Merge branch 'master' of https://gitlab.kitware.com/vtk/vtk-m

.gitlab-ci.yml

@@ -106,7 +106,7 @@
     - .docker_image
 
 .ubuntu2004_hip_kokkos: &ubuntu2004_hip_kokkos
-  image: "kitware/vtkm:ci-ubuntu2004_hip_kokkos-20210827"
+  image: "kitware/vtkm:ci-ubuntu2004_hip_kokkos-20220620"
   extends:
     - .docker_image
 

.gitlab/ci/config/initial_config.cmake

@@ -144,6 +144,9 @@ foreach(option IN LISTS options)
       if(VTKm_ENABLE_CUDA)
         set(CMAKE_CUDA_COMPILER_LAUNCHER "${CCACHE_COMMAND}" CACHE STRING "")
       endif()
+      if(VTKm_ENABLE_KOKKOS_HIP)
+        set(CMAKE_HIP_COMPILER_LAUNCHER "${CCACHE_COMMAND}" CACHE STRING "")
+      endif()
     else()
       message(FATAL_ERROR "CCACHE version [${CCACHE_VERSION}] is <= 4")
     endif()
@@ -165,10 +168,6 @@ if(SCCACHE_COMMAND)
   set(CMAKE_C_COMPILER_LAUNCHER "${SCCACHE_COMMAND}" CACHE STRING "")
   set(CMAKE_CXX_COMPILER_LAUNCHER "${SCCACHE_COMMAND}" CACHE STRING "")
 
-  if(DEFINED VTKm_ENABLE_KOKKOS_HIP)
-    set(CMAKE_HIP_COMPILER_LAUNCHER "${SCCACHE_COMMAND}" CACHE STRING "")
-  endif()
-
   # Use VTKm_CUDA_Architecture to determine if we need CUDA sccache setup
   # since this will also capture when kokkos is being used with CUDA backing
   if(DEFINED VTKm_CUDA_Architecture OR DEFINED CMAKE_CUDA_ARCHITECTURES)

.gitlab/ci/docker/ubuntu2004/kokkos-hip/Dockerfile

@@ -2,24 +2,35 @@ FROM rocm/dev-ubuntu-20.04
 LABEL maintainer "Vicente Adolfo Bolea Sanchez<vicente.bolea@kitware.com>"
 
 # Base dependencies for building VTK-m projects
-RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
-      cmake \
-      curl \
-      g++ \
-      git \
-      git-lfs \
-      libmpich-dev \
-      libomp-dev \
-      mpich \
-      ninja-build \
-      rsync \
-      ssh \
-      software-properties-common
+RUN apt update && \
+    DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends \
+    curl \
+    g++ \
+    git \
+    git-lfs \
+    libmpich-dev \
+    libomp-dev \
+    mpich \
+    ninja-build \
+    rsync \
+    ssh \
+    && \
+    apt clean
 
 # Need to run git-lfs install manually on ubuntu based images when using the
 # system packaged version
 RUN git-lfs install
 
+# Provide CCACHE
+ENV CCACHE_DIR "/ccache"
+ENV PATH "/opt/ccache/bin:${PATH}"
+ARG CCACHE_VERSION=4.6.1
+RUN mkdir /opt/ccache/ && \
+    curl -L https://github.com/ccache/ccache/releases/download/v$CCACHE_VERSION/ccache-$CCACHE_VERSION-linux-x86_64.tar.xz | tar -vxJ && \
+    make -C ccache-$CCACHE_VERSION-linux-x86_64 install prefix=/opt/ccache && \
+    rm -rf ccache-$CCACHE_VERSION-linux-x86_64 && \
+    ccache -z && ccache -s
+
 # Provide CMake
 ARG CMAKE_VERSION=3.21.1
 RUN mkdir /opt/cmake/ && \
@@ -33,11 +44,10 @@ ENV CMAKE_PREFIX_PATH "/opt/rocm/lib/cmake:/opt/rocm/lib:${CMAKE_PREFIX_PATH}"
 ENV CMAKE_GENERATOR "Ninja"
 
 # Build and install Kokkos
-ARG KOKKOS_VERSION=3.4.01
+ARG KOKKOS_VERSION=3.6.00
 COPY kokkos_cmake_config.cmake kokkos_cmake_config.cmake
 RUN curl -L https://github.com/kokkos/kokkos/archive/refs/tags/$KOKKOS_VERSION.tar.gz | tar -xzf - && \
-		cmake -S kokkos-$KOKKOS_VERSION -B build -C kokkos_cmake_config.cmake                          && \
-		cmake --build build -v                                                                         && \
-		sudo cmake --install build
-
-RUN rm -rf build
+    cmake -S kokkos-$KOKKOS_VERSION -B build -C kokkos_cmake_config.cmake                          && \
+    cmake --build build -v                                                                         && \
+    cmake --install build                                                                          && \
+    rm -rf build kokkos-$KOKKOS_VERSION

