Merge branch 'master' of bitbucket.org:glavaux/cosmotool

2017-08-17 10:07:29 +02:00 · 2017-08-17 10:07:29 +02:00 · c2059ea118
commit c2059ea118
parent af50c49dbf e80cf11f92
16 changed files with 162 additions and 138 deletions
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@ -1,6 +1,5 @@
 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)
@ -54,7 +53,7 @@ IF(YORICK_SUPPORT)
  ENDIF((EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") OR (INTERNAL_NETCDF))
 ENDIF(YORICK_SUPPORT)

-find_program(CYTHON cython)
+find_program(CYTHON cython3 cython)
 find_library(ZLIB z)
 find_library(DL_LIBRARY dl)
 find_library(MATH_LIBRARY m)
--- a/FindPyLibs.cmake
+++ b/FindPyLibs.cmake
@ -1,10 +1,12 @@
 execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
-    "import distutils.sysconfig as cs;  import os; v=cs.get_config_vars(); print(os.path.join(v['LIBDIR'],v['LDLIBRARY']));"
+	"import distutils.sysconfig as cs; import os; import sys; v=cs.get_config_vars(); print(os.path.join(v['LIBDIR'],v['LDLIBRARY'])); sys.exit(0)"
    RESULT_VARIABLE _PYLIB_SEARCH_SUCCESS
    OUTPUT_VARIABLE _PYLIB_VALUES_OUTPUT
    ERROR_VARIABLE _PYLIB_ERROR_VALUE
    OUTPUT_STRIP_TRAILING_WHITESPACE)

+message(${_PYLIB_SEARCH_SUCCESS})
+
 execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
    "import distutils.sysconfig as cs;  import os; v=cs.get_config_vars(); print(v['INCLUDEPY']);"
    RESULT_VARIABLE _PYINC_SEARCH_SUCCESS
--- a/external/external_build.cmake
+++ b/external/external_build.cmake
@ -5,8 +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/3.2.10.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")
+SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.gz" CACHE STRING "URL to download HDF5 from")
+SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.4.1.1.tar.gz" CACHE STRING "URL to download NetCDF from")
+SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.0.tar.gz" CACHE STRING "URL to download NetCDF-C++ 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)
@ -77,13 +78,14 @@ if (INTERNAL_HDF5)
  ExternalProject_Add(hdf5
    PREFIX ${BUILD_PREFIX}/hdf5-prefix
    URL ${HDF5_URL}
-    CONFIGURE_COMMAND ${HDF5_SOURCE_DIR}/configure
-           --disable-shared --enable-cxx --with-pic
-	   --prefix=${HDF5_BIN_DIR} --libdir=${HDF5_BIN_DIR}/lib 
-	   CPPFLAGS=${CONFIGURE_CPP_FLAGS} CC=${CMAKE_C_COMPILER} 
-	   CXX=${CMAKE_CXX_COMPILER}
-    BUILD_IN_SOURCE 1
-    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+    CMAKE_ARGS
+       -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
+       -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+       -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+       -DHDF5_BUILD_CPP_LIB=ON
