Merge pull request #1634 from glotzerlab/test-gcc13-py312

Test gcc 13 and Python 3.12.
glotzerlab · Oct 11, 2023 · d03e41a · d03e41a
2 parents 7385be6 + 488043f
commit d03e41a
Show file tree

Hide file tree

Showing 10 changed files with 51 additions and 45 deletions.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -36,7 +36,7 @@ jobs:
     name: Build release tarball
     runs-on: ubuntu-latest
     container:
-      image: glotzerlab/ci:2023.07.24-ubuntu20.04
+      image: glotzerlab/ci:2023.10.09-ubuntu20.04
 
     steps:
       - name: Checkout

diff --git a/.github/workflows/templates/configurations.yml b/.github/workflows/templates/configurations.yml
@@ -4,10 +4,10 @@
 # - The build options are `mpi`, `tbb`, `llvm`, `nomd`, and `nohpmc`.
 unit_test_configurations:
 - config: "[clang14_py311, mpi, tbb, llvm]"
-- config: "[gcc12_py311]"
-- config: "[gcc12_py311, nomd]"
-- config: "[gcc12_py311, nohpmc]"
-- config: "[gcc12_py311, nomd, nohpmc]"
+- config: "[gcc13_py312]"
+- config: "[gcc13_py312, nomd]"
+- config: "[gcc13_py312, nohpmc]"
+- config: "[gcc13_py312, nomd, nohpmc]"
 - config: "[cuda120_gcc11_py310, mpi, llvm, debug]"
 - config: "[cuda120_gcc11_py310, mpi, llvm]"
 - config: "[cuda120_gcc11_py310]"
@@ -17,13 +17,14 @@ unit_test_configurations:
 # `unit_test_configurations`
 validate_configurations:
 - config: "[clang14_py311, mpi, tbb, llvm]"
-- config: "[gcc12_py311]"
+- config: "[gcc13_py312]"
 - config: "[cuda120_gcc11_py310, mpi, llvm]"
 - config: "[cuda120_gcc11_py310]"
 
 # Configurations to build and test only rarely, such as just before a release.
 # There should be no overlap between this list and `unit_test_configurations`
 release_test_configurations:
+- config: "[gcc12_py311]"
 - config: "[clang16_py311, mpi, llvm]"
 - config: "[clang15_py311, mpi, llvm]"
 - config: "[clang13_py310, llvm]"

diff --git a/.github/workflows/templates/workflow.yml b/.github/workflows/templates/workflow.yml
@@ -1,5 +1,5 @@
 <% block name %><% endblock %>
-<% set container_prefix="glotzerlab/ci:2023.07.24" %>
+<% set container_prefix="glotzerlab/ci:2023.10.09" %>
 
 <% block concurrency %>
 concurrency:

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -59,15 +59,15 @@ jobs:
     name: Build [${{ join(matrix.config, '_') }}]
     runs-on: ${{ matrix.build_runner }}
     container:
-      image: glotzerlab/ci:2023.07.24-${{ matrix.config[0] }}
+      image: glotzerlab/ci:2023.10.09-${{ matrix.config[0] }}
     strategy:
       matrix:
         include:
         - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
         - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
         - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
@@ -168,16 +168,16 @@ jobs:
     needs: build
     runs-on: ${{ matrix.test_runner }}
     container:
-      image: glotzerlab/ci:2023.07.24-${{ matrix.config[0] }}
+      image: glotzerlab/ci:2023.10.09-${{ matrix.config[0] }}
       options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
     strategy:
       matrix:
         include:
         - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
         - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
         - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
@@ -229,16 +229,16 @@ jobs:
     needs: build
     runs-on: ${{ matrix.test_runner }}
     container:
-      image: glotzerlab/ci:2023.07.24-${{ matrix.config[0] }}
+      image: glotzerlab/ci:2023.10.09-${{ matrix.config[0] }}
       options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
     strategy:
       matrix:
         include:
         - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312, nomd], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312, nomd, nohpmc], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [cuda120_gcc11_py310, mpi, llvm, debug], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
         - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
         - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
@@ -283,13 +283,13 @@ jobs:
     needs: build
     runs-on: ${{ matrix.test_runner }}
     container:
-      image: glotzerlab/ci:2023.07.24-${{ matrix.config[0] }}
+      image: glotzerlab/ci:2023.10.09-${{ matrix.config[0] }}
       options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
     strategy:
       matrix:
         include:
         - {config: [clang14_py311, mpi, tbb, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
-        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
+        - {config: [gcc13_py312], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [cuda120_gcc11_py310, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
         - {config: [cuda120_gcc11_py310], build_runner: [self-hosted,jetstream2,CPU], test_runner: [self-hosted,GPU], test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' }
 