.gitlab/ci/ubuntu2004.yml

@@ -72,10 +72,20 @@ build:ubuntu2004_hip_kokkos:
     - .run_scheduled
   variables:
     CMAKE_BUILD_TYPE: RelWithDebInfo
-    VTKM_SETTINGS: "benchmarks+kokkos+hip+no_virtual+no_rendering"
+    VTKM_SETTINGS: "benchmarks+kokkos+hip+no_virtual+no_rendering+ccache"
     CMAKE_PREFIX_PATH: "/opt/rocm/lib/cmake"
-    CTEST_MAX_PARALLELISM: "1"
-  timeout: 12 hours
+
+    CCACHE_BASEDIR: "$CI_PROJECT_DIR"
+
+    # -isystem= is not affected by CCACHE_BASEDIR, thus we must ignore it
+    CCACHE_IGNOREOPTIONS: "-isystem=*"
+    CCACHE_COMPILERCHECK: "content"
+    CCACHE_NOHASHDIR: "true"
+    CCACHE_RESHARE: "true"
+  after_script:
+    - ccache -v -s
+    - ccache -z
+  timeout: 10 hours
 
 test:ubuntu2004_hip_kokkos:
   tags:

CMake/testing/VTKmTestWrappers.cmake

@@ -144,8 +144,7 @@ function(vtkm_unit_tests)
     if(VTKm_ENABLE_KOKKOS AND (enable_all_backends OR NOT per_device_suffix))
       list(APPEND per_device_command_line_arguments --vtkm-device=kokkos)
       list(APPEND per_device_suffix "KOKKOS")
-      #may require more time because of kernel generation.
-      list(APPEND per_device_timeout 1500)
+      list(APPEND per_device_timeout 600)
       list(APPEND per_device_serial FALSE)
     endif()
     if(VTKm_ENABLE_TBB AND (enable_all_backends OR NOT per_device_suffix))

vtkm/filter/Probe.h

@@ -11,7 +11,7 @@
 #define vtk_m_filter_Probe_h
 
 #include <vtkm/Deprecated.h>
-#include <vtkm/filter/resampling //Probe.h>
+#include <vtkm/filter/resampling/Probe.h>
 
 namespace vtkm
 {

vtkm/filter/connected_components/testing/CMakeLists.txt

@@ -14,6 +14,7 @@ set(unit_tests
 
 set(unit_tests_device
   UnitTestCellSetConnectivityFilter.cxx # uses vtkm::cont::Algorithm
+  UnitTestGraphConnectivityWorklet.cxx
   )
 
