Merge branch 'master' of github.com:dilawar/moose-core

Author: dilawar

.travis.yml

@@ -1,16 +1,12 @@
 language: cpp
 sudo: required
-group: travis_lts
-dist: xenial
-
-os:
-    - linux
-    - osx
 
 matrix:
     include:
+        - os : linux
+          dist: xenial
         - os : osx
-          osx_image: xcode10
+          osx_image: xcode10.1
 
 notifications:
   email:

.travis/travis_build_linux.sh

@@ -59,14 +59,14 @@ if type $PYTHON3 > /dev/null; then
     # GSL.
     (
         mkdir -p _GSL_BUILD_PY3 && cd _GSL_BUILD_PY3 && \
-            cmake -DPYTHON_EXECUTABLE="$PYTHON3" -DDEBUG=ON ..
+            cmake -DWITH_NSDF=ON -DPYTHON_EXECUTABLE="$PYTHON3" -DDEBUG=ON ..
         $MAKE && ctest --output-on-failure -E ".*socket_streamer.*"
     )
 
     # BOOST
     (
         mkdir -p _BOOST_BUILD_PY3 && cd _BOOST_BUILD_PY3 && \
-            cmake -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
+            cmake -DWITH_NSDF=ON -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
         $MAKE && ctest --output-on-failure -E ".*socket_streamer.*"
     )
     echo "All done"

.travis/travis_prepare_linux.sh

@@ -27,11 +27,14 @@ apt-get install -qq python3-lxml python-lxml
 apt-get install -qq python3-numpy python3-matplotlib python3-dev
 apt-get install -qq python-pip python3-pip
 apt-get install -qq python-tk python3-tk
-apt-get install -qq libgraphviz-dev
+apt-get install -qq libgraphviz-dev 
 
 # Gsl
 apt-get install -qq libgsl0-dev || apt-get install -qq libgsl-dev
 
+# hdf5
+apt-get install -qq libhdf5-serial-dev
+
 # Boost related.
 apt-get install -qq liblapack-dev
 apt-get install -qq libboost-all-dev

CMakeLists.txt

@@ -181,72 +181,6 @@ if(WITH_BOOST_ODE)
     add_definitions(-DUSE_BOOST_ODE -UUSE_GSL)
 endif()
 
-# NSDF5 support. Disabled by default.
-if(WITH_NSDF)
-    find_package(HDF5 COMPONENTS CXX HL)
-    if(NOT HDF5_FOUND)
-        message(
-            "==================================================================\n"
-            " HDF5 not found. Disabling NSDF support.\n\n"
-            " If you need NSDF support, please install hdf5-dev or hdf5-devel\n"
-            " package or equivalent.\n\n"
-            "     $ sudo apt-get install libhdf5-dev \n"
-            "     $ sudo yum install libhdf5-devel \n"
-            "     $ brew install hdf5 \n\n"
-            " Otherwise, continue with 'make' and 'make install' \n"
-            " If you install hdf5 to non-standard path, export environment \n"
-            " variable HDF5_ROOT to the location. Rerun cmake \n"
-            "================================================================ \n"
-            )
-    endif(NOT HDF5_FOUND)
-
-    if(HDF5_FOUND)
-        include_directories( ${HDF5_INCLUDE_DIRS} )
-        add_definitions( -DUSE_HDF5 -DENABLE_NSDF )
-        if(HDF5_USE_STATIC_LIBRARIES)
-            message(STATUS "Finding static HDF5 libraries in $ENV{HDF5_ROOT}")
-            find_library(HDF5_CXX_LIBRARIES NAMES libhdf5.a
-                PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
-                )
-            find_library(HDF5_HL_LIBRARIES NAMES libhdf5_hl.a
-                PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
-                )
-            set(HDF5_LIBRARIES ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES})
-        endif()
-
-
-        # Make sure, HDF5_HL_LIBRARIES are set. The COMPONENTS in find_package may
-        # or may not work. See BhallaLab/moose-core#163.
-        if(NOT HDF5_HL_LIBRARIES)
-            set(HDF5_HL_LIBRARIES ${HDF5_HL_LIBRARIES})
-        endif(NOT HDF5_HL_LIBRARIES)
-        list(APPEND HDF5_LIBRARIES ${HDF5_HL_LIBRARIES})
-
-        # message(STATUS "MOOSE will use following HDF5 ${HDF5_LIBRARIES}" )
-        foreach(HDF5_LIB ${HDF5_LIBRARIES})
-            if(HDF5_LIB)
-                get_filename_component( HDF5_LIB_EXT ${HDF5_LIB} EXT )
-                if(HDF5_LIB_EXT)
-                    if(${HDF5_LIB_EXT} STREQUAL ".a")
-                        list(APPEND STATIC_LIBRARIES ${HDF5_LIB} )
-                    else( )
-                        list(APPEND SYSTEM_SHARED_LIBS ${HDF5_LIB} )
-                    endif( )
-                endif()
-            endif( )
-        endforeach( )
-    else( HDF5_FOUND )
-        message(STATUS "HDF5 is not found" )
-    endif( HDF5_FOUND )
-    # This is a fix for new HDF5 package on Debian/Ubuntu which installs hdf5
-    # headers in non-standard path. issue #80.
-    if(HDF5_LIBRARY_DIRS)
-        set_target_properties( libmoose PROPERTIES LINK_FLAGS "-L${HDF5_LIBRARY_DIRS}" )
-    endif()
-else(WITH_NSDF)
-    message(STATUS "NSDF support is disabled" )
-endif(WITH_NSDF)
-
 # Openmpi
 if(WITH_MPI)
     find_package(MPI REQUIRED)