+       -DHDF5_BUILD_TOOLS=ON
+       -DHDF5_BUILD_HL_LIB=ON
+       -DBUILD_SHARED_LIBS=OFF
  )
  SET(cosmotool_DEPS ${cosmotool_DEPS} hdf5)
  SET(hdf5_built hdf5)
@ -112,7 +114,12 @@ else (INTERNAL_HDF5)
    cmessage(STATUS "HDF5 lib: ${HDF5_LIBRARIES}")
    cmessage(STATUS "HDF5 includes: ${HDF5_INCLUDE_DIRS}")
    cmessage(STATUS "HDF5 C lib: ${HDF5_C_LIBRARY}")
-    get_filename_component(HDF5_BIN_DIR ${HDF5_C_LIBRARY} DIRECTORY)
+    cmessage(STATUS "HDF5 BIN: ${HDF5_BIN_DIR}")
+    foreach(hdf5lib IN LISTS HDF5_LIBRARIES)
+      if (${hdf5lib} MATCHES "(hdf5)|(HDF5)")
+        get_filename_component(HDF5_BIN_DIR ${hdf5lib} DIRECTORY)
+      endif()
+    endforeach()
    cmessage(STATUS "HDF5 libpath: ${HDF5_BIN_DIR}")
  else()
    cmessage(STATUS "Found HDF5 cmake config.")
@ -137,7 +144,7 @@ endforeach(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})
  SET(NETCDF_CONFIG_COMMAND ${NETCDF_SOURCE_DIR}/configure
@ -150,15 +157,36 @@ if (INTERNAL_NETCDF)
    DEPENDS ${hdf5_built}
    PREFIX ${BUILD_PREFIX}/netcdf-prefix
    URL ${NETCDF_URL}
-    CONFIGURE_COMMAND  ${NETCDF_CONFIG_COMMAND}
-    BUILD_IN_SOURCE 1
-    INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
+	CMAKE_ARGS
+		-DCMAKE_PREFIX_PATH=${EXT_INSTALL}
+		-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+		-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+		-DBUILD_SHARED_LIBS=OFF
+		-DBUILD_TESTING=OFF
+		-DCMAKE_BUILD_TYPE=Release
+		-DENABLE_NETCDF4=ON
+                -DENABLE_DAP=OFF
+		-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
+  )
+  
+  SET(NETCDFCXX_SOURCE_DIR ${BUILD_PREFIX}/netcdf-c++-prefix/src/netcdf-c++)
+  ExternalProject_Add(netcdf-c++
+    DEPENDS ${hdf5_built} netcdf
+    PREFIX ${BUILD_PREFIX}/netcdf-c++-prefix
+    URL ${NETCDFCXX_URL}
+	CMAKE_ARGS
+		-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+		-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+		-DBUILD_SHARED_LIBS=OFF
+		-DBUILD_TESTING=OFF
+		-DCMAKE_BUILD_TYPE=Release
+		-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
  )
 #  SET(CONFIGURE_CPP_LDFLAGS "${CONFIGURE_LDFLAGS}")
 #  SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_CPP_LDFLAGS})
-  SET(cosmotool_DEPS ${cosmotool_DEPS} netcdf)
+  SET(cosmotool_DEPS ${cosmotool_DEPS} netcdf netcdf-c++)
  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)
+  SET(NETCDFCPP_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf-cxx4.a CACHE STRING "NetCDF-C++ lib" FORCE)
  SET(NETCDF_INCLUDE_PATH ${NETCDF_BIN_DIR}/include CACHE STRING "NetCDF include" FORCE)
  SET(NETCDFCPP_INCLUDE_PATH ${NETCDF_INCLUDE_PATH} CACHE STRING "NetCDF C++ include path" FORCE)

