...

.github/workflows/cmake.yml

@@ -80,7 +80,8 @@ jobs:
         cmake $GITHUB_WORKSPACE \
               -DENABLE_SAMRAI_TESTS=OFF -DCMAKE_C_COMPILER_LAUNCHER=ccache \
               -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DlowResourceTests=ON \
-              -DCMAKE_CXX_FLAGS="-DPHARE_DIAG_DOUBLES=1 -O2"
+              -DCMAKE_CXX_FLAGS="-DPHARE_DIAG_DOUBLES=1 -O2" \
+              -DtestDuringBuild=ON
 
     - name: Build
       working-directory: ${{runner.workspace}}/build

.gitignore

@@ -1,3 +1,4 @@
+.mkn*
 bin
 build
 subprojects

CMakeLists.txt

@@ -1,6 +1,10 @@
 cmake_minimum_required (VERSION 3.9)
 
 project(PHARE VERSION 0.1 LANGUAGES CXX)
+set(PHARE_PROJECT_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+
+include("${PHARE_PROJECT_DIR}/res/cmake/policies.cmake" NO_POLICY_SCOPE)
+include(CheckCXXCompilerFlag)
 
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "Debug" CACHE STRING "" FORCE)
@@ -10,31 +14,21 @@ if(NOT CMAKE_BUILD_TYPE)
   endif()
 endif()
 
-if (POLICY CMP0074) # hides warning about ${PACKAGE}_ROOT variables
-  cmake_policy(SET CMP0074 NEW)
-endif()
-if (POLICY CMP0069) # allow LTO if available, requires cmake 3.9 (released August 2017)
-  cmake_policy(SET CMP0069 NEW)
-endif()
+find_package(PythonInterp  3.0 REQUIRED)
+include("${PHARE_PROJECT_DIR}/res/cmake/options.cmake")
+include("${PHARE_PROJECT_DIR}/res/cmake/def.cmake")
+include("${PHARE_PROJECT_DIR}/res/cmake/coverage.cmake")
+include("${PHARE_PROJECT_DIR}/res/cmake/dep.cmake")
 
 # Enables -fPIC  typically required for shared libraries with dependencies. e.g. pybind modules
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-
-include(CheckCXXCompilerFlag)
-find_program(Git git)
-find_package(PythonInterp  3.0 REQUIRED)
-
-set(PHARE_PROJECT_DIR ${CMAKE_CURRENT_SOURCE_DIR})
 set(CMAKE_EXPORT_COMPILE_COMMANDS 1)
 
 include_directories(${PHARE_PROJECT_DIR}/src)
 
-include("${PHARE_PROJECT_DIR}/res/cmake/options.cmake")
-include("${PHARE_PROJECT_DIR}/res/cmake/def.cmake")
-include("${PHARE_PROJECT_DIR}/res/cmake/coverage.cmake")
-include("${PHARE_PROJECT_DIR}/res/cmake/dep.cmake")
 include("${PHARE_PROJECT_DIR}/res/cmake/cppcheck.cmake")
 
+# set standard after dependencies to avoid potential conflicts
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 

mkn.cuda.sh

@@ -0,0 +1,36 @@
+#! /usr/bin/env bash
+
+set -ex
+
+CWD="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+mkdir -p $CWD/build
+[ ! -d  "$CWD/build" ] && echo "mkn expects cmake configured build directory" && exit 1
+
+MKN_X_FILE=${MKN_X_FILE:-settings}
+MKN_MPI_X_FILE=${MKN_MPI_X_FILE:-res/mkn/mpi}
+MKN_GPU_X_FILE=${MKN_GPU_X_FILE:-res/mkn/clang_cuda}
+export MKN_LIB_LINK_LIB=1
+
+exit 0
+
+# verify compiler setup
+# mkn clean build -x ${MKN_GPU_X_FILE} -ga -DKUL_GPU_CUDA dbg -p mkn.gpu_depositor run test
+
+[ ! -d ./subprojects/thrust ] && \
+  git clone https://github.com/NVIDIA/thrust \
+    -b main subprojects/thrust --depth 10 --shallow-submodules --recursive
+[ ! -d ./subprojects/cuda-samples ] && \
+  git clone https://github.com/NVIDIA/cuda-samples \
+    -b main subprojects/cuda-samples --depth 10 --shallow-submodules --recursive
+
+
+# gtest doens't like mpi compilers
+#mkn clean build -x ${MKN_X_FILE} -p test_diagnostics -tKOd google.test,+
+
+#mkn clean build -x ${MKN_MPI_X_FILE} -dtKOp py
+
+# mkn clean build -x ${MKN_MPI_X_FILE} -p test_diagnostics -KO 9 test run
+# mkn clean build -x ${MKN_GPU_X_FILE} -Oa -DKUL_GPU_CUDA run
+
+#mkn clean build -x ${MKN_GPU_X_FILE} -Op cpp

