Deps rcmtool (#25)

* feat: add generic read_env with optional type

* fix(mc): remove conflict pool_type and MC::pool_type

* feat(prng): add uniform distribution

* feat(udf): clean udf loader with reduced conditional build, final warning with the use of get_config

* feat(wip): try sort SoA, not working yet

* fix(serde): correct scalar init w and w/o gas

* feat(cma): wip changes but fully working with cmtool rust implem

* refractor(worker): clean signal handling and callback

* wip: opti mpi

* feat(cma): clean all unsued and better rust integration

* feat(params): remove recursive flag for cma load not needed with rust impl

* fix(mpi): ensure to_wait=false when no comm

* feat(simulation): checkScalar to ensure positive concentrations

* refactor: clean up previously added code

* fix(api): udf namespace + Python raise runtimeerror

* chore: remove wrap for cmtool

* fix(udf): same namespace for forward declartion w/o udf features

* chore: update dockerfile for rust deps

* chore: rmctool wrapfile from git

* chore: remove cmtool clone from ci

* ci: token

* ci: token

* ci: token

* ci: token

* ci: token

* ci: token

* ci: token

* ci: token

* ci: token

* ci: token

* ci: token

* fix(docker): cargo install

* fix: typo

* fix(test): updated test and cma_case

* chore: clean up code

Author: Benncs

.github/workflows/container.yml

@@ -25,15 +25,9 @@ jobs:
             tag: biocma_omp_base:latest
             output: /tmp/biocma_omp_base.tar
     steps:
+
       - name: Checkout code
         uses: actions/checkout@v4
-        #with:
-          #token: '${{ secrets.PAT_TOKEN }}'
-#
-      - name: Clone GitLab submodule
-        run: |
-          git config --global credential.helper '!f() { echo "username=${{ secrets.USER_GITLAB }}"; echo "password=${{ secrets.PAT_GITLAB }}"; }; f'
-          #git submodule update --init --recursive
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
@@ -56,15 +50,12 @@ jobs:
     runs-on: ubuntu-latest
     needs: build-docker-base-images
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-        #with:
-          #token: '${{ secrets.PAT_TOKEN }}'
-#
-      - name: Clone GitLab submodule
+
+      - uses: actions/checkout@v1  
+      
+      - name: Clone RMCTool
         run: |
-          git config --global credential.helper '!f() { echo "username=${{ secrets.USER_GITLAB }}"; echo "password=${{ secrets.PAT_GITLAB }}"; }; f'
-          git clone https://gitlab.com/codes_tim/compartment-modelling-tool.git subprojects/cmtool
+          git clone --branch v1.3 https://${{ secrets.RCMTTOKEN }}@github.com/Benncs/rcmtool.git subprojects/rcmtool
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2

.github/workflows/main.yml

@@ -17,13 +17,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
-        with:
-          token: '${{ secrets.PAT_TOKEN }}'
-      - name: Add token GitLab 
-        run: >
-          git config --global credential.helper '!f() { echo "username=${{
-          secrets.USER_GITLAB }}"; echo "password=${{ secrets.PAT_GITLAB }}"; };
-          f'
+        
         run: |
           sudo sh devutils/install_dep.sh
       - name: Configure project

.gitignore

@@ -8,6 +8,7 @@ compile_commands.json
 # Env
 .bmc_info
 results/
+results
 cma_data/
 *.h5
 #Benchs

apps/api/includes/udf_handle.hpp

@@ -0,0 +1,19 @@
+#ifndef __UDF_HANDLE_HPP__
+#define __UDF_HANDLE_HPP__
+
+#include <common/results.hpp>
+#include <memory>
+#ifdef USE_UDF
+#  include <udf_includes.hpp>
+#endif
+
+#ifndef USE_UDF
+struct DynamicLibrary;
+#endif
+
+namespace Unsafe
+{
+  Result<std::shared_ptr<DynamicLibrary>, std::string>
+  load_udf(std::string_view model_name);
+} // namespace Unsafe
+#endif

apps/api/meson.build

@@ -2,10 +2,14 @@ src_dir = './src'
 
 name = f'@project_name@_api'
 
-api_source = files(f'@src_dir@/api.cpp')
+api_source = files(f'@src_dir@/api.cpp', f'@src_dir@/udf_handle.cpp')
 
-includes = include_directories('./includes', 'public')
+includes = [include_directories('./includes', 'public'), ext_include]
 
