hbuesing@cluster-x2:~/Code/firedrake$ PETSC_DIR=~/petsc_opt PETSC_ARCH=arch-linux2-c-opt CC=mpicc CFLAGS=-I/opt/MPI/openmpi-1.6.5/linux/gcc/include make Building extension modules running build_ext skipping 'firedrake/dmplex.c' Cython extension (up-to-date) skipping 'firedrake/spatialindex.cpp' Cython extension (up-to-date) building 'firedrake.spatialindex' extension mpicc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/MPI/openmpi-1.6.5/linux/gcc/include -fPIC -I/home/hbuesing/.local/lib/python2.7/site-packages/numpy/core/include -I/rwthfs/rz/SW/UTIL.common/Python/2.7.9/x86_64/include/python2.7 -c firedrake/spatialindex.cpp -o build/temp.linux-x86_64-2.7/firedrake/spatialindex.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ In file included from /home/hbuesing/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1781, from /home/hbuesing/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/hbuesing/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/spatialindex.cpp:251: /home/hbuesing/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" firedrake/spatialindex.cpp:259:39: error: spatialindex/SpatialIndex.h: No such file or directory firedrake/spatialindex.cpp:805: error: 'SpatialIndex' has not been declared firedrake/spatialindex.cpp:805: error: ISO C++ forbids declaration of 'IStorageManager' with no type firedrake/spatialindex.cpp:805: error: expected ';' before '*' token firedrake/spatialindex.cpp:806: error: 'SpatialIndex' has not been declared firedrake/spatialindex.cpp:806: error: ISO C++ forbids declaration of 'ISpatialIndex' with no type firedrake/spatialindex.cpp:806: error: expected ';' before '*' token firedrake/spatialindex.cpp: In function 'int __pyx_pf_9firedrake_12spatialindex_12SpatialIndex___cinit__(__pyx_obj_9firedrake_12spatialindex_SpatialIndex*, uint32_t)': firedrake/spatialindex.cpp:1359: error: 'Tools' has not been declared firedrake/spatialindex.cpp:1359: error: expected ';' before '__pyx_v_ps' firedrake/spatialindex.cpp:1360: error: 'Tools' has not been declared firedrake/spatialindex.cpp:1360: error: expected ';' before '__pyx_v_var' firedrake/spatialindex.cpp:1364: error: 'SpatialIndex' has not been declared firedrake/spatialindex.cpp:1364: error: '__pyx_t_2' was not declared in this scope firedrake/spatialindex.cpp:1365: error: 'SpatialIndex' has not been declared firedrake/spatialindex.cpp:1365: error: '__pyx_t_3' was not declared in this scope firedrake/spatialindex.cpp:1378: error: 'struct __pyx_obj_9firedrake_12spatialindex_SpatialIndex' has no member named 'storage_manager' firedrake/spatialindex.cpp:1387: error: 'struct __pyx_obj_9firedrake_12spatialindex_SpatialIndex' has no member named 'spatial_index' firedrake/spatialindex.cpp:1396: error: '__pyx_v_var' was not declared in this scope firedrake/spatialindex.cpp:1396: error: 'Tools' has not been declared firedrake/spatialindex.cpp:1415: error: '__pyx_v_ps' was not declared in this scope firedrake/spatialindex.cpp:1425: error: 'SpatialIndex' has not been declared firedrake/spatialindex.cpp:1430: error: 'struct __pyx_obj_9firedrake_12spatialindex_SpatialIndex' has no member named 'storage_manager' firedrake/spatialindex.cpp:1440: error: 'SpatialIndex' has not been declared firedrake/spatialindex.cpp:1440: error: 'struct __pyx_obj_9firedrake_12spatialindex_SpatialIndex' has no member named 'storage_manager' firedrake/spatialindex.cpp:1445: error: 'struct __pyx_obj_9firedrake_12spatialindex_SpatialIndex' has no member named 'spatial_index' firedrake/spatialindex.cpp: In function 'void __pyx_pf_9firedrake_12spatialindex_12SpatialIndex_2__dealloc__(__pyx_obj_9firedrake_12spatialindex_SpatialIndex*)': firedrake/spatialindex.cpp:1496: error: 'struct __pyx_obj_9firedrake_12spatialindex_SpatialIndex' has no member named 'spatial_index' firedrake/spatialindex.cpp:1505: error: 'struct __pyx_obj_9firedrake_12spatialindex_SpatialIndex' has no member named 'storage_manager' firedrake/spatialindex.cpp: In function 'PyObject* __pyx_pf_9firedrake_12spatialindex_12SpatialIndex_4ctypes(__pyx_obj_9firedrake_12spatialindex_SpatialIndex*)': firedrake/spatialindex.cpp:1567: error: 'struct __pyx_obj_9firedrake_12spatialindex_SpatialIndex' has no member named 'spatial_index' firedrake/spatialindex.cpp: In function 'PyObject* __pyx_pf_9firedrake_12spatialindex_from_regions(PyObject*, PyArrayObject*, PyArrayObject*)': firedrake/spatialindex.cpp:1701: error: 'SpatialIndex' has not been declared firedrake/spatialindex.cpp:1701: error: expected ';' before '__pyx_v_region' firedrake/spatialindex.cpp:1719: error: 'SpatialIndex' has not been declared firedrake/spatialindex.cpp:1719: error: expected ';' before '__pyx_t_10' firedrake/spatialindex.cpp:1853: error: '__pyx_t_10' was not declared in this scope firedrake/spatialindex.cpp:1853: error: 'SpatialIndex' has not been declared firedrake/spatialindex.cpp:1858: error: '__pyx_v_region' was not declared in this scope firedrake/spatialindex.cpp:1858: error: '__pyx_t_10' was not declared in this scope firedrake/spatialindex.cpp:1866: error: 'struct __pyx_obj_9firedrake_12spatialindex_SpatialIndex' has no member named 'spatial_index' /home/hbuesing/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h: At global scope: /home/hbuesing/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1634: warning: 'int _import_array()' defined but not used error: command 'mpicc' failed with exit status 1 hbuesing@cluster-x2:~/Code/firedrake$