Add signedVolume() to Polyhedron class, add intel oneAPI config (#1186)

LLNL · Sep 19, 2023 · 9a25422 · 9a25422
1 parent 80889b6
commit 9a25422
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diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
@@ -26,6 +26,11 @@ The Axom project release numbers follow [Semantic Versioning](http://semver.org/
   - `DistributedClosestPoint::computeClosestPoints`
   - `MarchingCubes::MarchingCubes`
   - `MarchingCubesSingleDomain::MarchingCubesSingleDomain`
+- Primal: `Polyhedron::volume()` function changed from returning a signed
+  volume to an unsigned volume. The added `Polyhedron::signedVolume()` function
+  returns the signed volume.
+- Primal: `intersection_volume()` operators changed from returning a signed
+  volume to an unsigned volume.
 
 ### Fixed
 - quest's `SamplingShaper` now properly handles material names containing underscores

diff --git a/host-configs/rzwhippet-toss_4_x86_64_ib-intel@2022.1.0.cmake b/host-configs/rzwhippet-toss_4_x86_64_ib-intel@2022.1.0.cmake
@@ -0,0 +1,110 @@
+#------------------------------------------------------------------------------
+# !!!! This is a generated file, edit at own risk !!!!
+#------------------------------------------------------------------------------
+# CMake executable path: /usr/tce/bin/cmake
+#------------------------------------------------------------------------------
+
+set(CMAKE_PREFIX_PATH "/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/umpire-2023.06.0-6wmifjy5c2er4kkfqw7m5s4in7esiln5;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/raja-2023.06.0-urtfojwbjummyvyev7k4zn2oix53f4up;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/camp-2023.06.0-ovewmmz43udq34jrdlokh2zuzgkzrum4;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/mfem-4.5.2-dbvjel6jhwnwf6wzm76w6ghbjpy3v4gj;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/hypre-2.24.0-qdjyl5ibcpl4nxb6t5godfgvi5bb6hac;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/conduit-0.8.8-22refnw4twba4zznewcuczky2udimj7i;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/parmetis-4.0.3-nqxoj5gqogj32hfo5ognkcb6vg24zdlc;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/metis-5.1.0-tb5bijmooj2d6d2npjpajcj4fyu4yd4y;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/hdf5-1.8.22-6oeginq7kyyix35utjgsfxeghcnujtpg;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/c2c-1.8.0-gvlftgplgmtput3k4fy2nssecldmmlsa;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/gmake-4.4.1-e3r4ry6vgi7zp4mbwfokypkutqwpctek;/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0/blt-0.5.3-i7qltms7ksyz4xltznzbtsafywrykq7b;/collab/usr/gapps/axom/devtools/toss_4_x86_64_ib/latest/python-3.10.10;/collab/usr/gapps/axom/devtools/toss_4_x86_64_ib/latest/python-3.10.10;/collab/usr/gapps/axom/devtools/toss_4_x86_64_ib/latest/python-3.10.10;/collab/usr/gapps/axom/devtools/toss_4_x86_64_ib/latest/llvm-10.0.0;/collab/usr/gapps/axom/devtools/toss_4_x86_64_ib/latest/doxygen-1.8.14;/collab/usr/gapps/axom/devtools/toss_4_x86_64_ib/latest/cppcheck-2.9;/usr/tce/packages/mvapich2/mvapich2-2.3.6-intel-2022.1.0;/usr/tce" CACHE PATH "")
+
+set(CMAKE_BUILD_TYPE "Release" CACHE STRING "")
+
+#------------------------------------------------------------------------------
+# Compilers
+#------------------------------------------------------------------------------
+# Compiler Spec: intel@=2022.1.0
+#------------------------------------------------------------------------------
+if(DEFINED ENV{SPACK_CC})
+
+  set(CMAKE_C_COMPILER "/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/spack/lib/spack/env/intel/icc" CACHE PATH "")
+
+  set(CMAKE_CXX_COMPILER "/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/spack/lib/spack/env/intel/icpc" CACHE PATH "")
+
+  set(CMAKE_Fortran_COMPILER "/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/spack/lib/spack/env/intel/ifort" CACHE PATH "")
+
+else()
+
