Initial MIR component

.gitlab/build_ruby.yml

@@ -24,13 +24,13 @@
 # Template
 .src_build_on_ruby:
   variables:
-    ALLOC_TIME: "30"
+    ALLOC_TIME: "40"
   extends: [.src_build_script, .on_ruby, .src_workflow]
   needs: []
 
 .full_build_on_ruby:
   variables:
-    ALLOC_TIME: "60"
+    ALLOC_TIME: "70"
   extends: [.full_build_script, .on_ruby, .full_workflow]
   needs: []
 

RELEASE-NOTES.md

@@ -20,6 +20,11 @@ The Axom project release numbers follow [Semantic Versioning](http://semver.org/
 ## [Unreleased] - Release date yyyy-mm-dd
 
 ###  Added
+- Added a new "Mir" Axom component for accelerated Material Interface Reconstruction (MIR) algorithms.
+  MIR algorithms take Blueprint meshes with a matset and they use the matset's material information
+  to split any input zones that contain multiple materials into zones that contain a single material.
+  The Mir component provides an implementation of the Equi-Z MIR algorithm, which is a visualization-
+  oriented algorithm that produces smooth interfaces between zones and their neighbors.
 - Support in `quest::IntersectionShaper` for Blueprint mesh stored in a `conduit::Node`
   or `sidre::Group`.
 - Adds new CMake configuration options, `AXOM_ENABLE_ASAN` and `AXOM_ENABLE_UBSAN`, to enable/disable AddressSanitizer and UndefinedBehaviorSanitizer respectively in Axom. Default is OFF for both.

azure-pipelines.yml

@@ -17,7 +17,7 @@ variables:
 jobs:
 - job: Build_and_Test
 
-  timeoutInMinutes: 90
+  timeoutInMinutes: 120
 
   strategy:
     matrix:
@@ -48,7 +48,7 @@ jobs:
       linux_clang14_noraja:
         VM_ImageName: 'ubuntu-22.04'
         Compiler_ImageName: '$(CLANG14_IMAGENAME)'
-        CMAKE_EXTRA_FLAGS: '-DBUILD_SHARED_LIBS=ON -DAXOM_QUEST_ENABLE_EXTRA_REGRESSION_TESTS:BOOL=ON -U RAJA_DIR'
+        CMAKE_EXTRA_FLAGS: '-DBUILD_SHARED_LIBS=ON -DAXOM_QUEST_ENABLE_EXTRA_REGRESSION_TESTS:BOOL=ON -DAXOM_ENABLE_MIR:BOOL=OFF -U RAJA_DIR'
         BUILD_TYPE: 'Debug'
         COMPILER: 'clang++'
         TEST_TARGET: 'linux_clang14'
@@ -64,7 +64,7 @@ jobs:
       linux_clang14_noraja_noumpire:
         VM_ImageName: 'ubuntu-22.04'
         Compiler_ImageName: '$(CLANG14_IMAGENAME)'
-        CMAKE_EXTRA_FLAGS: '-DBUILD_SHARED_LIBS=ON -DAXOM_QUEST_ENABLE_EXTRA_REGRESSION_TESTS:BOOL=ON -U RAJA_DIR -U UMPIRE_DIR'
+        CMAKE_EXTRA_FLAGS: '-DBUILD_SHARED_LIBS=ON -DAXOM_QUEST_ENABLE_EXTRA_REGRESSION_TESTS:BOOL=ON -DAXOM_ENABLE_MIR:BOOL=OFF -U RAJA_DIR -U UMPIRE_DIR'
         BUILD_TYPE: 'Debug'
         COMPILER: 'clang++'
         TEST_TARGET: 'linux_clang14'
@@ -79,11 +79,11 @@ jobs:
         HOST_CONFIG: 'clang@14.0.0'
       osx_gcc:
         VM_ImageName: 'macos-13'
-        CMAKE_EXTRA_FLAGS: '-DAXOM_ENABLE_SIDRE:BOOL=OFF -DAXOM_ENABLE_INLET:BOOL=OFF -DAXOM_ENABLE_KLEE:BOOL=OFF -DAXOM_ENABLE_SINA:BOOL=OFF'
+        CMAKE_EXTRA_FLAGS: '-DAXOM_ENABLE_SIDRE:BOOL=OFF -DAXOM_ENABLE_INLET:BOOL=OFF -DAXOM_ENABLE_KLEE:BOOL=OFF -DAXOM_ENABLE_SINA:BOOL=OFF -DAXOM_ENABLE_MIR:BOOL=OFF'
         TEST_TARGET: 'osx_gcc'
       windows:
         VM_ImageName: 'windows-2019'
-        CMAKE_EXTRA_FLAGS: '-DAXOM_ENABLE_SIDRE:BOOL=OFF -DAXOM_ENABLE_INLET:BOOL=OFF -DAXOM_ENABLE_KLEE:BOOL=OFF -DAXOM_ENABLE_SINA:BOOL=OFF'
+        CMAKE_EXTRA_FLAGS: '-DAXOM_ENABLE_SIDRE:BOOL=OFF -DAXOM_ENABLE_INLET:BOOL=OFF -DAXOM_ENABLE_KLEE:BOOL=OFF -DAXOM_ENABLE_SINA:BOOL=OFF -DAXOM_ENABLE_MIR:BOOL=OFF'
         TEST_TARGET: 'win_vs'
 
