...

.cuda-gdbinit

@@ -0,0 +1,2 @@
+break abort
+break __assert_fail

.gdbinit

@@ -0,0 +1,4 @@
+
+break __assert_fail
+break abort
+catch throw

.github/build.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+set -ex
+
+(
+  cd /github/workspace
+  mkdir build && cd build
+  cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
+        -DlowResourceTests=ON            \
+        -DCMAKE_CXX_FLAGS="-DPHARE_DIAG_DOUBLES=1 -O2" ..
+  make VERBOSE=1
+  ctest -j 2 --output-on-failure
+)

.github/workflows/cmake_macos.yml

@@ -87,13 +87,14 @@ jobs:
               -DCMAKE_BUILD_TYPE=RelWithDebInfo \
               -DENABLE_SAMRAI_TESTS=OFF -DCMAKE_C_COMPILER_LAUNCHER=ccache \
               -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DlowResourceTests=ON \
-              -DCMAKE_CXX_FLAGS="-DPHARE_DIAG_DOUBLES=1 "
+              -DCMAKE_CXX_FLAGS="-DPHARE_DIAG_DOUBLES=1 " \
+              -DtestDuringBuild=ON
 
     - name: Build
       working-directory: ${{runner.workspace}}/build
       env:
         LIBRARY_PATH: ${{ matrix.dylib_path }} # used by clang, needed to find libquadmath - else link error
-      run: cmake --build . -j 2
+      run: cmake --build . -j 1
 
     - name: Test
       working-directory: ${{runner.workspace}}/build

.gitignore

@@ -1,3 +1,4 @@
+.mkn*
 bin
 build
 subprojects
@@ -22,3 +23,5 @@ perf.*
 .vscode
 .phare*
 PHARE_REPORT.zip
+*.mkn
+.cache

CMakeLists.txt

@@ -1,37 +1,32 @@
 cmake_minimum_required (VERSION 3.20.1) # released April 8, 2021 - https://www.kitware.com/cmake-3-20-1-available-for-download/
 
 project(PHARE VERSION 0.1 LANGUAGES CXX C)
+set(PHARE_PROJECT_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+
+include("${PHARE_PROJECT_DIR}/res/cmake/policies.cmake" NO_POLICY_SCOPE)
+include(CheckCXXCompilerFlag)
+
 
 # Release mode default
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "Release" CACHE STRING "" FORCE)
 endif()
 
-if (POLICY CMP0074) # hides warning about ${PACKAGE}_ROOT variables
-  cmake_policy(SET CMP0074 NEW)
-endif()
-if (POLICY CMP0069) # allow LTO if available, requires cmake 3.9 (released August 2017)
-  cmake_policy(SET CMP0069 NEW)
-endif()
+find_package(Python 3.8 COMPONENTS Interpreter Development.Module REQUIRED)
+include("${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(Python 3.8 COMPONENTS Interpreter Development.Module 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 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 

doc/obs/.obsidian/app.json

@@ -0,0 +1 @@
+{}

doc/obs/.obsidian/appearance.json

@@ -0,0 +1 @@
+{}

doc/obs/.obsidian/core-plugins-migration.json

@@ -0,0 +1,30 @@
+{
+  "file-explorer": true,
+  "global-search": true,
+  "switcher": true,
+  "graph": true,
+  "backlink": true,
+  "canvas": true,
+  "outgoing-link": true,
+  "tag-pane": true,
+  "properties": false,
+  "page-preview": true,
+  "daily-notes": true,
+  "templates": true,
+  "note-composer": true,
+  "command-palette": true,
+  "slash-command": false,
+  "editor-status": true,
+  "bookmarks": true,
+  "markdown-importer": false,
+  "zk-prefixer": false,
+  "random-note": false,
+  "outline": true,
+  "word-count": true,
+  "slides": false,
+  "audio-recorder": false,
+  "workspaces": false,
+  "file-recovery": true,
+  "publish": false,
+  "sync": false
+}

doc/obs/.obsidian/core-plugins.json

@@ -0,0 +1,20 @@
+[
+  "file-explorer",
+  "global-search",
+  "switcher",
+  "graph",
+  "backlink",
+  "canvas",
+  "outgoing-link",
+  "tag-pane",
+  "page-preview",
+  "daily-notes",
+  "templates",
+  "note-composer",
+  "command-palette",
+  "editor-status",
+  "bookmarks",
+  "outline",
+  "word-count",
+  "file-recovery"
+]

