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hranihrani
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Merge branch 'master' of http://github.com/hrani/moose-core 
2 parents f723a63 + 1dfbbeb commit a812045

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5 files changed

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‎.travis.yml‎

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

‎.travis/travis_build_linux.sh‎

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

‎.travis/travis_prepare_linux.sh‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -27,11 +27,14 @@ apt-get install -qq python3-lxml python-lxml
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apt-get install -qq python3-numpy python3-matplotlib python3-dev
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apt-get install -qq python-pip python3-pip
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apt-get install -qq python-tk python3-tk
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apt-get install -qq libgraphviz-dev
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apt-get install -qq libgraphviz-dev
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# Gsl
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apt-get install -qq libgsl0-dev || apt-get install -qq libgsl-dev
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# hdf5
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apt-get install -qq libhdf5-serial-dev
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# Boost related.
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apt-get install -qq liblapack-dev
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apt-get install -qq libboost-all-dev

‎CMakeLists.txt‎

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Original file line numberDiff line numberDiff line change
@@ -181,72 +181,6 @@ if(WITH_BOOST_ODE)
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add_definitions(-DUSE_BOOST_ODE -UUSE_GSL)
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endif()
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# NSDF5 support. Disabled by default.
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if(WITH_NSDF)
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find_package(HDF5 COMPONENTS CXX HL)
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if(NOT HDF5_FOUND)
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message(
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"==================================================================\n"
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" HDF5 not found. Disabling NSDF support.\n\n"
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" If you need NSDF support, please install hdf5-dev or hdf5-devel\n"
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" package or equivalent.\n\n"
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" $ sudo apt-get install libhdf5-dev \n"
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" $ sudo yum install libhdf5-devel \n"
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" $ brew install hdf5 \n\n"
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" Otherwise, continue with 'make' and 'make install' \n"
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" If you install hdf5 to non-standard path, export environment \n"
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" variable HDF5_ROOT to the location. Rerun cmake \n"
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"================================================================ \n"
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)
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endif(NOT HDF5_FOUND)
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if(HDF5_FOUND)
204-
include_directories( ${HDF5_INCLUDE_DIRS} )
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add_definitions( -DUSE_HDF5 -DENABLE_NSDF )
206-
if(HDF5_USE_STATIC_LIBRARIES)
207-
message(STATUS "Finding static HDF5 libraries in $ENV{HDF5_ROOT}")
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find_library(HDF5_CXX_LIBRARIES NAMES libhdf5.a
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PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
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)
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find_library(HDF5_HL_LIBRARIES NAMES libhdf5_hl.a
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PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
213-
)
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set(HDF5_LIBRARIES ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES})
215-
endif()
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217-
218-
# Make sure, HDF5_HL_LIBRARIES are set. The COMPONENTS in find_package may
219-
# or may not work. See BhallaLab/moose-core#163.
220-
if(NOT HDF5_HL_LIBRARIES)
221-
set(HDF5_HL_LIBRARIES ${HDF5_HL_LIBRARIES})
222-
endif(NOT HDF5_HL_LIBRARIES)
223-
list(APPEND HDF5_LIBRARIES ${HDF5_HL_LIBRARIES})
224-
225-
# message(STATUS "MOOSE will use following HDF5 ${HDF5_LIBRARIES}" )
226-
foreach(HDF5_LIB ${HDF5_LIBRARIES})
227-
if(HDF5_LIB)
228-
get_filename_component( HDF5_LIB_EXT ${HDF5_LIB} EXT )
229-
if(HDF5_LIB_EXT)
230-
if(${HDF5_LIB_EXT} STREQUAL ".a")
231-
list(APPEND STATIC_LIBRARIES ${HDF5_LIB} )
232-
else( )
233-
list(APPEND SYSTEM_SHARED_LIBS ${HDF5_LIB} )
234-
endif( )
235-
endif()
236-
endif( )
237-
endforeach( )
238-
else( HDF5_FOUND )
239-
message(STATUS "HDF5 is not found" )
240-
endif( HDF5_FOUND )
241-
# This is a fix for new HDF5 package on Debian/Ubuntu which installs hdf5
242-
# headers in non-standard path. issue #80.
243-
if(HDF5_LIBRARY_DIRS)
244-
set_target_properties( libmoose PROPERTIES LINK_FLAGS "-L${HDF5_LIBRARY_DIRS}" )
245-
endif()
246-
else(WITH_NSDF)
247-
message(STATUS "NSDF support is disabled" )
248-
endif(WITH_NSDF)
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# Openmpi
251185
if(WITH_MPI)
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find_package(MPI REQUIRED)

‎builtins/CMakeLists.txt‎

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,52 @@
11
cmake_minimum_required(VERSION 2.8)
22
include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
33

4+
# NSDF5 support. Disabled by default.
5+
if(WITH_NSDF)
6+
find_package(HDF5 COMPONENTS CXX HL)
7+
if(NOT HDF5_FOUND)
8+
message(
9+
"==================================================================\n"
10+
" HDF5 not found. Disabling NSDF support.\n\n"
11+
" If you need NSDF support, please install hdf5-dev or hdf5-devel\n"
12+
" package or equivalent.\n\n"
13+
" $ sudo apt-get install libhdf5-dev \n"
14+
" $ sudo yum install libhdf5-devel \n"
15+
" $ brew install hdf5 \n\n"
16+
" Otherwise, continue with 'make' and 'make install' \n"
17+
" If you install hdf5 to non-standard path, export environment \n"
18+
" variable HDF5_ROOT to the location. Rerun cmake \n"
19+
"================================================================ \n"
20+
)
21+
endif(NOT HDF5_FOUND)
22+
23+
if(HDF5_FOUND)
24+
include_directories(${HDF5_CXX_INCLUDE_DIRS} )
25+
add_definitions(-DUSE_HDF5 -DENABLE_NSDF )
26+
add_definitions(${HDF5_CXX_DEFINITIONS})
27+
if(HDF5_USE_STATIC_LIBRARIES)
28+
message(STATUS "Finding static HDF5 libraries in $ENV{HDF5_ROOT}")
29+
find_library(HDF5_CXX_LIBRARIES NAMES libhdf5.a
30+
PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
31+
)
32+
find_library(HDF5_HL_LIBRARIES NAMES libhdf5_hl.a
33+
PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
34+
)
35+
set(HDF5_LIBRARIES ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES})
36+
endif()
37+
38+
# Make sure, HDF5_HL_LIBRARIES are set. The COMPONENTS in find_package may
39+
# or may not work. See BhallaLab/moose-core#163.
40+
if(NOT HDF5_HL_LIBRARIES)
41+
set(HDF5_HL_LIBRARIES ${HDF5_HL_LIBRARIES})
42+
endif(NOT HDF5_HL_LIBRARIES)
43+
list(APPEND HDF5_LIBRARIES ${HDF5_HL_LIBRARIES})
44+
45+
else(HDF5_FOUND)
46+
message(STATUS "HDF5 is not found. Disabling NSDF support." )
47+
endif( HDF5_FOUND )
48+
endif(WITH_NSDF)
49+
450
set(SRCS
551
Arith.cpp
652
Group.cpp
@@ -33,3 +79,6 @@ if(WITH_NSDF AND HDF5_FOUND)
3379
endif()
3480

3581
add_library(moose_builtins ${SRCS} )
82+
if(WITH_NSDF AND HDF5_FOUND)
83+
target_link_libraries(moose_builtins ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES})
84+
endif()

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