Bump up to Kokkos 5.1

.github/workflows/actions/pre-install-py-packages/action.yml

@@ -0,0 +1,15 @@
+name: Install python packages
+
+description: "Action installing the Idefix python packages before running the tests."
+
+inputs: {}
+
+runs:
+  using: "composite"
+  steps:
+    - name: Create venv
+      shell: bash
+      run: |
+        python3 -m venv .venv
+        source .venv/bin/activate
+        python3 -m pip install -r ./test/python_requirements.txt

.github/workflows/idefix-ci-jobs.yml

@@ -32,6 +32,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Sod test
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/sod -all $TESTME_OPTIONS
       - name: Isothermal Sod test
@@ -49,6 +51,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Viscous flow past cylinder
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/ViscousFlowPastCylinder -all $TESTME_OPTIONS
       - name: Viscous disk
@@ -64,6 +68,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: MHD Sod test
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/sod -all $TESTME_OPTIONS
       - name: MHD Isothermal Sod test
@@ -85,6 +91,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Ambipolar C Shock
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/AmbipolarCshock -all $TESTME_OPTIONS
       - name: Ambipolar C Shock 3D
@@ -105,6 +113,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Fargo + planet
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/FargoPlanet -all $TESTME_OPTIONS
       - name: Fargo MHD spherical
@@ -119,6 +129,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Hydro shearing box
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/ShearingBox -all $TESTME_OPTIONS
       - name: MHD shearing box
@@ -133,6 +145,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Jeans Instability
         run: scripts/ci/run-tests $IDEFIX_DIR/test/SelfGravity/JeansInstability -all $TESTME_OPTIONS
       - name: Random sphere spherical
@@ -153,6 +167,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: 3 body
         run: scripts/ci/run-tests $IDEFIX_DIR/test/Planet/Planet3Body -all $TESTME_OPTIONS
       - name: migration
@@ -175,6 +191,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Energy conservation
         run: scripts/ci/run-tests $IDEFIX_DIR/test/Dust/DustEnergy -all $TESTME_OPTIONS
       - name: Dusty wave
@@ -189,6 +207,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: MTI
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/MTI -all $TESTME_OPTIONS
       - name: Spherical anisotropic diffusion
@@ -207,6 +227,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Run examples test
         run: cd test && ./checks_examples.sh $TEST_OPTIONS
 
@@ -219,6 +241,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Lookup table
         run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/lookupTable -all $TESTME_OPTIONS
       - name: Dump Image
@@ -235,6 +259,8 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
+      - name: Prep python
+        uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Restart dumps
         run: scripts/ci/run-tests $IDEFIX_DIR/test/IO/dump -all $TESTME_OPTIONS
       - name: Pydefix

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.16)
 if (NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE "Release" CACHE STRING "" FORCE)
 endif()
-set (CMAKE_CXX_STANDARD 17)
+set (CMAKE_CXX_STANDARD 20)
 
 set(Idefix_VERSION_MAJOR 2)
 set(Idefix_VERSION_MINOR 3)

doc/source/index.rst

@@ -20,11 +20,11 @@ algorithm is essentially the same (but with some major modification to its struc
 ================
 Requirements
 ================
-*Idefix* is written is standard C++17 and does not rely on any external library in serial (non MPI).
+*Idefix* is written is standard C++20 and does not rely on any external library in serial (non MPI).
 
 Compiler
-  *Idefix* requires a C++17 compatible compiler. It has been tested successfully with GCC (>8), Intel compiler suite (>2018) and
-  Clang on both Intel and AMD CPUs. *Idefix* has also been tested on NVIDIA GPUs (Pascal, Volta and Ampere architectures) using the nvcc (>10) compiler, and on AMD GPUs (Radeon Mi50, Mi210, Mi250) using the hipcc compiler.
+  *Idefix* requires a C++20 compatible compiler. It has been tested successfully with GCC (>11), Intel compiler suite (>2022) and
+  Clang on both Intel and AMD CPUs. *Idefix* has also been tested on NVIDIA GPUs (Pascal, Volta and Ampere architectures) using the nvcc (>12) compiler, and on AMD GPUs (Radeon Mi50, Mi210, Mi250, Mi300) using the hipcc compiler.
 