+  set(CMAKE_C_COMPILER "/usr/tce/packages/intel/intel-2022.1.0/compiler/2022.1.0/linux/bin/icx" CACHE PATH "")
+
+  set(CMAKE_CXX_COMPILER "/usr/tce/packages/intel/intel-2022.1.0/compiler/2022.1.0/linux/bin/icpx" CACHE PATH "")
+
+  set(CMAKE_Fortran_COMPILER "/usr/tce/packages/intel/intel-2022.1.0/compiler/2022.1.0/linux/bin/ifx" CACHE PATH "")
+
+endif()
+
+set(CMAKE_GENERATOR "Unix Makefiles" CACHE STRING "")
+
+set(ENABLE_FORTRAN ON CACHE BOOL "")
+
+#------------------------------------------------------------------------------
+# MPI
+#------------------------------------------------------------------------------
+
+set(MPI_C_COMPILER "/usr/tce/packages/mvapich2/mvapich2-2.3.6-intel-2022.1.0/bin/mpicc" CACHE PATH "")
+
+set(MPI_CXX_COMPILER "/usr/tce/packages/mvapich2/mvapich2-2.3.6-intel-2022.1.0/bin/mpicxx" CACHE PATH "")
+
+set(MPI_Fortran_COMPILER "/usr/tce/packages/mvapich2/mvapich2-2.3.6-intel-2022.1.0/bin/mpif90" CACHE PATH "")
+
+set(MPIEXEC_NUMPROC_FLAG "-n" CACHE STRING "")
+
+set(ENABLE_MPI ON CACHE BOOL "")
+
+set(MPIEXEC_EXECUTABLE "/usr/bin/srun" CACHE PATH "")
+
+#------------------------------------------------------------------------------
+# Hardware
+#------------------------------------------------------------------------------
+
+#------------------------------------------------
+# Hardware Specifics
+#------------------------------------------------
+
+set(ENABLE_OPENMP ON CACHE BOOL "")
+
+set(ENABLE_GTEST_DEATH_TESTS ON CACHE BOOL "")
+
+#------------------------------------------------------------------------------
+# TPLs
+#------------------------------------------------------------------------------
+
+set(TPL_ROOT "/usr/WS1/axom/libs/toss_4_x86_64_ib/2023_08_30_10_09_12/intel-2022.1.0" CACHE PATH "")
+
+set(CONDUIT_DIR "${TPL_ROOT}/conduit-0.8.8-22refnw4twba4zznewcuczky2udimj7i" CACHE PATH "")
+
+set(C2C_DIR "${TPL_ROOT}/c2c-1.8.0-gvlftgplgmtput3k4fy2nssecldmmlsa" CACHE PATH "")
+
+set(MFEM_DIR "${TPL_ROOT}/mfem-4.5.2-dbvjel6jhwnwf6wzm76w6ghbjpy3v4gj" CACHE PATH "")
+
+set(HDF5_DIR "${TPL_ROOT}/hdf5-1.8.22-6oeginq7kyyix35utjgsfxeghcnujtpg" CACHE PATH "")
+
+set(LUA_DIR "/usr" CACHE PATH "")
+
+set(RAJA_DIR "${TPL_ROOT}/raja-2023.06.0-urtfojwbjummyvyev7k4zn2oix53f4up" CACHE PATH "")
+
+set(UMPIRE_DIR "${TPL_ROOT}/umpire-2023.06.0-6wmifjy5c2er4kkfqw7m5s4in7esiln5" CACHE PATH "")
+
+set(CAMP_DIR "${TPL_ROOT}/camp-2023.06.0-ovewmmz43udq34jrdlokh2zuzgkzrum4" CACHE PATH "")
+
+# scr not built
+
+#------------------------------------------------------------------------------
+# Devtools
+#------------------------------------------------------------------------------
+
+set(DEVTOOLS_ROOT "/collab/usr/gapps/axom/devtools/toss_4_x86_64_ib/2023_05_18_11_52_05/._view/btoxy5ovdbouub2brzxcmjwzdhvzatlc" CACHE PATH "")
+
+set(CLANGFORMAT_EXECUTABLE "/collab/usr/gapps/axom/devtools/toss_4_x86_64_ib/latest/llvm-10.0.0/bin/clang-format" CACHE PATH "")
+
+set(PYTHON_EXECUTABLE "${DEVTOOLS_ROOT}/python-3.10.10/bin/python3.10" CACHE PATH "")
+
+set(ENABLE_DOCS ON CACHE BOOL "")
+
+set(SPHINX_EXECUTABLE "${DEVTOOLS_ROOT}/python-3.10.10/bin/sphinx-build" CACHE PATH "")
+
+set(SHROUD_EXECUTABLE "${DEVTOOLS_ROOT}/python-3.10.10/bin/shroud" CACHE PATH "")
+
+set(CPPCHECK_EXECUTABLE "${DEVTOOLS_ROOT}/cppcheck-2.9/bin/cppcheck" CACHE PATH "")
+
+set(DOXYGEN_EXECUTABLE "${DEVTOOLS_ROOT}/doxygen-1.8.14/bin/doxygen" CACHE PATH "")
+
+
diff --git a/scripts/azure-pipelines/linux-build_and_test.sh b/scripts/azure-pipelines/linux-build_and_test.sh
@@ -33,9 +33,9 @@ if [[ "$DO_BUILD" == "yes" ]] ; then
     or_die cd build-$HOST_CONFIG-${BUILD_TYPE,,}
     echo "~~~~~~ BUILDING ~~~~~~~~"
     if [[ ${CMAKE_EXTRA_FLAGS} == *COVERAGE* ]] ; then
-        or_die make -j 10
+        or_die make -j 8
     else
-        or_die make -j 10 VERBOSE=1
+        or_die make -j 8 VERBOSE=1
     fi
     if [[ "${DO_TEST}" == "yes" ]] ; then
         echo "~~~~~~ RUNNING TESTS ~~~~~~~~"