doc/obs/.obsidian/workspace.json

@@ -0,0 +1,153 @@
+{
+  "main": {
+    "id": "ebdfe6166647b6c1",
+    "type": "split",
+    "children": [
+      {
+        "id": "0d59da3f5e2f6cc6",
+        "type": "tabs",
+        "children": [
+          {
+            "id": "aab21fbc2ddacce1",
+            "type": "leaf",
+            "state": {
+              "type": "markdown",
+              "state": {
+                "file": "todo.md",
+                "mode": "source",
+                "source": false
+              }
+            }
+          }
+        ]
+      }
+    ],
+    "direction": "vertical"
+  },
+  "left": {
+    "id": "e35d4318c9016fd8",
+    "type": "split",
+    "children": [
+      {
+        "id": "0b0082ef75efe82d",
+        "type": "tabs",
+        "children": [
+          {
+            "id": "7dc1b9cb3eccb73e",
+            "type": "leaf",
+            "state": {
+              "type": "file-explorer",
+              "state": {
+                "sortOrder": "alphabetical"
+              }
+            }
+          },
+          {
+            "id": "50e136fb58f0f54f",
+            "type": "leaf",
+            "state": {
+              "type": "search",
+              "state": {
+                "query": "",
+                "matchingCase": false,
+                "explainSearch": false,
+                "collapseAll": false,
+                "extraContext": false,
+                "sortOrder": "alphabetical"
+              }
+            }
+          },
+          {
+            "id": "d313742985bf39d7",
+            "type": "leaf",
+            "state": {
+              "type": "bookmarks",
+              "state": {}
+            }
+          }
+        ]
+      }
+    ],
+    "direction": "horizontal",
+    "width": 300
+  },
+  "right": {
+    "id": "cc54f2482c16b8a4",
+    "type": "split",
+    "children": [
+      {
+        "id": "0747445f8f878360",
+        "type": "tabs",
+        "children": [
+          {
+            "id": "34bdda6cd146cf63",
+            "type": "leaf",
+            "state": {
+              "type": "backlink",
+              "state": {
+                "file": "todo.md",
+                "collapseAll": false,
+                "extraContext": false,
+                "sortOrder": "alphabetical",
+                "showSearch": false,
+                "searchQuery": "",
+                "backlinkCollapsed": false,
+                "unlinkedCollapsed": true
+              }
+            }
+          },
+          {
+            "id": "83058547a4e6c739",
+            "type": "leaf",
+            "state": {
+              "type": "outgoing-link",
+              "state": {
+                "file": "todo.md",
+                "linksCollapsed": false,
+                "unlinkedCollapsed": true
+              }
+            }
+          },
+          {
+            "id": "451e733254a59cc0",
+            "type": "leaf",
+            "state": {
+              "type": "tag",
+              "state": {
+                "sortOrder": "frequency",
+                "useHierarchy": true
+              }
+            }
+          },
+          {
+            "id": "df2f29a5241eb034",
+            "type": "leaf",
+            "state": {
+              "type": "outline",
+              "state": {
+                "file": "todo.md"
+              }
+            }
+          }
+        ]
+      }
+    ],
+    "direction": "horizontal",
+    "width": 300,
+    "collapsed": true
+  },
+  "left-ribbon": {
+    "hiddenItems": {
+      "switcher:Open quick switcher": false,
+      "graph:Open graph view": false,
+      "canvas:Create new canvas": false,
+      "daily-notes:Open today's daily note": false,
+      "templates:Insert template": false,
+      "command-palette:Open command palette": false
+    }
+  },
+  "active": "7dc1b9cb3eccb73e",
+  "lastOpenFiles": [
+    "todo.md"
+  ]
+}

doc/obs/docker.md

@@ -0,0 +1,7 @@
+# just docker things
+
+### set shm size for mpi
+
+```shell
+docker run --shm-size=3256m -w /io  --rm -it -v $PWD:/io --name phare registry.lpp.polytechnique.fr/phare/teamcity-fedora_dep:40
+```

doc/obs/perf.md

@@ -0,0 +1,52 @@
+## Performance analyses
+
+### via perf
+
+See: https://man7.org/linux/man-pages/man1/perf-record.1.html
+
+```shell
+# build with the following
+CMAKE_CXX_FLAGS="-g3 -O3 -march=native -mtune=native -fno-omit-frame-pointer"
+CMAKE_BUILD_TYPE="RelWithDebInfo"
+
+# build...
+
+perf record -Tga -F 1000 ./build/src/phare/phare-exe path/to/python/script.py
+ls -lah perf.data # check file is new/exists
+perf script report flamegraph
+```
+
+### via perf in vtune
+
+installation see
+https://www.intel.com/content/www/us/en/docs/vtune-profiler/installation-guide/2023-0/package-managers.html
+
+
+```shell
+# see above, but rename perf.data to data.perf (vtune only reads .perf files)
+```
+
+### via scalasca / scorep
+
+```shell
+# install
+sudo dnf install scorep-openmpi scalasca-openmpi libunwind-devel binutils-devel elfutils-devel
+```
+
+```shell
+# usage
+CMAKE_CXX_FLAGS="-g3 -O3 -march=native -mtune=native -fno-omit-frame-pointer"
+CMAKE_BUILD_TYPE="RelWithDebInfo"
+export CXX=scorep-mpicxx CC=scorep-mpicc FC=scorep-gfortran
+
+# build...
+
+# run
+# see https://vampir.eu/public/files/pdf/spcheatsheet_a4.pdf
+export SCOREP_EXPERIMENT_DIRECTORY=scorep_run_trace
+export SCOREP_TOTAL_MEMORY=500M # default is 16MB which will fail
+scalasca -analyze mpirun -n 8 ./build/src/phare/phare-exe path/to/python/script.py
+
+# view
+scalasca -examine scorep_run_trace
+```

doc/obs/todo.md

@@ -0,0 +1 @@
+multiple gpu https://enccs.github.io/gpu-programming/8-multiple_gpu/