Fixed HDF5 support in cmake. Fixed fortran.

2017-05-05 09:09:51 +02:00 · 2017-05-05 09:09:51 +02:00 · d720854361
commit d720854361
parent 537a68b668
8 changed files with 63 additions and 106 deletions
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@ -9,11 +9,13 @@ include(GetGitRevisionDescription)
 include(ExternalProject)
 include(FindPkgConfig)
 include(FindPackageHandleStandardArgs)
+include(color_msg)

 option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
 option(BUILD_STATIC_LIBS "Build static libraries." ON)
 option(ENABLE_SHARP "Enable SHARP support." ON)
 option(INTERNAL_HDF5 "Build internal version of HDF5" OFF)
+option(INTERNAL_EIGEN "Build internal version of Eigen" ON)
 option(INTERNAL_NETCDF "Build internal version of NETCDF" OFF)
 option(INTERNAL_BOOST "Build internal version of BOOST" OFF)
 option(USE_GIT_VERSION "Use GIT version to pad version number" OFF)
--- a/FindHDF5.cmake
+++ b/FindHDF5.cmake
@ -1,86 +0,0 @@
-#
-# To be used by projects that make use of Cmakeified hdf5-1.8.17
-#
-
-#
-# Find the HDF5 includes and get all installed hdf5 library settings from
-# HDF5-config.cmake file : Requires a CMake compatible hdf5-1.8.5 or later 
-# for this feature to work. The following vars are set if hdf5 is found.
-#
-# HDF5_FOUND               - True if found, otherwise all other vars are undefined
-# HDF5_INCLUDE_DIR         - The include dir for main *.h files
-# HDF5_FORTRAN_INCLUDE_DIR - The include dir for fortran modules and headers
-# HDF5_VERSION_STRING      - full version (e.g. 1.8.17)
-# HDF5_VERSION_MAJOR       - major part of version (e.g. 1.8)
-# HDF5_VERSION_MINOR       - minor part (e.g. 17)
-# 
-# The following boolean vars will be defined
-# HDF5_ENABLE_PARALLEL  - 1 if HDF5 parallel supported
-# HDF5_BUILD_FORTRAN    - 1 if HDF5 was compiled with fortran on
-# HDF5_BUILD_CPP_LIB    - 1 if HDF5 was compiled with cpp on
-# HDF5_BUILD_TOOLS      - 1 if HDF5 was compiled with tools on
-# HDF5_BUILD_HL_LIB     - 1 if HDF5 was compiled with high level on
-# HDF5_BUILD_HL_CPP_LIB - 1 if HDF5 was compiled with high level and cpp on
-# 
-# Target names that are valid (depending on enabled options)
-# will be the following
-#
-# hdf5              : HDF5 C library
-# hdf5_tools        : the tools library
-# hdf5_f90cstub     : used by Fortran to C interface
-# hdf5_fortran      : Fortran HDF5 library
-# hdf5_cpp          : HDF5 cpp interface library
-# hdf5_hl           : High Level library
-# hdf5_hl_f90cstub  : used by Fortran to C interface to High Level library
-# hdf5_hl_fortran   : Fortran High Level library
-# hdf5_hl_cpp       : High Level cpp interface library
-# 
-# To aid in finding HDF5 as part of a subproject set
-# HDF5_ROOT_DIR_HINT to the location where hdf5-config.cmake lies
-
-include (SelectLibraryConfigurations)
-include (FindPackageHandleStandardArgs)
-
-# The HINTS option should only be used for values computed from the system.
-set (_HDF5_HINTS
-    $ENV{HOME}/.local
-    $ENV{HDF5_ROOT}
-    $ENV{HDF5_ROOT_DIR_HINT}
-)
-# Hard-coded guesses should still go in PATHS. This ensures that the user
-# environment can always override hard guesses.
-set (_HDF5_PATHS
-    $ENV{HOME}/.local
-    $ENV{HDF5_ROOT}
-    $ENV{HDF5_ROOT_DIR_HINT}
-    /usr/lib/hdf5
-    /usr/share/hdf5
-    /usr/local/hdf5
-    /usr/local/hdf5/share
-)
-
-FIND_PATH (HDF5_ROOT_DIR "hdf5-config.cmake"
-    HINTS ${_HDF5_HINTS}
-    PATHS ${_HDF5_PATHS}
-    PATH_SUFFIXES
-        cmake/hdf5
-        lib/cmake/hdf5
-        share/cmake/hdf5
-)
-
-FIND_PATH (HDF5_INCLUDE_DIRS "H5public.h"
-    HINTS ${_HDF5_HINTS}
-    PATHS ${_HDF5_PATHS}
-    PATH_SUFFIXES
-        include
-        Include
-)
-
-# For backwards compatibility we set HDF5_INCLUDE_DIR to the value of
-# HDF5_INCLUDE_DIRS
-set ( HDF5_INCLUDE_DIR "${HDF5_INCLUDE_DIRS}" )
-
-if (HDF5_INCLUDE_DIR)
-  set (HDF5_FOUND "YES")
-  include (${HDF5_ROOT_DIR}/hdf5-config.cmake)
-endif (HDF5_INCLUDE_DIR)
--- a/external/external_build.cmake
+++ b/external/external_build.cmake
@ -3,7 +3,7 @@ include(FindOpenMP)
 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(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.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 "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")
@ -12,6 +12,25 @@ SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to dow
 mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL)


