Merge pull request #2 from trilinos/develop

Trilinos Merge 6/5/19

cmake/std/atdm/sems-rhel7/environment.sh

@@ -160,6 +160,20 @@ elif [[ "$ATDM_CONFIG_COMPILER" == "INTEL-17.0.1" ]] ; then
   if [[ "${ATDM_CONFIG_LM_LICENSE_FILE_OVERRIDE}" != "" ]] ; then
     export LM_LICENSE_FILE=${ATDM_CONFIG_LM_LICENSE_FILE_OVERRIDE}
   fi
+elif [[ "$ATDM_CONFIG_COMPILER" == "INTEL-18.0.5" ]] ; then
+  module load sems-gcc/7.2.0
+  module load sems-intel/18.0.5
+  module load atdm-env
+  module load atdm-mkl/18.0.5
+  export OMPI_CXX=`which icpc`
+  export OMPI_CC=`which icc`
+  export OMPI_FC=`which ifort`
+  export ATDM_CONFIG_LAPACK_LIBS="-mkl"
+  export ATDM_CONFIG_BLAS_LIBS="-mkl"
+  export [email protected]
+  if [[ "${ATDM_CONFIG_LM_LICENSE_FILE_OVERRIDE}" != "" ]] ; then
+    export LM_LICENSE_FILE=${ATDM_CONFIG_LM_LICENSE_FILE_OVERRIDE}
+  fi
 elif [[ "$ATDM_CONFIG_COMPILER" == "CUDA-9.2" ]] ; then
   module load sems-gcc/7.2.0
   module load sems-cuda/9.2

packages/stk/stk_balance/stk_balance/CMakeLists.txt

@@ -65,6 +65,11 @@ FILE(GLOB SOURCES *.cpp)
 FILE(GLOB HEADERS_INTERNAL ${CMAKE_CURRENT_SOURCE_DIR}/internal/*.hpp)
 FILE(GLOB SOURCES_INTERNAL ${CMAKE_CURRENT_SOURCE_DIR}/internal/*.cpp)
 
+IF(NOT TPL_ENABLE_BoostLib)
+LIST(REMOVE_ITEM HEADERS_INTERNAL "${CMAKE_CURRENT_SOURCE_DIR}/internal/balanceCommandLine.hpp")
+LIST(REMOVE_ITEM SOURCES_INTERNAL "${CMAKE_CURRENT_SOURCE_DIR}/internal/balanceCommandLine.cpp")
+ENDIF()
+
 FILE(GLOB HEADERS_SEARCH_TOLERANCE ${CMAKE_CURRENT_SOURCE_DIR}/search_tolerance/*.hpp)
 
 FILE(GLOB HEADERS_SEARCH_TOLERANCE_ALGS ${CMAKE_CURRENT_SOURCE_DIR}/search_tolerance_algs/*.hpp)
@@ -88,12 +93,7 @@ TRIBITS_ADD_LIBRARY(
   DEPLIBS
   )
 
-# TRIBITS_ADD_LIBRARY(
-#   stk_balance_search_tolerance_algs
-#   NOINSTALLHEADERS ${HEADERS_SEARCH_TOLERANCE_ALGS} 
-#   SOURCES ${SOURCES_SEARCH_TOLERANCE_ALGS}
-#   DEPLIBS
-#   )
+IF(TPL_ENABLE_BoostLib)
 
 TRIBITS_ADD_EXECUTABLE(
     stk_balance
@@ -109,6 +109,8 @@ TRIBITS_ADD_EXECUTABLE(
     NOEXEPREFIX INSTALLABLE
     )
 
+ENDIF()
+
 INSTALL(FILES ${HEADERS} DESTINATION
     ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_balance)
 INSTALL(FILES ${HEADERS_INTERNAL} DESTINATION