--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@ -1,5 +1,6 @@
 set(CMAKE_SHARED_MODULE_PREFIX)

+
 include_directories(${NUMPY_INCLUDE_DIRS} ${PYTHON_INCLUDE_PATH} ${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src ${CMAKE_SOURCE_DIR}/python)

 IF(CYTHON)
@ -39,7 +40,10 @@ add_library(_project MODULE ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp)



-SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Bsymbolic-functions")
+SET(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -Bsymbolic-functions")
+if(APPLE)
+  set(CMAKE_MODULE_LINKER_FLAGS "-undefined dynamic_lookup")
+endif()

 target_link_libraries(_cosmotool ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
 target_link_libraries(_cosmo_power ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
@ -74,6 +78,9 @@ if (NOT PYTHON_SITE_PACKAGES)
  mark_as_advanced(USER_PYTHON_SITE_PACKAGES SYSTEM_PYTHON_SITE_PACKAGES)
 endif (NOT PYTHON_SITE_PACKAGES)

+message(STATUS "System python site: ${SYSTEM_PYTHON_SITE_PACKAGES}")
+message(STATUS "User python site: ${USER_PYTHON_SITE_PACKAGES}")
+
 OPTION(INSTALL_PYTHON_LOCAL OFF)

 IF (NOT INSTALL_PYTHON_LOCAL)
@ -81,6 +88,7 @@ IF (NOT INSTALL_PYTHON_LOCAL)
 ELSE (NOT INSTALL_PYTHON_LOCAL)
  SET(PYTHON_SITE_PACKAGES ${USER_PYTHON_SITE_PACKAGES})
 ENDIF(NOT INSTALL_PYTHON_LOCAL)
+cmessage(STATUS "Python install location: ${PYTHON_SITE_PACKAGES}")


 if (WIN32 AND NOT CYGWIN)
--- a/python/_cosmo_bispectrum.cpp
+++ b/python/_cosmo_bispectrum.cpp
@ -1,4 +1,6 @@
+#ifdef _OPENMP
 #include <omp.h>
+#endif
 #include <iostream>
 #include <boost/format.hpp>
 #include <boost/multi_array.hpp>
@ -171,7 +173,11 @@ void CosmoTool_compute_bispectrum(
 {
    // First remap to multi_array for easy access
    size_t kNz = Nz/2+1;
+#ifdef _OPENMP
    int Ntasks = omp_get_max_threads();
+#else
+    int Ntasks = 1;
+#endif
    boost::multi_array_ref<std::complex<double>, 3> a_delta(reinterpret_cast<std::complex<double>*>(delta_hat), boost::extents[Nx][Ny][kNz]); 
    boost::multi_array_ref<size_t, 3> a_Nt(Ntriangles, boost::extents[Nk][Nk][Nk]); 
    boost::multi_array_ref<std::complex<double>, 3> a_B(reinterpret_cast<std::complex<double>*>(B), boost::extents[Nk][Nk][Nk]); 
@ -190,6 +196,7 @@ void CosmoTool_compute_bispectrum(
      delta_mirror[n1.i1][n1.i2][n1.i3] = std::conj(delta_mirror[n2.i1][n2.i2][n2.i3]);
    }

+#ifdef _OPENMP
    // First loop over m1
 #pragma omp parallel
    {
@ -236,6 +243,9 @@ void CosmoTool_compute_bispectrum(
      a_B_p[q] += b_B_p[q];
    }
  }
+#else
+#warning Serial version not implemented
+#endif
 }


--- a/python/_cosmotool.pyx
+++ b/python/_cosmotool.pyx
@ -9,6 +9,9 @@ cimport cython

 np.import_array()

+cdef extern from "sys/types.h":
+   ctypedef np.int64_t int64_t
+
 cdef extern from "loadSimu.hpp" namespace "CosmoTool":

  cdef cppclass SimuData:
@ -20,7 +23,7 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool":
    np.float_t Omega_Lambda
    np.int64_t TotalNumPart
    np.int64_t NumPart
-    np.int64_t *Id
+    int64_t *Id
    float *Pos[3]
    float *Vel[3]
    int *type
@ -323,7 +326,7 @@ cdef object wrap_array(void *p, np.uint64_t s, int typ):
 cdef object wrap_float_array(float *p, np.uint64_t s):
    return wrap_array(<void *>p, s, np.NPY_FLOAT32)

-cdef object wrap_int64_array(np.int64_t* p, np.uint64_t s):
+cdef object wrap_int64_array(int64_t* p, np.uint64_t s):
    return wrap_array(<void *>p, s, np.NPY_INT64)

 cdef object wrap_int_array(int* p, np.uint64_t s):
@ -388,6 +391,7 @@ def loadGadget(str filename, int snapshot_id, int gadgetFormat = 1, bool loadPos
    cdef int flags
    cdef SimuData *data
    cdef Simulation simu
+    cdef const char *filename_bs

    flags = 0
    if loadPosition:
@ -401,7 +405,10 @@ def loadGadget(str filename, int snapshot_id, int gadgetFormat = 1, bool loadPos
    if loadMass:
        flags |= NEED_MASS

-    data = loadGadgetMulti(filename, snapshot_id, flags, gadgetFormat)
+    filename_b = bytes(filename, 'utf-8')
+    filename_bs = filename_b
+    with nogil:
+      data = loadGadgetMulti(filename_bs, snapshot_id, flags, gadgetFormat)
    if data == <SimuData*>0:
        return None

@ -497,7 +504,7 @@ def writeGadget(str filename, object simulation):
    simdata.Vel[j] = <float *>vel.data
  
  ids = simulation.getIdentifiers()
-  simdata.Id = <np.int64_t *>ids.data
+  simdata.Id = <int64_t *>ids.data
  simdata.BoxSize = simulation.getBoxsize()
  simdata.time = simulation.getTime()
  simdata.Hubble = simulation.getHubble()
--- a/python/_project.pyx
+++ b/python/_project.pyx
@ -389,7 +389,8 @@ cdef void INTERNAL_project_cic_no_mass(npx.ndarray[DTYPE_t, ndim=3] g,
                                       npx.ndarray[DTYPE_t, ndim=2] x, int Ngrid, double Lbox, double shifter):
    cdef double delta_Box = Ngrid/Lbox
    cdef int i
-    cdef double a[3], c[3]
+    cdef double a[3]
+    cdef double c[3]
    cdef int b[3]
    cdef int do_not_put

