Merge branch '1.2.0rc' into dev/1dsr-sugon

Author: StaticObserver

.gitmodules

@@ -7,3 +7,6 @@
 [submodule "extern/Kokkos"]
 	path = extern/Kokkos
 	url = https://github.com/kokkos/kokkos.git
+[submodule "extern/entity-pgens"]
+	path = extern/entity-pgens
+	url = https://github.com/entity-toolkit/entity-pgens.git

.vscode/.taplo.toml

@@ -1,4 +1,4 @@
-include = ["input.example.toml", "setups/**/*.toml"]
+include = ["input.example.toml", "pgens/**/*.toml"]
 exclude = [".taplo.toml"]
 
 [formatting]

LICENSE

@@ -1,19 +1,8 @@
 BSD 3-Clause License
 
-Copyright (c) 2024, Princeton University (PU), and
-Princeton Plasma Physics Lab (PPPL).
+Copyright (c) 2021-present, Entity development team.
 All rights reserved.
 
-Core developers (alphabetical order):
-* Alexander Chernoglazov
-* Benjamin Crinquand
-* Alisa Galishnikova
-* Hayk Hakobyan
-* Jens Mahlmann
-* Sasha Philippov
-* Arno Vanthieghem
-* Muni Zhou
-
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 

README.md

@@ -14,10 +14,10 @@ Our [detailed documentation](https://entity-toolkit.github.io/) includes everyth
 
 * :guitar: Ludwig Böss {[@LudwigBoess](https://github.com/LudwigBoess)}
 * :eyes: Yangyang Cai {[@StaticObserver](https://github.com/StaticObserver)}
-* :person_tipping_hand: Alexander Chernoglazov {[@SChernoglazov](https://github.com/SChernoglazov)}
+* :tipping_hand_person: Alexander Chernoglazov {[@SChernoglazov](https://github.com/SChernoglazov)}
 * :tea: Benjamin Crinquand {[@bcrinquand](https://github.com/bcrinquand)}
 * :bubble_tea: Alisa Galishnikova {[@alisagk](https://github.com/alisagk)}
-* :locomotive: Evgeny Gorbunov {[@Alcauchy](https://github.com/Alcauchy)}
+* :steam_locomotive: Evgeny Gorbunov {[@Alcauchy](https://github.com/Alcauchy)}
 * :coffee: Hayk Hakobyan {[@haykh](https://github.com/haykh)}
 * :potato: Jens Mahlmann {[@jmahlmann](https://github.com/jmahlmann)}
 * :dolphin: Sasha Philippov {[@sashaph](https://github.com/sashaph)}

cmake/config.cmake

@@ -18,25 +18,60 @@ endfunction()
 
 # ---------------------------- Problem generator --------------------------- #
 function(set_problem_generator pgen_name)
-  file(GLOB_RECURSE PGENS "${CMAKE_CURRENT_SOURCE_DIR}/setups/**/pgen.hpp"
-       "${CMAKE_CURRENT_SOURCE_DIR}/setups/pgen.hpp")
+  if(pgen_name STREQUAL ".")
+    message(FATAL_ERROR "Problem generator not specified")
+  endif()
+
+  file(GLOB_RECURSE PGENS "${CMAKE_CURRENT_SOURCE_DIR}/pgens/**/pgen.hpp")
+
   foreach(PGEN ${PGENS})
     get_filename_component(PGEN_NAME ${PGEN} DIRECTORY)
-    string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/setups/" "" PGEN_NAME
-                   ${PGEN_NAME})
-    string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/setups" "" PGEN_NAME
+    string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/pgens/" "" PGEN_NAME
                    ${PGEN_NAME})
     list(APPEND PGEN_NAMES ${PGEN_NAME})
   endforeach()
+
   list(FIND PGEN_NAMES ${pgen_name} PGEN_FOUND)
-  if(NOT ${pgen_name} STREQUAL "." AND ${PGEN_FOUND} EQUAL -1)
-    message(FATAL_ERROR "Invalid problem generator: "
-                        "${pgen_name}\nValid options are: ${PGEN_NAMES}")
+
+  file(GLOB_RECURSE EXTRA_PGENS
+       "${CMAKE_CURRENT_SOURCE_DIR}/extern/entity-pgens/**/pgen.hpp")
+  foreach(EXTRA_PGEN ${EXTRA_PGENS})
+    get_filename_component(EXTRA_PGEN_NAME ${EXTRA_PGEN} DIRECTORY)
+    string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/extern/entity-pgens/" ""
+                   EXTRA_PGEN_NAME ${EXTRA_PGEN_NAME})
+    list(APPEND PGEN_NAMES "pgens/${EXTRA_PGEN_NAME}")
+  endforeach()
+
+  if(${PGEN_FOUND} EQUAL -1)
+    if(${pgen_name} MATCHES "^pgens/")
+      get_filename_component(pgen_name ${pgen_name} NAME)
+      set(pgen_path
+          "${CMAKE_CURRENT_SOURCE_DIR}/extern/entity-pgens/${pgen_name}")
+      set(pgen_name "pgens/${pgen_name}")
+    else()
+      set(pgen_path ${pgen_name})
+      get_filename_component(pgen_path ${pgen_path} ABSOLUTE)
+      string(REGEX REPLACE ".*/" "" pgen_name ${pgen_name})
+      list(APPEND PGEN_NAMES ${pgen_name})
+    endif()
+  else()
+    set(pgen_path ${CMAKE_CURRENT_SOURCE_DIR}/pgens/${pgen_name})
+  endif()
+
+  file(GLOB_RECURSE PGEN_FILES "${pgen_path}/pgen.hpp")
+  if(NOT PGEN_FILES)
+    message(FATAL_ERROR "pgen.hpp file not found in ${pgen_path}")
   endif()
+
+  add_library(ntt_pgen INTERFACE)
+  target_link_libraries(ntt_pgen INTERFACE ntt_global ntt_framework
+                                           ntt_archetypes ntt_kernels)
+
+  target_include_directories(ntt_pgen INTERFACE ${pgen_path})
+
   set(PGEN
       ${pgen_name}
       PARENT_SCOPE)
-  include_directories(${CMAKE_CURRENT_SOURCE_DIR}/setups/${pgen_name})
   set(PGEN_FOUND
       TRUE
       PARENT_SCOPE)

