Merge pull request #275 from awslabs/sjg/dependency-updates

Update dependency version tags

cmake/ExternalGSLIB.cmake

@@ -48,7 +48,7 @@ list(APPEND GSLIB_OPTIONS
   "BLAS=0"
 )
 
-# Configure BLAS dependency
+# # Configure BLAS dependency
 # if(NOT "${BLAS_LAPACK_LIBRARIES}" STREQUAL "")
 #   foreach(INCLUDE_DIR IN LISTS BLAS_LAPACK_INCLUDE_DIRS)
 #     set(GSLIB_CFLAGS "${GSLIB_CFLAGS} -I${INCLUDE_DIR}")

cmake/ExternalGitTags.cmake

@@ -20,7 +20,7 @@ set(EXTERN_ARPACK_GIT_BRANCH
   "Git branch for external ARPACK-NG build"
 )
 set(EXTERN_ARPACK_GIT_TAG
-  "217e25ac7c48b5d05d31120475c8e1eeaf543bbd" CACHE STRING
+  "0b3038d139f874a423ba6a1cdf5098fc15336848" CACHE STRING
   "Git tag for external ARPACK-NG build"
 )
 
@@ -34,7 +34,7 @@ set(EXTERN_BUTTERFLYPACK_GIT_BRANCH
   "Git branch for external ButterflyPACK build"
 )
 set(EXTERN_BUTTERFLYPACK_GIT_TAG
-  "7410fca61c188daab40f55c235ab7fad16ee5856" CACHE STRING
+  "28e9380ef938a46a6ac49427146fc0ea0cc9b0eb" 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
-  "0dcae3ec7c069785ea25d25aa0bc0c7aa8b0be8d" CACHE STRING
+  "5de2c5ceec9f68fa875f65bb3cfe605504c8229d" 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
-  "ef9a992f4cf09f2be4ec72f649495c67ec03f813" CACHE STRING
+  "80859cf565d67332b8cfd754474c121c2d43d208" 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
-  "953405207f32369cd74d757681ce476fe89768b6" CACHE STRING
+  "f5cb6f5d32a9527351dfce1b367e32055a1e759b" 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
-  "e20a6748d9e7067c0946036b9c6d5caa022051db" CACHE STRING
+  "5b7fc4ee3421de71393935751112a939b718c0a4" 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
-  "9a327eeca6472254e8bdefc1527aa130250e528e" CACHE STRING  # master @ 05/18/2024
+  "e13989a2934e8895bd01f2ebbc8d78102f0c0e8f" 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
-  "b00cc7c9fc6127e07d6583a8c50c727508ea1c6e" CACHE STRING
+  "c997fd6236ec157e66ede97c52a296e3930db285" 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
-  "e6938432041f05a2617386d95f6ba21e1677d3e7" CACHE STRING
+  "96e7d5cfaa07a5d3427e87ca13c8795e24a0e757" 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
-  "2c2766ada27519a79c9f9d9634b730afb4010d95" CACHE STRING
+  "ffa1d78448240d13360ff0555c46d4e767792d2c" 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
-  "c318456692bf25ff2781c48fc89297a7c7ff6c3d" CACHE STRING
+  "cf768ce0977904f2991ea9844e5164dd39a15102" 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
-  "2e39ceca001f594dc63426f2b500c82f5ce312a3" CACHE STRING
+  "ea4d47b206387a1592eea46493519d57cf3984d6" 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
-  "6aa2dae1c1bf700f062f386e81cc71796929c30e" CACHE STRING
+  "5c976d8da013988174f931845862b6f94119cade" CACHE STRING
   "Git tag for external ZFP build"
 )
 

cmake/ExternalMFEM.cmake

@@ -357,7 +357,6 @@ set(MFEM_PATCH_FILES
   "${CMAKE_SOURCE_DIR}/extern/patch/mfem/patch_mfem_device_fixes.diff"
   "${CMAKE_SOURCE_DIR}/extern/patch/mfem/patch_mesh_vis_dev.diff"
   "${CMAKE_SOURCE_DIR}/extern/patch/mfem/patch_mesh_prism_vtu_fix.diff"
-  "${CMAKE_SOURCE_DIR}/extern/patch/mfem/patch_mesh_part_const.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/ExternalMUMPS.cmake

