Merge commit 'ca96fdc0b59e27c3bd51baca8034c24bc347ae89' into feature-…

…openmp

* commit 'ca96fdc0b59e27c3bd51baca8034c24bc347ae89': (58 commits)
  Arte 2D ready for use
  Revert "Merge pull request #96 from UG4/95-avoid-slicing"
  Member variable  m_passOnBehaviour now moved to abstract base. Menat to avoid slicing.
  NULL => nullptr
  Some cosmetics to the previous bug fix. Note that the bug fix is due to Shuai Lu.
  Bug fix: The bug prevented the subset handlers to be registered in the domain.
  Protecting LUA specific.
  An auxiliary function to check if a point is in a bounding box.
  Tools for conversion of different Lua types to ConstUserData objects.
  Add every status in PBS scheduler
  static asserts auskommentiert
  additional help classes for arte implementation
  Übertragen von arte24 auf master vorbereiten
  empty function to allow Jenkins to be successful
  removed static_asserts and other compiler warning reasons
  Bug fix: Releasing set but not cleared ip's in the local discretizations. ToDo: Should this be also done for the error estimators?
  Introducing the object names for the userdata class. This is a debugging facility.
  Restoring master version
  Revert "Merge branch 'master' into arte-merge"
  Fixing Out-of-line definition
  ...

.github/workflows/jenkins-trigger.yml

@@ -1,25 +1,24 @@
 name: Trigger Jenkins CI
+
 # Controls when the workflow will run
 on:
   # Triggers the workflow on push or pull request events but only for the main branch
   push:
     branches: [ master ]
   pull_request:
     branches: [ master ]
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+
 jobs:
-  # This workflow contains a single job called "build"
-  build:
-    name: Build
+  trigger-jenkins-job:
     runs-on: ubuntu-latest
     steps:
-      - name: Trigger jenkins job
-        uses: anaegel/jenkins-githubaction@master
+      - id: triggerjenkinsjob
+        uses: mickeygoussetorg/trigger-jenkins-job@v1
         with:
-          url: ${{ secrets.JENKINS_URL }}
-          job_name: ug-build-pipeline
-          username: ${{ secrets.JENKINS_USER }}
-          api_token: ${{ secrets.JENKINS_TOKEN }}
-          timeout: "3600"
-          interval: "300"
+          jenkins-server:  ${{ secrets.JENKINS_URL }} # URL of the jenkins server. ex: http://myjenkins.acme.com:8080
+          jenkins-job: "ug-build-pipeline" # The name of the jenkins job to run
+          jenkins-username: ${{ secrets.JENKINS_USER }} # user name for accessing jenkins
+          jenkins-pat: ${{ secrets.JENKINS_TOKEN }} # personal Access token for accessing Jenkins
+          poll-time: 90 # how often (seconds) to poll the jenkins server for results
+          timeout-value: 3600 # How long (seconds) to poll before timing out the action
+          verbose: true # true/false - turns on extra logging

scripts/shell/schedulers/pbs-generic

@@ -34,7 +34,7 @@ function UJS_Submit
 
 
 	# PBSnodes="-l select=$nnodes:node_type=rome:mpiprocs=$nppn"
-	PBSnodes=""
+	PBSnodes="-l select=$nnodes:ncpus=$nppn:mpiprocs=$nppn"
 
 
 	if [ -z "$queue" ]; then
@@ -110,13 +110,15 @@ function UJS_Info
 			sub(/\..*$/, "", $1)
 
 			status = $10
-			if (status == "R") {
+			if (status == "R" || status == "E") {
 			status = "RUNNING"
-			} else if (status == "Q") {
+			} else if (status == "Q" || status == "H" || status == "W" || status == "T" || status == "S") {
+			status = "PENDING"
+			} else {
 			status = "PENDING"
 			}
 			print $1, $2, $3, $4, $5, $6, $7, $8, $9, status, $11
-		}'  # change status to RUNNING or PENDING
+		}'  # change every status to RUNNING or PENDING, fallback to PENDING
 	) | column -t  # format output as table
 }
 

scripts/util/user_data_util.lua

@@ -111,9 +111,79 @@ function FreeUserData()
    collectgarbage("collect")
 end
 
+--------------------------------------------------------------------------------
+-- Conversion of types
+--------------------------------------------------------------------------------
+
+function ToUserNumber (o, my_dim)
+	if my_dim == nil then my_dim = GetUGDim() end
+
+	if type(o) == "number" then
+		return _G["ConstUserNumber"..my_dim.."d"](o)
+	elseif type(o) == "function" then
+		return _G["LuaUserNumber"..my_dim.."d"](o)
+	elseif type(o) == "string" then
+		return _G["LuaUserNumber"..my_dim.."d"](_G[o]) -- we assume a function as the argument
+	elseif type(o) == "userdata" then -- ToDo: Provide a better condition!
+		return o
+	end
+	return nil -- this indicates an error
+end
 