   pool:

config-build.py

@@ -84,6 +84,10 @@ def parse_arguments():
         help="Create an eclipse project file.",
     )
 
+    parser.add_argument(
+        "-n", "--ninja", action="store_true", help="Create a Ninja project."
+    )
+
     parser.add_argument(
         "-x", "--xcode", action="store_true", help="Create an xcode project."
     )
@@ -270,6 +274,9 @@ def create_cmake_command_line(
     if args.eclipse:
         cmakeline += ' -G "Eclipse CDT4 - Unix Makefiles"'
 
+    if args.ninja:
+        cmakeline += ' -G "Ninja"'
+
     if args.xcode:
         cmakeline += ' -G "Xcode"'
 

scripts/azure-pipelines/linux-build_and_test.sh

@@ -28,18 +28,21 @@ export BUILD_TYPE=${BUILD_TYPE:-Debug}
 
 
 if [[ "$DO_BUILD" == "yes" ]] ; then
+    echo "~~~~~~ FIND NUMPROCS ~~~~~~~~"
+    NUMPROCS=`python3 -c "import os; print(f'{os.cpu_count()}')"`
+    NUM_BUILD_PROCS=`python3 -c "import os; print(f'{max(2, os.cpu_count() * 8 // 10)}')"`
     echo "~~~~~~ RUNNING CMAKE ~~~~~~~~"
     or_die python3 ./config-build.py -hc /home/axom/axom/host-configs/docker/${HOST_CONFIG}.cmake -bt ${BUILD_TYPE} -DENABLE_GTEST_DEATH_TESTS=ON ${CMAKE_EXTRA_FLAGS}
     or_die cd build-$HOST_CONFIG-${BUILD_TYPE,,}
     echo "~~~~~~ BUILDING ~~~~~~~~"
     if [[ ${CMAKE_EXTRA_FLAGS} == *COVERAGE* ]] ; then
-        or_die make -j 8
+        or_die make -j $NUM_BUILD_PROCS
     else
-        or_die make -j 8 VERBOSE=1
+        or_die make -j $NUM_BUILD_PROCS VERBOSE=1
     fi
     if [[ "${DO_TEST}" == "yes" ]] ; then
         echo "~~~~~~ RUNNING TESTS ~~~~~~~~"
-        make CTEST_OUTPUT_ON_FAILURE=1 test ARGS='-T Test -VV -j8'
+        make CTEST_OUTPUT_ON_FAILURE=1 test ARGS='-T Test -VV -j$NUM_BUILD_PROCS'
     fi
     if [[ "${DO_BENCHMARKS}" == "yes" ]] ; then
         echo "~~~~~~ RUNNING BENCHMARKS ~~~~~~~~"

