Tons of build updates

CMakeLists.txt

@@ -1,4 +1,6 @@
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 3.6)
+set(CMAKE_CXX_STANDARD 11)
+cmake_policy(SET CMP0012 OLD)
 list(INSERT CMAKE_MODULE_PATH 0 "${CMAKE_CURRENT_SOURCE_DIR}")
 
 project(CosmoToolbox)

external/external_build.cmake

@@ -5,9 +5,9 @@ OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
 SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE URL "URL to download FFTW from")
 SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.1.4.tar.gz" CACHE URL "URL to download Eigen from")
 SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
-SET(HDF5_URL "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.15/src/hdf5-1.8.15.tar.gz" CACHE STRING "URL to download HDF5 from")
+SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from")
 SET(NETCDF_URL "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz" CACHE STRING "URL to download NetCDF from")
-SET(BOOST_URL "http://sourceforge.net/projects/boost/files/boost/1.60.0/boost_1_60_0.tar.gz/download" CACHE STRING "URL to download Boost from")
+SET(BOOST_URL "http://sourceforge.net/projects/boost/files/boost/1.61.0/boost_1_61_0.tar.gz/download" CACHE STRING "URL to download Boost from")
 SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ")
 mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL)
 
@@ -26,8 +26,9 @@ ENDIF(ENABLE_OPENMP)
 
 SET(BUILD_PREFIX ${CMAKE_BINARY_DIR}/external_build)
 SET(EXT_INSTALL ${CMAKE_BINARY_DIR}/ext_install)
-SET(CONFIGURE_LIBS)
+SET(CONFIGURE_LIBS )
-SET(CONFIGURE_CPP_FLAGS)
+SET(CONFIGURE_CPP_FLAGS "")
+SET(CONFIGURE_LDFLAGS "")
 
 if (ENABLE_SHARP)
   SET(SHARP_SOURCE ${CMAKE_SOURCE_DIR}/external/sharp)
@@ -71,16 +72,26 @@ if (INTERNAL_HDF5)
   SET(HDF5_ROOTDIR ${HDF5_BIN_DIR})
   SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib")
   SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl")
-  MESSAGE("Internal HDF5 directory: $ENV{HDF5_ROOT}")
+  set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE)
+  set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl.a CACHE STRING "HDF5 HL lib" FORCE)
+  set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp.a CACHE STRING "HDF5 C++ lib" FORCE)
+  SET(HDF5_INCLUDE_DIR ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE)
+  mark_as_advanced(HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIR)
+
+  MESSAGE(STATUS "Internal HDF5 directory: $ENV{HDF5_ROOT}")
+  MESSAGE(STATUS "Libs: ${HDF5_LIBRARIES}")
+  SET(HDF5_FOUND TRUE)
 else (INTERNAL_HDF5)
+  mark_as_advanced(CLEAR HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIR)
   if(HDF5_ROOTDIR)
     SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})
   endif(HDF5_ROOTDIR)
+  find_package(HDF5 COMPONENTS C CXX HL)
 endif (INTERNAL_HDF5)
-find_package(HDF5 COMPONENTS C CXX HL)
-mark_as_advanced(HDF5_INCLUDE_DIR HDF5_LIBRARY HDF5_HL_LIBRARY)
 
-SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${HDF5_INCLUDE_DIR}")
+foreach(include_dir ${HDF5_INCLUDE_DIR})
+  SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${include_dir}")
+endforeach(include_dir)
 