 Kokkos library
   *Idefix* relies internally on the `Kokkos <https://github.com/kokkos/kokkos>`_ library, which is bundled with *Idefix* as a git submodule and compiled on the fly, hence no external installation is required.
@@ -90,6 +90,9 @@ Jean Kempf, Victor Reville, François Rincon
 Marc Coiffier
   Continuous integration, automatic benchmarking
 
+Sébastien Valat
+   Continuous integration
+
 ========================
 About this documentation
 ========================

doc/source/programmingguide.rst

@@ -355,31 +355,31 @@ fills the following arrays (essentially grid information) with data from its par
 
 .. code-block:: c++
 
-  IdefixArray1D<real>::HostMirror x[3];   // geometrical central points
-  IdefixArray1D<real>::HostMirror xr[3];  // cell right interface
-  IdefixArray1D<real>::HostMirror xl[3];  // cell left interface
-  IdefixArray1D<real>::HostMirror dx[3];  // cell width
+  IdefixArray1D<real>::host_mirror_type x[3];   // geometrical central points
+  IdefixArray1D<real>::host_mirror_type xr[3];  // cell right interface
+  IdefixArray1D<real>::host_mirror_type xl[3];  // cell left interface
+  IdefixArray1D<real>::host_mirror_type dx[3];  // cell width
 
-  IdefixArray3D<real>::HostMirror dV;     // cell volume
-  IdefixArray3D<real>::HostMirror A[3];   // cell right interface area
+  IdefixArray3D<real>::host_mirror_type dV;     // cell volume
+  IdefixArray3D<real>::host_mirror_type A[3];   // cell right interface area
 
 
 Note however that the physics arrays are not automatically synchronized when ``DataBlockHost`` is
 created, that is:
 
 .. code-block:: c++
 
-  IdefixArray4D<real>::HostMirror Vc;     // Main cell-centered primitive variables index
-  IdefixArray4D<real>::HostMirror Vs;     // Main face-centered primitive variables index
-  IdefixArray4D<real>::HostMirror J;      // Current (only when haveCurrent is enabled)
-  IdefixArray4D<real>::HostMirror Uc;     // Main cell-centered conservative variables
-  IdefixArray3D<real>::HostMirror InvDt;
+  IdefixArray4D<real>::host_mirror_type Vc;     // Main cell-centered primitive variables index
+  IdefixArray4D<real>::host_mirror_type Vs;     // Main face-centered primitive variables index
+  IdefixArray4D<real>::host_mirror_type J;      // Current (only when haveCurrent is enabled)
+  IdefixArray4D<real>::host_mirror_type Uc;     // Main cell-centered conservative variables
+  IdefixArray3D<real>::host_mirror_type InvDt;
 
-  IdefixArray3D<real>::HostMirror Ex1;    // x1 electric field
-  IdefixArray3D<real>::HostMirror Ex2;    // x2 electric field
-  IdefixArray3D<real>::HostMirror Ex3;    // x3 electric field
+  IdefixArray3D<real>::host_mirror_type Ex1;    // x1 electric field
+  IdefixArray3D<real>::host_mirror_type Ex2;    // x2 electric field
+  IdefixArray3D<real>::host_mirror_type Ex3;    // x3 electric field
 
-need to be synchronized *manually*. These IdefixArrays are all defined as ``HostMirror``, implying that they are accessible
+need to be synchronized *manually*. These IdefixArrays are all defined as ``host_mirror_type``, implying that they are accessible
 from the host only. If modifications are performed on the arrays of the
 parent ``DataBlock``, one can call ``DataBlockHost::SyncFromDevice()`` to refresh the host arrays,
 and inversely one can call ``DataBlockHost::SyncToDevice()`` to send data from ``DataBlockHost``

scripts/ci/run-tests

@@ -1,7 +1,20 @@
 #!/usr/bin/env bash
+
+# load ICC compiler env
 if [ "$IDEFIX_COMPILER" == icc ]; then
     source /opt/intel/oneapi/setvars.sh
 fi
+
+# enable bash features
 set -ue
+
+# load python venv if present
+if [ -d .venv ]; then
+    source .venv/bin/activate
+fi
+
+# jump in test directory
 cd "$1"
+
+# run the test
 ./testme.py "${@:2}"

src/dataBlock/dumpToFile.cpp

@@ -45,13 +45,13 @@ void DataBlock::DumpToFile(std::string filebase)  {
 
 
   // TODO(lesurg) Make datablock a friend of hydro to get the Riemann flux?
-  //IdefixArray4D<real>::HostMirror locFlux = Kokkos::create_mirror_view(Kokkos::HostSpace(),
+  //IdefixArray4D<real>::host_mirror_type locFlux = Kokkos::create_mirror_view(Kokkos::HostSpace(),
   //                                                                     this->hydro->FluxRiemann);
   //Kokkos::deep_copy(locFlux, this->FluxRiemann);
 #if MHD == YES
 