+MACRO(CHECK_CHANGE_STATE VAR) 
+  IF (DEFINED _PREVIOUS_${VAR})
+    IF (NOT ${_PREVIOUS_${VAR}} EQUAL ${${VAR}})
+      foreach(loopvar ${ARGN})
+         UNSET(${loopvar} CACHE)
+      endforeach()
+    ENDIF (NOT ${_PREVIOUS_${VAR}} EQUAL ${${VAR}})
+  ENDIF (DEFINED _PREVIOUS_${VAR})
+  SET(_PREVIOUS_${VAR} ${${VAR}} CACHE INTERNAL "Internal value")
+ENDMACRO(CHECK_CHANGE_STATE)
+
+CHECK_CHANGE_STATE(INTERNAL_BOOST Boost_LIBRARIES Boost_INCLUDE_DIRS)
+CHECK_CHANGE_STATE(INTERNAL_EIGEN EIGEN3_INCLUDE_DIRS)
+CHECK_CHANGE_STATE(INTERNAL_GSL GSL_LIBRARY GSL_CBLAS_LIBRARY GSL_INCLUDE)
+CHECK_CHANGE_STATE(INTERNAL_HDF5 
+    HDF5_INCLUDE_DIR HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_DIR 
+    HDF5_C_STATIC_LIBRARY HDF5_HL_STATIC_LIBRARY HDF5_CXX_STATIC_LIBRARY)
+CHECK_CHANGE_STATE(INTERNAL_DLIB DLIB_INCLUDE_DIR DLIB_LIBRARIES)
+

 IF(ENABLE_OPENMP)
  IF (NOT OPENMP_FOUND)
@ -75,24 +94,35 @@ if (INTERNAL_HDF5)
  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)
+  SET(HDF5_INCLUDE_DIRS ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE)
+  mark_as_advanced(HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIRS)

  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)
+  mark_as_advanced(CLEAR HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIRS)
  if(HDF5_ROOTDIR)
    SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})
  endif(HDF5_ROOTDIR)
-  find_package(HDF5 COMPONENTS C CXX HL static)
+  find_package(HDF5 COMPONENTS C CXX HL CONFIG QUIET)
+  if (NOT HDF5_FOUND)
+    cmessage(CWARNING "Could not find HDF5 cmake config. Try classical exploration")
+    find_package(HDF5 COMPONENTS C CXX HL)
+    cmessage(STATUS "HDF5 lib: ${HDF5_LIBRARIES}")
+    cmessage(STATUS "HDF5 includes: ${HDF5_INCLUDE_DIRS}")
+    get_filename_component(HDF5_BIN_DIR ${HDF5_C_LIBRARY_hdf5} DIRECTORY)
+    cmessage(STATUS "HDF5 libpath: ${HDF5_BIN_DIR}")
+  else()
    set(HDF5_LIBRARIES ${HDF5_C_STATIC_LIBRARY} CACHE STRING "HDF5 lib" FORCE)
    set(HDF5_HL_LIBRARIES ${HDF5_HL_STATIC_LIBRARY} CACHE STRING "HDF5 HL lib" FORCE)
    set(HDF5_CXX_LIBRARIES ${HDF5_CXX_STATIC_LIBRARY} CACHE STRING "HDF5 C++ lib" FORCE)
+    get_filename_component(HDF5_BIN_DIR ${HDF5_C_STATIC_LIBRARY} DIRECTORY)
+  endif()
+  SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}")
 endif (INTERNAL_HDF5)

-foreach(include_dir ${HDF5_INCLUDE_DIR})
+foreach(include_dir ${HDF5_INCLUDE_DIRS})
  SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${include_dir}")
 endforeach(include_dir)

@ -161,8 +191,11 @@ if (INTERNAL_BOOST)
  set(Boost_DEP boost)

 ELSE (INTERNAL_BOOST)
-  find_package(Boost 1.53)
+  find_package(Boost 1.53 QUIET)
  set(Boost_DEP)
+  if (NOT Boost_FOUND)
+    cmessage(CWARNING "Boost >= 1.53 was not found")
+  endif()
 endif (INTERNAL_BOOST)
 mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES)