+function ToUserVector (o, my_dim)
+	if my_dim == nil then my_dim = GetUGDim() end
+
+	if type(o) == "table" then
+		return _G["ConstUserVector"..my_dim.."d"](o)
+	elseif type(o) == "function" then
+		return _G["LuaUserVector"..my_dim.."d"](o)
+	elseif type(o) == "string" then
+		return _G["LuaUserVector"..my_dim.."d"](_G[o]) -- we assume a function as the argument
+	elseif type(o) == "userdata" then -- ToDo: Provide a better condition!
+		return o
+	end
+	return nil -- this indicates an error
+end
 
-function __ug__CheckUserDataArgType(r, l)
+function ToUserMatrix (o, my_dim)
+	if my_dim == nil then my_dim = GetUGDim() end
+
+	if type(o) == "number" then
+		return _G["ConstUserMatrix"..my_dim.."d"](o)
+	elseif type(o) == "table" then
+		local i, j
+		local m = _G["ConstUserMatrix"..my_dim.."d"]()
+		for i = 0, my_dim-1 do
+			if type(o[i+1]) ~= "table" then
+				print ("Illegal specification of a matrix by a table: Specify the rows as subtables.\n")
+				return nil
+			end
+			for j = 0, my_dim-1 do
+				local val = o [i+1] [j+1]
+				if type(val) ~= "number" then
+					print ("Illegal specification of a matrix by a table at (" .. i+1 .. ", " .. j+1 ..").\n")
+					return nil
+				end
+				m:set_entry (i, j, val)
+			end
+		end
+		return m
+	elseif type(o) == "function" then
+		return LuaUserMatrix(o)
+	elseif type(o) == "string" then
+		return LuaUserMatrix(_G[o])
+	elseif type(o) == "userdata" then -- ToDo: Provide a better condition!
+		return o
+	end
+	return nil -- this indicates an error
+end
+
+--------------------------------------------------------------------------------
+---- Overloading Lua arithmetics operators for UserData
+--------------------------------------------------------------------------------
+
+
+local function __ug__CheckUserDataArgType(r, l)
 	local rType = ug_class_name(r)
 	local lType = ug_class_name(l)
 	local rDim = -1
@@ -175,11 +245,11 @@ function __ug__CheckUserDataArgType(r, l)
 end
 
 --------------------------------------------------------------------------------
--- Function to add/subtract UserData
+-- Function to Add/Subtract UserData
 --------------------------------------------------------------------------------
 
 --! functions user when '+/-' is called on an UserData (or a derived implementation)
-function __ug__UserNumber_sum(lScale, l, rScale, r)
+local function __ug__UserNumber_sum(lScale, l, rScale, r)
 	local rType, lType, rDim, lDim, Dim, rData, lData, Data = __ug__CheckUserDataArgType(r, l)
 
 	if l == nil or r == nil then
@@ -253,12 +323,12 @@ function __ug__UserNumber_sum(lScale, l, rScale, r)
 end
 
 --! functions used when '+' is called on an UserData (or a derived implementation)
-function __ug__UserNumber_add(l,r)
+local function __ug__UserNumber_add(l,r)
 	return __ug__UserNumber_sum(1.0, l, 1.0, r)
 end
 
 --! functions used when '-' is called on an UserData (or a derived implementation)
-function __ug__UserNumber_sub(l,r)
+local function __ug__UserNumber_sub(l,r)
 	return __ug__UserNumber_sum(1.0, l, -1.0, r)
 end
 
@@ -267,7 +337,7 @@ end
 --------------------------------------------------------------------------------
 
 --! functions user when '*' is called on an UserData (or a derived implementation)
-function __ug__UserNumber_mul(l, r)
+local function __ug__UserNumber_mul(l, r)
 	local rType, lType, rDim, lDim, Dim, rData, lData, Data = __ug__CheckUserDataArgType(r, l)
 
 	if l == nil or r == nil then
@@ -321,7 +391,7 @@ function __ug__UserNumber_mul(l, r)
 end
 
 --! functions user when '/' is called on an UserData (or a derived implementation)
-function __ug__UserNumber_div(l, r)
+local function __ug__UserNumber_div(l, r)
 	local rType, lType, rDim, lDim, Dim, rData, lData, Data = __ug__CheckUserDataArgType(r, l)
 
 	if l == nil or r == nil then
@@ -382,11 +452,11 @@ function __ug__UserNumber_div(l, r)
 end
 
