Merging develop into master

.github/workflows/simmetrix_enabled_pr_comment_trigger_self_hosted.yml

@@ -2,7 +2,7 @@ name: simmetrx_enabled_pr_comment_trigger_self_hosted
 
 # Controls when the workflow will run
 on:
-  issue_comment:                                     
+  issue_comment:
     types: [created]
 
   # Allows you to run this workflow manually from the Actions tab
@@ -26,45 +26,79 @@ jobs:
           ref: refs/pull/${{ github.event.issue.number }}/head
           submodules: recursive
           path: 'core_${{ github.event.issue.number }}'
-
-      - name: build
-        id: build        
+
+      - name: build_sim
+        id: build_sim
+        shell: bash
+        run: |
+          set +e #avoid exiting when lua modules return non-zero on 'warning' messages
+          module use /opt/scorec/spack/rhel9/v0201_4/lmod/linux-rhel9-x86_64/Core/
+          module load gcc/12.3.0-iil3lno
+          module load mpich/4.1.1-xpoyz4t
+          module load simmetrix-simmodsuite/2024.0-240119dev-7abimo4
+          module load zoltan/3.83-hap4ggo
+          module load cmake/3.26.3-2duxfcd
+          set -e
+
+          cmake -S core_${{ github.event.issue.number }} \
+            -B ${RUNNER_TEMP}/buildSim \
+            -DCMAKE_CXX_COMPILER=mpicxx \
+            -DCMAKE_C_COMPILER=mpicc \
+            -DCMAKE_VERBOSE_MAKEFILE=ON \
+            -DENABLE_ZOLTAN=ON \
+            -DENABLE_SIMMETRIX=ON \
+            -DSIM_MPI=mpich4.1.1 \
+            -DSIM_PARASOLID=ON \
+            -DSIM_ACIS=ON \
+            -DSKIP_SIMMETRIX_VERSION_CHECK=ON \
+            -DMESHES=${{github.workspace}}/core_${{ github.event.issue.number }}/pumi-meshes \
+            -DIS_TESTING=ON \
+            -DSCOREC_CXX_WARNINGS=ON \
+            -DCMAKE_BUILD_TYPE=Release
+          cmake --build ${RUNNER_TEMP}/buildSim -j 4
+          ctest --test-dir ${RUNNER_TEMP}/buildSim --output-on-failure
+
+      - name: build_sim_cgns
+        id: build_sim_cgns
         shell: bash
         run: |
           set +e #avoid exiting when lua modules return non-zero on 'warning' messages
           module use /opt/scorec/spack/rhel9/v0201_4/lmod/linux-rhel9-x86_64/Core/
-          module load gcc/12.3.0-iil3lno 
+          module load gcc/12.3.0-iil3lno
           module load mpich/4.1.1-xpoyz4t
           module load simmetrix-simmodsuite/2024.0-240119dev-7abimo4
           module load zoltan/3.83-hap4ggo
           module load cmake/3.26.3-2duxfcd
+          module load cgns/develop-cc4dfwp
           set -e
-          
+
           cmake -S core_${{ github.event.issue.number }} \
-            -B ${RUNNER_TEMP}/build \
+            -B ${RUNNER_TEMP}/buildSimCgns\
             -DCMAKE_CXX_COMPILER=mpicxx \
             -DCMAKE_C_COMPILER=mpicc \
             -DCMAKE_VERBOSE_MAKEFILE=ON \
             -DENABLE_ZOLTAN=ON \
             -DENABLE_SIMMETRIX=ON \
             -DSIM_MPI=mpich4.1.1 \
             -DSIM_PARASOLID=ON \
+            -DENABLE_CGNS=on \
             -DSIM_ACIS=ON \
             -DSKIP_SIMMETRIX_VERSION_CHECK=ON \
             -DMESHES=${{github.workspace}}/core_${{ github.event.issue.number }}/pumi-meshes \
             -DIS_TESTING=ON \
             -DSCOREC_CXX_WARNINGS=ON \
-            -DCMAKE_BUILD_TYPE=Release 
-          cmake --build ${RUNNER_TEMP}/build -j 4
-          ctest --test-dir ${RUNNER_TEMP}/build --output-on-failure
+            -DCMAKE_BUILD_TYPE=Release
+          cmake --build ${RUNNER_TEMP}/buildSimCgns -j 4
+          ctest --test-dir ${RUNNER_TEMP}/buildSimCgns --output-on-failure
 
