Dear Lawrence, I'm afraid I'm still having problems, so that doesn't seem to have fixed it. The error looks the same (I've attached the install log) Tom On 01/11/16 17:32, Lawrence Mitchell wrote:
On 01/11/16 15:41, T. M. Bendall wrote:
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/firedrake/hdf5interface.o -lpetsc -o build/lib.linux-x86_64-2.7/firedrake/hdf5interface.so -L/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib -Wl,-rpath,/home/tmb15/src/firedrake/lib cythoning firedrake/spatialindex.pyx to firedrake/spatialindex.c building 'firedrake.spatialindex' extension mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include -I/home/tmb15/src/firedrake/include -I/usr/include/python2.7 -c firedrake/spatialindex.c -o build/temp.linux-x86_64-2.7/firedrake/spatialindex.o In file included from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from firedrake/spatialindex.c:406:
/home/tmb15/src/firedrake/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" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from /usr/include/spatialindex/SpatialIndex.h:30:0, from /usr/include/spatialindex/capi/sidx_config.h:56, from /usr/include/spatialindex/capi/sidx_api.h:34, from firedrake/spatialindex.c:409: /usr/include/spatialindex/tools/Tools.h:59:20: fatal error: iostream: No such file or directory compilation terminated. error: command 'mpicc' failed with exit status 1
This is the problem. The version of spatialindex shipped with ubuntu has a broken C API. We include our own, but you appear to be picking up the system version.
Does it work if you do "apt-get remove libspatialindex-dev"?
Lawrence
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