 
-  IdefixArray4D<real>::HostMirror locJ;
+  IdefixArray4D<real>::host_mirror_type locJ;
   if(hydro->haveCurrent) {
     locJ = Kokkos::create_mirror_view(Kokkos::HostSpace(), this->hydro->J);
     Kokkos::deep_copy(locJ, this->hydro->J);
@@ -82,7 +82,7 @@ void DataBlock::DumpToFile(std::string filebase)  {
   fwrite (header, sizeof(char), HEADERSIZE, fileHdl);
 
   // Write Vc
-  IdefixArray4D<real>::HostMirror locVc = Kokkos::create_mirror_view(this->hydro->Vc);
+  IdefixArray4D<real>::host_mirror_type locVc = Kokkos::create_mirror_view(this->hydro->Vc);
   Kokkos::deep_copy(locVc,this->hydro->Vc);
   dims[0] = this->np_tot[IDIR];
   dims[1] = this->np_tot[JDIR];
@@ -94,7 +94,7 @@ void DataBlock::DumpToFile(std::string filebase)  {
   WriteVariable(fileHdl, 4, dims, fieldName, locVc.data());
 
   if (this->gravity->haveSelfGravityPotential) {
-    IdefixArray3D<real>::HostMirror locPot = Kokkos::create_mirror_view(this->gravity->phiP);
+    IdefixArray3D<real>::host_mirror_type locPot = Kokkos::create_mirror_view(this->gravity->phiP);
     Kokkos::deep_copy(locPot, this->gravity->phiP);
 
     dims[3] = 1;
@@ -121,7 +121,7 @@ void DataBlock::DumpToFile(std::string filebase)  {
   // Write Vs
 #if MHD == YES
   // Write Vs
-  IdefixArray4D<real>::HostMirror locVs = Kokkos::create_mirror_view(Kokkos::HostSpace(),
+  IdefixArray4D<real>::host_mirror_type locVs = Kokkos::create_mirror_view(Kokkos::HostSpace(),
                                                                      this->hydro->Vs);
   Kokkos::deep_copy(locVs,this->hydro->Vs);
   dims[0] = this->np_tot[IDIR]+IOFFSET;
@@ -139,7 +139,7 @@ void DataBlock::DumpToFile(std::string filebase)  {
   dims[2] = this->np_tot[KDIR];
 
   std::snprintf(fieldName,NAMESIZE,"Ex3");
-  IdefixArray3D<real>::HostMirror locE = Kokkos::create_mirror_view(Kokkos::HostSpace(),
+  IdefixArray3D<real>::host_mirror_type locE = Kokkos::create_mirror_view(Kokkos::HostSpace(),
                                                                     this->hydro->emf->ez);
   Kokkos::deep_copy(locE,this->hydro->emf->ez);
   WriteVariable(fileHdl, 3, dims, fieldName, locE.data());
@@ -155,7 +155,7 @@ void DataBlock::DumpToFile(std::string filebase)  {
 
 
   if(hydro->haveCurrent) {
-    IdefixArray4D<real>::HostMirror locJ = Kokkos::create_mirror_view(Kokkos::HostSpace(),
+    IdefixArray4D<real>::host_mirror_type locJ = Kokkos::create_mirror_view(Kokkos::HostSpace(),
                                                                       this->hydro->J);
     Kokkos::deep_copy(locJ,this->hydro->J);
     dims[0] = this->np_tot[IDIR];

src/dataBlock/planetarySystem/planetStructs.hpp

@@ -19,7 +19,7 @@ struct Force {
     real f_ex_inner[3];
     real f_outer[3];
     real f_ex_outer[3];
-    KOKKOS_FUNCTION void operator+=(Force const volatile& f) volatile {
+    KOKKOS_FUNCTION void operator+=(const Force & f) {
         for (int i = 0; i < 3; ++i) {
             f_inner[i] += f.f_inner[i];
             f_ex_inner[i] += f.f_ex_inner[i];

src/fluid/boundary/axis.hpp

@@ -126,7 +126,7 @@ Axis::Axis(Boundary<Phys> *boundary) {
 
   // Init the symmetry array (used to flip the signs of arrays accross the axis)
   symmetryVc = IdefixArray1D<int>("Axis:SymmetryVc",nVar);
-  IdefixArray1D<int>::HostMirror symmetryVcHost = Kokkos::create_mirror_view(symmetryVc);
+  IdefixArray1D<int>::host_mirror_type symmetryVcHost = Kokkos::create_mirror_view(symmetryVc);
   // Init the array
   for (int nv = 0; nv < nVar; nv++) {
     symmetryVcHost(nv) = 1;
@@ -143,7 +143,7 @@ Axis::Axis(Boundary<Phys> *boundary) {
 
