#1221 Add Seldon and Ops as embedded libraries.

CMakeLists.txt

@@ -96,8 +96,8 @@ endif()
 
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/Sources /
                     ${CMAKE_CURRENT_SOURCE_DIR}/Sources/ThirdParty/Source/Tclap/include /
-                    ${OPS_DIR} /
-                    ${SELDON_DIR} /
+                    ${CMAKE_CURRENT_SOURCE_DIR}/Sources/ThirdParty/Source/Ops /
+                    ${CMAKE_CURRENT_SOURCE_DIR}/Sources/ThirdParty/Source/Seldon /
                     ${OPEN_MPI_INCL_DIR} /
                     ${PETSC_GENERAL_INCL_DIR} /
                     ${PETSC_SPECIFIC_INCL_DIR} /

MoReFEM.xcodeproj/xcshareddata/xcschemes/Stokes.xcscheme

@@ -65,7 +65,7 @@
       </BuildableProductRunnable>
       <CommandLineArguments>
          <CommandLineArgument
-            argument = "--input_parameters ${HOME}/Codes/MoReFEM/Sources/ModelInstances/Stokes/demo_input_stokes.lua"
+            argument = "--input_parameters ${HOME}/Codes/MoReFEM/CoreLibrary/Sources/ModelInstances/Stokes/demo_input_stokes.lua"
             isEnabled = "YES">
          </CommandLineArgument>
       </CommandLineArguments>

README.md

 A HPC finite element library developed for the implementation of the models of M3DISIM Inria team.
+
+
+# Dependencies
+
+MoReFEM relies on several third party libraries:
+
+- An optimized Blas library. On macos you may use the Accelerate framework; Openblas has also been successfully tested.
+- Ops: 
+    third_party_build.BuildLibrary("Lua")
+    third_party_build.BuildLibrary("Boost")
+    third_party_build.CopyOps()
+    third_party_build.CopySeldon()
+    third_party_build.BuildLibrary("Openmpi")
+    third_party_build.BuildLibrary("Parmetis")
+
+    third_party_build.BuildLibrary("Superlu_dist")
+    third_party_build.BuildLibrary("Scalapack")
+    third_party_build.BuildLibrary("Mumps")
+    third_party_build.BuildLibrary("Petsc")

SCons/configuration_file.py

@@ -66,9 +66,6 @@ def ReadConfigurationFile(configuration_file):
     vars.Add(SCons.Variables.PathVariable('LUA_LIB_DIR', "Path to Lua library.", None))
     vars.Add(SCons.Variables.PathVariable('BOOST_LIB_DIR', "Path to Boost library.", None))
 
-    vars.Add(SCons.Variables.PathVariable('OPS_DIR', "Path to Ops source files.", None))
-    vars.Add(SCons.Variables.PathVariable('SELDON_DIR', "Path to Seldon source files.", None))
-    
     vars.Add(SCons.Variables.BoolVariable('PHILLIPS_LINKER', "True if you want to link with the Phillips Library. Only works with gcc.", 0))
     vars.Add(SCons.Variables.PathVariable('PHILLIPS_DIR', "Path to Phillips library and header. Might be 'None' if irrelevant", None, PathOrNone))
     

SCons/custom_scons_functions.py

@@ -335,8 +335,8 @@ def DefineEnvironment(vars, morefem_root = None):
         env['PARMETIS_INCL_DIR'],
         env['LUA_INCL_DIR'],
         env['BOOST_INCL_DIR'],
-        env['OPS_DIR'],
-        env['SELDON_DIR'],
+        os.path.join(env['MOREFEM_ROOT'], 'Sources', 'ThirdParty', 'Source', 'Ops'),
+        os.path.join(env['MOREFEM_ROOT'], 'Sources', 'ThirdParty', 'Source', 'Seldon')
     ]    
     
     if env['PHILLIPS_DIR']:

Scripts/GenerateSourceList4CMake.py

@@ -89,7 +89,7 @@ if __name__ == "__main__":
     morefem_path = "${HOME}/Codes/Morefem/CoreLibrary"
     