mkn.rocm.sh

@@ -0,0 +1,28 @@
+#! /usr/bin/env bash
+
+set -ex
+
+CWD="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+MKN_X_FILE=${MKN_X_FILE:-settings}
+MKN_MPI_X_FILE=${MKN_MPI_X_FILE:-res/mkn/mpi}
+MKN_GPU_X_FILE=${MKN_GPU_X_FILE:-res/mkn/hip}
+
+mkdir -p $CWD/build
+[ ! -d  "$CWD/build" ] && echo "mkn expects cmake configured build directory" && exit 1
+
+export MKN_LIB_LINK_LIB=1
+
+# verify compiler setup
+# mkn clean build -x ${MKN_GPU_X_FILE} -ga -DKUL_GPU_ROCM dbg -p mkn.gpu_depositor run test
+
+# git clone https://github.com/NVIDIA/thrust -b 1.13.0 subprojects/thrust --depth 10 --shallow-submodules --recursive
+
+# gtest doens't like mpi compilers
+mkn clean build -x ${MKN_X_FILE} -p test_diagnostics -tKOd google.test,+
+
+mkn clean build -x ${MKN_MPI_X_FILE} -dtKOp py
+
+mkn clean build -x ${MKN_MPI_X_FILE} -p test_diagnostics -KO 9 test run
+
+mkn clean build -x ${MKN_GPU_X_FILE} -Oa -DKUL_GPU_ROCM run