       - name: Save Result Link
         if: ${{ !cancelled() }} #prepare report unless the job was cancelled
         run: |
           mkdir -p ./pr
           echo "${{ github.event.issue.number }}"  > ./pr/issueNumber
-          echo -n "Test Result: ${{ steps.build.outcome }} "  > ./pr/message
-          echo "[(details)](https://github.com/${{github.repository}}/actions/runs/${{ github.run_id }})" >> ./pr/message
+          echo "[Build Log](https://github.com/${{github.repository}}/actions/runs/${{ github.run_id }})" >> ./pr/message
+          echo "Simmetrix Test Result: ${{ steps.build_sim.outcome }} "  > ./pr/message
+          echo "Simmetrix + CGNS Test Result: ${{ steps.build_sim_cgns.outcome }} "  > ./pr/message
 
       - name: Upload result
         if: ${{ !cancelled() }} #upload unless the job was cancelled

apf/apfCGNS.cc

@@ -1051,11 +1051,11 @@ void WriteCGNS(const char *prefix, apf::Mesh *m, const apf::CGNSBCMap &cgnsBCMap
   auto communicator = PCU_Get_Comm();
   cgp_mpi_comm(communicator);
   //
-  cgp_pio_mode(CGNS_ENUMV(CGP_INDEPENDENT));
+  cgp_pio_mode(CGP_INDEPENDENT);
 
   CGNS cgns;
   cgns.fname = std::string(prefix);
-  if (cgp_open(prefix, CGNS_ENUMV(CG_MODE_WRITE), &cgns.index))
+  if (cgp_open(prefix, CG_MODE_WRITE, &cgns.index))
     cgp_error_exit();
 
   {

apf/apfElement.cc

@@ -121,9 +121,12 @@ void Element::getNodeData()
 
 void Element::getElementNodeData(NewArray<double>& d)
 {
-  d.allocated() ? d.resize(nen) : d.allocate(nen);
-  for (int i = 0; i < nen; i++)
-    d[i] = nodeData[i];
+  d.resize(nodeData.size());
+  // to get the iterator 1 past the end without indexing one past the
+  // end we get the address to the last element then do ptr arithmetic
+  // to get one past that. Indexing at nodeData.size() can lead to segfault
+  // as you are actually accessing that memory.
+  std::copy(&nodeData[0], (&nodeData[nodeData.size()-1])+1, &d[0]);
 }
 
 }//namespace apf

cdash/nightly.cmake

@@ -5,14 +5,14 @@ SET(CTEST_TEST_TYPE Nightly)
 set(CTEST_BUILD_CONFIGURATION RelWithDebInfo)
 
 set(CTEST_NIGHTLY_START_TIME "17:00:00 EST")
-set(CTEST_SITE "cranium.scorec.rpi.edu" )
+set(CTEST_SITE "checkers.scorec.rpi.edu" )
 set(CTEST_DROP_METHOD "http")
 set(CTEST_DROP_SITE "my.cdash.org")
 set(CTEST_DROP_LOCATION "/submit.php?project=SCOREC")
 set(CTEST_DROP_SITE_CDASH TRUE)
 set(CTEST_BUILD_NAME  "linux-gcc-${CTEST_BUILD_CONFIGURATION}")
 
-set(CTEST_DASHBOARD_ROOT "/lore/cwsmith/nightlyBuilds/" )
+set(CTEST_DASHBOARD_ROOT "/lore/smithc11/nightlyBuilds/" )
 set(CTEST_CMAKE_GENERATOR "Unix Makefiles")
 set(CTEST_BUILD_FLAGS -j4)
 
@@ -123,6 +123,11 @@ function(check_current_branch BRANCH_NAME CONFIG_OPTS
     ERRVAR)
   file(MAKE_DIRECTORY "${CTEST_BINARY_DIRECTORY}/${BRANCH_NAME}")
 
+  execute_process(COMMAND df -h /tmp OUTPUT_VARIABLE outVar)
+  message(STATUS "df result {\n${outVar}}")
+  execute_process(COMMAND pwd OUTPUT_VARIABLE outVar)
+  message(STATUS "pwd result output {\n${outVar}}")
+
   ctest_configure(
       BUILD "${CTEST_BINARY_DIRECTORY}/${BRANCH_NAME}"
       SOURCE "${CTEST_SOURCE_DIRECTORY}/${CTEST_PROJECT_NAME}"
@@ -134,6 +139,11 @@ function(check_current_branch BRANCH_NAME CONFIG_OPTS
     message("${BRANCH_NAME} config passed")
   endif()
 