@ -248,13 +281,17 @@ ENDIF(INTERNAL_FFTW)
 IF (INTERNAL_EIGEN)
  ExternalProject_Add(eigen
     URL ${EIGEN_URL}
+     URL_HASH SHA256=04f8a4fa4afedaae721c1a1c756afeea20d3cdef0ce3293982cf1c518f178502 
     PREFIX ${BUILD_PREFIX}/eigen-prefix
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
  )
-  SET(EIGEN_INCLUDE_PATH ${EXT_INSTALL}/include/eigen3)
+  SET(EIGEN3_INCLUDE_DIRS ${EXT_INSTALL}/include/eigen3)

 ELSE (INTERNAL_EIGEN)
-  pkg_check_modules(EIGEN3 eigen3)
+  pkg_check_modules(EIGEN3 QUIET eigen3 )
+  if (NOT  EIGEN3_FOUND)
+    cmessage(CWARNING "Eigen library not found")
+  endif()
 ENDIF(INTERNAL_EIGEN)


--- a/python/cosmotool/fftw.py
+++ b/python/cosmotool/fftw.py
@ -12,8 +12,8 @@ class CubeFT(object):
      self.max_cpu = multiprocessing.cpu_count() if max_cpu < 0 else max_cpu
      self._dhat = pyfftw.n_byte_align_empty((self.N,self.N,self.N/2+1), self.align, dtype='complex64')
      self._density = pyfftw.n_byte_align_empty((self.N,self.N,self.N), self.align, dtype='float32')
-      self._irfft = pyfftw.FFTW(self._dhat, self._density, axes=(0,1,2), direction='FFTW_BACKWARD', threads=self.max_cpu, normalize_idft=False)
-      self._rfft = pyfftw.FFTW(self._density, self._dhat, axes=(0,1,2), threads=self.max_cpu, normalize_idft=False)
+      self._irfft = pyfftw.FFTW(self._dhat, self._density, axes=(0,1,2), direction='FFTW_BACKWARD', threads=self.max_cpu)#, normalize_idft=False)
+      self._rfft = pyfftw.FFTW(self._density, self._dhat, axes=(0,1,2), threads=self.max_cpu) #, normalize_idft=False)

  def rfft(self):
      return ne.evaluate('c*a', out=self._dhat, local_dict={'c':self._rfft(normalise_idft=False),'a':(self.L/self.N)**3}, casting='unsafe')
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@ -76,7 +76,6 @@ if(YORICK_SUPPORT)
  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_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES} ${ZLIB})
  include_directories(${HDF5_INCLUDE_DIRS})
--- a/src/fortran.cpp
+++ b/src/fortran.cpp
@ -136,8 +136,9 @@ void UnformattedRead::endCheckpoint(bool autodrop)
 {
  if (checkPointRef != checkPointAccum)
    {
-      if (!autodrop || checkPointAccum > checkPointRef)
+      if (!autodrop || checkPointAccum > checkPointRef) {
 	throw InvalidUnformattedAccess();
+      }
      f->seekg(checkPointRef-checkPointAccum, ios::cur);
    }

@ -145,10 +146,11 @@ void UnformattedRead::endCheckpoint(bool autodrop)

  checkPointRef = (cSize == Check_32bits) ? 4 : 8;
  checkPointAccum = 0;
-  checkPointRef = (cSize == Check_32bits) ? readInt32() : readInt64();
+  checkPointRef = (cSize == Check_32bits) ? readUint32() : readInt64();
  
-  if (oldCheckPoint != checkPointRef)
+  if (oldCheckPoint != checkPointRef) {
    throw InvalidUnformattedAccess();
+  }

  checkPointAccum = checkPointRef = 0;
 }
--- a/src/fortran.hpp
+++ b/src/fortran.hpp
@ -46,6 +46,9 @@ namespace CosmoTool
 {
  class InvalidUnformattedAccess : public Exception
  {
+  public:
+    InvalidUnformattedAccess()
+       : Exception("Invalid unformatted fortran file format") {}
  };

  class FortranTypes
--- a/src/loadGadget.cpp
+++ b/src/loadGadget.cpp
@ -146,14 +146,14 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
  if (GadgetFormat == 2) {
    int64_t startBlock = 0;
    char block[5];
-    int32_t blocksize;
+    uint32_t blocksize;

    try {
      while (true) {
        f->beginCheckpoint();
        f->readOrderedBuffer(block, 4);
        block[4] = 0;
-        blocksize = f->readInt32();
+        blocksize = f->readUint32();
        f->endCheckpoint();
        blockTable[block].position = f->position();
        blockTable[block].size = blocksize;