@ -404,9 +405,6 @@ cdef void INTERNAL_project_cic_no_mass(npx.ndarray[DTYPE_t, ndim=3] g,
            if b[j] < 0 or b[j]+1 >= Ngrid:
              do_not_put = True

-        print("b = %g %g %g" % (b[0], b[1], b[2]))
-        print("a = %g %g %g" % (a[0], a[1], a[2]))
-
        if not do_not_put:
            g[b[0],b[1],b[2]] += c[0]*c[1]*c[2]
            g[b[0]+1,b[1],b[2]] += a[0]*c[1]*c[2]
@ -424,8 +422,10 @@ cdef void INTERNAL_project_cic_no_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g,
                                                npx.ndarray[DTYPE_t, ndim=2] x, int Ngrid, double Lbox, double shifter):
    cdef double delta_Box = Ngrid/Lbox
    cdef int i
-    cdef double a[3], c[3]
-    cdef int b[3], b1[3]
+    cdef double a[3]
+    cdef double c[3]
+    cdef int b[3]
+    cdef int b1[3]
    cdef int do_not_put
    cdef DTYPE_t[:,:] ax
    cdef DTYPE_t[:,:,:] ag
@ -465,7 +465,8 @@ cdef void INTERNAL_project_cic_with_mass(npx.ndarray[DTYPE_t, ndim=3] g,
                                         int Ngrid, double Lbox, double shifter):
    cdef double delta_Box = Ngrid/Lbox
    cdef int i
-    cdef double a[3], c[3]
+    cdef double a[3]
+    cdef double c[3]
    cdef DTYPE_t m0
    cdef int b[3]

@ -502,8 +503,10 @@ cdef void INTERNAL_project_cic_with_mass_periodic(npx.ndarray[DTYPE_t, ndim=3] g
    cdef double half_Box = 0.5*Lbox, m0
    cdef double delta_Box = Ngrid/Lbox
    cdef int i
-    cdef double a[3], c[3]
-    cdef int b[3], b1[3]
+    cdef double a[3]
+    cdef double c[3]
+    cdef int b[3]
+    cdef int b1[3]

    for i in range(x.shape[0]):

@ -550,18 +553,18 @@ def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, nd
    if x.shape[1] != 3:
        raise ValueError("Invalid shape for x array")

-    if mass != None and mass.shape[0] != x.shape[0]:
+    if mass is not None and mass.shape[0] != x.shape[0]:
        raise ValueError("Mass array and coordinate array must have the same number of elements")

    g = np.zeros((Ngrid,Ngrid,Ngrid),dtype=DTYPE)

    if not periodic:
-      if mass == None:
+      if mass is None:
        INTERNAL_project_cic_no_mass(g, x, Ngrid, Lbox, shifter)
      else:
        INTERNAL_project_cic_with_mass(g, x, mass, Ngrid, Lbox, shifter)       
    else:
-      if mass == None:
+      if mass is None:
        INTERNAL_project_cic_no_mass_periodic(g, x, Ngrid, Lbox, shifter)
      else:
        INTERNAL_project_cic_with_mass_periodic(g, x, mass, Ngrid, Lbox, shifter)       
@ -629,7 +632,8 @@ cdef DTYPE_t cube_integral(DTYPE_t u[3], DTYPE_t u0[3], int r[1], DTYPE_t alpha_
@cython.cdivision(True)
 cdef DTYPE_t cube_integral_trilin(DTYPE_t u[3], DTYPE_t u0[3], int r[1], DTYPE_t vertex_value[8], DTYPE_t alpha_max) nogil:
    cdef DTYPE_t I, tmp_a
-    cdef DTYPE_t v[3], term[4]
+    cdef DTYPE_t v[3]
+    cdef DTYPE_t term[4]
    cdef int i, j, q