diff --git a/scripts/spack/configs/toss_4_x86_64_ib/spack.yaml b/scripts/spack/configs/toss_4_x86_64_ib/spack.yaml
@@ -46,6 +46,19 @@ spack:
         fc: /usr/tce/packages/gcc/gcc-10.3.1/bin/gfortran
       spec: gcc@10.3.1
       target: x86_64
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      modules: []
+      operating_system: rhel8
+      paths:
+        cc: /usr/tce/packages/intel/intel-2022.1.0/compiler/2022.1.0/linux/bin/icx
+        cxx: /usr/tce/packages/intel/intel-2022.1.0/compiler/2022.1.0/linux/bin/icpx
+        f77: /usr/tce/packages/intel/intel-2022.1.0/compiler/2022.1.0/linux/bin/ifx
+        fc: /usr/tce/packages/intel/intel-2022.1.0/compiler/2022.1.0/linux/bin/ifx
+      spec: intel@2022.1.0
+      target: x86_64
 
   packages:
     all:
@@ -86,6 +99,8 @@ spack:
         prefix: /usr/tce/packages/mvapich2/mvapich2-2.3.6-clang-14.0.6
       - spec: mvapich2@2.3.6%gcc@10.3.1 process_managers=slurm arch=linux-rhel8-ivybridge
         prefix: /usr/tce/packages/mvapich2/mvapich2-2.3.6-gcc-10.3.1
+      - spec: mvapich2@2.3.6%intel@2022.1.0 process_managers=slurm arch=linux-rhel8-ivybridge
+        prefix: /usr/tce/packages/mvapich2/mvapich2-2.3.6-intel-2022.1.0
 
     netlib-lapack:
       buildable: false

diff --git a/scripts/spack/specs.json b/scripts/spack/specs.json
@@ -22,7 +22,8 @@
 
     "toss_4_x86_64_ib":
     [ "gcc@10.3.1+devtools+hdf5+mfem+c2c",
-      "clang@14.0.6+devtools+hdf5+mfem+c2c" ],
+      "clang@14.0.6+devtools+hdf5+mfem+c2c",
+      "intel@2022.1.0+devtools+hdf5+mfem+c2c" ],
 
     "__comment__":"# Use amdgpu_target=gfx90a for tioga/rzvernal; and gfx908 for rznevada",
     "__comment__":"# -Wno-int-conversion flag needed for building HDF5",

diff --git a/src/axom/primal/geometry/Polyhedron.hpp b/src/axom/primal/geometry/Polyhedron.hpp
@@ -501,16 +501,18 @@ class Polyhedron
   }
 
   /*!
-   * \brief Finds the volume of the polyhedron.
+   * \brief Computes the signed volume of the polyhedron.
    *
-   * \return The volume of the polyhedron
+   * \return The signed volume of the polyhedron
    *
    * \note Function is based off moments() in Mike Owen's PolyClipper.
    *
    * \pre polyhedron vertex neighbors are defined, and polyhedron is 3D
+   *
+   * \sa volume()
    */
   AXOM_HOST_DEVICE
-  double volume() const
+  double signedVolume() const
   {
     double retVol = 0.0;
 