builtins/CMakeLists.txt

@@ -1,6 +1,52 @@
 cmake_minimum_required(VERSION 2.8)
 include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
 
+# NSDF5 support. Disabled by default.
+if(WITH_NSDF)
+    find_package(HDF5 COMPONENTS CXX HL)
+    if(NOT HDF5_FOUND)
+        message(
+            "==================================================================\n"
+            " HDF5 not found. Disabling NSDF support.\n\n"
+            " If you need NSDF support, please install hdf5-dev or hdf5-devel\n"
+            " package or equivalent.\n\n"
+            "     $ sudo apt-get install libhdf5-dev \n"
+            "     $ sudo yum install libhdf5-devel \n"
+            "     $ brew install hdf5 \n\n"
+            " Otherwise, continue with 'make' and 'make install' \n"
+            " If you install hdf5 to non-standard path, export environment \n"
+            " variable HDF5_ROOT to the location. Rerun cmake \n"
+            "================================================================ \n"
+            )
+    endif(NOT HDF5_FOUND)
+
+    if(HDF5_FOUND)
+        include_directories(${HDF5_CXX_INCLUDE_DIRS} )
+        add_definitions(-DUSE_HDF5 -DENABLE_NSDF )
+        add_definitions(${HDF5_CXX_DEFINITIONS})
+        if(HDF5_USE_STATIC_LIBRARIES)
+            message(STATUS "Finding static HDF5 libraries in $ENV{HDF5_ROOT}")
+            find_library(HDF5_CXX_LIBRARIES NAMES libhdf5.a
+                PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
+                )
+            find_library(HDF5_HL_LIBRARIES NAMES libhdf5_hl.a
+                PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
+                )
+            set(HDF5_LIBRARIES ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES})
+        endif()
+
+        # Make sure, HDF5_HL_LIBRARIES are set. The COMPONENTS in find_package may
+        # or may not work. See BhallaLab/moose-core#163.
+        if(NOT HDF5_HL_LIBRARIES)
+            set(HDF5_HL_LIBRARIES ${HDF5_HL_LIBRARIES})
+        endif(NOT HDF5_HL_LIBRARIES)
+        list(APPEND HDF5_LIBRARIES ${HDF5_HL_LIBRARIES})
+
+    else(HDF5_FOUND)
+        message(STATUS "HDF5 is not found. Disabling NSDF support." )
+    endif( HDF5_FOUND )
+endif(WITH_NSDF)
+
 set(SRCS
     Arith.cpp
     Group.cpp
@@ -33,3 +79,6 @@ if(WITH_NSDF AND HDF5_FOUND)
 endif()
 
 add_library(moose_builtins ${SRCS} )
+if(WITH_NSDF AND HDF5_FOUND)
+    target_link_libraries(moose_builtins ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES})
+endif()

builtins/SocketStreamer.cpp

@@ -224,7 +224,7 @@ void SocketStreamer::configureSocketServer( )
     // for details. We are making it 'reusable'.
     int on = 1;
 
-#ifdef SO_REUSEADDR
+#ifdef SO_REUSEPORT
     if(0 > setsockopt(sockfd_, SOL_SOCKET, SO_REUSEPORT, (const char *)&on, sizeof(on)))
         LOG(moose::warning, "Warn: setsockopt() failed");
 #endif