packages/stk/stk_io/stk_io/InputFile.cpp

@@ -33,6 +33,7 @@
 
 // #######################  Start Clang Header Tool Managed Headers ########################
 // clang-format off
+#include <stk_util/stk_config.h>
 #include <stk_io/InputFile.hpp>
 #include <math.h>                                  // for fmod
 #include <stddef.h>                                // for size_t
@@ -46,7 +47,9 @@
 #include <stk_mesh/base/FieldBase.hpp>             // for FieldBase, etc
 #include <stk_mesh/base/FindRestriction.hpp>       // for find_restriction
 #include <stk_mesh/base/MetaData.hpp>              // for MetaData
+#if defined(STK_HAVE_BOOSTLIB)
 #include <stk_util/environment/FileUtils.hpp>
+#endif
 #include <stk_util/util/ReportHandler.hpp>  // for ThrowErrorMsgIf
 #include <utility>                                 // for pair
 #include "Ioss_DBUsage.h"                          // for DatabaseUsage, etc
@@ -132,8 +135,10 @@ namespace stk {
       Ioss::DatabaseUsage db_usage = Ioss::READ_MODEL;
       if (m_db_purpose == stk::io::READ_RESTART)
         db_usage = Ioss::READ_RESTART;
-
+
+#if defined(STK_HAVE_BOOSTLIB)
       stk::util::filename_substitution(mesh_filename);
+#endif
       m_database = Teuchos::rcp(Ioss::IOFactory::create(mesh_type, mesh_filename,
 							db_usage, communicator,
 							properties));

packages/stk/stk_io/stk_io/StkMeshIoBroker.cpp

@@ -33,6 +33,7 @@
 
 // #######################  Start Clang Header Tool Managed Headers ########################
 // clang-format off
+#include <stk_util/stk_config.h>
 #include <stk_io/StkMeshIoBroker.hpp>
 #include <stk_util/environment/Env.hpp>
 #include <Ionit_Initializer.h>                       // for Initializer
@@ -55,7 +56,9 @@
 #include <stk_mesh/base/Field.hpp>                   // for Field
 #include <stk_mesh/base/GetEntities.hpp>
 #include <stk_mesh/base/MetaData.hpp>                // for MetaData, etc
+#if defined(STK_HAVE_BOOSTLIB)
 #include <stk_util/environment/FileUtils.hpp>
+#endif
 #include <stk_util/util/ReportHandler.hpp>    // for ThrowErrorMsgIf, etc
 #include <utility>                                   // for pair, make_pair
 #include "Ioss_CodeTypes.h"                          // for NameList
@@ -505,7 +508,9 @@ size_t StkMeshIoBroker::create_output_mesh(const std::string &filename, Database
     }
 
     std::string out_filename = filename;
+#if defined(STK_HAVE_BOOSTLIB)
     stk::util::filename_substitution(out_filename);
+#endif
     Ioss::Region *input_region = nullptr;
     if (is_index_valid(m_inputFiles, m_activeMeshIndex)) {
         input_region = get_input_io_region().get();
@@ -1157,7 +1162,9 @@ size_t StkMeshIoBroker::add_heartbeat_output(const std::string &filename, Heartb
                                              const Ioss::PropertyManager &properties, bool openFileImmediately)
 {
     std::string out_filename = filename;
+#if defined(STK_HAVE_BOOSTLIB)
     stk::util::filename_substitution(out_filename);
+#endif
     auto heartbeat = Teuchos::rcp(new impl::Heartbeat(out_filename, hb_type,
                                                       properties, m_communicator, openFileImmediately));
     m_heartbeat.push_back(heartbeat);

packages/stk/stk_search/CMakeLists.txt

@@ -1,13 +1,11 @@
 
 TRIBITS_SUBPACKAGE(Search)
 
-
 ADD_SUBDIRECTORY(stk_search)
 
 IF(Trilinos_ENABLE_STKNGP_TEST)
 TRIBITS_ADD_TEST_DIRECTORIES(unit_tests)
 TRIBITS_ADD_TEST_DIRECTORIES(integrationtest)
 ENDIF()
 
-
 TRIBITS_SUBPACKAGE_POSTPROCESS()

packages/stk/stk_search/cmake/Dependencies.cmake

@@ -3,6 +3,6 @@ SET(LIB_OPTIONAL_DEP_PACKAGES)
 SET(TEST_REQUIRED_DEP_PACKAGES STKUnit_test_utils Gtest)
 SET(TEST_OPTIONAL_DEP_PACKAGES)
 SET(LIB_REQUIRED_DEP_TPLS MPI)
-SET(LIB_OPTIONAL_DEP_TPLS Boost)
+SET(LIB_OPTIONAL_DEP_TPLS Boost BoostLib)
 SET(TEST_REQUIRED_DEP_TPLS)
 SET(TEST_OPTIONAL_DEP_TPLS Boost)

packages/stk/stk_search/integrationtest/CMakeLists.txt

@@ -38,12 +38,36 @@ FILE(GLOB SOURCES *.cpp)
 LIST(REMOVE_ITEM SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/UnitTestPerformance.cpp)
 LIST(REMOVE_ITEM SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/UnitTestNaluPerformance.cpp)
 
