Merge branch 'develop' into pgrete/pmd-output

.github/workflows/check-compilers.yml

@@ -1,6 +1,14 @@
 name: Check compilers
 
-on: [push, pull_request]
+on:
+  # run every day at 06:00 UTC
+  schedule:
+    - cron: '0 6 * * *'
+  # when triggered manually
+  workflow_dispatch:
+  # when auto merge is enabled (hack to make sure it's run before merging)
+  pull_request:
+    types: [auto_merge_enabled]
 
 # Cancel "duplicated" workflows triggered by pushes to internal
 # branches with associated PRs.
@@ -14,7 +22,7 @@ jobs:
     strategy:
       matrix:
         cxx: ['g++', 'clang++-15']
-        cmake_build_type: ['Release', 'Debug']
+        cmake_build_type: ['Release', 'DbgNoSym']
         device: ['cuda', 'host']
         parallel: ['serial', 'mpi']
         exclude:
@@ -23,7 +31,7 @@ jobs:
           # https://github.com/lanl/parthenon/issues/630
           - cxx: clang++-15
             device: cuda
-            cmake_build_type: Debug
+            cmake_build_type: DbgNoSym
     runs-on: ubuntu-latest
     container:
       image: ghcr.io/parthenon-hpc-lab/cuda11.6-mpi-hdf5-ascent
@@ -48,25 +56,29 @@ jobs:
     strategy:
       matrix:
         cxx: ['hipcc']
-        cmake_build_type: ['Release', 'Debug']
+        cmake_build_type: ['Release', 'DbgNoSym']
         device: ['hip']
         parallel: ['serial', 'mpi']
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/parthenon-hpc-lab/rocm5.4.3-mpi-hdf5
+      image: ghcr.io/parthenon-hpc-lab/rocm6.2-mpi-hdf5
     env:
       CMAKE_GENERATOR: Ninja
     steps:
       - uses: actions/checkout@v2
         with:
           submodules: 'true'
       - name: CMake
+        # Manually chaning the arch for this (debug) build as the
+        # -O0 option causes compiler issue for the navi 1030 GPU at
+        # compile time, see https://github.com/parthenon-hpc-lab/parthenon/pull/1191#issuecomment-2492035364
         run: |
           cmake -B builddir \
             -DCMAKE_CXX_COMPILER=${{ matrix.cxx }} \
             -DCMAKE_BUILD_TYPE=${{ matrix.cmake_build_type }} \
             -DMACHINE_CFG=${PWD}/cmake/machinecfg/GitHubActions.cmake \
-            -DMACHINE_VARIANT=${{ matrix.device }}_${{ matrix.parallel }}
+            -DMACHINE_VARIANT=${{ matrix.device }}_${{ matrix.parallel }} \
+            -DKokkos_ARCH_AMD_GFX90A=ON -DKokkos_ARCH_NAVI1030=OFF
       - name: Build
         run: |
           cmake --build builddir --parallel 2

.github/workflows/ci-extended.yml

@@ -21,6 +21,8 @@ env:
   CMAKE_BUILD_PARALLEL_LEVEL: 5 # num threads for build
   MACHINE_CFG: cmake/machinecfg/CI.cmake
   OMPI_MCA_mpi_common_cuda_event_max: 1000
+  # CUDA IPC within docker repeated seem to cause issue on the CI machine
+  OMPI_MCA_btl_smcuda_use_cuda_ipc: 0
   # https://github.com/open-mpi/ompi/issues/4948#issuecomment-395468231
   OMPI_MCA_btl_vader_single_copy_mechanism: none
 
@@ -34,7 +36,7 @@ jobs:
     container:
       image: ghcr.io/parthenon-hpc-lab/cuda11.6-mpi-hdf5-ascent
       # map to local user id on CI  machine to allow writing to build cache
-      options: --user 1001
+      options: --user 1001 --cap-add CAP_SYS_PTRACE --shm-size="8g" --ulimit memlock=134217728
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/ci-short.yml