+exe_link_args=[flto_flag]
+if not use_cuda and build_udf
+exe_link_args=[exe_link_args,'-rdynamic']
+endif
 
 lib_api_shared = static_library(
   f'@name@_shared',
@@ -14,6 +18,7 @@ lib_api_shared = static_library(
   dependencies: [core_shared_dependency],
   # cpp_args: ['-DNO_MPI'],
   install_rpath: project_name,
+  link_args:exe_link_args
 )
 
 lib_api_distributed = static_library(
@@ -23,18 +28,21 @@ lib_api_distributed = static_library(
   dependencies: [core_distributed_dependency_static, mpi_wrap_dependency],
   # cpp_args: ['-DNO_MPI'],
   install_rpath: project_name,
+  link_args:exe_link_args
 )
 
 lib_api_shared_dep = declare_dependency(
   link_with: lib_api_shared,
   include_directories: includes,
   dependencies: [core_shared_dependency, kokkos],
+  link_args:exe_link_args
 )
 
 lib_api_distributed_dep = declare_dependency(
   link_with: lib_api_distributed,
   include_directories: includes,
   dependencies: [core_distributed_dependency_static],
+  link_args:exe_link_args
 )
 
 build_python = get_option('build_python_api')
@@ -106,4 +114,4 @@ endif
 
 if build_test
   subdir('tests')
-endif
+endif

apps/api/public/api/api.hpp

@@ -136,7 +136,7 @@ namespace Api
      * @param recursive Flag indicating if recursive registration is required.
      * @return True if the path was successfully registered; false otherwise.
      */
-    bool register_cma_path(std::string_view path, bool recursive = false);
+    bool register_cma_path(std::string_view path);
 
     /**
      * @brief Register a serialization/deserialization (serde) path.

apps/api/public/api/api_raw.h

@@ -51,7 +51,6 @@ typedef struct Opaque* Handle; // NOLINT //In C we only need ptr type so Opaque
 
   /* REGISTER */
   int register_result_path(Handle handle, const char* c);
-  int register_cma_path_recursive(Handle handle, const char* c);
   int register_cma_path(Handle handle, const char* c);
   int register_serde(Handle handle, const char* c);
   int register_model_name(Handle handle, const char* c);
@@ -67,7 +66,6 @@ typedef struct Opaque* Handle; // NOLINT //In C we only need ptr type so Opaque
     uint64_t number_particle; ///< Number of particles in the simulation.
     int32_t n_thread;         ///< Number of threads to use for simulation.
     uint32_t number_exported_result; ///< Number of results to be exported.
-    int recursive;                   ///< Flag to enable recursive processing.
     int force_override; ///< Flag to allow overwriting of existing results.
     int load_serde;
     int save_serde;

apps/api/python/__init__.py

@@ -35,7 +35,6 @@ def init_simulation(
     simulation_name: str,
     cma_path: str,
     params,
-    is_recursive: bool = False,
     _id: Optional[int] = None,
 ):
     sim_id = 0
@@ -58,7 +57,7 @@ def init_simulation(
     handle_module.register_result_path(handle, f"{full_out_dir}/{simulation_name}")
 
     # Register the CMA path
-    handle_module.register_cma_path(handle, cma_path, is_recursive)
+    handle_module.register_cma_path(handle, cma_path)
 
     return handle
 
@@ -83,7 +82,6 @@ def fast_run(
     n_compartment: int,
     s_feed: float,
     liquid_flow_rate: float = 0.0,
-    is_recursive: bool = False,
     is_serde: bool = False,
     f_init=None,
     serde_path=None,
@@ -93,7 +91,7 @@ def fast_run(
     # Prepare parameters
     params = handle_module.make_params(**params)
     handle = handle_module.init_simulation(
-        outfolder, name, cma_path, params, is_recursive
+        outfolder, name, cma_path, params
     )
 
     # Liquid feed configuration

apps/api/src/api.cpp

@@ -1,3 +1,4 @@
+#include "simulation/mass_transfer.hpp"
 #include <Kokkos_Core.hpp>
 #include <api/api.hpp>
 #include <api/results.hpp>
@@ -20,8 +21,10 @@
 #include <span>
 #include <stdexcept>
 #include <string>
+#include <udf_handle.hpp>
 #include <utility>
 #include <vector>
+static std::shared_ptr<DynamicLibrary> udf_handle = nullptr;
 constexpr int ID_VERIF = 2025;
 
 #define CHECK_OR_RETURN(cond, msg)                                             \
@@ -65,6 +68,7 @@ namespace Api
 
   void finalise()
   {
+
     if (!Kokkos::is_finalized() && Kokkos::is_initialized())
     {
       Kokkos::finalize();
@@ -131,14 +135,15 @@ namespace Api
                                          std::optional<std::size_t> run_id)
       : id(ID_VERIF)
   {
+
     _data.exec_info = Core::runtime_init(argc, argv, run_id);
     std::atexit(Api::finalise);
   }
 
   SimulationInstance::~SimulationInstance()
   {
-
     _data = Core::CaseData(); // Explicity delete everything before
+    udf_handle.reset();
   }
 
   std::optional<std::unique_ptr<SimulationInstance>> SimulationInstance::init(
@@ -156,10 +161,12 @@ namespace Api
 
   ApiResult SimulationInstance::exec() noexcept
   {
+
     if (loaded || (registered && applied))
     {
       try
       {
+
         if (logger)
         {
           logger->print(
@@ -174,6 +181,10 @@ namespace Api
       }
       catch (std::exception& e)
       {
+        if (logger)
+        {
+          logger->alert("EXEC", e.what());
+        }
         return ApiResult(e.what());
       }
     }
@@ -218,6 +229,7 @@ namespace Api
     Core::GlobalInitialiser global_initializer(_data.exec_info, params, logger);
 
     auto transitionner = global_initializer.init_transitionner();
+
     CHECK_OR_RETURN(!transitionner, "Error when apply: transitionner");
 