     GenerateInModule(morefem_path, "Utilities", "MOREFEM_UTILITIES", None)
-    GenerateInModule(morefem_path, "ThirdParty", "MOREFEM_UTILITIES", ['Tclap', 'Legacy'])
+    GenerateInModule(morefem_path, "ThirdParty", "MOREFEM_UTILITIES", ['Tclap', 'Source'])
     GenerateInModule(morefem_path, "Core", "MOREFEM_CORE")
     GenerateInModule(morefem_path, "Geometry", "MOREFEM_GEOMETRY")
     GenerateInModule(morefem_path, "FiniteElement", "MOREFEM_FELT")

Sources/CMakeLists.txt

@@ -31,8 +31,6 @@ endif()
 
 include(Utilities/SourceList.cmake)
 include(ThirdParty/SourceList.cmake)
-include(ThirdParty/Ops.cmake)
-include(ThirdParty/Seldon.cmake)
 include(ThirdParty/Source/CMakeLists.txt)
 
 include(Core/SourceList.cmake)

Sources/Core/SourceList.cmake

@@ -17,4 +17,3 @@ include(${CMAKE_CURRENT_LIST_DIR}/LinearAlgebra/SourceList.cmake)
 include(${CMAKE_CURRENT_LIST_DIR}/InputParameterData/SourceList.cmake)
 include(${CMAKE_CURRENT_LIST_DIR}/InputParameter/SourceList.cmake)
 include(${CMAKE_CURRENT_LIST_DIR}/TimeManager/SourceList.cmake)
-

Sources/ThirdParty/SConscript

@@ -67,7 +67,7 @@ for file in third_party_src_filter_out_warnings:
 # Fetch also Ops source files and add them in the list:
 third_party_build_directory = os.path.join(env['CURRENT_BUILD_INTERMEDIATE_DIR'], 'Ops')
 
-ops_obj_list = SConscript(os.path.join(env['OPS_DIR'], 'MoReFEMSConscript'),
+ops_obj_list = SConscript(os.path.join('Source', 'Ops', 'MoReFEMSConscript'),
                                        'env',
                                        variant_dir=third_party_build_directory,
                                        duplicate=0)
@@ -78,7 +78,7 @@ third_party_src_and_objects.extend(ops_obj_list)
 # Likewise for Seldon.
 third_party_build_directory = os.path.join(env['CURRENT_BUILD_INTERMEDIATE_DIR'], 'Seldon')
 
-seldon_obj_list = SConscript(os.path.join(env['SELDON_DIR'], 'MoReFEMSConscript'),
+seldon_obj_list = SConscript(os.path.join('Source', 'Seldon', 'MoReFEMSConscript'),
                              'env',
                              variant_dir=third_party_build_directory,
                              duplicate=0)

Sources/ThirdParty/Source/CMakeLists.txt

-
 include(${CMAKE_CURRENT_LIST_DIR}/Lm6/CMakeLists.txt)
+include(${CMAKE_CURRENT_LIST_DIR}/Ops/CMakeLists.txt)
+include(${CMAKE_CURRENT_LIST_DIR}/Seldon/CMakeLists.txt)
\ No newline at end of file

Sources/ThirdParty/Source/Lm6/SourceList.cmake

-target_sources(${MOREFEM_UTILITIES}
-
-	PUBLIC
-)
-

Sources/ThirdParty/Source/Ops/.sconf_temp/conftest_0.c

+
+
+
+int
+main() {
+  
+return 0;
+}

Sources/ThirdParty/Source/Ops/.sconf_temp/conftest_1.c

+
+
+
+int
+main() {
+  
+return 0;
+}

Sources/ThirdParty/Source/Ops/.sconf_temp/conftest_2.c

+
+
+
+int
+main() {
+  
+return 0;
+}

Sources/ThirdParty/Ops.cmake → Sources/ThirdParty/Source/Ops/CMakeLists.txt

@@ -2,9 +2,9 @@ add_library(Ops ${LIBRARY_TYPE} "")
 
 target_sources(Ops
     PRIVATE
-        ${OPS_DIR}/ClassOps.cpp  /
-        ${OPS_DIR}/Error.cpp /
-        ${OPS_DIR}/Ops.cpp 
+        "${CMAKE_CURRENT_LIST_DIR}/ClassOps.cpp"
+        "${CMAKE_CURRENT_LIST_DIR}/Error.cpp"
+        "${CMAKE_CURRENT_LIST_DIR}/Ops.cpp"
 )
 
 # Suppress all warnings from this third party library. PRIVATE is important not to propagate that to the MoReFEM libraries!