@@ -13,6 +13,8 @@ env:
   CMAKE_BUILD_PARALLEL_LEVEL: 5 # num threads for build
   MACHINE_CFG: cmake/machinecfg/CI.cmake
   OMPI_MCA_mpi_common_cuda_event_max: 1000
+  # CUDA IPC within docker repeated seem to cause issue on the CI machine
+  OMPI_MCA_btl_smcuda_use_cuda_ipc: 0
   # https://github.com/open-mpi/ompi/issues/4948#issuecomment-395468231
   OMPI_MCA_btl_vader_single_copy_mechanism: none
 
@@ -22,7 +24,7 @@ jobs:
     container:
       image: ghcr.io/parthenon-hpc-lab/cuda11.6-mpi-hdf5-ascent
       # map to local user id on CI  machine to allow writing to build cache
-      options: --user 1001
+      options: --user 1001 --cap-add CAP_SYS_PTRACE --shm-size="8g" --ulimit memlock=134217728
     steps:
       - uses: actions/checkout@v3
         with:
@@ -47,7 +49,7 @@ jobs:
     container:
       image: ghcr.io/parthenon-hpc-lab/cuda11.6-mpi-hdf5-ascent
       # map to local user id on CI  machine to allow writing to build cache
-      options: --user 1001
+      options: --user 1001 --cap-add CAP_SYS_PTRACE --shm-size="8g" --ulimit memlock=134217728
     steps:
       - uses: actions/checkout@v3
         with:
@@ -79,7 +81,7 @@ jobs:
     container:
       image: ghcr.io/parthenon-hpc-lab/cuda11.6-mpi-hdf5-ascent
       # map to local user id on CI  machine to allow writing to build cache
-      options: --user 1001
+      options: --user 1001 --cap-add CAP_SYS_PTRACE --shm-size="8g" --ulimit memlock=134217728
     steps:
       - uses: actions/checkout@v3
         with:

CHANGELOG.md

@@ -3,23 +3,26 @@
 ## Current develop
 
 ### Added (new features/APIs/variables/...)
-- [[PR 1185]](https://github.com/parthenon-hpc-lab/parthenon/pull/1185/files) Bugfix to particle defragmentation
+- [[PR 1103]](https://github.com/parthenon-hpc-lab/parthenon/pull/1103) Add sparsity to vector wave equation test
+- [[PR 1185]](https://github.com/parthenon-hpc-lab/parthenon/pull/1185) Bugfix to particle defragmentation
 - [[PR 1184]](https://github.com/parthenon-hpc-lab/parthenon/pull/1184) Fix swarm block neighbor indexing in 1D, 2D
 - [[PR 1183]](https://github.com/parthenon-hpc-lab/parthenon/pull/1183) Fix particle leapfrog example initialization data
 - [[PR 1179]](https://github.com/parthenon-hpc-lab/parthenon/pull/1179) Make a global variable for whether simulation is a restart
 - [[PR 1171]](https://github.com/parthenon-hpc-lab/parthenon/pull/1171) Add PARTHENON_USE_SYSTEM_PACKAGES build option
 - [[PR 1161]](https://github.com/parthenon-hpc-lab/parthenon/pull/1161) Make flux field Metadata accessible, add Metadata::CellMemAligned flag, small perfomance upgrades
 
 ### Changed (changing behavior/API/variables/...)
+- [[PR 1191]](https://github.com/parthenon-hpc-lab/parthenon/pull/1191) Update Kokkos version to 4.4.1
+- [[PR 1209]](https://github.com/parthenon-hpc-lab/parthenon/pull/1209) Ordered history output
 - [[PR 1206]](https://github.com/parthenon-hpc-lab/parthenon/pull/1206) Leapfrog fix
-- [[PR1203]](https://github.com/parthenon-hpc-lab/parthenon/pull/1203) Pin Ubuntu CI image
-- [[PR1177]](https://github.com/parthenon-hpc-lab/parthenon/pull/1177) Make mesh-level boundary conditions usable without the "user" flag
+- [[PR 1203]](https://github.com/parthenon-hpc-lab/parthenon/pull/1203) Pin Ubuntu CI image
+- [[PR 1177]](https://github.com/parthenon-hpc-lab/parthenon/pull/1177) Make mesh-level boundary conditions usable without the "user" flag
 - [[PR 1187]](https://github.com/parthenon-hpc-lab/parthenon/pull/1187) Make DataCollection::Add safer and generalize MeshBlockData::Initialize
-- [[Issue 1165]](https://github.com/parthenon-hpc-lab/parthenon/issues/1165) Bump Kokkos submodule to 4.4.1
 - [[PR 1171]](https://github.com/parthenon-hpc-lab/parthenon/pull/1171) Add PARTHENON_USE_SYSTEM_PACKAGES build option
 - [[PR 1172]](https://github.com/parthenon-hpc-lab/parthenon/pull/1172) Make parthenon manager robust against external MPI init and finalize calls
 
