Merging develop into master

Author: Nightly Bot

cmake/FindParmetis.cmake

@@ -12,6 +12,12 @@ if(NOT EXISTS "${PARMETIS_INCLUDE_DIR}")
   message(FATAL_ERROR "parmetis include dir not found")
 endif()
 
+find_path(METIS_INCLUDE_DIR metis.h PATHS "${PARMETIS_PREFIX}/include")
+if(NOT EXISTS "${METIS_INCLUDE_DIR}")
+  message(FATAL_ERROR "metis include dir not found")
+endif()
+
+
 find_library(PARMETIS_LIBRARY parmetis PATHS "${PARMETIS_PREFIX}/lib")
 if(NOT EXISTS "${PARMETIS_LIBRARY}")
   message(FATAL_ERROR "parmetis library not found")
@@ -23,7 +29,7 @@ if(NOT EXISTS "${METIS_LIBRARY}")
 endif()
 
 set(PARMETIS_LIBRARIES ${PARMETIS_LIBRARY} ${METIS_LIBRARY})
-set(PARMETIS_INCLUDE_DIRS ${PARMETIS_INCLUDE_DIR} )
+set(PARMETIS_INCLUDE_DIRS ${PARMETIS_INCLUDE_DIR} ${METIS_INCLUDE_DIR})
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set PARMETIS_FOUND to TRUE

gmi_sim/gmi_sim.cc

@@ -14,6 +14,7 @@
 #include <gmi.h>
 #include <SimModel.h>
 #include <vector>
+#include <set>
 
 #include "gmi_sim_config.h"
 
@@ -182,8 +183,7 @@ static gmi_set* region_faces(pGRegion region)
   return s;
 }
 
-/* getting the region adj to an edge. This version
- * does not support non-manifold models
+/* getting the region adj to an edge.
  */
 // NOTE: the corresponding functionality does not exist
 // in gmi_base!
@@ -192,22 +192,23 @@ static gmi_set* edge_regions(pGEdge e)
 {
   pPList list = GE_faces((pGEdge)e);
 
-  // do the first one outside of the loop
-  gmi_set* regions_set = face_regions((pGFace)PList_item(list, 0));
-  if (regions_set->n > 1)
-    gmi_fail("no support for non-manifold surfaces!\n");
-  pGRegion r = (pGRegion)regions_set->e[0];
-
-  // do the rest inside of the loop
-  for (int i = 1; i < PList_size(list); i++) {
-    regions_set = face_regions((pGFace)PList_item(list, i));
-    if (regions_set->n > 1)
-      gmi_fail("no support for non-manifold surfaces!\n");
-    if (r != (pGRegion)regions_set->e[0])
-      gmi_fail("no support for non-manifold surfaces!\n");
+  std::set<pGRegion> rgns;
+  gmi_set* regions_set;
+  for (int i = 0; i < PList_size(list); i++) {
+   regions_set = face_regions((pGFace)PList_item(list, i));
+   for (int j = 0; j < regions_set->n; j++) {
+     rgns.insert( (pGRegion) regions_set->e[j] );
+   }
   }
-  PList_delete(list);
-  return regions_set;
+
+  int count = 0;
+  gmi_set* s = gmi_make_set(rgns.size());
+  for (std::set<pGRegion>::iterator it=rgns.begin(); it!=rgns.end(); ++it) {
+    s->e[count] = (gmi_ent*)*it;
+    count++;
+  }
+
+  return s;
 }
 
 static gmi_set* adjacent(gmi_model* m, gmi_ent* e, int dim)

phasta/CMakeLists.txt

@@ -47,12 +47,25 @@ if(NOT ENABLE_SIMMETRIX # no simmetrix
   set(SOURCES ${SOURCES} phGrowthCurves_empty.cc)
 endif()
 
+# Package headers
+set(HEADERS
+  chef.h
+  phInput.h
+  phstream.h
+  phiotimer.h
+  phastaChef.h
+)
+
+# Add the ph library
+add_library(ph ${SOURCES})
 
 #determine which timer to use based on the target system and compiler
 if(CMAKE_SYSTEM_NAME MATCHES BlueGeneQ*)
   add_definitions(-DUSE_PCU_TIME)
+  target_compile_definitions(ph INTERFACE -DUSE_PCU_TIME)
 elseif(CMAKE_CXX_COMPILER_ID MATCHES Intel)
   add_definitions(-DHAVE_INTEL_RDTSC)
+  target_compile_definitions(ph INTERFACE -DHAVE_INTEL_RDTSC)
 else()
   #from https://github.com/abduld/libwb/issues/5
   include(CheckFunctionExists)
@@ -63,23 +76,13 @@ else()
   endif(NOT HAVE_CLOCK_GETTIME)
   if( HAVE_CLOCK_GETTIME OR LIBRT_LIBRARIES )
     add_definitions(-DHAVE_CLOCK_GETTIME)
+    target_compile_definitions(ph INTERFACE -DHAVE_CLOCK_GETTIME)
   else()
     add_definitions(-DUSE_PCU_TIME)
+    target_compile_definitions(ph INTERFACE -DUSE_PCU_TIME)
   endif()
 endif()
 
-# Package headers
-set(HEADERS
-  chef.h
-  phInput.h
-  phstream.h
-  phiotimer.h
-  phastaChef.h
-)
-
-# Add the ph library
-add_library(ph ${SOURCES})
-
 # Include directories
 target_include_directories(ph INTERFACE
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>

test/measureAnisoStats.cc

@@ -219,7 +219,8 @@ void getStats(
 
   std::stringstream ss, sse, ssq, ssm, ssl;
   ss << outputPrefix << "/" << "linear_tables";
-  const char* pathName = ss.str().c_str();
+  const std::string& tmp = ss.str();
+  const char* pathName = tmp.c_str();
   safe_mkdir(pathName);
 
   ssq << pathName << "/linearQTable_" << PCU_Comm_Self() << ".dat";