     CHECK_OR_RETURN(!global_initializer.init_feed(feed),
@@ -243,6 +255,8 @@ namespace Api
 
     mtr_type = Simulation::MassTransfer::Type::FixedKla{kla};
 
+    // mtr_type = Simulation::MassTransfer::Type::FlowmapTurbulence{};
+
     if (mtr_type)
     {
       simulation->setMtrModel(std::move(*mtr_type));
@@ -268,6 +282,11 @@ namespace Api
 
   ApiResult SimulationInstance::apply(bool to_load) noexcept
   {
+    auto opt_udf = Unsafe::load_udf(params.model_name);
+    if (opt_udf.valid())
+    {
+      udf_handle = opt_udf.gets();
+    }
     if (to_load)
     {
       return apply_load();
@@ -299,8 +318,7 @@ namespace Api
     return ApiResult(); // TODO
   }
 
-  bool SimulationInstance::register_cma_path(std::string_view path,
-                                             bool recursive)
+  bool SimulationInstance::register_cma_path(std::string_view path)
   {
 
     std::filesystem::path p(path);
@@ -316,7 +334,6 @@ namespace Api
       normalized += std::filesystem::path::preferred_separator;
     }
 
-    this->params.recursive = recursive;
     this->params.cma_case_path = normalized;
 
     return true;

apps/api/src/api_python.cpp

@@ -4,6 +4,7 @@
 #include <core/scalar_factory.hpp>
 #include <cstddef>
 #include <cstdlib>
+#include <exception>
 #include <memory>
 #include <pybind11/cast.h>
 #include <pybind11/detail/common.h>
@@ -52,9 +53,12 @@ namespace PythonBindings
   auto exec(std::shared_ptr<Api::SimulationInstance>& handle)
   {
     pybind11::gil_scoped_release release; // TODO check if really usefull ?
-    handle->exec();
+    const auto ret = handle->exec();
     pybind11::gil_scoped_acquire acquire;
-    return 0;
+    if (ret.invalid())
+    {
+      throw std::runtime_error(ret.get());
+    }
   }
 
   auto apply(std::shared_ptr<Api::SimulationInstance>& handle, bool to_load)
@@ -66,13 +70,10 @@ namespace PythonBindings
   }
 
   auto register_cma_path(std::shared_ptr<Api::SimulationInstance>& handle,
-                         const std::string& cma_path,
-                         bool recursive)
+                         const std::string& cma_path)
   {
 
-    return (recursive)
-               ? register_cma_path_recursive(handle.get(), cma_path.data())
-               : ::register_cma_path(handle.get(), cma_path.data());
+    return ::register_cma_path(handle.get(), cma_path.data());
   }
 
   auto
@@ -109,7 +110,6 @@ namespace PythonBindings
       .def_readwrite("force_override", &wrap_c_param_t::force_override)
       .def_readwrite("n_thread", &wrap_c_param_t::n_thread)
       .def_readwrite("number_exported_result", &wrap_c_param_t::number_exported_result)
-      .def_readwrite("recursive", &wrap_c_param_t::recursive)
       .def_readwrite("biomass_initial_concentration",
                      &wrap_c_param_t::biomass_initial_concentration)
       .def_readwrite("number_particle", &wrap_c_param_t::number_particle)
@@ -128,13 +128,12 @@ namespace PythonBindings
                                   p.force_override,
                                   p.n_thread,
                                   p.number_exported_result,
-                                  p.recursive,
                                   p.biomass_initial_concentration,
                                   p.number_particle,
                                   p.save_serde);
           },
           [](const py::tuple& t) { // __setstate__
-            constexpr std::size_t n_attributes = 9;
+            constexpr std::size_t n_attributes = 8;
             if (t.size() != n_attributes)
             {
               throw std::runtime_error("Pickle param invalid state, "
@@ -151,10 +150,9 @@ namespace PythonBindings
             p.force_override = static_cast<int>(t[2].cast<bool>());
             p.n_thread = t[3].cast<int>();
             p.number_exported_result = t[4].cast<int>();
-            p.recursive = static_cast<int>(t[5].cast<bool>());
-            p.biomass_initial_concentration = t[6].cast<double>();
-            p.number_particle = t[7].cast<int>();
-            p.save_serde = t[8].cast<int>();
+            p.biomass_initial_concentration = t[5].cast<double>();
+            p.number_particle = t[6].cast<int>();
+            p.save_serde = t[7].cast<int>();
             // NOLINTEND
             return p;
           }));
@@ -198,8 +196,7 @@ PYBIND11_MODULE(handle_module, m) // NOLINT (Pybind11 MACRO)
   m.def("register_cma_path",
         &PythonBindings::register_cma_path,
         py::arg("handle"),
-        py::arg("cma_path"),
-        py::arg("recursive") = false);
+        py::arg("cma_path"));
 
   m.def("register_serde", &register_serde);
   m.def("register_parameters", &register_parameters);