 ### Fixed (not changing behavior/API/variables/...)
+- [[PR 1188]](https://github.com/parthenon-hpc-lab/parthenon/pull/1188) Fix hdf5 output issue for metadata none variables, update test.
 - [[PR 1170]](https://github.com/parthenon-hpc-lab/parthenon/pull/1170) Fixed incorrect initialization of array by a const not constexpr
 - [[PR 1189]](https://github.com/parthenon-hpc-lab/parthenon/pull/1189) Address CUDA MPI/ICP issue with Kokkos <=4.4.1
 - [[PR 1178]](https://github.com/parthenon-hpc-lab/parthenon/pull/1178) Fix issue with mesh pointer when using relative residual tolerance in BiCGSTAB solver.
@@ -32,7 +35,7 @@
 
 
 ### Incompatibilities (i.e. breaking changes)
-- [[PR1177]](https://github.com/parthenon-hpc-lab/parthenon/pull/1177) Make mesh-level boundary conditions usable without the "user" flag
+- [[PR 1177]](https://github.com/parthenon-hpc-lab/parthenon/pull/1177) Make mesh-level boundary conditions usable without the "user" flag
 
 ## Release 24.08
 Date: 2024-08-30
@@ -156,12 +159,12 @@ Date: 2024-03-21
 - [[PR 973]](https://github.com/parthenon-hpc-lab/parthenon/pull/973) Multigrid performance upgrades
 
 ### Fixed (not changing behavior/API/variables/...)
-- [[PR1023]](https://github.com/parthenon-hpc-lab/parthenon/pull/1023) Fix broken param of a scalar bool
-- [[PR1012]](https://github.com/parthenon-hpc-lab/parthenon/pull/1012) Remove accidentally duplicated code
-- [[PR992]](https://github.com/parthenon-hpc-lab/parthenon/pull/992) Allow custom PR ops with sparse pools
-- [[PR988]](https://github.com/parthenon-hpc-lab/parthenon/pull/988) Fix bug in neighbor finding routine for small, periodic, refined meshes
-- [[PR986]](https://github.com/parthenon-hpc-lab/parthenon/pull/986) Fix bug in sparse boundary communication BndInfo cacheing
-- [[PR978]](https://github.com/parthenon-hpc-lab/parthenon/pull/978) remove erroneous sparse check
+- [[PR 1023]](https://github.com/parthenon-hpc-lab/parthenon/pull/1023) Fix broken param of a scalar bool
+- [[PR 1012]](https://github.com/parthenon-hpc-lab/parthenon/pull/1012) Remove accidentally duplicated code
+- [[PR 992]](https://github.com/parthenon-hpc-lab/parthenon/pull/992) Allow custom PR ops with sparse pools
+- [[PR 988]](https://github.com/parthenon-hpc-lab/parthenon/pull/988) Fix bug in neighbor finding routine for small, periodic, refined meshes
+- [[PR 986]](https://github.com/parthenon-hpc-lab/parthenon/pull/986) Fix bug in sparse boundary communication BndInfo cacheing
+- [[PR 978]](https://github.com/parthenon-hpc-lab/parthenon/pull/978) remove erroneous sparse check
 
 ### Infrastructure (changes irrelevant to downstream codes)
 - [[PR 1027]](https://github.com/parthenon-hpc-lab/parthenon/pull/1027) Refactor RestartReader as abstract class
@@ -228,7 +231,7 @@ Date: 2023-11-16
 - [[PR 901]](https://github.com/parthenon-hpc-lab/parthenon/pull/901) Implement shared element ownership model
 
 ### Removed (removing behavior/API/varaibles/...)
-- [[PR 930](https://github.com/parthenon-hpc-lab/parthenon/pull/930) Remove ParthenonManager::ParthenonInit as it is error-prone and the split functions are the recommended usage.
+- [[PR 930]](https://github.com/parthenon-hpc-lab/parthenon/pull/930) Remove ParthenonManager::ParthenonInit as it is error-prone and the split functions are the recommended usage.
 
