GIT_TAG
-  "9a45f304f21e1d9c44c6fa50ac2f044ab15cf342" CACHE STRING
+  "115b152be9a5d0d77846e3694f699c53c93fe394" CACHE STRING
   "Git tag for external STRUMPACK build"
 )
 
@@ -230,7 +230,7 @@ set(EXTERN_SUPERLU_GIT_BRANCH
   "Git branch for external SuperLU_DIST build"
 )
 set(EXTERN_SUPERLU_GIT_TAG
-  "b3193e8615b5364f4e5650297d9e2aaf2e49c909" CACHE STRING
+  "fe0e4e8968c58309fd75b4d6999580c44fffc26d" CACHE STRING
   "Git tag for external SuperLU_DIST build"
 )
 
@@ -244,7 +244,7 @@ set(EXTERN_ZFP_GIT_BRANCH
   "Git branch for external ZFP build"
 )
 set(EXTERN_ZFP_GIT_TAG
-  "a46fa8b91bf2d69f4ffcf04af4f908383828ba79" CACHE STRING
+  "71490d236e29af2968dc9e11f14cb46af37f1dd3" CACHE STRING
   "Git tag for external ZFP build"
 )
 
@@ -276,6 +276,6 @@ set(EXTERN_SUNDIALS_GIT_BRANCH
   "Git branch for external SUNDIALS build"
 )
 set(EXTERN_SUNDIALS_GIT_TAG
-  "aaeab8d907c6b7dfca86041401fdc1448f35f826" CACHE STRING
+  "0eff39663606f2ff280c4059a947ed62ae38180a" CACHE STRING
   "Git tag for external SUNDIALS build"
 )
diff --git a/cmake/ExternalMFEM.cmake b/cmake/ExternalMFEM.cmake
@@ -388,6 +388,7 @@ set(MFEM_PATCH_FILES
   "${CMAKE_SOURCE_DIR}/extern/patch/mfem/patch_mesh_prism_vtu_fix.diff"
   "${CMAKE_SOURCE_DIR}/extern/patch/mfem/patch_par_tet_mesh_fix_dev.diff"
   "${CMAKE_SOURCE_DIR}/extern/patch/mfem/patch_gmsh_parser_performance.diff"
+  "${CMAKE_SOURCE_DIR}/extern/patch/mfem/patch_gmsh_reader_periodic_bugfix.diff"
 )
 
 include(ExternalProject)

diff --git a/extern/patch/mfem/patch_gmsh_parser_performance.diff b/extern/patch/mfem/patch_gmsh_parser_performance.diff
@@ -1,8 +1,8 @@
 diff --git a/mesh/mesh_readers.cpp b/mesh/mesh_readers.cpp
-index 377cc906e..cf06e5456 100644
+index d21bc481e..62bd0b8d8 100644
 --- a/mesh/mesh_readers.cpp
 +++ b/mesh/mesh_readers.cpp
-@@ -1548,7 +1548,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1549,7 +1549,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
     // A map between a serial number of the vertex and its number in the file
     // (there may be gaps in the numbering, and also Gmsh enumerates vertices
     // starting from 1, not 0)
@@ -11,7 +11,7 @@ index 377cc906e..cf06e5456 100644
 
     // A map containing names of physical curves, surfaces, and volumes.
     // The first index is the dimension of the physical manifold, the second
-@@ -1566,9 +1566,10 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1567,9 +1567,10 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
     // is non-trivial. Note that with these assumptions a 2D mesh parallel to the
     // yz plane will be considered a surface mesh embedded in 3D whereas the same
     // 2D mesh parallel to the xy plane will be considered a 2D mesh.
@@ -25,15 +25,15 @@ index 377cc906e..cf06e5456 100644
 
     // Mesh order
     int mesh_order = 1;
-@@ -1589,7 +1590,6 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1590,7 +1591,6 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
           getline(input, buff);
           vertices.SetSize(NumOfVertices);
           int serial_number;
 -         const int gmsh_dim = 3; // Gmsh always outputs 3 coordinates
           real_t coord[gmsh_dim];
           for (int ver = 0; ver < NumOfVertices; ++ver)
           {
-@@ -1651,7 +1651,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1652,7 +1652,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
 
