manual installation error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

[Miguel Calpe]

Hello,

I am new in dedalus.
I wanted to install manually the package, but I always get the same error : error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
I guess the problem comes from an import in module libraries.fftw (in bold below).
Does someone have an idea of the problem?

Thank you!
Miguel

Looking for fftw prefix
  Found matching library in /usr/lib
Looking for mpi prefix
  Found matching library in /usr/lib/openmpi/lib
Looking for fftw prefix
  Found matching library in /usr/lib
missing cimport in module '..libraries.fftw': dedalus/core/transposes.pyx
running build_ext
building 'dedalus.libraries.fftw.fftw_wrappers' extension
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Idedalus/libraries/fftw/ -I/home/users/calpelin7m/opt/mypy3/lib/python3.5/site-packages/numpy/core/include -I/opt/python/3.5.1/lib/python3.5/site-packages/mpi4py/include -I/usr/include -I/usr/lib/openmpi/include -I/opt/python/3.5.1/include/python3.5m -c dedalus/libraries/fftw/fftw_wrappers.c -o build/temp.linux-x86_64-3.5/dedalus/libraries/fftw/fftw_wrappers.o -Wno-error=declaration-after-statement
In file included from /home/users/calpelin7m/opt/mypy3/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /home/users/calpelin7m/opt/mypy3/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /home/users/calpelin7m/opt/mypy3/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from dedalus/libraries/fftw/fftw_wrappers.c:301:
/home/users/calpelin7m/opt/mypy3/lib/python3.5/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 " \
  ^
dedalus/libraries/fftw/fftw_wrappers.c:1043:3: error: unknown type name 'MPI_Message'
   MPI_Message ob_mpi;
   ^
dedalus/libraries/fftw/fftw_wrappers.c: In function '__pyx_pf_7dedalus_9libraries_4fftw_13fftw_wrappers_23DiscreteCosineTransform___init__':
dedalus/libraries/fftw/fftw_wrappers.c:6060:163: warning: passing argument 7 of 'fftw_plan_guru_r2r' from incompatible pointer type
   __pyx_v_self->forward_plan = fftw_plan_guru_r2r(__pyx_v_trans_rank, __pyx_v_trans_struct, __pyx_v_vec_rank, __pyx_v_vec_struct_f, __pyx_v_gdata, __pyx_v_cdata, __pyx_v_kind_f, (__pyx_v_intflags | __pyx_e_7dedalus_9libraries_4fftw_10fftw_c_api_FFTW_DESTROY_INPUT));
                                                                                                                                                                   ^
In file included from dedalus/libraries/fftw/fftw_wrappers.c:306:0:
/usr/include/fftw3.h:355:1: note: expected 'const enum fftw_r2r_kind *' but argument is of type 'int *'
 FFTW_DEFINE_API(FFTW_MANGLE_DOUBLE, double, fftw_complex)
 ^
dedalus/libraries/fftw/fftw_wrappers.c:6069:164: warning: passing argument 7 of 'fftw_plan_guru_r2r' from incompatible pointer type
   __pyx_v_self->backward_plan = fftw_plan_guru_r2r(__pyx_v_trans_rank, __pyx_v_trans_struct, __pyx_v_vec_rank, __pyx_v_vec_struct_b, __pyx_v_cdata, __pyx_v_gdata, __pyx_v_kind_b, (__pyx_v_intflags | __pyx_e_7dedalus_9libraries_4fftw_10fftw_c_api_FFTW_DESTROY_INPUT));
                                                                                                                                                                    ^
In file included from dedalus/libraries/fftw/fftw_wrappers.c:306:0:
/usr/include/fftw3.h:355:1: note: expected 'const enum fftw_r2r_kind *' but argument is of type 'int *'
 FFTW_DEFINE_API(FFTW_MANGLE_DOUBLE, double, fftw_complex)
 ^
dedalus/libraries/fftw/fftw_wrappers.c: In function '__pyx_pf_7dedalus_9libraries_4fftw_13fftw_wrappers_21DiscreteSineTransform___init__':
dedalus/libraries/fftw/fftw_wrappers.c:7328:163: warning: passing argument 7 of 'fftw_plan_guru_r2r' from incompatible pointer type
   __pyx_v_self->forward_plan = fftw_plan_guru_r2r(__pyx_v_trans_rank, __pyx_v_trans_struct, __pyx_v_vec_rank, __pyx_v_vec_struct_f, __pyx_v_gdata, __pyx_v_cdata, __pyx_v_kind_f, (__pyx_v_intflags | __pyx_e_7dedalus_9libraries_4fftw_10fftw_c_api_FFTW_DESTROY_INPUT));
                                                                                                                                                                   ^
In file included from dedalus/libraries/fftw/fftw_wrappers.c:306:0:
/usr/include/fftw3.h:355:1: note: expected 'const enum fftw_r2r_kind *' but argument is of type 'int *'
 FFTW_DEFINE_API(FFTW_MANGLE_DOUBLE, double, fftw_complex)
 ^
dedalus/libraries/fftw/fftw_wrappers.c:7337:164: warning: passing argument 7 of 'fftw_plan_guru_r2r' from incompatible pointer type
   __pyx_v_self->backward_plan = fftw_plan_guru_r2r(__pyx_v_trans_rank, __pyx_v_trans_struct, __pyx_v_vec_rank, __pyx_v_vec_struct_b, __pyx_v_cdata, __pyx_v_gdata, __pyx_v_kind_b, (__pyx_v_intflags | __pyx_e_7dedalus_9libraries_4fftw_10fftw_c_api_FFTW_DESTROY_INPUT));
                                                                                                                                                                    ^
In file included from dedalus/libraries/fftw/fftw_wrappers.c:306:0:
/usr/include/fftw3.h:355:1: note: expected 'const enum fftw_r2r_kind *' but argument is of type 'int *'
 FFTW_DEFINE_API(FFTW_MANGLE_DOUBLE, double, fftw_complex)
 ^
In file included from /home/users/calpelin7m/opt/mypy3/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                 from /home/users/calpelin7m/opt/mypy3/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from dedalus/libraries/fftw/fftw_wrappers.c:301:
dedalus/libraries/fftw/fftw_wrappers.c: At top level:
/home/users/calpelin7m/opt/mypy3/lib/python3.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:1453:1: warning: '_import_array' defined but not used [-Wunused-function]
 _import_array(void)
 ^
dedalus/libraries/fftw/fftw_wrappers.c:25553:18: warning: '__pyx_convert__to_py_fftw_iodim' defined but not used [-Wunused-function]
 static PyObject* __pyx_convert__to_py_fftw_iodim(fftw_iodim s) {
                  ^
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