cmake/report.cmake

@@ -4,7 +4,7 @@ if(${PGEN_FOUND})
     "pgen"
     "${problem_generators}"
     ${PGEN}
-    ${default_pgen}
+    ""
     "${Blue}"
     PGEN_REPORT
     0)

dev/nix/adios2.nix

@@ -19,10 +19,12 @@ let
     BUILD_TESTING = "OFF";
     ADIOS2_BUILD_EXAMPLES = "OFF";
     ADIOS2_USE_MPI = if mpi then "ON" else "OFF";
+    ADIOS2_HAVE_HDF5_VOL = if mpi then "ON" else "OFF";
     CMAKE_BUILD_TYPE = "Release";
-  } // (if !mpi then { ADIOS2_HAVE_HDF5_VOL = "OFF"; } else { });
+  };
+  stdenv = pkgs.gcc13Stdenv;
 in
-pkgs.stdenv.mkDerivation {
+stdenv.mkDerivation {
   pname = "${name}${if hdf5 then "-hdf5" else ""}${if mpi then "-mpi" else ""}";
   version = "${version}";
   src = pkgs.fetchgit {
@@ -36,12 +38,10 @@ pkgs.stdenv.mkDerivation {
     perl
   ];
 
-  propagatedBuildInputs =
-    [
-      pkgs.gcc13
-    ]
-    ++ (if hdf5 then (if mpi then [ pkgs.hdf5-mpi ] else [ pkgs.hdf5 ]) else [ ])
-    ++ (if mpi then [ pkgs.openmpi ] else [ ]);
+  propagatedBuildInputs = [
+    pkgs.gcc13
+  ] ++ (if hdf5 then (if mpi then [ pkgs.hdf5-mpi ] else [ pkgs.hdf5-cpp ]) else [ ]);
+  # ++ (if mpi then [ pkgs.openmpi ] else [ ]);
 
   configurePhase = ''
     cmake -B build $src ${

dev/nix/kokkos.nix

@@ -20,15 +20,24 @@ let
     "CUDA" = with pkgs.cudaPackages; [
       cudatoolkit
       cuda_cudart
+      pkgs.gcc13
     ];
     "NONE" = [
       pkgs.gcc13
     ];
   };
+  getArch =
+    _:
+    if gpu != "NONE" && arch == "NATIVE" then
+      throw "Please specify an architecture when the GPU support is enabled. Available architectures: https://kokkos.org/kokkos-core-wiki/get-started/configuration-guide.html#gpu-architectures"
+    else
+      arch;
   cmakeExtraFlags = {
     "HIP" = [
       "-D Kokkos_ENABLE_HIP=ON"
       "-D Kokkos_ARCH_${getArch { }}=ON"
+      # remove leading AMD_
+      "-D AMDGPU_TARGETS=${builtins.replaceStrings [ "amd_" ] [ "" ] (pkgs.lib.toLower (getArch { }))}"
       "-D CMAKE_C_COMPILER=hipcc"
       "-D CMAKE_CXX_COMPILER=hipcc"
     ];
@@ -39,13 +48,6 @@ let
     ];
     "NONE" = [ ];
   };
-  getArch =
-    _:
-    if gpu != "NONE" && arch == "NATIVE" then
-      throw "Please specify an architecture when the GPU support is enabled. Available architectures: https://kokkos.org/kokkos-core-wiki/keywords.html#architectures"
-    else
-      arch;
-
 in
 pkgs.stdenv.mkDerivation rec {
   pname = "${name}";

dev/nix/shell.nix

@@ -42,7 +42,8 @@ pkgs.mkShell {
     zlib
     cmake
 
-    clang-tools
+    llvmPackages_18.clang-tools
+    libgcc
 
     adios2Pkg
     kokkosPkg