   if constexpr(Phys::mhd) {
     symmetryVs = IdefixArray1D<int>("Axis:SymmetryVs",DIMENSIONS);
-    IdefixArray1D<int>::HostMirror symmetryVsHost = Kokkos::create_mirror_view(symmetryVs);
+    IdefixArray1D<int>::host_mirror_type symmetryVsHost = Kokkos::create_mirror_view(symmetryVs);
     // Init the array
     for(int nv = 0; nv < DIMENSIONS; nv++) {
       symmetryVsHost(nv) = 1;

src/gravity/laplacian.cpp

@@ -170,7 +170,7 @@ void Laplacian::InitInternalGrid() {
      });
 
   // Check that all is well
-  IdefixArray1D<real>::HostMirror xH = Kokkos::create_mirror_view(x1l);
+  IdefixArray1D<real>::host_mirror_type xH = Kokkos::create_mirror_view(x1l);
   Kokkos::deep_copy(xH, x1l);
 
   if(xH(0)<0.0) {

src/mpi/mpi.cpp

@@ -131,7 +131,7 @@ void Mpi::CheckConfig() {
 
   // Run-time check that we can do a reduce on device arrays
   IdefixArray1D<int64_t> src("MPIChecksrc",1);
-  IdefixArray1D<int64_t>::HostMirror srcHost = Kokkos::create_mirror_view(src);
+  IdefixArray1D<int64_t>::host_mirror_type srcHost = Kokkos::create_mirror_view(src);
 
   if(idfx::prank == 0) {
     srcHost(0) = 0;

test/MHD/AmbipolarWind/setup.cpp

@@ -373,7 +373,7 @@ void ComputeUserVars(DataBlock & data, UserDefVariablesContainer &variables) {
   IdefixHostArray1D<real> x1=d.x[IDIR];
   IdefixHostArray1D<real> x2=d.x[JDIR];
   IdefixHostArray4D<real> Vc=d.Vc;
-  IdefixArray3D<real>::HostMirror scrhHost = Kokkos::create_mirror_view(scrh);
+  IdefixArray3D<real>::host_mirror_type scrhHost = Kokkos::create_mirror_view(scrh);
   Kokkos::deep_copy(scrhHost,scrh);
 
   for(int k = d.beg[KDIR]; k < d.end[KDIR] ; k++) {

test/python_requirements.txt

@@ -8,7 +8,7 @@ scipy>=1.2.3
 
 # note that no version of inifix supports Python older than 3.6
 inifix>=0.11.2
-
+pybind11 >= 3.0.4
 # To run the test suite, we can use pytest, mostly any version
 # 6.0 is the one available on system available on debian-11
 pytest >= 6.0

test/skeleton/main.cpp

@@ -37,7 +37,7 @@ void testReduction() {
 
   // Init an array on device, and image on host
   IdefixArray3D<real> rho = IdefixArray3D<real>("rho",nx3,nx2,nx1);
-  IdefixArray3D<real>::HostMirror rhoHost = Kokkos::create_mirror_view(rho);
+  IdefixArray3D<real>::host_mirror_type rhoHost = Kokkos::create_mirror_view(rho);
 
   // Fill the host array, and compute the theoretical results
   real theoreticalResult = 0;

test/utils/columnDensity/setup.cpp

@@ -33,7 +33,7 @@ void Analysis(DataBlock & data) {
   columnX3Right->ComputeColumn(rho);
 
   IdefixArray3D<real> columnDensityLeft, columnDensityRight;
-  IdefixArray3D<real>::HostMirror columnDensityLeftHost, columnDensityRightHost;
+  IdefixArray3D<real>::host_mirror_type columnDensityLeftHost, columnDensityRightHost;
   // IDIR
   columnDensityLeft = columnX1Left->GetColumn();
   columnDensityRight = columnX1Right->GetColumn();

test/utils/lookupTable/main.cpp

@@ -38,7 +38,7 @@ int main( int argc, char* argv[] )
     idfx::cout << "--------------------------------------" << std::endl;
     idfx::cout << "Testing 2D CSV file on device." << std::endl;
     IdefixArray1D<real> arr = IdefixArray1D<real>("Test",1);
-    IdefixArray1D<real>::HostMirror arrHost = Kokkos::create_mirror_view(arr);
+    IdefixArray1D<real>::host_mirror_type arrHost = Kokkos::create_mirror_view(arr);
 
     LookupTable<2> csv("toto.csv",',');