 set(libraries

vtkm/filter/connected_components/testing/UnitTestGraphConnectivityWorklet.cxx

@@ -0,0 +1,141 @@
+//============================================================================
+//  Copyright (c) Kitware, Inc.
+//  All rights reserved.
+//  See LICENSE.txt for details.
+//
+//  This software is distributed WITHOUT ANY WARRANTY; without even
+//  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+//  PURPOSE.  See the above copyright notice for more information.
+//============================================================================
+
+#include <vtkm/cont/testing/Testing.h>
+
+#include <vtkm/filter/connected_components/worklet/GraphConnectivity.h>
+
+class AdjacentDifference : public vtkm::worklet::WorkletMapField
+{
+public:
+  using ControlSignature = void(FieldIn index, WholeArrayIn counts, FieldOut outputCount);
+  using ExecutionSignature = void(_1, _2, _3);
+  using InputDomain = _1;
+
+  template <typename WholeArrayType>
+  VTKM_EXEC void operator()(const vtkm::Id& index,
+                            const WholeArrayType& counts,
+                            int& difference) const
+  {
+    difference = counts.Get(index + 1) - counts.Get(index);
+  }
+};
+
+class SameComponent : public vtkm::worklet::WorkletMapField
+{
+public:
+  using ControlSignature = void(FieldIn start,
+                                FieldIn degree,
+                                WholeArrayIn conns,
+                                WholeArrayIn comps,
+                                AtomicArrayInOut same);
+  using ExecutionSignature = void(WorkIndex, _1, _2, _3, _4, _5);
+
+  template <typename Conn, typename Comp, typename AtomicSame>
+  VTKM_EXEC void operator()(vtkm::Id index,
+                            int start,
+                            int degree,
+                            const Conn& conns,
+                            const Comp& comps,
+                            AtomicSame& same) const
+  {
+    for (vtkm::Id offset = start; offset < start + degree; ++offset)
+    {
+      vtkm::Id neighbor = conns.Get(offset);
+      if (comps.Get(index) != comps.Get(neighbor))
+      {
+        same.Set(0, 0);
+      }
+    }
+  }
+};
+
+class TestGraphConnectivity
+{
+public:
+  void TestECL_CC(const std::string& filename, int ncomps) const
+  {
+    auto pathname =
+      vtkm::cont::testing::Testing::GetTestDataBasePath() + "/third_party/ecl_cc/" + filename;
+    std::ifstream stream(pathname, std::ios_base::in | std::ios_base::binary);
+
+    int nnodes;
+    stream.read(reinterpret_cast<char*>(&nnodes), sizeof(nnodes));
+
+    int nedges;
+    stream.read(reinterpret_cast<char*>(&nedges), sizeof(nedges));
+
+    // CSR, there is one more element in offsets than the actual number of nodes.
+    std::vector<int> offsets(nnodes + 1);
+    std::vector<int> conns(nedges);
+
+    stream.read(reinterpret_cast<char*>(offsets.data()), (nnodes + 1) * sizeof(int));
+    stream.read(reinterpret_cast<char*>(conns.data()), nedges * sizeof(int));
+
+    vtkm::cont::ArrayHandle<int> counts_h;
+    vtkm::cont::Invoker invoke;
+    invoke(AdjacentDifference{},
+           vtkm::cont::make_ArrayHandleCounting(0, 1, nnodes),
+           vtkm::cont::make_ArrayHandle<int>(offsets, vtkm::CopyFlag::On),
+           counts_h);
+
+    offsets.pop_back();
+    vtkm::cont::ArrayHandle<int> offsets_h =
+      vtkm::cont::make_ArrayHandle(offsets, vtkm::CopyFlag::On);
+
+    vtkm::cont::ArrayHandle<int> conns_h = vtkm::cont::make_ArrayHandle(conns, vtkm::CopyFlag::Off);
+
+    vtkm::cont::ArrayHandle<vtkm::Id> comps_h;
+    vtkm::worklet::connectivity::GraphConnectivity().Run(counts_h, offsets_h, conns_h, comps_h);
+
+    VTKM_TEST_ASSERT(vtkm::cont::Algorithm::Reduce(comps_h, vtkm::Id(0), vtkm::Maximum{}) ==
+                       ncomps - 1,
+                     "number of components mismatch");
+
+    vtkm::cont::ArrayHandle<vtkm::UInt32> atomicSame;
+    atomicSame.Allocate(1);
+    atomicSame.WritePortal().Set(0, 1);
+
+    invoke(SameComponent{}, offsets_h, counts_h, conns_h, comps_h, atomicSame);
+    VTKM_TEST_ASSERT(atomicSame.ReadPortal().Get(0) == 1,
+                     "Neighboring nodes don't have the same component id");
+  }
+
+  void TestECL_CC_DataSets() const { TestECL_CC("internet.egr", 1); }
+
+  void TestSimpleGraph() const
+  {
+    vtkm::cont::ArrayHandle<vtkm::Id> counts_h =
+      vtkm::cont::make_ArrayHandle<vtkm::Id>({ 1, 1, 2, 2, 2 });
+    vtkm::cont::ArrayHandle<vtkm::Id> offsets_h =
+      vtkm::cont::make_ArrayHandle<vtkm::Id>({ 0, 1, 2, 4, 6 });
+    vtkm::cont::ArrayHandle<vtkm::Id> conn_h =
+      vtkm::cont::make_ArrayHandle<vtkm::Id>({ 2, 4, 0, 3, 2, 4, 1, 3 });
+    vtkm::cont::ArrayHandle<vtkm::Id> comps;
+
+    vtkm::worklet::connectivity::GraphConnectivity().Run(counts_h, offsets_h, conn_h, comps);
+
+    for (int i = 0; i < comps.GetNumberOfValues(); i++)
+    {
+      VTKM_TEST_ASSERT(comps.ReadPortal().Get(i) == 0, "Components has unexpected value.");
+    }
+  }
+
+  void operator()() const
+  {
+    TestSimpleGraph();
+    TestECL_CC_DataSets();
+  }
+};
+
+int UnitTestGraphConnectivityWorklet(int argc, char* argv[])
+{
+  return vtkm::cont::testing::Testing::Run(TestGraphConnectivity{}, argc, argv);
+}

vtkm/filter/resampling/Probe.h

@@ -7,8 +7,8 @@
 //  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
 //  PURPOSE.  See the above copyright notice for more information.
 //============================================================================
-#ifndef vtk_m_filter_Probe_h
-#define vtk_m_filter_Probe_h
+#ifndef vtk_m_filter_resampling_Probe_h
+#define vtk_m_filter_resampling_Probe_h
 
 #include <vtkm/filter/NewFilterField.h>
 #include <vtkm/filter/resampling/vtkm_filter_resampling_export.h>
@@ -62,4 +62,4 @@ class VTKM_DEPRECATED(1.8, "Use vtkm::filter::resampling::Probe.") Probe
 } // namespace filter
 } // namespace vtkm
 
-#endif // vtk_m_filter_Probe_h
+#endif // vtk_m_filter_resampling_Probe_h