Update dependencies and patches

cmake/ExternalGitTags.cmake

@@ -34,7 +34,7 @@ set(EXTERN_BUTTERFLYPACK_GIT_BRANCH
   "Git branch for external ButterflyPACK build"
 )
 set(EXTERN_BUTTERFLYPACK_GIT_TAG
-  "28e9380ef938a46a6ac49427146fc0ea0cc9b0eb" CACHE STRING
+  "36e1f4a1b98451df0f561349f899e0f5d0e0b6bc" CACHE STRING
   "Git tag for external ButterflyPACK build"
 )
 
@@ -62,7 +62,7 @@ set(EXTERN_HYPRE_GIT_BRANCH
   "Git branch for external HYPRE build"
 )
 set(EXTERN_HYPRE_GIT_TAG
-  "5de2c5ceec9f68fa875f65bb3cfe605504c8229d" CACHE STRING
+  "3caa81955eb8d1b4e35d9b450e27cf6d07b50f6e" 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
-  "80859cf565d67332b8cfd754474c121c2d43d208" CACHE STRING
+  "83862665467081d1f29e1ddefe74326356b818f0" CACHE STRING
   "Git tag for external libCEED build"
 )
 
@@ -90,7 +90,7 @@ set(EXTERN_LIBXSMM_GIT_BRANCH
   "Git branch for external LIBXSMM build"
 )
 set(EXTERN_LIBXSMM_GIT_TAG
-  "f5cb6f5d32a9527351dfce1b367e32055a1e759b" CACHE STRING
+  "d10cd5d59b03c04d1b0aa2aa44f28a21cd60a062" CACHE STRING
   "Git tag for external LIBXSMM build"
 )
 
@@ -104,7 +104,7 @@ set(EXTERN_MAGMA_GIT_BRANCH
   "Git branch for external MAGMA build"
 )
 set(EXTERN_MAGMA_GIT_TAG
-  "5b7fc4ee3421de71393935751112a939b718c0a4" CACHE STRING
+  "6573c5a752da571b9c5a5c5f7cd68cc24d3c2c6d" 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
-  "e13989a2934e8895bd01f2ebbc8d78102f0c0e8f" CACHE STRING
+  "957ca0d50089795b219e4701312355f875af6019" 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
-  "c997fd6236ec157e66ede97c52a296e3930db285" CACHE STRING
+  "8cfe473232bd45a660e247ea909a670ea9186ec3" 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
-  "96e7d5cfaa07a5d3427e87ca13c8795e24a0e757" CACHE STRING
+  "4bbe91384854fec5c16b677958fdcd4ec4bdaf6b" CACHE STRING
   "Git tag for external PETSc build"
 )
 
@@ -188,7 +188,7 @@ set(EXTERN_SCALAPACK_GIT_BRANCH
   "Git branch for external ScaLAPACK build"
 )
 set(EXTERN_SCALAPACK_GIT_TAG
-  "0234af94c6578c53ac4c19f2925eb6e5c4ad6f0f" CACHE STRING
+  "25935e1a7e022ede9fd71bd86dcbaa7a3f1846b7" CACHE STRING
   "Git tag for external ScaLAPACK build"
 )
 
@@ -202,7 +202,7 @@ set(EXTERN_SLEPC_GIT_BRANCH
   "Git branch for external SLEPc build"
 )
 set(EXTERN_SLEPC_GIT_TAG
-  "ffa1d78448240d13360ff0555c46d4e767792d2c" CACHE STRING
+  "e93850835cc2843553d5b759b2277856d10dbc97" 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
-  "cf768ce0977904f2991ea9844e5164dd39a15102" CACHE STRING
+  "b964011b77e1cf6bb087a6e049f61c1c77a8e256" 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
-  "ea4d47b206387a1592eea46493519d57cf3984d6" CACHE STRING
+  "a66f013e468524b0f1508447fa2c9e9ff605c3ec" 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
-  "5c976d8da013988174f931845862b6f94119cade" CACHE STRING
+  "3b6eb55c775e8c22d89c2a584160e3fe81cf9f5a" CACHE STRING
   "Git tag for external ZFP build"
 )
 

