Generic fix and path update

external/external_build.cmake

@@ -5,7 +5,7 @@ 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(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 "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/1.61.0/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 ")

python/CMakeLists.txt

@@ -74,6 +74,9 @@ 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 +84,7 @@ 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)

python/_cosmotool.pyx

@@ -388,6 +388,7 @@ 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 +402,10 @@ 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
 

python/_project.pyx

@@ -404,9 +404,6 @@ 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]

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._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='float32')
+      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)
 

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()
@@ -53,11 +54,15 @@ 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