 --------------------------------------------------------------------------------
--- Function to Multiply/Devide UserData
+-- Function to Raise UserData to a power
 --------------------------------------------------------------------------------
 
 --! functions user when '^' is called on an UserData (or a derived implementation)
-function __ug__UserNumber_pow(l, r)
+local function __ug__UserNumber_pow(l, r)
 	if l == nil or r == nil then
 		error("Error in '^': nil value (possibly uninitialized value?)")
 	end
@@ -430,28 +500,28 @@ function __ug__UserNumber_pow(l, r)
 end
 
 --------------------------------------------------------------------------------
--- Loop to set the __add functions for UserData
+-- Loop to set the arithmetic functions for UserData
 --------------------------------------------------------------------------------
 
-function set_user_data_overloads(name)
+local function set_user_data_overloads(name)
 	-- request metatable for the classname
 	mt = ug_get_metatable(name)
 	if mt == nil then return end
 
 	-- set __add function in metatable
-	mt.__add = _G["__ug__UserNumber_add"]
+	mt.__add = __ug__UserNumber_add
 
 	-- set __sub function in metatable
-	mt.__sub = _G["__ug__UserNumber_sub"]
+	mt.__sub = __ug__UserNumber_sub
 
 	-- set __mul function in metatable
-	mt.__mul = _G["__ug__UserNumber_mul"]
+	mt.__mul = __ug__UserNumber_mul
 
 	-- set __div function in metatable
-	mt.__div = _G["__ug__UserNumber_div"]
+	mt.__div = __ug__UserNumber_div
 
 	-- set __pow function in metatable
-	mt.__pow = _G["__ug__UserNumber_pow"]
+	mt.__pow = __ug__UserNumber_pow
 end
 
 -- loop some kinds of UserData implementation

ugbase/bindings/lua/lua_user_data_impl.h

@@ -33,7 +33,9 @@
 #ifndef __H__UG_BRIDGE__BRIDGES__USER_DATA__USER_DATA_IMPL_
 #define __H__UG_BRIDGE__BRIDGES__USER_DATA__USER_DATA_IMPL_
 
+#ifdef UG_FOR_LUA
 #include "lua_user_data.h"
+#endif
 #include "lib_disc/spatial_disc/user_data/linker/linker_traits.h"
 #include "lib_disc/spatial_disc/user_data/const_user_data.h"
 

ugbase/bridge/disc_bridges/user_data_bridge.cpp

@@ -597,7 +597,9 @@ static void Common(Registry& reg, string grp)
 
 //	UserDataInfo
 	{
-		reg.add_class_<UserDataInfo>("UserDataInfo", grp);
+		reg.add_class_<UserDataInfo>("UserDataInfo", grp)
+			.add_method("set_obj_name", &UserDataInfo::set_obj_name)
+			.add_method("obj_name", &UserDataInfo::obj_name);
 	}
 
 #ifdef UG_DIM_2

ugbase/bridge/grid_bridges/file_io_bridge.cpp

@@ -35,6 +35,7 @@
 #include "lib_grid/multi_grid.h"
 #include "lib_grid/file_io/file_io.h"
 #include "lib_grid/file_io/file_io_ugx.h"
+#include "lib_grid/file_io/file_io_vtu.h"
 
 using namespace std;
 
@@ -77,6 +78,13 @@ bool SaveGridHierarchy(MultiGrid& mg, const char* filename)
 	return SaveGridToFile(mg, mg.get_hierarchy_handler(), filename);
 }
 
+void SetVTURegionOfInterestIdentifier( char const * regOfInt )
+{
+	PROFILE_FUNC_GROUP("grid");
+	GridReaderVTU::setRegionOfInterestIdentifier( std::string( regOfInt ) );
+	return;
+}
+
 
 void RegisterGridBridge_FileIO(Registry& reg, string parentGroup)
 {
@@ -129,7 +137,8 @@ void RegisterGridBridge_FileIO(Registry& reg, string parentGroup)
 		.add_function("SaveParallelGridLayout", &SaveParallelGridLayout,
 				grp, "", "mg#filename#offset")
 		.add_function("SaveSurfaceViewTransformed", &SaveSurfaceViewTransformed)
-		.add_function("SaveGridLevelToFile", &SaveGridLevelToFile);
+		.add_function("SaveGridLevelToFile", &SaveGridLevelToFile)
+		.add_function("SetVTURegionOfInterestIdentifier", static_cast<void (*)(char const *)>(&SetVTURegionOfInterestIdentifier) );
 }
 
