Merge branch 'master' into arte-merge

.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
@@ -82,7 +82,7 @@ function UJS_Submit
 			exit
 		fi
 		jobid=`echo $jobid | sed 's/\([0-9]*\).*/\1/'`
-	fi	
+	fi
 }
 
 

ugbase/bridge/grid_bridges/file_io_bridge.cpp

@@ -35,7 +35,6 @@
 #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;
 
@@ -78,13 +77,6 @@ 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)
 {
@@ -137,8 +129,7 @@ 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("SetVTURegionOfInterestIdentifier", static_cast<void (*)(char const *)>(&SetVTURegionOfInterestIdentifier) );
+		.add_function("SaveGridLevelToFile", &SaveGridLevelToFile);
 }
 
 }//	end of namespace

ugbase/lib_grid/file_io/file_io_vtu.cpp

@@ -31,8 +31,6 @@
  */
 
 #include "file_io_vtu.h"
-#include <string>
-#include <iostream>
 
 using namespace std;
 using namespace rapidxml;
@@ -413,8 +411,7 @@ GridReaderVTU::~GridReaderVTU()
 {
 }
 
-#if 0
-// original function
+
 bool GridReaderVTU::
 parse_file(const char* filename)
 {
@@ -445,81 +442,6 @@ parse_file(const char* filename)
 //	notify derived classes that a new document has been parsed.
 	return new_document_parsed();
 }
-#else
-
-bool GridReaderVTU::
-parse_file(const char* filename)
-{
-	ifstream in(filename, ios::binary);
-	if(!in)
-		return false;
-
-	m_filename = filename;
-
-//	get the length of the file
-	streampos posStart = in.tellg();
-	in.seekg(0, ios_base::end);
-	streampos posEnd = in.tellg();
-	streamsize size = posEnd - posStart;
-
-//	go back to the start of the file
-	in.seekg(posStart);
-
-	char * fileContentOriginal = new char[size + 1];
-
-	in.read(fileContentOriginal,size);
-	fileContentOriginal[size] = 0;
-	in.close();
-
-	std::string fiCo2Str(fileContentOriginal);
-
-	delete [] fileContentOriginal;
-	fileContentOriginal = NULL;
-
-	std::string regInf("RegionInfo");
-
-	if ( fiCo2Str.find(regInf) == std::string::npos && fiCo2Str.find(m_regionOfInterest) != std::string::npos  )
-	{
-		// we need to insert the additional string
-
-		std::string regInfLines;
-
-		regInfLines.append( "\n<RegionInfo Name=\"" );
-
-		regInfLines.append( m_regionOfInterest );
-
-		regInfLines.append("\">\n");
-
-		regInfLines.append( "</RegionInfo>" );
-
-		std::string insAft( "</CellData>" );
-
-		size_t cedava = fiCo2Str.find( insAft );
-
-		if( cedava == std::string::npos )
-			return false;
-
-		size_t insVal = cedava + insAft.size();
-
-		fiCo2Str.insert( insVal, regInfLines );
-
-	}
-
-	char* fileContent = m_doc.allocate_string(0, fiCo2Str.size() );
-
-	strcpy(fileContent, fiCo2Str.c_str());
-
-
-//	parse the xml-data
-	m_doc.parse<0>(fileContent);
-
-//	notify derived classes that a new document has been parsed.
-	return new_document_parsed();
-}
-
-#endif
-
-
 
 bool GridReaderVTU::
 new_document_parsed()
@@ -539,7 +461,6 @@ new_document_parsed()
 		m_entries.push_back(GridEntry(curNode));
 		GridEntry& gridEntry = m_entries.back();
 
-
 	//	collect associated subset handlers
 		xml_node<>* curSHNode = curNode->first_node("RegionInfo");
 		while(curSHNode){
@@ -648,14 +569,6 @@ subset_handler(ISubsetHandler& shOut,
 	vector<int> subsetIndices;
 	read_scalar_data(subsetIndices, regionDataNode, true);
 