+  execute_process(COMMAND df -h /tmp OUTPUT_VARIABLE outVar)
+  message(STATUS "df result {\n${outVar}}")
+  execute_process(COMMAND pwd OUTPUT_VARIABLE outVar)
+  message(STATUS "pwd result output {\n${outVar}}")
+
   ctest_build(
       BUILD "${CTEST_BINARY_DIRECTORY}/${BRANCH_NAME}"
       NUMBER_ERRORS NUM_BUILD_ERRORS
@@ -313,7 +323,7 @@ SET(CONFIGURE_OPTIONS-sim
   "${CONFIGURE_OPTIONS}"
   "-DENABLE_SIMMETRIX:BOOL=ON"
   "-DSIM_PARASOLID:BOOL=ON"
-  "-DSIM_MPI:STRING=mpich3.3.2"
+  "-DSIM_MPI:STRING=mpich4.1.1"
 )
 
 setup_repo()

cdash/nightly.sh

@@ -1,24 +1,23 @@
 #!/bin/bash -x
 source /etc/profile
-source /users/cwsmith/.bash_profile
+source /users/smithc11/.bash_profile
 
 #setup lmod
 export PATH=/usr/share/lmod/lmod/libexec:$PATH
 
 #setup spack modules
 unset MODULEPATH
 
-module unuse /opt/scorec/spack/lmod/linux-rhel7-x86_64/Core
-module use /opt/scorec/modules
-module use /opt/scorec/spack/v0154_2/lmod/linux-rhel7-x86_64/Core
-module load gcc/10.1.0
-module load mpich/3.3.2
-module load simmetrix-simmodsuite/17.0-220516
-module load zoltan/3.83-int32
-module load cmake/3.20.0
+module use /opt/scorec/spack/rhel9/v0201_4/lmod/linux-rhel9-x86_64/Core/
+module load gcc/12.3.0-iil3lno
+module load mpich/4.1.1-xpoyz4t
+module load simmetrix-simmodsuite/2024.0-240119dev-7abimo4
+module load zoltan/3.83-hap4ggo
+module load cmake/3.26.3-2duxfcd
+module load cgns/develop-cc4dfwp
 
 #cdash output root
-d=/lore/cwsmith/nightlyBuilds/
+d=/lore/smithc11/nightlyBuilds/
 cd $d
 #remove compilation directories created by previous nightly.cmake runs
 [ -d build ] && rm -rf build/

cmake/FindSimModSuite.cmake

@@ -84,7 +84,7 @@ string(REGEX REPLACE
   "${SIM_VERSION}")
 
 set(MIN_VALID_SIM_VERSION 15.0.191017)
-set(MAX_VALID_SIM_VERSION 2024.0.240219)
+set(MAX_VALID_SIM_VERSION 2024.1.240606)
 if( ${SKIP_SIMMETRIX_VERSION_CHECK} )
   message(STATUS "Skipping Simmetrix SimModSuite version check."
     " This may result in undefined behavior")
@@ -124,10 +124,10 @@ endif()
 option(SIM_PARASOLID "Use Parasolid through Simmetrix" OFF)
 if (SIM_PARASOLID)
   set(MIN_SIM_PARASOLID_VERSION 290)
-  set(MAX_SIM_PARASOLID_VERSION 350)
+  set(MAX_SIM_PARASOLID_VERSION 361)
   foreach(version RANGE
       ${MAX_SIM_PARASOLID_VERSION}
-      ${MIN_SIM_PARASOLID_VERSION} -10)
+      ${MIN_SIM_PARASOLID_VERSION} -1)
     set(SIM_PARASOLID_VERSION ${version})
     getSimCadLib("${SIMMODSUITE_INSTALL_DIR}/lib/${SIM_ARCHOS}"
       SimParasolid${SIM_PARASOLID_VERSION} simParaLib FALSE)

mds/mdsCGNS.cc

@@ -177,19 +177,19 @@ struct MeshDataGroup
     if (components.size() == 1)
     {
       std::cout << "Scalar Group has " << components.size() << " related componenets: " << std::endl;
-      for (const auto m : components)
+      for (const auto& m : components)
         std::cout << "Field " << m.second.name << " @ " << m.second.si << " " << m.second.fi << std::endl;
     }
     else if (components.size() == 3)
     {
       std::cout << "Vector Group has " << components.size() << " related componenets: " << std::endl;
-      for (const auto m : components)
+      for (const auto& m : components)
         std::cout << "Field " << m.second.name << " @ " << m.second.si << " " << m.second.fi << std::endl;
     }
     else if (components.size() == 9)
     {
       std::cout << "Matrix Group has " << components.size() << " related componenets: " << std::endl;
-      for (const auto m : components)
+      for (const auto&  m : components)
         std::cout << "Field " << m.second.name << " @ " << m.second.si << " " << m.second.fi << std::endl;
     }
     else
@@ -1056,8 +1056,8 @@ apf::Mesh2 *DoIt(gmi_model *g, const std::string &fname, apf::CGNSBCMap &cgnsBCM
   int cgid = -1;
   auto comm = PCU_Get_Comm();
   cgp_mpi_comm(comm);
-  cgp_pio_mode(CGNS_ENUMV(CGP_INDEPENDENT));
-  cgp_open(fname.c_str(), CGNS_ENUMV(CG_MODE_READ), &cgid);
+  cgp_pio_mode(CGP_INDEPENDENT);
+  cgp_open(fname.c_str(), CG_MODE_READ, &cgid);
 