@@ -334,10 +334,11 @@ jobs:
     name: Build [${{ join(matrix.config, '_') }}]
     runs-on: ${{ matrix.build_runner }}
     container:
-      image: glotzerlab/ci:2023.07.24-${{ matrix.config[0] }}
+      image: glotzerlab/ci:2023.10.09-${{ matrix.config[0] }}
     strategy:
       matrix:
         include:
+        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [clang16_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [clang15_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [clang13_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
@@ -447,11 +448,12 @@ jobs:
     needs: build_release
     runs-on: ${{ matrix.test_runner }}
     container:
-      image: glotzerlab/ci:2023.07.24-${{ matrix.config[0] }}
+      image: glotzerlab/ci:2023.10.09-${{ matrix.config[0] }}
       options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
     strategy:
       matrix:
         include:
+        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [clang16_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [clang15_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [clang13_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
@@ -516,11 +518,12 @@ jobs:
     needs: build_release
     runs-on: ${{ matrix.test_runner }}
     container:
-      image: glotzerlab/ci:2023.07.24-${{ matrix.config[0] }}
+      image: glotzerlab/ci:2023.10.09-${{ matrix.config[0] }}
       options: ${{ matrix.test_docker_options }} -e CUDA_VISIBLE_DEVICES
     strategy:
       matrix:
         include:
+        - {config: [gcc12_py311], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [clang16_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [clang15_py311, mpi, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }
         - {config: [clang13_py310, llvm], build_runner: [self-hosted,jetstream2,CPU], test_runner: ubuntu-latest, test_docker_options: '' }

diff --git a/BUILDING.rst b/BUILDING.rst
@@ -77,7 +77,7 @@ Install prerequisites
 
 **General requirements:**
 
-- C++17 capable compiler (tested with ``gcc`` 9 - 12 and ``clang`` 10 - 16)
+- C++17 capable compiler (tested with ``gcc`` 9 - 13 and ``clang`` 10 - 16)
 - Python >= 3.8
 - NumPy >= 1.17.3
 - pybind11 >= 2.2

diff --git a/hoomd/MeshGroupData.cc b/hoomd/MeshGroupData.cc
@@ -76,7 +76,7 @@ MeshGroupData<group_size, Group, name, snap>::MeshGroupData(std::shared_ptr<Part
                           &BondedGroupData<group_size, Group, name, true>::setDirty>(this);
 
     // initialize from snapshot
-    initializeFromSnapshot(snapshot);
+    initializeFromTriangleSnapshot(snapshot);
 
 #ifdef ENABLE_MPI
     if (this->m_pdata->getDomainDecomposition())
@@ -106,7 +106,7 @@ MeshGroupData<group_size, Group, name, snap>::~MeshGroupData()
 
 //! Initialize from a snapshot
 template<unsigned int group_size, typename Group, const char* name, typename snap>
-void MeshGroupData<group_size, Group, name, snap>::initializeFromSnapshot(
+void MeshGroupData<group_size, Group, name, snap>::initializeFromTriangleSnapshot(
     const TriangleData::Snapshot& snapshot)
     {
     // check that all fields in the snapshot have correct length
@@ -590,7 +590,7 @@ void export_MeshGroupData(pybind11::module& m,
         .def(pybind11::init<std::shared_ptr<ParticleData>, unsigned int>())
         .def(
             pybind11::init<std::shared_ptr<ParticleData>, const typename TriangleData::Snapshot&>())
-        .def("initializeFromSnapshot", &T::initializeFromSnapshot)
+        .def("initializeFromTriangleSnapshot", &T::initializeFromTriangleSnapshot)
         .def("takeSnapshot", &T::takeSnapshot)
         .def("getN", &T::getN)
         .def("getNGlobal", &T::getNGlobal)

diff --git a/hoomd/MeshGroupData.h b/hoomd/MeshGroupData.h
@@ -61,11 +61,13 @@ class MeshGroupData : public BondedGroupData<group_size, Group, name, true>
 
     virtual ~MeshGroupData();
 