@@ -519,13 +521,13 @@ class Polyhedron
       return retVol;
     }
 
-    // Finds the volume of tetrahedrons formed from vertices of the Polyhedron
-    // faces and an arbitrary origin (the first vertex)
+    // Computes the signed volume of tetrahedra formed from vertices of the
+    // Polyhedron faces and an arbitrary origin (the first vertex)
     else
     {
       SLIC_CHECK_MSG(
         hasNeighbors(),
-        "Polyhedron::volume() is only valid with vertex neighbors.");
+        "Polyhedron::signedVolume() is only valid with vertex neighbors.");
 
       // faces is an overestimation
       int faces[MAX_VERTS * MAX_VERTS];
@@ -555,6 +557,13 @@ class Polyhedron
     return retVol / 6.;
   }
 
+  /*!
+   * \brief Returns the absolute (unsigned) volume of the polyhedron
+   * \sa signedVolume()
+   */
+  AXOM_HOST_DEVICE
+  double volume() const { return axom::utilities::abs(signedVolume()); }
+
   /*!
    * \brief Simple formatted print of a polyhedron instance
    *
@@ -661,9 +670,9 @@ class Polyhedron
  * \brief Creates a Polyhedron from a given Hexahedron's vertices.
  *
  * \param [in] hex The hexahedron
- * \param [in] checkSign If true (default is false), checks the volume of the
- *             Polyhedron is positive. If volume is negative, order of some
- *             vertices will be swapped.
+ * \param [in] checkSign If true (default is false), checks if the
+ *             signed volume of the Polyhedron is positive. If signed volume
+ *             is negative, order of some vertices will be swapped.
  *
  * \return A Polyhedron with the Hexahedron's vertices and added
  *         vertex neighbors
@@ -714,10 +723,10 @@ class Polyhedron
     poly.addNeighbors(6, {2, 7, 5});
     poly.addNeighbors(7, {3, 4, 6});
 
-    // Reverses order of vertices 1,3 and 5,7 if volume is negative
+    // Reverses order of vertices 1,3 and 5,7 if signed volume is negative
     if(checkSign)
     {
-      if(poly.volume() < 0)
+      if(poly.signedVolume() < 0)
       {
         axom::utilities::swap<Point<T, NDIMS>>(poly[1], poly[3]);
         axom::utilities::swap<Point<T, NDIMS>>(poly[5], poly[7]);
@@ -731,9 +740,9 @@ class Polyhedron
  * \brief Creates a Polyhedron from a given Octahedron's vertices.
  *
  * \param [in] oct The octahedron
- * \param [in] checkSign If true (default is false), checks the volume of the
- *             Polyhedron is positive. If volume is negative, order of some
- *             vertices will be swapped.
+ * \param [in] checkSign If true (default is false), checks if the
+ *             signed volume of the Polyhedron is positive. If signed volume
+ *             is negative, order of some vertices will be swapped.
  *
  * \return A Polyhedron with the Octahedron's vertices and added
  *         vertex neighbors
@@ -781,27 +790,12 @@ class Polyhedron
     poly.addNeighbors(5, {0, 1, 3, 4});
 
     // Reverses order of vertices 1,2 and 4,5 if volume is negative.
-    // Expanded swap operations for HIP workaround.
     if(checkSign)
     {
-      double vol = poly.volume();
-      if(vol < 0)
+      if(poly.signedVolume() < 0)
       {
-        PointType p2({poly[4][0], poly[4][1], poly[4][2]});
-        poly[4][0] = poly[5][0];
-        poly[4][1] = poly[5][1];
-        poly[4][2] = poly[5][2];
-        poly[5][0] = p2[0];
-        poly[5][1] = p2[1];
-        poly[5][2] = p2[2];
-
-        PointType p1({poly[1][0], poly[1][1], poly[1][2]});
-        poly[1][0] = poly[2][0];
-        poly[1][1] = poly[2][1];
-        poly[1][2] = poly[2][2];
-        poly[2][0] = p1[0];
-        poly[2][1] = p1[1];
-        poly[2][2] = p1[2];
+        axom::utilities::swap<PointType>(poly[1], poly[2]);
+        axom::utilities::swap<PointType>(poly[4], poly[5]);
       }
     }
 