    j = 0
@ -671,7 +675,8 @@ cdef DTYPE_t integrator1(DTYPE_t[:,:,:] density,
                         DTYPE_t u[3], DTYPE_t u0[3], int u_delta[3], int iu0[3], int jumper[1], DTYPE_t alpha_max) nogil:
    cdef DTYPE_t vertex_value[8]
    cdef DTYPE_t d
-    cdef int a[3][2], i
+    cdef int a[3][2]
+    cdef int i
    
    for i in xrange(3):
      a[i][0] = iu0[i]
@ -697,7 +702,10 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
                             DTYPE_t min_distance,
                             DTYPE_t max_distance, DTYPE_t[:] shifter, int integrator_id) nogil except? 0:

-    cdef DTYPE_t u[3], ifu0[3], u0[3], utot[3]
+    cdef DTYPE_t u[3] 
+    cdef DTYPE_t ifu0[3]
+    cdef DTYPE_t u0[3]
+    cdef DTYPE_t utot[3]
    cdef int u_delta[3]
    cdef int iu0[3]
    cdef int i
--- a/python/cosmotool/fftw.py
+++ b/python/cosmotool/fftw.py
@ -4,14 +4,23 @@ import numpy as np
 import numexpr as ne

 class CubeFT(object):
-  def __init__(self, L, N, max_cpu=-1):
+  def __init__(self, L, N, max_cpu=-1, width=32):
+  
+      if width==32:
+        fourier_type='complex64'
+        real_type='float32'
+      elif width==64:
+        fourier_type='complex128'
+        real_type='float64'
+      else:
+        raise ValueError("Invalid bitwidth (must be 32 or 64)")

      self.N = N
      self.align = pyfftw.simd_alignment
      self.L = float(L)
      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._dhat = pyfftw.n_byte_align_empty((self.N,self.N,self.N//2+1), self.align, dtype=fourier_type)
+      self._density = pyfftw.n_byte_align_empty((self.N,self.N,self.N), self.align, dtype=real_type)
      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)

--- a/python/cosmotool/simu.py
+++ b/python/cosmotool/simu.py
@ -14,6 +14,7 @@ class SimulationBare(PySimulationBase):
    self.positions = [q.copy() for q in s.getPositions()] if s.getPositions() is not None else None
    self.velocities = [q.copy() for q in s.getVelocities()] if s.getVelocities() is not None else None
    self.identifiers = s.getIdentifiers().copy() if s.getIdentifiers() is not None else None
+    self.types = s.getTypes().copy() if s.getTypes() is not None else None
    self.boxsize = s.getBoxsize()
    self.time = s.getTime()
    self.Hubble = s.getHubble()
@ -53,12 +54,16 @@ class SimulationBare(PySimulationBase):
    self.positions = _safe_merge(self.positions, other.getPositions())
    self.velocities = _safe_merge(self.velocities, other.getVelocities())
    self.identifiers = _safe_merge0(self.identifiers, other.getIdentifiers())
+    self.types = _safe_merge0(self.types, other.getTypes())
    try:
      self.masses = _safe_merge0(self.masses, other.getMasses())
    except Exception as e:
      warnings.warn("Unexpected exception: " + repr(e));
      self.masses = None

+  def getTypes(self):
+    return self.types
+    
  def getPositions(self):
    return self.positions
    
--- a/sample/simple3DFilter.cpp
+++ b/sample/simple3DFilter.cpp
@ -62,7 +62,7 @@ void computeInterpolatedField(MyTree *tree1, double boxsize, int Nres, double cx
              {
                double px = (rx)*boxsize/Nres-cx;
                
-                MyTree::coords c = { px, py, pz };
+                MyTree::coords c = { float(px), float(py), float(pz) };

                double r2 = c[0]*c[0]+c[1]*c[1]+c[2]*c[2];
                if (r2 > rLimit2)
@ -179,7 +179,7 @@ int main(int argc, char **argv)
              {
                double px = (rx)*boxsize/Nres-cx;
                