           // number of nodes for each type of Gmsh elements, type is the index of
           // the array + 1
@@ -42,7 +42,7 @@ index 377cc906e..cf06e5456 100644
           {
              2,   // 2-node line.
              3,   // 3-node triangle.
-@@ -1861,97 +1861,324 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1862,97 +1862,324 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
 
               This corresponds to the quad9 mapping below.
           */
@@ -443,7 +443,7 @@ index 377cc906e..cf06e5456 100644
              while (n_elem_part < num_of_all_elements)
              {
                 input.read(reinterpret_cast<char*>(header),
-@@ -1959,11 +2186,10 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1960,11 +2187,10 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
                 type_of_element = header[0];
                 n_elem_one_type = header[1];
                 n_tags          = header[2];
@@ -456,7 +456,7 @@ index 377cc906e..cf06e5456 100644
                 for (int el = 0; el < n_elem_one_type; ++el)
                 {
                    input.read(reinterpret_cast<char*>(&data[0]),
-@@ -1981,218 +2207,26 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1982,218 +2208,26 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
                    n_partitions = (n_tags > 2) ? data[dd++] : 0;
                    // we currently just skip the partitions if they exist, and go
                    // directly to vertices describing the mesh element
@@ -680,7 +680,7 @@ index 377cc906e..cf06e5456 100644
                 for (int i = 0; i < n_tags; ++i) { input >> data[i]; }
                 // physical domain - the most important value (to distinguish
                 // materials with different properties)
-@@ -2206,210 +2240,19 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -2207,210 +2241,19 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
                 // we currently just skip the partitions if they exist, and go
                 // directly to vertices describing the mesh element
                 const int n_elem_nodes = nodes_of_gmsh_element[type_of_element-1];
@@ -896,7 +896,7 @@ index 377cc906e..cf06e5456 100644
              } // el (all elements)
           } // if ASCII
 
-@@ -2533,81 +2376,106 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -2534,81 +2377,106 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
              Nodes_gf.SetSpace(nfes);
              Nodes_gf.MakeOwner(nfec);
 
@@ -1026,7 +1026,7 @@ index 377cc906e..cf06e5456 100644
                       }
                       vm = ho_pyr[el_order];
                       break;
-@@ -2615,62 +2483,47 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -2616,62 +2484,47 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
                       MFEM_WARNING("Unsupported Gmsh element type.");
                       break;
                 }
@@ -1121,7 +1121,7 @@ index 377cc906e..cf06e5456 100644
           }
 
           // Suppress warnings (MFEM_CONTRACT_VAR does not work here with nvcc):
-@@ -2808,7 +2661,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -2809,7 +2662,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
                 v[j] = v2v[v[j]];
              }
           }

diff --git a/extern/patch/mfem/patch_gmsh_reader_periodic_bugfix.diff b/extern/patch/mfem/patch_gmsh_reader_periodic_bugfix.diff
@@ -0,0 +1,15 @@
+diff --git a/mesh/mesh_readers.cpp b/mesh/mesh_readers.cpp
+index 62bd0b8d8..d04762567 100644
+--- a/mesh/mesh_readers.cpp
++++ b/mesh/mesh_readers.cpp
+@@ -2690,10 +2690,6 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+    }
+
+    this->RemoveUnusedVertices();
+-   if (periodic)
+-   {
+-      this->RemoveInternalBoundaries();
+-   }
+    this->FinalizeTopology();
+
+    // If a high order coordinate field was created project it onto the mesh
diff --git a/extern/patch/mfem/patch_mesh_prism_vtu_fix.diff b/extern/patch/mfem/patch_mesh_prism_vtu_fix.diff
@@ -1,8 +1,8 @@
 diff --git a/mesh/mesh.cpp b/mesh/mesh.cpp
-index 2c6f144e9..a32ba38e8 100644
+index c852cb52e..5270e8c71 100644
 --- a/mesh/mesh.cpp
 +++ b/mesh/mesh.cpp
-@@ -11856,7 +11856,7 @@ void Mesh::PrintVTU(std::ostream &os, int ref, VTKFormat format,
+@@ -11908,7 +11908,7 @@ void Mesh::PrintVTU(std::ostream &os, int ref, VTKFormat format,
              const int *p = VTKGeometry::VertexPermutation[geom];
              for (int k = 0; k < nv; k++, j++)
              {