 
 ## Release 0.8.0

CMakeLists.txt

@@ -76,9 +76,9 @@ include(cmake/Format.cmake)
 include(cmake/Lint.cmake)
 
 # regression test reference data
-set(REGRESSION_GOLD_STANDARD_VER 24 CACHE STRING "Version of gold standard to download and use")
+set(REGRESSION_GOLD_STANDARD_VER 25 CACHE STRING "Version of gold standard to download and use")
 set(REGRESSION_GOLD_STANDARD_HASH
-  "SHA512=e220df92a335131131e42ddb52dc221a6dbd6bb56361483b4af0292620eeb82ffb21ef3b95fd9a7c5cc158fb754da0bf1a1015bec98b5bbad05f4bceb1ee99bc"
+  "SHA512=314dc8312366d81ba33d1fde25812e9a7697b2f529de29e22662df0d458f1c4bc5b5bb4e649888170f66ffec0df1be20a9cf401944531c1c1ad835e26eaad28f"
   CACHE STRING "Hash of default gold standard file to download")
 option(REGRESSION_GOLD_STANDARD_SYNC "Automatically sync gold standard files." ON)
 

README.md

@@ -30,7 +30,7 @@ Parthenon -- a performance portable block-structured adaptive mesh refinement fr
 
 * CMake 3.16 or greater
 * C++17 compatible compiler
-* Kokkos 4.0.1 or greater
+* Kokkos 4.4.1 or greater
 
 ## Optional (enabling features)
 

cmake/machinecfg/GitHubActions.cmake

@@ -19,6 +19,9 @@ message(STATUS "Loading machine configuration for GitHub Actions CI. ")
 
 # common options
 set(NUM_MPI_PROC_TESTING "2" CACHE STRING "CI runs tests with 2 MPI ranks")
+set(Kokkos_ENABLE_ROCTHRUST OFF CACHE BOOL "Temporarily disabled as the container needs to be updated to the `-complete` base image.")
+
+set(CMAKE_CXX_FLAGS_DBGNOSYM "-O0" CACHE STRING "Debug build without symbols")
 
 set(MACHINE_CXX_FLAGS "")
 if (${MACHINE_VARIANT} MATCHES "cuda")

doc/sphinx/src/development.rst

@@ -21,7 +21,10 @@ Kokkos wrappers/abstractions
 -  ``par_for`` wrappers use inclusive bounds, i.e., the loop will
    include the last index given
 -  ``ParArrayND`` arrays by default allocate on the *device* using
-   default precision configured
+   default precision configured and come with a `State` that can
+   be used to store additional metadata.
+- ``ParArray#DRaw`` directly map to Kokkos ``Views`` that are allocated
+   on *device* using default precision.
 -  To create an array on the host with identical layout to the device
    array either use
 
@@ -62,6 +65,42 @@ parallelism interface that is needed for managing memory cached in
 tightly nested loops. The wrappers are documented
 :ref:`here <nested par for>`.
 
+View of Views
+-------------
+
+Special care needs to be taken when working with a ``View`` of ``Views``.
+
+To repeat the Kokkos documenation: `Don't use them <https://kokkos.org/kokkos-core-wiki/ProgrammingGuide/View.html#can-i-make-a-view-of-views>`__
+
+But if you have to (which is the case in some places inside Parthenon)
+then follow this pattern:
+
+.. code:: c++
+
+   ParArray1DRaw<ParArray1D<Real>> view_of_pararrays(parthenon::ViewOfViewAlloc("myname"), 10);
+
+The ``ViewOfViewAlloc`` ensures that the ``Kokkos::SequentialHostInit`` property is added,
+which results in the (inner ``View`` ) deallocators being called on the host (rather than on
+the device by default).
+Also note the use of the "raw" ``ParArray1DRaw``, which directly maps to a Kokkos ``View``
+(that is required to process the allocation property as this interface is not exposed
+in the more generic ``ParArrayND``).
+
+Similarly, when you create a host mirror of said ``View`` of ``View`` add the additional
+property for the same reason.
+
+.. code:: c++
+
+   // explicit theoretical example -- don't use this
+   auto view_of_pararrays_h =
+        Kokkos::create_mirror_view(Kokkos::view_alloc(Kokkos::SequentialHostInit), view_of_pararrays);
+
+   // but instead use this interface provided by Parthenon:
+   auto view_of_pararrays_h = create_view_of_view_mirror(view_of_pararrays);
+
+
+Note that the ``SequentialHostInit`` was only added in Kokkos 4.4.1 (which is now the default in Parthenon).
+
 The need for reductions within function handling ``MeshBlock`` data
 -------------------------------------------------------------------
 