-	if( subsetIndices.size() != cells.size() )
-	{
-		vector<double> subsetIndicesDbl;
-		read_scalar_data(subsetIndicesDbl, regionDataNode, true);
-
-		trafoDblVec2Int( subsetIndicesDbl, subsetIndices );
-	}
-
 	UG_COND_THROW(subsetIndices.size() != cells.size(),
 				  "Mismatch regarding number of cells and number of region-indices!");
 
@@ -859,17 +772,6 @@ create_cells(std::vector<GridObject*>& cellsOut,
 	return true;
 }
 
-void GridReaderVTU::
-trafoDblVec2Int( std::vector<double> const & dblVec, std::vector<int> & intVec )
-{
-	intVec = std::vector<int>();
-
-	for( auto d : dblVec )
-	{
-		intVec.push_back( static_cast<int>( d ) );
-	}
-}
-
 
 xml_node<>* GridReaderVTU::
 find_child_node_by_argument_value(rapidxml::xml_node<>* parent,

ugbase/lib_grid/file_io/file_io_vtu.h

@@ -220,12 +220,6 @@ class GridReaderVTU
 							size_t refGridIndex,
 							size_t subsetHandlerIndex);
 
-		static std::string const getRegionOfInterestIdentifyer()
-		{ return m_regionOfInterest; }
-
-		static void setRegionOfInterestIdentifier( std::string const & regOfInt )
-		{ m_regionOfInterest = regOfInt; }
-
 	protected:
 		struct SubsetHandlerEntry
 		{
@@ -275,8 +269,6 @@ class GridReaderVTU
 							  rapidxml::xml_node<>* dataNode,
 							  bool clearData = true);
 
-		void trafoDblVec2Int( std::vector<double> const & dblVec, std::vector<int> & intVec );
-
 		template <class T>
 		void check_indices(std::vector<T>& inds, size_t first, size_t num, size_t max);
 
@@ -295,8 +287,6 @@ class GridReaderVTU
 	///	holds grids which already have been created
 		std::vector<GridEntry>		m_entries;
 
-
-
 		static std::string m_regionOfInterest; // ProMesh standard = "regions", in Braunschweig case	often "Material Id", but not always
 
 };

ugbase/lib_grid/tools/creator_grid_util.h

@@ -40,7 +40,9 @@ namespace ug{
 ////////////////////////////////////////////////////////////////////////
 /**
  * To Create GridObject directly under UG4-C++ 
- * instead of ProMesh 
+ * instead of ProMesh:
+ *  
+ *  Functions are copied from plugins/ProMesh/tools/grid_generation_tools.cpp
  */
 template<typename TPosition>
 Vertex* CreateVertex(Grid& grid,const TPosition& pos,Grid::VertexAttachmentAccessor<Attachment<TPosition> >& aaPos )
@@ -56,7 +58,7 @@ Vertex* CreateVertex(Grid& grid,const TPosition& pos,Grid::VertexAttachmentAcces
 
 
 
-Edge* CreateEdge(Grid& grid, Vertex* vrts[], const size_t, numVrts){
+Edge* CreateEdge(Grid& grid, Vertex* vrts[], const size_t numVrts){
     //uniquify vrts by hash_value: no
     //The vrts can't be simply uniquified by hash_values since it will change the orientation of vrts. 
     // Hence,it should be generated by aaPos before using this function.
@@ -144,7 +146,7 @@ Face* CreateFace(Grid& grid, Vertex* vrts[], const size_t numVrts){
     //return CreateFace(grid, avrts, numVrts);
 }*/
 
-Volume* CreateVolume(Grid& grid, Vertex* vrts, const size_t numVrts){
+Volume* CreateVolume(Grid& grid, Vertex* vrts[], const size_t numVrts){
 //if(numVrts < 4 || numVrts > 8){
 	UG_ASSERT(numVrts>3 || numVrts<9,"Bad number of vertices! Can't create a volume element from " << numVrts << " vertices.");
 
@@ -209,7 +211,7 @@ void CreatePlane(Grid& grid,
                  const TPosition& upRight,
                  const TPosition& lowLeft,
                  const TPosition& lowRight,
-                 Grid::VertexAttachmentAccessor<Attachment<TPosition> >& aaPos
+                 Grid::VertexAttachmentAccessor<Attachment<TPosition> >& aaPos,
                  bool fill)
 {   
     Vertex* vrts[4];