-                MyTree::coords c = { px, py, pz };
+                MyTree::coords c = { float(px), float(py), float(pz) };

                double r2 = c[0]*c[0]+c[1]*c[1]+c[2]*c[2];
                if (r2 > rLimit2)
--- a/sample/testSmooth.cpp
+++ b/sample/testSmooth.cpp
@ -75,7 +75,7 @@ int main()
      cout << "iy=" << iy << endl;
      for (uint32_t ix = 0; ix < NX; ix++)
        {
-           MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX };
+           MyTree::coords c = { 1.0f*ix/NX, 1.0f*iy/NX };
           smooth.fetchNeighbours(c);
           smooth.addGridSite(c);
        }
@ -92,7 +92,7 @@ int main()
      cout << "iy=" << iy << endl;
      for (uint32_t ix = 0; ix < NX; ix++)
        {
-           MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX };
+           MyTree::coords c = { 1.0f*ix/NX, 1.0f*iy/NX };
           smooth.fetchNeighbours(c, &state);
           out.put(smooth.computeSmoothedValue(c, unit_fun, &state));

--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@ -78,7 +78,7 @@ endif(YORICK_SUPPORT)

 if (HDF5_FOUND)
  set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES} ${ZLIB})
-  include_directories(${HDF5_INCLUDE_DIRS})
+  include_directories(${HDF5_INCLUDE_DIR})
  message(STATUS "CosmoTool_LIBS: ${CosmoTool_LIBS}")
 endif (HDF5_FOUND)

--- a/src/fortran.cpp
+++ b/src/fortran.cpp
@ -43,7 +43,6 @@ using namespace std;
 using namespace CosmoTool;

 UnformattedRead::UnformattedRead(const string& fname)
-  throw(NoSuchFileException)
 {
  f = new ifstream(fname.c_str());
  if (!*f)
@ -55,7 +54,6 @@ UnformattedRead::UnformattedRead(const string& fname)
 }

 UnformattedRead::UnformattedRead(const char *fname)
-  throw(NoSuchFileException)
 {
  f = new ifstream(fname);
  if (!*f)
@ -100,7 +98,6 @@ void UnformattedRead::setCheckpointSize(CheckpointSize cs)
 }
    
 void UnformattedRead::skip(int64_t off)
-  throw (InvalidUnformattedAccess)
 {
  if (checkPointAccum == 0 && checkPointRef == 0)
    {
@ -119,7 +116,6 @@ void UnformattedRead::skip(int64_t off)
 }

 void UnformattedRead::beginCheckpoint(bool bufferRecord)
-  throw (InvalidUnformattedAccess,EndOfFileException)
 {
  if (checkPointAccum != 0)
    throw InvalidUnformattedAccess();
@ -140,7 +136,6 @@ void UnformattedRead::beginCheckpoint(bool bufferRecord)
 }

 void UnformattedRead::endCheckpoint(bool autodrop)
-  throw (InvalidUnformattedAccess)
 {
  if (recordBuffer != 0) {
    delete[] recordBuffer;
@ -169,7 +164,6 @@ void UnformattedRead::endCheckpoint(bool autodrop)
 }

 void UnformattedRead::readOrderedBuffer(void *buffer, int size)
-      throw (InvalidUnformattedAccess)
 {
  if ((checkPointAccum+(uint64_t)size) > checkPointRef)
       throw InvalidUnformattedAccess();
@ -190,7 +184,6 @@ void UnformattedRead::readOrderedBuffer(void *buffer, int size)
 }
  
 double UnformattedRead::readReal64()
-  throw (InvalidUnformattedAccess)
 {
  union
  {
@ -204,7 +197,6 @@ double UnformattedRead::readReal64()
 }

 float UnformattedRead::readReal32()
-  throw (InvalidUnformattedAccess)
 {
  union
  {
@ -218,7 +210,6 @@ float UnformattedRead::readReal32()
 }

 uint32_t UnformattedRead::readUint32()
-  throw (InvalidUnformattedAccess)
 {
  union
  {
@ -232,7 +223,6 @@ uint32_t UnformattedRead::readUint32()
 }

 int32_t UnformattedRead::readInt32()
-  throw (InvalidUnformattedAccess)
 {
  union
  {
@ -246,7 +236,6 @@ int32_t UnformattedRead::readInt32()
 }

 int64_t UnformattedRead::readInt64()
-  throw (InvalidUnformattedAccess)
 {
  union
  {
@ -262,7 +251,6 @@ int64_t UnformattedRead::readInt64()
 //// UnformattedWrite