scripts/benchmarks/mir_concentric_circles.py

@@ -0,0 +1,80 @@
+import os, sys
+
+runs = {
+  "build-rzansel-blueos_3_ppc64le_ib_p9-clang@10.0.1.2_cuda-release" : ["seq", "omp", "cuda"],
+  "build-rzwhippet-toss_4_x86_64_ib-clang@14.0.6-release" : ["seq", "omp"],
+  "build-rzwhippet-toss_4_x86_64_ib-gcc@10.3.1-release" : ["seq", "omp"],
+  "build-rzwhippet-toss_4_x86_64_ib-intel@2022.1.0-release" : ["seq", "omp"],
+  "build-rzvernal-toss_4_x86_64_ib_cray-clang@17.0.0_hip-release" : ["seq", "hip"],
+  "build-rzadams-toss_4_x86_64_ib_cray-cce@18.0.0_hip-release" :["seq", "hip"]
+}
+
+sizes = (50, 100, 200, 500, 1000, 1500, 2000, 4000, 8000)
+
+def generate():
+  for r in runs:
+    filename = os.path.join(r, "run_concentric_circles.bash")
+    f = open(filename, "wt")
+    f.write("#!/bin/bash\n\n")
+    f.write("CONCENTRIC_CIRCLES=./examples/mir_concentric_circles\n\n")
+
+    for s in sizes:
+      f.write(f"# Size {s}\n")
+      for policy in runs[r]:
+        f.write(f'echo "Running --gridsize {s} --numcircles 5 --policy {policy}"\n')
+        f.write(f'$CONCENTRIC_CIRCLES --gridsize {s} --numcircles 5 --policy {policy} > result_{policy}_{s}.txt\n\n')
+
+    f.close()
+    os.chmod(filename, 0o700)
+    print(f"Wrote {filename}")
+
+def read_timings(filename):
+  retval = "" # no data
+  try:
+    lines = open(filename, "rt").readlines()
+    for line in lines:
+      pos = line.find("runMIR")
+      if pos != -1:
+        toks = [x for x in line.split() if x != '']
+        retval = float(toks[2]) # timings (I)
+        break
+  except:
+    pass
+  return retval
+
+def make_csv(outputfile):
+  columns = []
+  # Add sizes column
+  sc = ["Sizes"]
+  for s in sizes:
+    sc.append(s)
+  columns.append(sc)
+
+  # Gather data.
+  for r in sorted(runs.keys()):
+    for policy in runs[r]:
+      buildname = r[6:-8]
+      name = f"{buildname} {policy.upper()}"
+      data = [name]
+      for s in sizes:
+        filename = os.path.join(r, f"result_{policy}_{s}.txt")
+        value = read_timings(filename)
+        data.append(value)
+      columns.append(data)
+
+  # Write data
+  f = open(outputfile, "wt")
+  nrows = len(columns[0])
+  for i in range(nrows):
+    rowdata = [str(c[i]) for c in columns]
+    line = ",".join(rowdata)
+    f.write(f"{line}\n")
+  f.close()
+
+def main():
+  if "--generate" in sys.argv:
+    generate()
+  else:
+    make_csv("concentric_circle_timings.csv")
+
+main()

scripts/copyrightPrepender.py

@@ -34,7 +34,7 @@ def reject(line):
 
   # Skip some autogenerated bindings, example code, and thirdparty code that
   # should not get a header.
-  for suppression in ("c_fortran", "lulesh2", "thirdparty"):
+  for suppression in ("c_fortran", "lulesh2", "thirdparty", "src/cmake", "clipping/ClipCases"):
     if filename.find(suppression) != -1:
       print("  Processing file:", filename, end=' ')
       print(skipMsg)

scripts/spack/packages/axom/package.py

@@ -602,6 +602,8 @@ def cmake_args(self):
         options.append(self.define_from_variant("BUILD_SHARED_LIBS", "shared"))
         options.append(self.define_from_variant("AXOM_ENABLE_EXAMPLES", "examples"))
         options.append(self.define_from_variant("AXOM_ENABLE_TOOLS", "tools"))
+        if "+raja" not in spec or "+umpire" not in spec:
+            options.append("-DAXOM_ENABLE_MIR:BOOL=OFF")
 
         return options
 

src/axom/CMakeLists.txt

@@ -32,6 +32,7 @@ axom_add_component(COMPONENT_NAME sina   DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONE
 axom_add_component(COMPONENT_NAME slam   DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
 axom_add_component(COMPONENT_NAME primal DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
 axom_add_component(COMPONENT_NAME sidre  DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
+axom_add_component(COMPONENT_NAME mir    DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
 axom_add_component(COMPONENT_NAME mint   DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
 axom_add_component(COMPONENT_NAME spin   DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
 axom_add_component(COMPONENT_NAME inlet  DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})