-TRIBITS_ADD_EXECUTABLE_AND_TEST(
+TRIBITS_ADD_EXECUTABLE(
     search_integration_tests
     SOURCES ${SOURCES}
     TESTONLYLIBS stk_unit_main
+    COMM serial mpi
+    )
+
+IF(TPL_ENABLE_BoostLib)
+
+TRIBITS_ADD_TEST(
+    search_integration_tests
+    NAME STKSearch_integration_tests
     ARGS ""
     COMM serial mpi
+    PASS_REGULAR_EXPRESSION "PASS"
+    FAIL_REGULAR_EXPRESSION "FAIL"
     NUM_MPI_PROCS 1
-    )
+)
+
+else()
+
+TRIBITS_ADD_TEST(
+    search_integration_tests
+    NAME STKSearch_integration_tests
+    ARGS "--gtest_filter=*KDTREE"
+    COMM serial mpi
+    PASS_REGULAR_EXPRESSION "PASS"
+    FAIL_REGULAR_EXPRESSION "FAIL"
+    NUM_MPI_PROCS 1
+)
+
+ENDIF()
 

packages/stk/stk_search/stk_search/CoarseSearch.hpp

@@ -34,9 +34,13 @@
 #ifndef stk_search_CoarseSearch_hpp
 #define stk_search_CoarseSearch_hpp
 
+#include <stk_util/stk_config.h>
+#include <stk_util/util/ReportHandler.hpp>
 #include <stk_search/IdentProc.hpp>
 #include <stk_search/BoundingBox.hpp>
+#if defined(STK_HAVE_BOOSTLIB)
 #include <stk_search/CoarseSearchBoostRTree.hpp>
+#endif
 #include <stk_search/CoarseSearchKdTree.hpp>
 #include <stk_search/SearchMethod.hpp>
 #include <vector>
@@ -73,7 +77,11 @@ void coarse_search_nonIdentProc(
   switch( method )
   {
   case BOOST_RTREE:
+#if defined(STK_HAVE_BOOSTLIB)
     coarse_search_boost_rtree_output_locally<DomainBox, DomainIdent, RangeBox, RangeIdent>(domain,range,comm,intersections);
+#else
+    ThrowRequireMsg(false,"ERROR, the BOOST_RTREE option in stk_search requires that Trilinos was configured with TPL_ENABLE_BoostLib:BOOL=ON");
+#endif
     break;
   default:
     std::cerr << "coarse_search(..) interface used does not support std::search::coarse_search_nonIdentProc(..) yet" << method << std::endl;
@@ -115,7 +123,11 @@ void coarse_search( std::vector<std::pair<DomainBox,DomainIdent> > const& domain
   {
   case BOOST_RTREE:
 #ifndef __NVCC__
+#if defined(STK_HAVE_BOOSTLIB)
     coarse_search_boost_rtree(domain,range,comm,intersections,communicateRangeBoxInfo);
+#else
+    ThrowRequireMsg(false,"ERROR, the BOOST_RTREE option in stk_search requires that Trilinos was configured with TPL_ENABLE_BoostLib:BOOL=ON");
+#endif
     break;
 #endif
   case KDTREE:

packages/stk/stk_search/unit_tests/CMakeLists.txt

@@ -37,12 +37,23 @@ FILE(GLOB SOURCES *.cpp)
 #removing due to dependence on geometry toolkit which is not available to Trilinos
 LIST(REMOVE_ITEM SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/UnitTestCoarseSearch.cpp")
 
-TRIBITS_ADD_EXECUTABLE_AND_TEST(
+IF(NOT TPL_ENABLE_BoostLib)
+LIST(REMOVE_ITEM SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/UnitTestCoarseSearchBoostImpl.cpp")
+ENDIF()
+
+TRIBITS_ADD_EXECUTABLE(
     search_unit_tests
     SOURCES ${SOURCES}
     TESTONLYLIBS stk_unit_main
-    ARGS ""
     COMM serial mpi
-    NUM_MPI_PROCS 1
     )
 
