From bf0874bbd36a9c9232ea0b89df4e47ebed0e9bdd Mon Sep 17 00:00:00 2001
From: Guilhem Lavaux <guilhem.lavaux@gmail.com>
Date: Wed, 9 Aug 2017 17:42:02 +0200
Subject: [PATCH] Fixes to compile on OSX

---
 python/CMakeLists.txt        |  6 +++++-
 python/_cosmo_bispectrum.cpp | 10 ++++++++++
 python/_cosmotool.pyx        |  9 ++++++---
 3 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index bb2f745..f5c963d 100644
--- 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})
diff --git a/python/_cosmo_bispectrum.cpp b/python/_cosmo_bispectrum.cpp
index 94e6491..db6a6e0 100644
--- 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
 }
 
 
diff --git a/python/_cosmotool.pyx b/python/_cosmotool.pyx
index 628e4e9..5ef1c1a 100644
--- 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):
@@ -501,7 +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()