src/axom/config.hpp.in

@@ -100,6 +100,7 @@
 #cmakedefine AXOM_USE_KLEE
 #cmakedefine AXOM_USE_LUMBERJACK
 #cmakedefine AXOM_USE_MINT
+#cmakedefine AXOM_USE_MIR
 #cmakedefine AXOM_USE_PRIMAL
 #cmakedefine AXOM_USE_QUEST
 #cmakedefine AXOM_USE_SIDRE

src/axom/core/ArrayView.hpp

@@ -73,7 +73,7 @@ class ArrayView : public ArrayBase<T, DIM, ArrayView<T, DIM, SPACE>>
     typename... Args,
     typename Enable = typename std::enable_if<
       sizeof...(Args) == DIM && detail::all_types_are_integral<Args...>::value>::type>
-  ArrayView(T* data, Args... args);
+  AXOM_HOST_DEVICE ArrayView(T* data, Args... args);
 
   /*!
    * \brief Generic constructor for an ArrayView of arbitrary dimension with external data
@@ -232,7 +232,7 @@ using MCArrayView = ArrayView<T, 2>;
 //------------------------------------------------------------------------------
 template <typename T, int DIM, MemorySpace SPACE>
 template <typename... Args, typename Enable>
-ArrayView<T, DIM, SPACE>::ArrayView(T* data, Args... args)
+AXOM_HOST_DEVICE ArrayView<T, DIM, SPACE>::ArrayView(T* data, Args... args)
   : ArrayView(data,
               StackArray<IndexType, DIM> {{static_cast<IndexType>(args)...}})
 {

src/axom/core/CMakeLists.txt

@@ -27,6 +27,7 @@ set(core_headers
     utilities/CommandLineUtilities.hpp
     utilities/FileUtilities.hpp
     utilities/RAII.hpp
+    utilities/Sorting.hpp
     utilities/StringUtilities.hpp
     utilities/System.hpp
     utilities/Timer.hpp
@@ -78,6 +79,7 @@ set(core_headers
     execution/for_all.hpp
     execution/nested_for_exec.hpp
     execution/runtime_policy.hpp
+    execution/scans.hpp
     execution/synchronize.hpp
 
     execution/internal/seq_exec.hpp

src/axom/core/StackArray.hpp

@@ -10,6 +10,8 @@
 #include "axom/core/Macros.hpp"  // for axom macros
 #include "axom/core/Types.hpp"   // for axom types
 
+#include <iostream>
+
 namespace axom
 {
 /*!
@@ -27,6 +29,14 @@ namespace axom
 template <typename T, int N>
 struct StackArray
 {
+  using value_type = T;
+
+  /*!
+   * \brief Return size of the array.
+   */
+  AXOM_HOST_DEVICE
+  constexpr static int size() { return N; }
+
   /*!
    * \brief Accessor, returns a reference to the value at the given index.
    *
@@ -55,6 +65,9 @@ struct StackArray
   AXOM_HOST_DEVICE
   constexpr operator const T*() const noexcept { return &m_data[0]; }
 
+  AXOM_HOST_DEVICE T* data() noexcept { return &m_data[0]; }
+  AXOM_HOST_DEVICE const T* data() const noexcept { return &m_data[0]; }
+
   /// @}
 
   /*!
@@ -135,6 +148,28 @@ AXOM_HOST_DEVICE bool operator<(const StackArray<T, N>& lhs,
   return false;
 }
 
+/**
+ * \brief Print the StackArray to a stream.
+ * \param os The stream to use.
+ * \param obj The StackArray to print.
+ * \return The input stream.
+ */
+template <typename T, int N>
+std::ostream& operator<<(std::ostream& os, const StackArray<T, N>& obj)
+{
+  os << "(";
+  for(int i = 0; i < N; i++)
+  {
+    if(i > 0)
+    {
+      os << ", ";
+    }
+    os << obj.m_data[i];
+  }
+  os << ")";
+  return os;
+}
+
 } /* namespace axom */
 
 #endif /* AXOM_STACKARRAY_HPP_ */