Merge pull request #7 from haykh/dev/main

Dev/main

Author: haykh

.gitmodules

@@ -21,4 +21,4 @@
 	branch = master
 [submodule "extern/fmt"]
 	path = extern/fmt
-	url = https://github.com/fmtlib/fmt.git
+	url = https://github.com/fmtlib/fmt.git

.vscode/c_cpp_properties.json

@@ -8,7 +8,7 @@
       "${workspaceFolder}/build/extern/kokkos/",
       "${workspaceFolder}/build/extern/adios2/source/"
     ],
-    "myCompilerPath": "/usr/bin/g++"
+    "myCompilerPath": "g++"
   },
   "configurations": [
     {

.vscode/settings.json

@@ -121,8 +121,8 @@
   "cmake.buildDirectory": "${workspaceFolder}/build",
   "cmake.configureSettings": {
     "output": "OFF",
-    "nttiny": "ON",
+    "nttiny": "OFF",
     "Kokkos_ENABLE_OPENMP": "ON",
-    "pgen": "langmuir"
+    "pgen": "weibel"
   },
 }

CMakeLists.txt

@@ -3,11 +3,12 @@ cmake_minimum_required(VERSION 3.16)
 set(PROJECT_NAME entity)
 
 project(${PROJECT_NAME}
-  VERSION 0.8.0.9
+  VERSION 0.8.2.1
   LANGUAGES CXX
 )
 
 # ----------------------------- Submodules ------------------------------- #
+# !TODO: this is quite ugly, update submodules as needed (below)
 find_package(Git QUIET)
 
 file(GLOB SUBMODULES_LOADED extern/kokkos/*)
@@ -24,6 +25,7 @@ if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git" AND NOT ${SUBMODULES_LOADED
 
   if(GIT_SUBMODULE)
     message(STATUS "Updating all the submodules")
+    message(STATUS "  During the first-time configure this may take a couple of minutes")
     execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --remote --recursive
       WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
       RESULT_VARIABLE GIT_SUBMOD_RESULT)
@@ -131,7 +133,7 @@ else()
   message(STATUS "Debug mode")
 endif()
 
-# ---------------------------------- tests --------------------------------- #
+# ---------------------------------- Tests --------------------------------- #
 set(BUILD_TESTING OFF CACHE BOOL "Build tests")
 
 if(${BUILD_TESTING} STREQUAL "OFF")
@@ -143,17 +145,11 @@ endif()
 # ----------------------------------- GUI ---------------------------------- #
 set(nttiny ${default_nttiny} CACHE BOOL "Use nttiny GUI")
 
-if(${nttiny} STREQUAL "ON")
-  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/extern/nttiny extern/nttiny)
-endif()
-
 # ----------------------------- Kokkos settings ---------------------------- #
 if(${Kokkos_ENABLE_CUDA})
   set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "Enable CUDA lambda")
 endif()
 
-add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/extern/kokkos extern/kokkos)
-
 # set memory space
 if(${Kokkos_ENABLE_CUDA})
   add_definitions(-DENABLE_GPU)
@@ -183,21 +179,40 @@ endif()
 set(output ${default_output} CACHE BOOL "Enable output")
 
 if(${output} STREQUAL "ON")
+  set(ADIOS2_BUILD_EXAMPLES OFF CACHE BOOL "Build ADIOS2 examples")
+  # Language support
   set(ADIOS2_USE_Python OFF CACHE BOOL "Use Python for ADIOS2")
   set(ADIOS2_USE_Fortran OFF CACHE BOOL "Use Fortran for ADIOS2")
+  # Format/compression support
+  set(ADIOS2_USE_MPI OFF CACHE BOOL "Use MPI for ADIOS2")
+  set(ADIOS2_USE_ZeroMQ OFF CACHE BOOL "Use ZeroMQ for ADIOS2")
+  set(ADIOS2_USE_SST OFF CACHE BOOL "Use SST for ADIOS2")
+  set(ADIOS2_USE_BZip2 OFF CACHE BOOL "Use BZip2 for ADIOS2")
+  set(ADIOS2_USE_ZFP OFF CACHE BOOL "Use ZFP for ADIOS2")
+  set(ADIOS2_USE_SZ OFF CACHE BOOL "Use SZ for ADIOS2")
+  set(ADIOS2_USE_MGARD OFF CACHE BOOL "Use MGARD for ADIOS2")
+  set(ADIOS2_USE_PNG OFF CACHE BOOL "Use PNG for ADIOS2")
+  set(ADIOS2_USE_Blosc OFF CACHE BOOL "Use Blosc for ADIOS2")
+
+  # !TODO: add MPI-enabled ADIOS2
   set(ADIOS2_USE_MPI OFF CACHE BOOL "Use MPI for ADIOS2")
-  set(ADIOS2_BUILD_EXAMPLES OFF CACHE BOOL "Build ADIOS2 examples")
 