@@ -14,7 +14,7 @@ list(APPEND MUMPS_OPTIONS
   "-DCMAKE_C_FLAGS=${CMAKE_C_FLAGS}"
   "-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}"
   "-DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}"
-  "-Dparallel=ON"
+  "-DMUMPS_parallel=ON"
   "-Dopenmp=${PALACE_WITH_OPENMP}"
   "-Dintsize64=OFF"
   "-DBUILD_SINGLE=OFF"

docs/src/developer.md

@@ -120,7 +120,7 @@ assembly routines. The unit tests source code is located in the
 [`test/unit/`](https://github.com/awslabs/palace/blob/main/test/unit/) directory, and can be
 built from within the *Palace* build directory using `make unit-tests`, or from the
 superbuild as `make palace-tests`. The unit tests can be accelerated using MPI and/or
-OpenMP parallelism(when configured with `PALACE_WITH_OPENMP=ON`), but in all cases they are
+OpenMP parallelism (when configured with `PALACE_WITH_OPENMP=ON`), but in all cases they are
 only testing the local operator assembly on each process. The 2D and 3D sample meshes in
 [`test/unit/mesh/`](https://github.com/awslabs/palace/blob/main/test/unit/mesh/) come from
 the [MFEM repository](https://github.com/mfem/mfem/tree/master/data).

docs/src/guide/parallelism.md

@@ -20,7 +20,7 @@ Lastly, *Palace* supports GPU-acceleration using NVIDIA and AMD GPUs, activated
 build options `-DPALACE_WITH_CUDA=ON` and `-DPALACE_WITH_HIP=ON`, respectively. At runtime,
 the [`config["Solver"]["Device"]`](../config/solver.md#config%5B%22Solver%22%5D) parameter
 in the configuration file can be set to `"CPU"` (the default) or `"GPU"` in order to
-configure *Palace* and MFEM to use the available GPU(s). The
+configure *Palace* and MFEM to use the available GPU device or devices. The
 [`config["Solver"]["Backend"]`](../config/solver.md#config%5B%22Solver%22%5D) parameter, on
 the other hand, controls the
 [libCEED backend](https://libceed.org/en/latest/gettingstarted/#backends). Users typically

docs/src/guide/postprocessing.md

@@ -58,7 +58,7 @@ These include:
     (associated with the specified domain attributes and indexed by the specified integer
     `"Index"`). These are from the electric and magnetic field solutions and written to the
     same `domain-E.csv` file in the specified postprocessing output directory used for the
-    global energies(described above).
+    global energies (described above).
   - [`config["Domains"]["Postprocessing"]["Probe"]`](../config/domains.md#domains%5B%22Postprocessing%22%5D%5B%22Probe%22%5D) :
     Probe the values of the computed electric field and magnetic flux density solutions at
     specified locations in the computational domain. The availability of the ``\bm{E}`` and

docs/src/guide/problem.md

@@ -62,7 +62,7 @@ type and stored in an ASCII file named `port-S.csv`, in the directory specified
 ``\text{dB}`` magnitude (``20\log_{10}(|S_{ij}|)``) and the phase ``\angle(S_{ij})``
 (in degrees) are written to the file. In the case that more than a single lumped or wave
 port is excited or surface current excitations are used, scattering parameter output will
-be disabled for the simulation(though other quantities of interest are still
+be disabled for the simulation (though other quantities of interest are still
 postprocessed). When lumped ports are present, the peak complex lumped port voltages and
 currents computed for each excitation frequency are written to ASCII files named
 `port-V.csv` and `port-I.csv`, respectively, Additionally, the surface current excitations

docs/src/reference.md

@@ -298,7 +298,7 @@ where ``\bm{D}_m = \varepsilon_r\bm{E}_m`` is the electric flux density for mode
 the second term on the right-hand side accounts for any lumped capacitive boundaries with
 nonzero circuit capacitance ``C_j``.
 