mkn.yaml

@@ -0,0 +1,214 @@
+#! clean build -x mpi -dtKOp py
+
+name: phare
+
+property:
+  MPI_INC: /usr/include #/hdf5/mpich #/usr/include/hdf5/openmpi #/usr/local/netcdf/include
+  MPI_LIB: hdf5
+  MPI_PTH: /usr/local/lib #/opt/conda/envs/vscode/lib
+  mkn.gpu: -DPHARE_HAVE_MKN_GPU=1 -DMKN_GPU_CUDA=1  -DPHARE_WITH_KUL=1
+  gpu.args: -DPHARE_HAVE_RAJA=1 -DPHARE_WITH_GPU=1  ${mkn.gpu} -DHAVE_RAJA=1 -DHAVE_CUDA=1
+
+profile:
+- name: umpira_raja_base
+  arg: -DPHARE_HAVE_RAJA=1 -DPHARE_HAVE_UMPIRE=1 
+
+- name: base
+  arg:  -Wno-macro-redefined -Wno-unknown-cuda-version  -DPHARE_HAS_HIGHFIVE=0
+
+- name: gpu_base
+  parent: base
+  dep: mkn.gpu llnl.raja[lib]
+  arg: ${gpu.args}
+
+- name: core
+  parent: base
+  inc: src subprojects
+  src: src/core
+  # dep: mkn.kul
+  out: phare_core
+
+
+- name: test_base
+  inc: .
+  dep: google.test
+
+- name: test_core
+  parent: test_base
+  self: core
+  # test: tests/core/(\w)/(test_.*).cpp
+
+- name: amr
+  parent: base
+  self: core
+  dep: llnl.samrai(https://github.com/mkn-nix/llnl.samrai) #llnl.raja[lib] mkn.gpu #llnl.umpire[lib]
+  lib: hdf5_openmpi
+  src: src/amr
+  out: phare_amr
+
+- name: test_amr
+  parent: test_base
+  self: amr
+
+- name: diagnostic
+  self: amr
+  dep: hpc.highfive(https://github.com/mkn-nix/hpc.highfive)
+  inc: build/subprojects/highfive/include
+       ${MPI_INC}
+  lib: ${MPI_LIB}
+  path: ${MPI_PTH}
+
+- name: simulator
+  parent: base
+  self: diagnostic
+  out: phare_simulator
+
+- name: exe
+  parent: gpu_base
+  self: simulator init
+  dep: lang.pybind11 
+  main: src/phare/phare.cpp
+  mod: lang.python3
+  env: PYTHONPATH=${MKN_ROOT}:${MKN_ROOT}/tests/diagnostic:${MKN_ROOT}/build:${MKN_ROOT}/pyphare
+
+- name: init
+  src: src/initializer/data_provider.cpp
+  self: core
+  out: phare_initializer
+  mode: shared # static singleton dict lives here
+
+- name: pybind
+  # parent: base
+  mode: shared
+  dep: lang.pybind11
+  mod: lang.pybind11 lang.python3
+
+- name: dictator
+  parent: pybind
+  self: init
+  src: src/initializer/dictator.cpp
+  install: build/pybindlibs
+  out: dictator
+
+- name: cpp
+  parent: pybind
+  # lib: numa
+  # arg: -DPHARE_WITH_GPU -DKUL_GPU_CUDA
+  arg: ${gpu.args}
+
+  self: simulator init gpu_base
+  src: src/python3/cpp_simulator.cpp
+  install: build/pybindlibs
+  #test: tests/amr/solvers/ppc/test_gpu_solverppc.cpp
+  out: cpp
+
+- name: cpp_etc
+  parent: pybind
+  self: simulator
+  src: src/python3/cpp_etc.cpp
+  install: build/pybindlibs
+  out: cpp_etc
+  arg:  -DPHARE_HAS_HIGHFIVE=0
+
+- name: py
+  self: dictator cpp_etc simulator
+
+- name: test
+  parent: base
+  self: init simulator
+  dep: lang.pybind11 google.test
+  mod: lang.python3
+  inc: .
+  link: -pthread
+
+- name: test_diagnostics
+  parent: test
+  mode: none
+  mod: lang.python3
+  test:
+    tests/diagnostic/test-diagnostics_1d.cpp
+    tests/diagnostic/test-diagnostics_2d.cpp
+  env: PYTHONPATH=${MKN_ROOT}:${MKN_ROOT}/build/tests/diagnostic:${MKN_ROOT}/build:${MKN_ROOT}/pyphare
+
+- name: bench
+  self: core
+  inc: . tools
+  dep: google.benchmark
+  main: tools/bench/core/data/particles/interop.cpp
+  link: -pthread
+
+- name: gpu_pusher
+  parent: test
+  self: bench
+  inc: .
+  dep: mkn.gpu
+  arg: -DPHARE_WITH_GPU
+  env: PYTHONPATH=${MKN_ROOT}:${MKN_ROOT}/tools/bench/core/numerics/pusher:${MKN_ROOT}/build:${MKN_ROOT}/pyphare
+
+- name: rocm_pusher
+  parent: gpu_pusher
+  main: tools/bench/core/numerics/pusher/gpu.cpp
+  arg: -DKUL_GPU_ROCM
+  env: PYTHONPATH=${MKN_ROOT}:${MKN_ROOT}/tools/bench/core/numerics/pusher:${MKN_ROOT}/build:${MKN_ROOT}/pyphare
+
+- name: cuda_pusher
+  parent: gpu_pusher
+  main: tests/amr/solvers/ppc/test_gpu_solverppc.cpp #tools/bench/core/numerics/pusher/gpu.cpp
+  arg: -DKUL_GPU_CUDA
+  inc: subprojects/thrust
+  env: PYTHONPATH=${MKN_ROOT}:${MKN_ROOT}/tools/bench/core/numerics/pusher:${MKN_ROOT}/build:${MKN_ROOT}/pyphare
+
+# - name: cuda_bandwidth_test
+#   main: subprojects/cuda-samples/Samples/bandwidthTest/bandwidthTest.cu
+#   inc: subprojects/cuda-samples/Common
+
+- name: c_depositor
+  test: tools/hw/gpu/bench/depositor.cpp
+
+- name: mkn.gpu_depositor
+  dep: mkn.gpu
+  test: tools/hw/gpu/bench/depositor.mkn.gpu.cpp
+
+# mkn clean build test run -p mkn.sheath.hip -x res/mkn/hcc.yaml -O
+- name: mkn.sheath.hip
+  dep: mkn.gpu
+  test: tools/hw/gpu/bench/sheath-gpu.hip.cpp
+
+- name: mkn.sheath.cuda
+  dep: mkn.gpu
+  test: tools/hw/gpu/bench/sheath-gpu.cuda.cpp
+
+- name: test_core_gpu_mkn
+  self: core
+  arg: -DPHARE_WITH_GPU=1 -DPHARE_HAVE_MKN_GPU=1 -DMKN_GPU_CUDA=1
+  dep: google.test mkn.gpu nvidia.thrust
+  main: tests/core/data/test_vector.cpp
+
+- name: gpu_test
+  parent: test
+  self: simulator init
+  arg: |
+      -DHAVE_RAJA
+      -DHAVE_UMPIRE
+      -DRAJA_ENABLE_CUDA=1
+      -DUMPIRE_ENABLE_CUDA=1
+      -DPHARE_WITH_GPU=1
+      -DPHARE_HAS_HIGHFIVE=1
+      -DPHARE_WITH_KUL=1
+      -DKUL_GPU_CUDA=1
+  test:
+    tests/core/data/ndarray/test_main.cpp
+
+# tests/core/numerics/ion_updater/test_updater.cpp
+# tests/core/numerics/interpolator/test_main.cpp
+# tests/core/data/field/test_field.cpp
+# tests/core/data/vecfield/test_main.cpp
+# tests/core/data/ions/test_ions.cpp
+# tests/core/data/electrons/test_electrons.cpp
+# tests/core/numerics/ampere/test_main.cpp
+# tests/core/numerics/faraday/test_main.cpp
+# tests/core/numerics/ohm/test_main.cpp
+
+- name: format
+  mod: |
+    clang.format{init{style: file, paths: src}}