-// mask the base class initializeFromSnapshot(const Snapshot& snapshot)
-#pragma clang diagnostic push
-#pragma clang diagnostic ignored "-Woverloaded-virtual"
-    void initializeFromSnapshot(const TriangleData::Snapshot& snapshot);
-#pragma clang diagnostic pop
+    virtual void initializeFromSnapshot(
+        const typename BondedGroupData<group_size, Group, name, true>::Snapshot& snapshot)
+        {
+        throw std::runtime_error("Not implemented");
+        }
+
+    void initializeFromTriangleSnapshot(const TriangleData::Snapshot& snapshot);
 
     //! Take a snapshot
     std::map<unsigned int, unsigned int> takeSnapshot(snap& snapshot) const;

diff --git a/hoomd/extern/quickhull b/hoomd/extern/quickhull
diff --git a/hoomd/hpmc/ShapeConvexPolyhedron.h b/hoomd/hpmc/ShapeConvexPolyhedron.h
@@ -55,10 +55,7 @@ struct PolyhedronVertices : ShapeParams
     PolyhedronVertices(unsigned int _N, bool managed = false) : ignore(0)
         {
         std::vector<vec3<ShortReal>> v(_N, vec3<ShortReal>(0, 0, 0));
-        x = ManagedArray<ShortReal>(1, managed);
-        y = ManagedArray<ShortReal>(1, managed);
-        z = ManagedArray<ShortReal>(1, managed);
-        setVerts(v, 0);
+        setVerts(v, 0, managed);
         }
 
     PolyhedronVertices(const std::vector<vec3<ShortReal>>& verts,
@@ -69,7 +66,7 @@ struct PolyhedronVertices : ShapeParams
           z((unsigned int)verts.size(), managed), n_hull_verts(0), N((unsigned int)verts.size()),
           diameter(0.0), sweep_radius(sweep_radius_), ignore(ignore_)
         {
-        setVerts(verts, sweep_radius_);
+        setVerts(verts, sweep_radius_, managed);
         }
 
     /** Set the shape vertices
@@ -79,12 +76,13 @@ struct PolyhedronVertices : ShapeParams
         @param verts Vertices to set
         @param sweep_radius_ Sweep radius
     */
-    void setVerts(const std::vector<vec3<ShortReal>>& verts, ShortReal sweep_radius_)
+    void setVerts(const std::vector<vec3<ShortReal>>& verts,
+                  ShortReal sweep_radius_,
+                  bool managed = false)
         {
         N = (unsigned int)verts.size();
         diameter = 0;
         sweep_radius = sweep_radius_;
-        bool managed = x.isManaged();
 
         unsigned int align_size = 8; // for AVX
         unsigned int N_align = ((N + align_size - 1) / align_size) * align_size;
@@ -166,7 +164,7 @@ struct PolyhedronVertices : ShapeParams
             vert_vector.push_back(vert);
             }
 
-        setVerts(vert_vector, v["sweep_radius"].cast<float>());
+        setVerts(vert_vector, v["sweep_radius"].cast<float>(), managed);
         }
 
     /// Convert parameters to a python dictionary

diff --git a/hoomd/managed_allocator.h b/hoomd/managed_allocator.h
@@ -143,6 +143,8 @@ template<class T> class managed_allocator
                 if (!result)
                     throw std::bad_alloc();
                 }
+
+            memset(result, 0, n * sizeof(T));
             allocation_bytes = n * sizeof(T);
             allocation_ptr = result;
             }