Sources/ThirdParty/Source/Ops/ClassOps.hxx

+// Copyright (C) 2010, Vivien Mallet
+//
+// This file is part of Ops, a library for parsing Lua configuration files.
+//
+// Ops is free software; you can redistribute it and/or modify it under the
+// terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 2.1 of the License, or (at your option)
+// any later version.
+//
+// Ops is distributed in the hope that it will be useful, but WITHOUT ANY
+// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for
+// more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with Ops. If not, see http://www.gnu.org/licenses/.
+
+
+#ifndef OPS_FILE_CLASSOPS_HXX
+
+
+namespace Ops
+{
+
+  class Ops
+  {
+  protected:
+    //! Path to the configuration file.
+    string file_path_;
+    //! Lua state.
+    lua_State* state_;
+    //! Prefix to be prepended to the entries names.
+    string prefix_;
+
+    //! Names and values of all Booleans read in the file.
+    std::map<string, bool> read_bool;
+    //! Names and values of all integer read in the file.
+    std::map<string, int> read_int;
+    //! Names and values of all floats read in the file.
+    std::map<string, float> read_float;
+    //! Names and values of all doubles read in the file.
+    std::map<string, double> read_double;
+    //! Names and values of all strings read in the file.
+    std::map<string, string> read_string;
+    //! Names and values of all vectors of Booleans read in the file.
+    std::map<string, std::vector<bool> > read_vect_bool;
+    //! Names and values of all vectors of integers read in the file.
+    std::map<string, std::vector<int> > read_vect_int;
+    //! Names and values of all vectors of floats read in the file.
+    std::map<string, std::vector<float> > read_vect_float;
+    //! Names and values of all vectors of doubles read in the file.
+    std::map<string, std::vector<double> > read_vect_double;
+    //! Names and values of all vectors of strings read in the file.
+    std::map<string, std::vector<string> > read_vect_string;
+
+  public:
+    // Constructor and destructor.
+    Ops();
+    Ops(string file_path);
+    ~Ops();
+
+    // Main methods.
+    void Open(string file_path, bool close_state = true);
+    void Reload(bool close_state = true);
+    void Close();
+    template<class TD, class T>
+    void
+    Set(string name, string constraint, const TD& default_value, T& value);
+    template<class T>
+    void Set(string name, string constraint, T& value);
+    template<class T>
+    void Set(string name, T& value);
+    template<class T>
+    T Get(string name);
+    template<class T>
+    T Get(string name, string constraint);
+    template<class T>
+    T Get(string name, string constraint, const T& default_value);
+    template<class Tin, class Tout>
+    void Apply(string name, const std::vector<Tin>& in,
+               std::vector<Tout>& OUTPUT);
+    template<class T>
+    T Apply(string name, const T& arg0);
+    template<class T>
+    T Apply(string name, const T& arg0, const T& arg1);
+    template<class T>
+    T Apply(string name, const T& arg0, const T& arg1, const T& arg2);
+    template<class T>
+    T Apply(string name, const T& arg0, const T& arg1, const T& arg2,
+            const T& arg3);
+    template<class T>
+    T Apply(string name, const T& arg0, const T& arg1, const T& arg2,
+            const T& arg3, const T& arg4);
+    std::vector<string> GetEntryList(string name = "");
+    bool CheckConstraint(string name, string constraint);
+    bool CheckConstraintOnValue(string value, string constraint);
+    void PutOnStack(string name);
+    bool Exists(string name);
+    void PushOnStack(bool value);
+    void PushOnStack(int value);
+    void PushOnStack(float value);
+    void PushOnStack(double value);
+    void PushOnStack(string value);
+    template<class T>
+    void PushOnStack(const std::vector<T>& v);
+    template<class T>
+    bool Is(string name);
+    bool IsTable(string name);
+    bool IsFunction(string name);
+    void ClearStack();
+
+    void DoFile(string file_path);
+    void DoString(string expression);
+
+    // Access methods.
+    string GetFilePath() const;
+    lua_State* GetState();
+#ifndef SWIG
+    const lua_State* GetState() const;
+#endif
+    string GetPrefix() const;
+    void SetPrefix(string prefix);
+    void ClearPrefix();
+    std::vector<string> GetReadEntryList();
+    void UpdateLuaDefinition();
+    string LuaDefinition(string name);
+    string LuaDefinition();
+    void WriteLuaDefinition(string file_name);
+
+  protected:
+    bool Convert(int index, std::vector<bool>::reference output,
+                 string name = "");
+    bool Convert(int index, bool& output, string name = "");
+    bool Convert(int index, int& output, string name = "");
+    bool Convert(int index, float& output, string name = "");
+    bool Convert(int index, double& output, string name = "");
+    bool Convert(int index, string& output, string name = "");
+    template<class TD, class T>
+    void SetValue(string name, string constraint,
+                  const TD& default_value, bool with_default, T& value);
+    template<class T>
+    void SetValue(string name, string constraint,
+                  const std::vector<T>& default_value, bool with_default,
+                  std::vector<T>& value);
+    string Constraint(string constraint) const;
+    string Name(const string& name) const;
+    string Entry(const string& name) const;
+    string Function(const string& name) const;
+    void WalkDown(string name);
+    template<class T>
+    bool IsParam(string name, T& value);
+    template<class T>
+    bool IsParam(string name, std::vector<T>&);
+    void Push(string name, const bool& value);
+    void Push(string name, const int& value);
+    void Push(string name, const float& value);
+    void Push(string name, const double& value);
+    void Push(string name, const string& value);
+    void Push(string name, const std::vector<bool>& value);
+    void Push(string name, const std::vector<int>& value);
+    void Push(string name, const std::vector<float>& value);
+    void Push(string name, const std::vector<double>& value);
+    void Push(string name, const std::vector<string>& value);
+    template<class TK, class T>
+    void AppendKey(const std::map<TK, T>& input, std::vector<TK>& vect);
+  };
+
+}
+
+
+#define OPS_FILE_CLASSOPS_HXX
+#endif