   int nbases = -1;
   cg_nbases(cgid, &nbases);

spr/spr.tex

@@ -11,7 +11,7 @@
 
 \section{Overview}
 An SPR-based error estimation procedure is defined in detail
-in Jie Wan's thesis.
+in Section 2.2.2 of Jie Wan's RPI thesis.
 We have reimplemented this system using the latest APF
 libraries and it supports the Albany adaptive cycle.
 This document details the inner workings of this estimator.

test/convert.cc

@@ -23,6 +23,7 @@
 #include <getopt.h>
 #include <string.h>
 #include <stdio.h>
+#include <array> //std::array
 
 using namespace std;
 
@@ -193,6 +194,7 @@ void addFathersTag(pGModel simModel, pParMesh sim_mesh, apf::Mesh* simApfMesh, c
       int id = GEN_tag(gface);
       if(id==ExtruRootId) ExtruRootFace=gface;
     }
+    GFIter_delete(gfIter);
     assert(ExtruRootFace != NULL);
     // all of the work so far assumes translation extrusion.  Rotation extrusion (sweeping extruded entiy over an arc of some angle about 
     // a given axis) is useful but this would require some code change.  The principle is the same.  Every root entity has another 
@@ -246,7 +248,7 @@ void addFathersTag(pGModel simModel, pParMesh sim_mesh, apf::Mesh* simApfMesh, c
       int nvert=i;
       PList_delete(listV);
 
-      double coordNewPt[nvert][3];
+      std::vector<std::array<double,3>> coordNewPt(nvert,{0,0,0});
       for(i=0; i< nvert ; i++) {
         int* markedData;
         if(!EN_getDataPtr((pEntity)vrts[i],myFather,(void**)&markedData)){  // not sure about marked yet
@@ -344,16 +346,16 @@ void addFathersTag(pGModel simModel, pParMesh sim_mesh, apf::Mesh* simApfMesh, c
 	   }
           PCU_ALWAYS_ASSERT(foundEETag != 0);
           count2D++;
-          int* vtxData = new int[1];
+          int* vtxData = new int;
           vtxData[0] = count2D;
           EN_attachDataPtr((pEntity)vrts[i],myFather,(void*)vtxData);
-          V_coord(vrts[i],coordNewPt[i]);
+          V_coord(vrts[i],coordNewPt[i].data());
 
           fprintf ( fcr, "%.15E %.15E %d %d %d %d  \n", coordNewPt[i][0],coordNewPt[i][1], vClassDim, foundESTag, foundETag, foundEETag );
         }
       }
 
-      double coordFather[nvert][3];
+      std::vector<std::array<double,3>> coordFather(nvert,{0,0,0});
       int fatherIds[4]; //store the ids of the fathers (vertices) on the root face
       for(i=0; i< nvert ; i++) {
         int* fatherIdPtr;
@@ -365,7 +367,7 @@ void addFathersTag(pGModel simModel, pParMesh sim_mesh, apf::Mesh* simApfMesh, c
         }
         assert(exists);
         fatherIds[i] = fatherIdPtr[0];
-        V_coord(vrts[i],coordFather[i]);
+        V_coord(vrts[i],coordFather[i].data());
         fprintf ( fcn, "%d ", fatherIds[i]);
       }
       fprintf ( fcn, "\n");
@@ -414,7 +416,7 @@ void addFathersTag(pGModel simModel, pParMesh sim_mesh, apf::Mesh* simApfMesh, c
               }
             }
             my2Dfath=fatherIds[iMin];
-            int* vtxData = new int[1];
+            int* vtxData = new int;
             vtxData[0] = my2Dfath;
             EN_attachDataPtr((pEntity)sonVtx,myFather,(void*)vtxData);
           }
@@ -424,6 +426,7 @@ void addFathersTag(pGModel simModel, pParMesh sim_mesh, apf::Mesh* simApfMesh, c
       }
       PList_delete(faces);
     } //end root face iterator
+    FIter_delete(fIter);
   }
   apf::MeshSIM* cake = reinterpret_cast<apf::MeshSIM*>(simApfMesh);
   cake->createIntTag("fathers2D", myFather, 1);

test/generate.cc

@@ -281,7 +281,6 @@ pNativeModel loadNativeModel() {
 }
 
 void simStart() {
-  SimModel_start();
   SimPartitionedMesh_start(NULL,NULL);
   if(should_log)
     Sim_logOn("generate_sim.log");