 UnformattedWrite::UnformattedWrite(const string& fname)
-  throw(NoSuchFileException)
 {
  f = new ofstream(fname.c_str());
  if (!*f)
@ -274,7 +262,6 @@ UnformattedWrite::UnformattedWrite(const string& fname)
 }

 UnformattedWrite::UnformattedWrite(const char *fname)
-  throw(NoSuchFileException)
 {
  f = new ofstream(fname);
  if (!*f)
@ -304,7 +291,6 @@ void UnformattedWrite::setCheckpointSize(CheckpointSize cs)
 }
    
 void UnformattedWrite::beginCheckpoint()
-  throw (InvalidUnformattedAccess,FilesystemFullException)
 {
  if (checkPointAccum != 0)
    throw InvalidUnformattedAccess();
@ -322,7 +308,6 @@ void UnformattedWrite::beginCheckpoint()
 }

 void UnformattedWrite::endCheckpoint()
-  throw (InvalidUnformattedAccess,FilesystemFullException)
 {
  if (checkPointAccum == 0)
    throw InvalidUnformattedAccess();
@ -354,7 +339,6 @@ void UnformattedWrite::endCheckpoint()
 }

 void UnformattedWrite::writeOrderedBuffer(void *buffer, int size)
-  throw (FilesystemFullException)
 {
  f->write((char *)buffer, size);
  
@ -371,7 +355,6 @@ void UnformattedWrite::writeOrderedBuffer(void *buffer, int size)
 }
  
 void UnformattedWrite::writeReal64(double d)
-  throw (FilesystemFullException)
 {
  union
  {
@ -385,7 +368,6 @@ void UnformattedWrite::writeReal64(double d)
 }

 void UnformattedWrite::writeReal32(float f)
-  throw (FilesystemFullException)
 {
  union
  {
@ -399,7 +381,6 @@ void UnformattedWrite::writeReal32(float f)
 }

 void UnformattedWrite::writeInt32(int32_t i)
-  throw (FilesystemFullException)
 {
  union
  {
@ -412,7 +393,6 @@ void UnformattedWrite::writeInt32(int32_t i)
 }

 void UnformattedWrite::writeInt64(int64_t i)
-  throw (FilesystemFullException)
 {
  union
  {
@ -425,7 +405,6 @@ void UnformattedWrite::writeInt64(int64_t i)
 }

 void UnformattedWrite::writeInt8(int8_t i)
-  throw (FilesystemFullException)
 {
  union { char b; int8_t i; } a;

--- a/src/fortran.hpp
+++ b/src/fortran.hpp
@ -67,10 +67,8 @@ namespace CosmoTool
  {
  public:

-    UnformattedRead(const std::string& fname)
-      throw (NoSuchFileException);
-    UnformattedRead(const char *fname)
-      throw (NoSuchFileException);
+    UnformattedRead(const std::string& fname);
+    UnformattedRead(const char *fname);
    ~UnformattedRead();

    // Todo implement primitive description
@ -79,30 +77,21 @@ namespace CosmoTool

    uint64_t getBlockSize() const { return checkPointRef; }
    
-    void beginCheckpoint(bool bufferRecord = false)
-      throw (InvalidUnformattedAccess,EndOfFileException);
-    void endCheckpoint(bool autodrop = false)
-      throw (InvalidUnformattedAccess);
+    void beginCheckpoint(bool bufferRecord = false);
+    void endCheckpoint(bool autodrop = false);
    
-    double readReal64()
-      throw (InvalidUnformattedAccess);
-    float readReal32()
-      throw (InvalidUnformattedAccess);
-    uint32_t readUint32()
-      throw (InvalidUnformattedAccess);
-    int32_t readInt32()
-      throw (InvalidUnformattedAccess);
-    int64_t readInt64()
-      throw (InvalidUnformattedAccess);
+    double readReal64();
+    float readReal32();
+    uint32_t readUint32();
+    int32_t readInt32();
+    int64_t readInt64();

-    void skip(int64_t off)
-      throw (InvalidUnformattedAccess);
+    void skip(int64_t off);

    int64_t position() const;
    void seek(int64_t pos);