pyphare/pyphare/core/phare_utilities.py

@@ -1,18 +1,24 @@
 import math
 import numpy as np
 
+
+
+def is_nd_array(arg):
+    return isinstance(arg, np.ndarray)
+
+
 def all_iterables(*args):
     """
     return true if all arguments are either lists or tuples
     """
-    return all([isinstance(arg, list) or isinstance(arg, tuple) for arg in args])
+    return all([isinstance(arg, (tuple, list)) or is_nd_array(arg) for arg in args])
 
 
 def none_iterable(*args):
     """
     return true if none of the arguments are either lists or tuples
     """
-    return all([not isinstance(arg, list) and not isinstance(arg, tuple) for arg in args])
+    return all([not isinstance(arg, (tuple, list)) and not is_nd_array(arg)  for arg in args])
 
 
 def equal_size(*args):
@@ -44,11 +50,9 @@ def listify(arg):
 
 
 def is_scalar(arg):
-    return not isinstance(arg, (list, tuple)) and not is_nd_array(arg)
+    return none_iterable(arg)
 
 
-def is_nd_array(arg):
-    return isinstance(arg, np.ndarray)
 
 
 def np_array_ify(arg, size = 1):
@@ -159,3 +163,8 @@ def deep_copy(item, memo, excludes=[]):
             setattr(that, key, deepcopy(value, memo))
     return that
 
+
+def NO_GUI():
+    import matplotlib as mpl
+    mpl.use("Agg")
+

requirements.txt

@@ -1,3 +1,5 @@
+# wheel might be need to build other deps
+wheel
 dill
 ddt
 h5py