+TRIBITS_ADD_TEST(
+    search_unit_tests
+    NAME STKSearch_unit_tests
+    ARGS ""
+    COMM serial mpi
+    PASS_REGULAR_EXPRESSION "PASS"
+    FAIL_REGULAR_EXPRESSION "FAIL"
+    NUM_MPI_PROCS 1
+)

packages/stk/stk_search/unit_tests/UnitTestUtils.hpp

@@ -47,6 +47,8 @@
 
 #include <stk_unit_test_utils/getOption.h>
 
+#include <iomanip>
+
 typedef stk::search::IdentProc<int,int> Ident;
 typedef stk::search::Point<double> Point;
 typedef stk::search::Sphere<double> Sphere;

packages/stk/stk_search_util/stk_search_util/PeriodicBoundarySearch.hpp

@@ -34,6 +34,7 @@
 #ifndef STK_SEARCH_UTIL_STK_MESH_PERIODIC_BOUNDARY_SEARCH_HPP
 #define STK_SEARCH_UTIL_STK_MESH_PERIODIC_BOUNDARY_SEARCH_HPP
 
+#include <stk_util/stk_config.h>
 #include <stk_search/CoarseSearch.hpp>
 #include <stk_search/BoundingBox.hpp>
 #include <stk_search/IdentProc.hpp>
@@ -160,6 +161,7 @@ class PeriodicBoundarySearch
       // Default is identity transform.
     }
 
+#if defined(STK_HAVE_BOOST)
     TransformHelper(const boost::array<double, 3> & trans_arg)
       : m_transform_type(TRANSLATION)
       , m_translation(3,0)
@@ -168,6 +170,7 @@ class PeriodicBoundarySearch
         m_translation[1] = trans_arg[1];
         m_translation[2] = trans_arg[2];
     }
+#endif
 
     TransformHelper(double angle, const double axis[3])
       : m_transform_type(ROTATIONAL)

packages/stk/stk_tools/stk_tools/block_extractor/main.cpp

@@ -1,6 +1,10 @@
 #include "mpi.h"
 #include <iosfwd>
 #include <vector>
+#include <stk_util/stk_config.h>
+
+#if defined(STK_HAVE_BOOSTLIB)
+
 #include <stk_tools/block_extractor/ParseCsv.hpp>
 #include <stk_util/command_line/CommandLineParserParallel.hpp>
 #include <stk_util/command_line/CommandLineParserUtils.hpp>
@@ -29,4 +33,14 @@ int main(int argc, const char**argv)
     return 0;
 }
 
+#else
+
+int main(int argc, const char**argv)
+{
+  std::cerr<<"ERROR, stk_block_extractor requires that Trilinos was configured with -DTPL_ENABLE_BoostLib:BOOL=ON"
+           << std::endl;
+  return -1;
+}
+
+#endif
 

packages/stk/stk_transfer/cmake/Dependencies.cmake

@@ -2,7 +2,7 @@ SET(LIB_REQUIRED_DEP_PACKAGES STKUtil STKSearch)
 SET(LIB_OPTIONAL_DEP_PACKAGES)
 SET(TEST_REQUIRED_DEP_PACKAGES)
 SET(TEST_OPTIONAL_DEP_PACKAGES)
-SET(LIB_REQUIRED_DEP_TPLS)
+SET(LIB_REQUIRED_DEP_TPLS BoostLib)
 SET(LIB_OPTIONAL_DEP_TPLS Boost)
 SET(TEST_REQUIRED_DEP_TPLS)
 SET(TEST_OPTIONAL_DEP_TPLS)

packages/stk/stk_util/stk_util/CMakeLists.txt

@@ -4,8 +4,8 @@ ADD_SUBDIRECTORY(util)
 IF(TPL_ENABLE_MPI)
 
 ADD_SUBDIRECTORY(parallel)
-ADD_SUBDIRECTORY(registry)
 ADD_SUBDIRECTORY(environment)
+ADD_SUBDIRECTORY(registry)
 ADD_SUBDIRECTORY(diag)
 
 IF ( ${PACKAGE_NAME}_ENABLE_SEACASIoss )