 }//	end of namespace

ugbase/common/math/math_vector_matrix/math_vector.h

@@ -7,7 +7,7 @@
  * UG4 is free software: you can redistribute it and/or modify it under the
  * terms of the GNU Lesser General Public License version 3 (as published by the
  * Free Software Foundation) with the following additional attribution
- * requirements (according to LGPL/GPL v3 ��7):
+ * requirements (according to LGPL/GPL v3 §7):
  * 
  * (1) The following notice must be displayed in the Appropriate Legal Notices
  * of covered and combined works: "Based on UG4 (www.ug4.org/license)".
@@ -20,7 +20,7 @@
  * "Reiter, S., Vogel, A., Heppner, I., Rupp, M., and Wittum, G. A massively
  *   parallel geometric multigrid solver on hierarchically distributed grids.
  *   Computing and visualization in science 16, 4 (2013), 151-164"
- * "Vogel, A., Reiter, S., Rupp, M., N��gel, A., and Wittum, G. UG4 -- a novel
+ * "Vogel, A., Reiter, S., Rupp, M., Nägel, A., and Wittum, G. UG4 -- a novel
  *   flexible software system for simulating pde based models on high performance
  *   computers. Computing and visualization in science 16, 4 (2013), 165-179"
  * 
@@ -101,7 +101,7 @@ class MathVector
 		static const std::size_t Size = N;
 
 	public:
-		MathVector() {for(std::size_t i = 0; i < N; ++i) m_data[i] =  0.0;}
+		MathVector() {for(std::size_t i = 0; i < N; ++i) m_data[i] = 0.0;}
 		MathVector(const value_type& val) {for(std::size_t i = 0; i < N; ++i) m_data[i] =  val;}
 		MathVector(const MathVector& v)	{assign(v);}
 
@@ -234,7 +234,7 @@ class MathVector<1, T>
 		static const std::size_t Size = 1;
 
 	public:
-		MathVector() 	{m_data[0] = 0.0; }
+		MathVector() 	{m_data[0] = 0.0;}
 		MathVector(value_type x) { m_data[0] = x; }
 		MathVector(const MathVector<1, T>& v)	{assign(v);}
 
@@ -298,7 +298,7 @@ class MathVector<2, T>
 		static const std::size_t Size = 2;
 
 	public:
-		MathVector()	{ m_data[0] = m_data[1] = 0.0; }
+		MathVector()	{m_data[0] = m_data[1] = 0.0;}
 		MathVector(const value_type& val) {m_data[0] = m_data[1] = val;}
 		MathVector(value_type x, value_type y)
 		{
@@ -370,7 +370,7 @@ class MathVector<3, T>
 		static const std::size_t Size = 3;
 
 	public:
-		MathVector()	{ m_data[0] = m_data[1] = m_data[2] = 0.0; }
+		MathVector()	{m_data[0] = m_data[1] = m_data[2] = 0.0;}
 		MathVector(const value_type& val) {m_data[0] = m_data[1] = m_data[2] = val;}
 		MathVector(value_type x, value_type y, value_type z)
 		{
@@ -448,7 +448,7 @@ class MathVector<4, T>
 		static const std::size_t Size = 4;
 
 	public:
-		MathVector()	{m_data[0] = m_data[1] = m_data[2] = m_data[3] =0.0;}
+		MathVector()	{m_data[0] = m_data[1] = m_data[2] = m_data[3] = 0.0;}
 		MathVector(const value_type& val) {m_data[0] = m_data[1] = m_data[2] = m_data[3] =val;}
 		MathVector(value_type x, value_type y, value_type z, value_type w)
 		{

ugbase/common/math/math_vector_matrix/math_vector_functions.h

@@ -405,6 +405,12 @@ inline
 bool
 VecAbsIsLess(const vector_t& v1, const typename vector_t::value_type s);
 
+/// checks if the given point is in the bounding box given by two other points
+template <typename vector_t>
+inline
+bool
+VecIsInBB(const vector_t& v, const vector_t& low, const vector_t& high);
+
 }//	end of namespace
 
 ////////////////////////////////////////////////////////////////////////

ugbase/common/math/math_vector_matrix/math_vector_functions_common_impl.hpp

@@ -699,6 +699,18 @@ VecAbsIsLess(const vector_t& v1, const typename vector_t::value_type s)
 	return true;
 }
 
+/// checks if the given point is in the bounding box given by two other points
+template <typename vector_t>
+inline
+bool
+VecIsInBB(const vector_t& v, const vector_t& low, const vector_t& high)
+{
+	for(typename vector_t::size_type i = 0; i < v.size(); ++i)
+		if (v[i] < low[i] || high[i] < v[i])
+			return false;
+	return true;
+}
+
 }//	end of namespace
 
 #endif /* __H__COMMON__MathVector_FUNCTIONS_COMMON_IMPL__ */