   # !TODO: add CUDA-enabled ADIOS2
   set(ADIOS2_USE_CUDA OFF CACHE BOOL "Use CUDA for ADIOS2")
 
   # set(ADIOS2_USE_CUDA ${Kokkos_ENABLE_CUDA} CACHE BOOL "Use CUDA for ADIOS2")
   add_compile_options("-D OUTPUT_ENABLED")
-  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/extern/adios2 extern/adios2)
 endif()
 
-# ----------------------------------- fmt ---------------------------------- #
+# ------------------------------ Dependencies ------------------------------ #
+if(${nttiny} STREQUAL "ON")
+  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/extern/nttiny extern/nttiny)
+endif()
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/extern/kokkos extern/kokkos)
 add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/extern/fmt extern/fmt)
+if (${output} STREQUAL "ON")
+  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/extern/adios2 extern/adios2)
+endif()
 
 # ------------------------------- Main source ------------------------------ #
 add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/src src)

README.md

@@ -1,7 +1,13 @@
 # `Entity` a.k.a. `ntt`
 One particle-in-cell code to rule them all. Find our detailed documentation [here](https://haykh.github.io/entity/).
 
-![image](assets/cover.gif)
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="assets/cover_dark.gif">
+    <source media="(prefers-color-scheme: light)" srcset="assets/cover_light.gif">
+    <img alt="cover" src="assets/cover_light.gif">
+  </picture>
+</p>
 
 ## Code contributors (alphabetical)
 

TASKLIST.md

@@ -5,13 +5,13 @@
 - [ ] add diagnostics for nans in fields and particles
 - [ ] add gravitationally bound atmosphere
 - [x] rewrite UniformInjector with global random pool
-- [ ] add particle deletion routine
+- [?] add particle deletion routine
 - [ ] make more user-friendly and understandable boundary conditions
 - [ ] refine output
 - [ ] fix bugs in `nttiny`
   - [x] delete plot removes all labels
   - [ ] add particles to `nttiny`
-  - [ ] state should also save skip interval
+  - [x] state should also save skip interval
   - [ ] (?) add autosave state
   - [x] why last cell does not work?
 - [ ] add different moments (momX, momY, momZ, meanGamma)

assets/cover.gif.REMOVED.git-id

@@ -9,7 +9,7 @@ qsph_r0         = <float: -infinity < ... < r_min>
 qsph_h          = <float: -1 < ... < 1>
 resolution      = <array of int of size 1, 2 or 3>
 extent          = <array of float of size 2, 4 or 6>, ex. [x1min, x1max, x2min, x2max, x3min, x3max]
-boundaries      = <array of strings of size 1, 2 or 3: { "PERIODIC" | "ABSORB" | "OPEN" | "USER_BC" }>
+boundaries      = <array of strings of size 1, 2 or 3: { "PERIODIC" | "ABSORB" | "OPEN" | "USER" }>
 
 [algorithm]
 CFL             = <float: 0.0 < ... < 1.0>
@@ -25,21 +25,25 @@ skindepth0      = <float>
 
 [particles]
 n_species       = <int>
+shuffle_step    = <int>
+max_dead_frac   = <float>
 
 [species_<INT>]
 label           = <string>
 mass            = <float>
 charge          = <float>
 maxnpart        = <int>
-pusher          = <string: { BORIS }>
+pusher          = <string: { "Boris" }>
 
 [problem]
 ...
 
 [visualization]
-fields          = <array of strings, ex. ["Dr", "Dtheta", ...], see vis/nttiny.cpp for ref>
+fields          = <array of strings, ex. ["Dr", "Dtheta", ...], see src/definitions.h for ref>
 fields_stride   = <int>
 
 [output]
+fields          = <array of strings, ex. ["Dr", "Dtheta", ...], see src/definitions.h for ref>
 format          = <string: { disabled, hdf5 }>
-interval        = <int>
+mom_smooth      = <int>
+interval        = <int>

assets/cover_dark.gif

@@ -224,36 +224,43 @@ PrintChoices("OpenMP"
   0
   42
 )
+
 PrintChoices("C++ compiler"
   "CMAKE_CXX_COMPILER"
-  "${CMAKE_CXX_COMPILER}"
-  ${CMAKE_CXX_COMPILER}
+  "${CMAKE_CXX_COMPILER} v${CMAKE_CXX_COMPILER_VERSION}"
+  "${CMAKE_CXX_COMPILER} v${CMAKE_CXX_COMPILER_VERSION}"
   "N/A"
   "${White}"
-  COMPILERS_REPORT
+  CXX_COMPILER_REPORT
   0
   42
 )
 