 ###############
 # Build NetCDF
@@ -90,24 +101,25 @@ SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${HDF5_INCLUDE_DIR}")
 if (INTERNAL_NETCDF)
   SET(NETCDF_SOURCE_DIR ${BUILD_PREFIX}/netcdf-prefix/src/netcdf)
   SET(NETCDF_BIN_DIR ${EXT_INSTALL})
-  SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${NETCDF_BIN_DIR}/include")
+#  SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${NETCDF_BIN_DIR}/include")
   SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${NETCDF_BIN_DIR}/lib")
   SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LIBS=${CONFIGURE_LIBS} LDFLAGS=${CONFIGURE_LDFLAGS})
-  ExternalProject_Add(netcdf
+  SET(NETCDF_CONFIG_COMMAND ${NETCDF_SOURCE_DIR}/configure
-    DEPENDS ${hdf5_built}
-    PREFIX ${BUILD_PREFIX}/netcdf-prefix
-    URL ${NETCDF_URL}
-    CONFIGURE_COMMAND ${NETCDF_SOURCE_DIR}/configure
          --prefix=${NETCDF_BIN_DIR} --libdir=${NETCDF_BIN_DIR}/lib
          --enable-netcdf-4  --with-pic --disable-shared --disable-dap 
          --disable-cdmremote --disable-rpc --enable-cxx-4 
          --disable-examples ${EXTRA_NC_FLAGS} CC=${CMAKE_C_COMPILER}
-         CXX=${CMAKE_CXX_COMPILER}
+         CXX=${CMAKE_CXX_COMPILER})
+  ExternalProject_Add(netcdf
+    DEPENDS ${hdf5_built}
+    PREFIX ${BUILD_PREFIX}/netcdf-prefix
+    URL ${NETCDF_URL}
+    CONFIGURE_COMMAND  ${NETCDF_CONFIG_COMMAND}
     BUILD_IN_SOURCE 1
     INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
   )
-  SET(CONFIGURE_CPP_LDFLAGS "${CONFIGURE_LDFLAGS}")
+#  SET(CONFIGURE_CPP_LDFLAGS "${CONFIGURE_LDFLAGS}")
-  SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_CPP_LDFLAGS})
+#  SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_CPP_LDFLAGS})
   SET(cosmotool_DEPS ${cosmotool_DEPS} netcdf)
   SET(NETCDF_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf.a CACHE STRING "NetCDF lib" FORCE)
   SET(NETCDFCPP_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf_c++4.a CACHE STRING "NetCDF-C++ lib" FORCE)
@@ -120,8 +132,7 @@ ELSE(INTERNAL_NETCDF)
   find_library(NETCDF_LIBRARY netcdf)
   find_library(NETCDFCPP_LIBRARY NAMES netcdf_c++ netcdf_c++4)
 
-  SET(CONFIGURE_CPP_FLAGS ${CONFIGURE_CPP_FLAGS} 
+  SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${NETCDF_INCLUDE_PATH} -I${NETCDFCPP_INCLUDE_PATH}")          
-          -I${NETCDF_INCLUDE_PATH} -I${NETCDFCPP_INCLUDE_PATH})          
 endif (INTERNAL_NETCDF)
 mark_as_advanced(NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH NETCDFCPP_INCLUDE_PATH)
 
@@ -130,6 +141,7 @@ mark_as_advanced(NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH NETCDFCPP_
 ##################
 
 if (INTERNAL_BOOST)
+  message(STATUS "Building Boost")
   SET(BOOST_SOURCE_DIR ${BUILD_PREFIX}/boost-prefix/src/boost)
   ExternalProject_Add(boost
     URL ${BOOST_URL}

python/CMakeLists.txt

@@ -36,7 +36,8 @@ add_library(_cosmo_power MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp)
 add_library(_cosmo_cic MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp)
 add_library(_fast_interp MODULE ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp)
 add_library(_project MODULE ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp)
-add_library(_cosmo_bispectrum MODULE _cosmo_bispectrum.cpp)
+
+
 
 SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Bsymbolic-functions")
 
@@ -45,7 +46,17 @@ target_link_libraries(_cosmo_power ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_
 target_link_libraries(_cosmo_cic ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
 target_link_libraries(_project ${PYTHON_LIBRARIES})
 target_link_libraries(_fast_interp ${CosmoTool_local} ${PYTHON_LIBRARIES})
-target_link_libraries(_cosmo_bispectrum ${MATH_LIBRARY})
+
+SET(ct_TARGETS   _cosmotool _project _cosmo_power _cosmo_cic _fast_interp )
+
+if (Boost_FOUND)
+  message(STATUS "Building bispectrum support (path = ${Boost_INCLUDE_DIRS})")
+  include_directories(${Boost_INCLUDE_DIRS})
+  add_library(_cosmo_bispectrum MODULE _cosmo_bispectrum.cpp)
+  target_link_libraries(_cosmo_bispectrum ${MATH_LIBRARY})
+  add_dependencies(_cosmo_bispectrum boost)
+  SET(ct_TARGETS ${ct_TARGETS} _cosmo_bispectrum)
+endif()
 
 # Discover where to put packages
 if (NOT PYTHON_SITE_PACKAGES)
@@ -71,7 +82,8 @@ if (WIN32 AND NOT CYGWIN)
   SET_TARGET_PROPERTIES(_cosmotool PROPERTIES SUFFIX ".pyd")
 endif (WIN32 AND NOT CYGWIN)
 