-    void readOrderedBuffer(void *buffer, int size)
-      throw (InvalidUnformattedAccess);
+    void readOrderedBuffer(void *buffer, int size);
  protected:
    bool swapOrdering;
    CheckpointSize cSize;
@ -117,34 +106,24 @@ namespace CosmoTool
  {
  public:

-    UnformattedWrite(const std::string& fname)
-      throw (NoSuchFileException);
-    UnformattedWrite(const char *fname)
-      throw (NoSuchFileException);
+    UnformattedWrite(const std::string& fname);
+    UnformattedWrite(const char *fname);
    ~UnformattedWrite();

    // Todo implement primitive description
    void setOrdering(Ordering o);
    void setCheckpointSize(CheckpointSize cs);
    
-    void beginCheckpoint()
-      throw (FilesystemFullException,InvalidUnformattedAccess);
-    void endCheckpoint()
-      throw (FilesystemFullException,InvalidUnformattedAccess);
+    void beginCheckpoint();
+    void endCheckpoint();
    
-    void writeReal64(double d)
-      throw (FilesystemFullException);
-    void writeReal32(float f)
-      throw (FilesystemFullException);
-    void writeInt32(int32_t i)
-      throw (FilesystemFullException);
-    void writeInt64(int64_t i)
-      throw (FilesystemFullException);
-    void writeInt8(int8_t c)
-      throw (FilesystemFullException);
+    void writeReal64(double d);
+    void writeReal32(float f);
+    void writeInt32(int32_t i);
+    void writeInt64(int64_t i);
+    void writeInt8(int8_t c);

-    void writeOrderedBuffer(void *buffer, int size)
-      throw(FilesystemFullException);
+    void writeOrderedBuffer(void *buffer, int size);
  protected:
    bool swapOrdering;
    CheckpointSize cSize;
--- a/src/interpolate.cpp
+++ b/src/interpolate.cpp
@ -66,7 +66,6 @@ Interpolate::~Interpolate()
 }

 double Interpolate::compute(double x)
-  throw (InvalidRangeException)
 {
  double y;
  
@ -85,7 +84,6 @@ double Interpolate::compute(double x)
 }

 double Interpolate::compute(double x) const
-  throw (InvalidRangeException)
 {
  double y;

@ -107,7 +105,6 @@ double Interpolate::compute(double x) const


 double Interpolate::derivative(double x)
-  throw (InvalidRangeException)
 {
  double y, dy, x0 = x;
  
@ -199,7 +196,6 @@ Interpolate CosmoTool::buildFromVector(const InterpolatePairs& v)
 }

 Interpolate CosmoTool::buildInterpolateFromFile(const char *fname)
-  throw (NoSuchFileException)
 {
  vector<MyPair> allData;
  ifstream f(fname);
@ -239,7 +235,6 @@ Interpolate CosmoTool::buildInterpolateFromFile(const char *fname)

 Interpolate CosmoTool::buildInterpolateFromColumns(const char *fname, uint32_t col1, uint32_t col2, bool logx,
 						   bool logy)
-  throw (NoSuchFileException,InvalidRangeException)
 {
  vector<MyPair> allData;
  ifstream f(fname);
--- a/src/interpolate.hpp
+++ b/src/interpolate.hpp
@ -54,12 +54,9 @@ namespace CosmoTool
 		bool logx = false, bool logy = false);
    ~Interpolate();

-    double compute(double x)
-      throw (InvalidRangeException);
-    double compute(double x) const
-      throw (InvalidRangeException);
-    double derivative(double x)
-      throw (InvalidRangeException);
+    double compute(double x);
+    double compute(double x) const;
+    double derivative(double x);

    const Interpolate& operator=(const Interpolate& a);

@ -77,10 +74,8 @@ namespace CosmoTool

  typedef std::vector< std::pair<double,double> > InterpolatePairs;

-  Interpolate buildInterpolateFromFile(const char *fname)
-    throw (NoSuchFileException);
-  Interpolate buildInterpolateFromColumns(const char *fname, uint32_t col1, uint32_t col2, bool logx = false, bool logy = false)
-    throw (NoSuchFileException,InvalidRangeException);
+  Interpolate buildInterpolateFromFile(const char *fname);
+  Interpolate buildInterpolateFromColumns(const char *fname, uint32_t col1, uint32_t col2, bool logx = false, bool logy = false);
  Interpolate buildFromVector(const InterpolatePairs& v);