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 c5f01b50d..645b7f167 100644
+index 377cc906e..cf06e5456 100644
 --- a/mesh/mesh_readers.cpp
 +++ b/mesh/mesh_readers.cpp
-@@ -1535,7 +1535,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1548,7 +1548,7 @@ 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 c5f01b50d..645b7f167 100644
 
     // A map containing names of physical curves, surfaces, and volumes.
     // The first index is the dimension of the physical manifold, the second
-@@ -1553,9 +1553,10 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1566,9 +1566,10 @@ 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 c5f01b50d..645b7f167 100644
 
     // Mesh order
     int mesh_order = 1;
-@@ -1576,7 +1577,6 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1589,7 +1590,6 @@ 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)
           {
-@@ -1638,7 +1638,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1651,7 +1651,7 @@ 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 c5f01b50d..645b7f167 100644
           {
              2,   // 2-node line.
              3,   // 3-node triangle.
-@@ -1848,97 +1848,324 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1861,97 +1861,324 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
 
               This corresponds to the quad9 mapping below.
           */
@@ -443,7 +443,7 @@ index c5f01b50d..645b7f167 100644
              while (n_elem_part < num_of_all_elements)
              {
                 input.read(reinterpret_cast<char*>(header),
-@@ -1946,11 +2173,10 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1959,11 +2186,10 @@ 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 c5f01b50d..645b7f167 100644
                 for (int el = 0; el < n_elem_one_type; ++el)
                 {
                    input.read(reinterpret_cast<char*>(&data[0]),
-@@ -1968,218 +2194,26 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -1981,218 +2207,26 @@ 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 c5f01b50d..645b7f167 100644
                 for (int i = 0; i < n_tags; ++i) { input >> data[i]; }
                 // physical domain - the most important value (to distinguish
                 // materials with different properties)
-@@ -2193,210 +2227,19 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -2206,210 +2240,19 @@ 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 c5f01b50d..645b7f167 100644
              } // el (all elements)
           } // if ASCII
 
-@@ -2520,81 +2363,106 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -2533,81 +2376,106 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
              Nodes_gf.SetSpace(nfes);
              Nodes_gf.MakeOwner(nfec);
 
@@ -1026,7 +1026,7 @@ index c5f01b50d..645b7f167 100644
                       }
                       vm = ho_pyr[el_order];
                       break;
-@@ -2602,62 +2470,47 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -2615,62 +2483,47 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
                       MFEM_WARNING("Unsupported Gmsh element type.");
                       break;
                 }
@@ -1121,7 +1121,7 @@ index c5f01b50d..645b7f167 100644
           }
 
           // Suppress warnings (MFEM_CONTRACT_VAR does not work here with nvcc):
-@@ -2795,7 +2648,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
+@@ -2808,7 +2661,7 @@ void Mesh::ReadGmshMesh(std::istream &input, int &curved, int &read_gf)
                 v[j] = v2v[v[j]];
              }
           }

extern/patch/mfem/patch_mesh_prism_vtu_fix.diff

@@ -1,8 +1,8 @@
 diff --git a/mesh/mesh.cpp b/mesh/mesh.cpp
-index 8b32f1eba..e18def619 100644
+index 2c6f144e9..a32ba38e8 100644
 --- a/mesh/mesh.cpp
 +++ b/mesh/mesh.cpp
-@@ -11811,7 +11811,7 @@ void Mesh::PrintVTU(std::ostream &os, int ref, VTKFormat format,
+@@ -11856,7 +11856,7 @@ void Mesh::PrintVTU(std::ostream &os, int ref, VTKFormat format,
              const int *p = VTKGeometry::VertexPermutation[geom];
              for (int k = 0; k < nv; k++, j++)
              {