Sources/ThirdParty/Source/Ops/Error.cpp

+// Copyright (C) 2010, Vivien Mallet
+//
+// This file is part of Ops, a library for parsing Lua configuration files.
+//
+// Ops is free software; you can redistribute it and/or modify it under the
+// terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 2.1 of the License, or (at your option)
+// any later version.
+//
+// Ops is distributed in the hope that it will be useful, but WITHOUT ANY
+// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for
+// more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with Ops. If not, see http://www.gnu.org/licenses/.
+
+
+#include "Ops.hxx"
+#include "Error.hxx"
+
+
+namespace Ops
+{
+
+
+  //! Constructor.
+  /*! Error associated with both a function and a comment.
+    \param[in] function function in which the error occurred.
+    \param[in] comment comment associated with the error.
+  */
+  Error::Error(string function, string comment):
+    function_(function), comment_(comment)
+  {
+#ifdef OPS_WITH_ABORT
+    this->CoutWhat();
+    abort();
+#endif
+  }
+
+
+  //! Destructor.
+  Error::~Error()
+  {
+  }
+
+
+  //! Delivers information about the error.
+  /*! \return The available information: the function and/or the comment.
+   */
+  string Error::What() const
+  {
+    string message;
+    if (!function_.empty())
+      message += "Error in Ops::" + function_ + ".\n";
+    if (!comment_.empty())
+      message += "   " + comment_;
+    return message;
+  }
+
+
+  //! Delivers information about the error.
+  /*! Displays available information: the function and/or the comment.
+   */
+  void Error::CoutWhat()
+  {
+    std::cout << this->What() << std::endl;
+  }
+
+
+} // namespace Ops.
+

Sources/ThirdParty/Source/Ops/Error.hxx

+// Copyright (C) 2010, Vivien Mallet
+//
+// This file is part of Ops, a library for parsing Lua configuration files.
+//
+// Ops is free software; you can redistribute it and/or modify it under the
+// terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 2.1 of the License, or (at your option)
+// any later version.
+//
+// Ops is distributed in the hope that it will be useful, but WITHOUT ANY
+// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for
+// more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with Ops. If not, see http://www.gnu.org/licenses/.
+
+
+#ifndef OPS_FILE_ERROR_HXX
+