doc/sphinx/src/outputs.rst

@@ -194,7 +194,9 @@ block might look like
 
 This will produce a text file (``.hst``) output file every 1 units of
 simulation time. The content of the file is determined by the functions
-enrolled by specific packages, see :ref:`state history output`.
+enrolled by specific packages, see :ref:`state history output`. Per-package history
+outputs will always be in alphabetical order by package name, which may not match
+the order in which packages were added to a simulation.
 
 Histograms
 ----------

example/advection/advection_package.cpp

@@ -196,6 +196,20 @@ std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin) {
   m = Metadata({Metadata::Cell, Metadata::OneCopy}, std::vector<int>({1}));
   pkg->AddField("my_derived_var", m);
 
+  // Create a Metadata::None variable for IO testing purposes.
+  // Only load if test_metadata_none is specified in the Advection block
+  auto test_metadata_none =
+      pin->GetOrAddBoolean("Advection", "test_metadata_none", false);
+  pkg->AddParam<bool>("test_metadata_none", test_metadata_none);
+  if (test_metadata_none) {
+    const int nx1 = pin->GetOrAddInteger("parthenon/meshblock", "nx1", 1);
+    const int nx2 = pin->GetOrAddInteger("parthenon/meshblock", "nx2", 1);
+    const int nx3 = pin->GetOrAddInteger("parthenon/meshblock", "nx3", 1);
+    std::vector<int> test_shape = {nx1 + 1, nx2 + 1, nx3 + 1, 3};
+    m = Metadata({Metadata::OneCopy, Metadata::None}, test_shape);
+    pkg->AddField("metadata_none_var", m);
+  }
+
   // List (vector) of HistoryOutputVar that will all be enrolled as output variables
   parthenon::HstVar_list hst_vars = {};
   // Now we add a couple of callback functions
@@ -281,6 +295,7 @@ AmrTag CheckRefinement(MeshBlockData<Real> *rc) {
 void PreFill(MeshBlockData<Real> *rc) {
   auto pmb = rc->GetBlockPointer();
   auto pkg = pmb->packages.Get("advection_package");
+  const bool test_metadata_none = pkg->Param<bool>("test_metadata_none");
   bool fill_derived = pkg->Param<bool>("fill_derived");
 
   if (fill_derived) {
@@ -302,6 +317,24 @@ void PreFill(MeshBlockData<Real> *rc) {
           v(out + n, k, j, i) = 1.0 - v(in + n, k, j, i);
         });
   }
+
+  // Fill the metadata::None var with index gymnastics.
+  if (test_metadata_none) {
+    const int nx1 = pmb->cellbounds.ncellsi(IndexDomain::interior);
+    const int nx2 = pmb->cellbounds.ncellsj(IndexDomain::interior);
+    const int nx3 = pmb->cellbounds.ncellsk(IndexDomain::interior);
+
+    // packing in principle unnecessary/convoluted here and just done for demonstration
+    std::vector<std::string> vars({"metadata_none_var"});
+    PackIndexMap imap;
+    const auto &v = rc->PackVariables(vars, imap);
+
+    pmb->par_for(
+        PARTHENON_AUTO_LABEL, 0, 2, 0, nx3, 0, nx2, 0, nx1,
+        KOKKOS_LAMBDA(const int n, const int k, const int j, const int i) {
+          v(n, k, j, i) = n + k + j + i;
+        });
+  }
 }
 
 // this is the package registered function to fill derived