-INSTALL(TARGETS _cosmotool _project _cosmo_power _cosmo_cic _fast_interp _cosmo_bispectrum
+INSTALL(TARGETS 
+  ${ct_TARGETS}
   LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool
 )
 

python_sample/test_bispectrum.py

@@ -1,19 +1,25 @@
+import timeit
 import numpy as np
 import cosmotool as ct
 
-N=32
+def myfun(N):
-f=0.10
+  f=0.10
-d=np.random.normal(size=(N,)*3)
+  d=np.random.normal(size=(N,)*3)
-rho = d + f *(d*d - np.average(d*d))
+  rho = d + f *(d*d - np.average(d*d))
   
-B = ct.bispectrum(rho, 1, N, fourier=False)
+  B = ct.bispectrum(rho, 1, N, fourier=False)
-P = ct.powerspectrum(rho, 1, N, fourier=False)
+  P = ct.powerspectrum(rho, 1, N, fourier=False)
-PP = P[1]/P[0]/N**3
+  PP = P[1]/P[0]/N**3
   
-x = PP[:,None,None] * PP[None,:,None] + PP[:,None,None]*PP[None,None,:] + PP[None,:,None]*PP[None,None,:]
+  x = PP[:,None,None] * PP[None,:,None] + PP[:,None,None]*PP[None,None,:] + PP[None,:,None]*PP[None,None,:]
   
-BB = B[1]/B[0]/N**6
+  BB = B[1]/B[0]/N**6
   
-y = BB/x
+  y = BB/x
+
+  np.savez("bispec_%d.npy" % N, y=y, B=B, P=P, rho=rho);
   
   
+print( timeit.timeit('from __main__ import myfun; myfun(16)', number=1) )
+print( timeit.timeit('from __main__ import myfun; myfun(32)', number=1) )
+print( timeit.timeit('from __main__ import myfun; myfun(64)', number=1) )

sample/CMakeLists.txt

@@ -43,9 +43,6 @@ if (HDF5_FOUND)
     add_executable(testHDF5 testHDF5.cpp)
     target_link_libraries(testHDF5 ${tolink})
 
-    add_executable(gadgetToArray gadgetToArray.cpp)
-    target_link_libraries(gadgetToArray ${tolink})
-
     add_executable(graficToDensity graficToDensity.cpp)
     target_link_libraries(graficToDensity ${tolink})
 endif (HDF5_FOUND)
@@ -94,6 +91,10 @@ if (Boost_FOUND)
     add_executable(simple3DFilter simple3DFilter.cpp)
     target_link_libraries(simple3DFilter ${tolink})
   ENDIF (YORICK_SUPPORT)
+  if (HDF5_FOUND)
+    add_executable(gadgetToArray gadgetToArray.cpp)
+    target_link_libraries(gadgetToArray ${tolink})
+  endif()
 endif (Boost_FOUND)
 
 IF (ENABLE_OPENMP AND YORICK_SUPPORT)

sample/gadgetToArray.cpp

@@ -33,6 +33,7 @@ The fact that you are presently reading this means that you have had
 knowledge of the CeCILL license and that you accept its terms.
 +*/
 #include <cmath>
+#include <algorithm>
 #include <iostream>
 #include <cstdlib>
 #include "cic.hpp"

sample/testHDF5.cpp

@@ -33,8 +33,8 @@ The fact that you are presently reading this means that you have had
 knowledge of the CeCILL license and that you accept its terms.
 +*/
 #include <iostream>
-#include <H5Cpp.h>
 #include "hdf5_array.hpp"
+#include <H5Cpp.h>
 
 using namespace std;
 

src/CMakeLists.txt

@@ -68,16 +68,19 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS}
 	growthFactor.hpp
 )
 
-include_directories(${Boost_INCLUDE_DIRS} ${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
+include_directories(${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
 
 set(CosmoTool_LIBS ${GSL_LIBRARIES})
 if(YORICK_SUPPORT)
   set(CosmoTool_LIBS ${CosmoTool_LIBS} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
   include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH})
 endif(YORICK_SUPPORT)
+
+message(STATUS "HDF5 ? ${HDF5_FOUND}")
 if (HDF5_FOUND)
-  set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_LIBRARIES} ${HDF5_C_LIBRARY} ${ZLIB})
+  set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES} ${ZLIB})
   include_directories(${HDF5_INCLUDE_DIRS})
+  message(STATUS "CosmoTool_LIBS: ${CosmoTool_LIBS}")
 endif (HDF5_FOUND)
 
 set(CosmoTool_LIBS ${CosmoTool_LIBS} PARENT_SCOPE)