-The EPR can also be used to estimate mode quality factors due to input-output(I-O) line
+The EPR can also be used to estimate mode quality factors due to input-output (I-O) line
 coupling. The mode coupling quality factor due to the ``j``-th I-O port is given by
 
 ```math

extern/patch/gslib/patch_build.diff

@@ -750,10 +750,10 @@ index 42c335c..62561ff 100644
  #define DIAGNOSTICS_1
  #define DIAGNOSTICS_2
 diff --git a/src/findpts_imp.h b/src/findpts_imp.h
-index b9759af..44b5c7d 100644
+index b9759af..8c08479 100644
 --- a/src/findpts_imp.h
 +++ b/src/findpts_imp.h
-@@ -1,45 +1,45 @@
+@@ -1,45 +1,44 @@
  #include <stdio.h>
  #include <float.h>
 -#define obbox           TOKEN_PASTE(obbox_,D)
@@ -834,11 +834,22 @@ index b9759af..44b5c7d 100644
 +#define findpts_free          GS_TOKEN_PASTE(GS_PREFIXED_NAME(findpts_free_ ),D)
 +#define findpts               GS_TOKEN_PASTE(GS_PREFIXED_NAME(findpts_      ),D)
 +#define findpts_eval          GS_TOKEN_PASTE(GS_PREFIXED_NAME(findpts_eval_ ),D)
-+#define findpts_local_eval    GS_TOKEN_PASTE(GS_PREFIXED_NAME(findpts_local_eval_ ),D)
 +#define setup_fev_aux         GS_TOKEN_PASTE(setup_fev_aux_,D)
 
  struct hash_data {
    ulong hash_n;
+@@ -279,7 +278,10 @@ void findptsms(        uint   *const        code_base, const unsigned       code
+                  const uint   *const session_id_match, const uint                   npt,
+                        struct findpts_data *const fd)
+ {
+-  if (fd->fevsetup==1) array_free(&fd->savpt); fd->fevsetup=0;
++  if (fd->fevsetup==1) {
++    array_free(&fd->savpt);
++    fd->fevsetup=0;
++  }
+   const uint np = fd->cr.comm.np, id=fd->cr.comm.id;
+   struct array hash_pt, src_pt, out_pt;
+   double *distv = tmalloc(double,npt);
 diff --git a/src/findpts_local.h b/src/findpts_local.h
 index 2a9d9da..30be675 100644
 --- a/src/findpts_local.h
@@ -899,7 +910,7 @@ index 2a9d9da..30be675 100644
    uint hash_n;
    struct dbl_range bnd[3];
 diff --git a/src/findpts_local_imp.h b/src/findpts_local_imp.h
-index e5310b1..0ca79fd 100644
+index e5310b1..401089d 100644
 --- a/src/findpts_local_imp.h
 +++ b/src/findpts_local_imp.h
 @@ -1,36 +1,36 @@
@@ -971,6 +982,15 @@ index e5310b1..0ca79fd 100644
  /*--------------------------------------------------------------------------
     Point to Possible Elements Hashing
 
+@@ -466,7 +466,7 @@ void findpts_local_eval(
+   const uint npt,
+   const double *const in, struct findpts_local_data *const fd)
+ {
+-  findpts_local_eval(
++  findptsms_local_eval(
+   out_base,out_stride,
+    el_base,el_stride,
+     r_base,r_stride,
 diff --git a/src/gs.c b/src/gs.c
 index 68581b3..e3a7b70 100644
 --- a/src/gs.c