-# check if empty
-if ("${CMAKE_CUDA_COMPILER}" STREQUAL "")
-  execute_process(COMMAND which nvcc OUTPUT_VARIABLE CUDACOMP)
-else()
-  set(CUDACOMP ${CMAKE_CUDA_COMPILER})
-endif()
-
 if(${Kokkos_ENABLE_CUDA})
+  # check if empty
+  if ("${CMAKE_CUDA_COMPILER}" STREQUAL "")
+    execute_process(COMMAND which nvcc OUTPUT_VARIABLE CUDACOMP)
+  else()
+    set(CUDACOMP ${CMAKE_CUDA_COMPILER})
+  endif()
+
+  message(STATUS "CUDA compiler: ${CUDACOMP}")
+  execute_process(COMMAND bash "-c" 
+                  "${CUDACOMP} --version | grep release | sed -e 's/.*release //' -e 's/,.*//'" 
+                  OUTPUT_VARIABLE CUDACOMP_VERSION 
+                  OUTPUT_STRIP_TRAILING_WHITESPACE)
+
   PrintChoices("CUDA compiler"
     "CMAKE_CUDA_COMPILER"
-    "${CUDACOMP}"
-    ${CUDACOMP}
+    "${CUDACOMP} v${CUDACOMP_VERSION}"
+    "${CUDACOMP} v${CUDACOMP_VERSION}"
     "N/A"
     "${White}"
     CUDA_COMPILER_REPORT
     0
     42
   )
-  set(COMPILERS_REPORT "${COMPILERS_REPORT}\n\n  ${CUDA_COMPILER_REPORT}")
+  # set(COMPILERS_REPORT "${COMPILERS_REPORT}\n\n  ${CUDA_COMPILER_REPORT}")
 endif()
 
 set(DOT_SYMBOL "${ColourReset}.")
@@ -280,42 +287,35 @@ ${DOT_SYMBOL}${Blue}                                                /\\___/
 ${DOT_SYMBOL}${Blue}                                                \\/__/                ${DOT_SYMBOL}
 ${DOT_SYMBOL}                                                                     ${DOT_SYMBOL}
 ${DOT_SYMBOL}${Blue}                              ${VERSION_SYMBOL}                             ${DOT_SYMBOL}
-${DOTTED_LINE_SYMBOL}
-
-${DASHED_LINE_SYMBOL}
+${DOTTED_LINE_SYMBOL}")
+message("${DASHED_LINE_SYMBOL}
 Main configurations ${Dim}[1]${ColourReset}
-${DASHED_LINE_SYMBOL}
-  ${ENGINE_REPORT}
-
-  ${METRIC_REPORT}
-
-  ${PGEN_REPORT}
-
-  ${PRECISION_REPORT}
-
-  ${OUTPUT_REPORT}
-
-  ${NTTINY_REPORT}
-${DASHED_LINE_SYMBOL}
+${DASHED_LINE_SYMBOL}")
+message("  ${ENGINE_REPORT}\n")
+message("  ${METRIC_REPORT}\n")
+message("  ${PGEN_REPORT}\n")
+message("  ${PRECISION_REPORT}\n")
+message("  ${OUTPUT_REPORT}\n")
+message("  ${NTTINY_REPORT}\n")
+message("${DASHED_LINE_SYMBOL}
 Framework configurations
-${DASHED_LINE_SYMBOL}
-  ${DEBUG_REPORT}
-
-  ${FRAMEWORK_REPORT}
-
-  ${ARCH_REPORT}
-
-  ${CUDA_REPORT}
-
-  ${OPENMP_REPORT}
-
-  ${COMPILERS_REPORT}
-${DASHED_LINE_SYMBOL}
+${DASHED_LINE_SYMBOL}")
+  message("  ${DEBUG_REPORT}\n")
+  message("  ${FRAMEWORK_REPORT}\n")
+  if (NOT "${ARCH_REPORT}" STREQUAL "")
+    message("  ${ARCH_REPORT}\n")
+  endif()
+  message("  ${CUDA_REPORT}\n")
+  message("  ${OPENMP_REPORT}\n")
+  message("  ${CXX_COMPILER_REPORT}\n")
+  if (NOT "${CUDA_COMPILER_REPORT}" STREQUAL "")
+    message("  ${CUDA_COMPILER_REPORT}\n")
+  endif()
+message("${DASHED_LINE_SYMBOL}
 Notes
 ${DASHED_LINE_SYMBOL}
   ${Dim}[1] Set with `cmake ... -D ${Magenta}<FLAG>${ColourReset}${Dim}=<VALUE>`, the ${Underline}default${ColourReset}${Dim} value
    :  will be used unless the variable is explicitly set.${ColourReset}
-
 ")
 
 # message("This is normal")

assets/cover_light.gif

@@ -50,6 +50,7 @@ add_library(${WRAPPER} STATIC)
 include_directories(${CMAKE_CURRENT_BINARY_DIR})
 include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/framework)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/framework/meshblock)
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/framework/io)
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/framework/utils)
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/framework/vec_transforms)

extern/adios2

@@ -9,10 +9,17 @@
 #  define STRINGIZE_DETAIL(x) #x
 #  define LINE_STRING         STRINGIZE(__LINE__)
 
+#  define NTTLog()                                                                            \
+    { PLOGV_(ntt::LogFile); }
+
+#  define NTTFatal()                                                                          \
+    { PLOGF_(ntt::LogFile); }
+
 #  define NTTHostError(msg)                                                                   \
     {                                                                                         \
       auto err                                                                                \
         = fmt::format("# ERROR: {}  : filename: {} : line: {}", msg, __FILE__, LINE_STRING);  \
+      NTTFatal();                                                                        \
       throw std::runtime_error(err);                                                          \
     }