@@ -812,9 +806,9 @@ class Polyhedron
  * \brief Creates a Polyhedron from a given Tetrahedron's vertices.
  *
  * \param [in] tet The tetrahedron
- * \param [in] checkSign If true (default is false), checks the volume of the
- *             Polyhedron is positive. If volume is negative, order of some
- *             vertices will be swapped.
+ * \param [in] checkSign If true (default is false), checks if the
+ *             signed volume of the Polyhedron is positive. If signed volume
+ *             is negative, order of some vertices will be swapped.
  *
  * \return A Polyhedron with the Tetrahedron's vertices and added
  *         vertex neighbors
@@ -858,7 +852,7 @@ class Polyhedron
     poly.addNeighbors(2, {0, 3, 1});
     poly.addNeighbors(3, {0, 1, 2});
 
-    // Reverses order of vertices 1 and 2 if volume is negative
+    // Reverses order of vertices 1 and 2 if signed volume is negative
     if(checkSign)
     {
       if(tet.signedVolume() < 0)

diff --git a/src/axom/primal/operators/clip.hpp b/src/axom/primal/operators/clip.hpp
@@ -117,9 +117,10 @@ Polygon<T, 3> clip(const Triangle<T, 3>& tri, const BoundingBox<T, 3>& bbox)
  * \param [in] hex The hexahedron to clip
  * \param [in] tet The tetrahedron to clip against
  * \param [in] eps The epsilon value
- * \param [in] checkSign If true (default is false), checks the volume of the
- *             shapes are positive. If volume is negative, order of some
- *             vertices will be swapped.
+ * \param [in] checkSign If true (default is false), checks if the
+ *             signed volume of each shape is positive. If the signed volume
+ *             of that shape is negative, order of some vertices will be
+ *             swapped for that shape.
  *
  * \return A polyhedron of the hexahedron clipped against the tetrahedron.
  *
@@ -157,9 +158,10 @@ AXOM_HOST_DEVICE Polyhedron<T, 3> clip(const Hexahedron<T, 3>& hex,
  * \param [in] tet The tetrahedron to clip against
  * \param [in] hex The hexahedron to clip
  * \param [in] eps The epsilon value
- * \param [in] checkSign If true (default is false), checks the volume of the
- *             shapes are positive. If volume is negative, order of some
- *             vertices will be swapped.
+ * \param [in] checkSign If true (default is false), checks if the
+ *             signed volume of each shape is positive. If the signed volume
+ *             of that shape is negative, order of some vertices will be
+ *             swapped for that shape.
  *
  * \return A polyhedron of the hexahedron clipped against the tetrahedron.
  *
@@ -197,9 +199,10 @@ AXOM_HOST_DEVICE Polyhedron<T, 3> clip(const Tetrahedron<T, 3>& tet,
  * \param [in] oct The octahedron to clip
  * \param [in] tet The tetrahedron to clip against
  * \param [in] eps The epsilon value
- * \param [in] checkSign If true (default is false), checks the volume of the
- *             shapes are positive. If volume is negative, order of some
- *             vertices will be swapped.
+ * \param [in] checkSign If true (default is false), checks if the
+ *             signed volume of each shape is positive. If the signed volume
+ *             of that shape is negative, order of some vertices will be
+ *             swapped for that shape.
  *
  * \return A polyhedron of the octahedron clipped against the tetrahedron.
  *
@@ -238,9 +241,10 @@ AXOM_HOST_DEVICE Polyhedron<T, 3> clip(const Octahedron<T, 3>& oct,
  * \param [in] oct The octahedron to clip
  * \param [in] tet The tetrahedron to clip against
  * \param [in] eps The epsilon value
- * \param [in] checkSign If true (default is false), checks the volume of the
- *             shapes are positive. If volume is negative, order of some
- *             vertices will be swapped.
+ * \param [in] checkSign If true (default is false), checks if the
+ *             signed volume of each shape is positive. If the signed volume
+ *             of that shape is negative, order of some vertices will be
+ *             swapped for that shape.
  *
  * \return A polyhedron of the octahedron clipped against the tetrahedron.
  *
@@ -277,9 +281,10 @@ AXOM_HOST_DEVICE Polyhedron<T, 3> clip(const Tetrahedron<T, 3>& tet,
  * \param [in] tet1 The tetrahedron to clip
  * \param [in] tet2 The tetrahedron to clip against
  * \param [in] eps The epsilon value
- * \param [in] checkSign If true (default is false), checks the volume of the
- *             shapes are positive. If volume is negative, order of some
- *             vertices will be swapped.
+ * \param [in] checkSign If true (default is false), checks if the
+ *             signed volume of each shape is positive. If the signed volume
+ *             of that shape is negative, order of some vertices will be
+ *             swapped for that shape.
  *
  * \return A polyhedron of the tetrahedron clipped against
  *         the other tetrahedron.