[Jeffrey S. Oishi]

Hi Miguel,

Welcome to Dedalus! I'd be happy to help. Could you explain a bit more about how you are doing the install? It looks like setuptools thinks your c compiler is called x86_64-linux-gnu-gcc, which is not the case (and would be quite unusual).

What OS are you using? How did you satisfy the dependencies ( via packages? Manually?) ?

Thanks,

Jeff

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[Miguel Calpe]

Hello Jeff,

Thak you for the email.
Today I solved the problem. My pc looked for the fftw3 library files in my "/usr/local/lib/" instead of "/usr/lib/x86_64-linux-gnu/" (where actually are).

(mypy3) calpelin7m@meige7pcjs225:/usr/lib/x86_64-linux-gnu$ ls libfftw3*
libfftw3.a                  libfftw3l_threads.so
libfftw3f.a                 libfftw3l_threads.so.3
libfftw3f_mpi.a             libfftw3l_threads.so.3.4.4
libfftw3f_mpi.so            libfftw3_mpi.a
libfftw3f_mpi.so.3          libfftw3_mpi.so
libfftw3f_mpi.so.3.4.4      libfftw3_mpi.so.3
libfftw3f_omp.a             libfftw3_mpi.so.3.4.4
libfftw3f_omp.so            libfftw3_omp.a
libfftw3f_omp.so.3          libfftw3_omp.so
libfftw3f_omp.so.3.4.4      libfftw3_omp.so.3
libfftw3f.so                libfftw3_omp.so.3.4.4
libfftw3f.so.3              libfftw3q.a
libfftw3f.so.3.4.4          libfftw3q_omp.a
libfftw3f_threads.a         libfftw3q_omp.so
libfftw3f_threads.so        libfftw3q_omp.so.3
libfftw3f_threads.so.3      libfftw3q_omp.so.3.4.4
libfftw3f_threads.so.3.4.4  libfftw3q.so
libfftw3l.a                 libfftw3q.so.3
libfftw3l_mpi.a             libfftw3q.so.3.4.4
libfftw3l_mpi.so            libfftw3q_threads.a
libfftw3l_mpi.so.3          libfftw3q_threads.so
libfftw3l_mpi.so.3.4.4      libfftw3q_threads.so.3
libfftw3l_omp.a             libfftw3q_threads.so.3.4.4
libfftw3l_omp.so            libfftw3.so
libfftw3l_omp.so.3          libfftw3.so.3
libfftw3l_omp.so.3.4.4      libfftw3.so.3.4.4
libfftw3l.so                libfftw3_threads.a
libfftw3l.so.3              libfftw3_threads.so
libfftw3l.so.3.4.4          libfftw3_threads.so.3
libfftw3l_threads.a         libfftw3_threads.so.3.4.4

Miguel

[snb...@york.ac.uk]

Hi Jeff / Miguel,

I have the same error message:

.
.
.
dedalus/core/transposes.pyx: cannot find cimported module '..libraries.fftw'
.
.
.
dedalus/libraries/fftw/fftw_wrappers.c:1349:3: error: unknown type name ‘MPI_Message’
MPI_Message ob_mpi;
^
.
.
.
error: command 'gcc' failed with exit status 1

I was using the install script so I have FFTW_PATH=/home/steve/Programs/dedalus/dedalus/

I have tried both MPI_PATH=/usr/lib/openmpi and MPI_PATH=/usr/lib/openmpi/lib where the contents are:

$ ls /usr/lib/openmpi
include lib

$ ls /usr/lib/openmpi/lib
libmca_common_sm.so libmpi_f77.so libmpi.so libopen-pal.so mpi.mod
libmca_common_sm.so.3.0.1 libmpi_f77.so.1.0.7 libmpi.so.1.0.8 libopen-pal.so.4.0.5 openmpi
libmpi_cxx.so libmpi_f90.so libompitrace.so libopen-rte.so pkgconfig
libmpi_cxx.so.1.0.2 libmpi_f90.so.1.3.0 libompitrace.so.0.0.0 libopen-rte.so.4.0.3

It's definitely supposed to be MPI_PATH=/usr/lib/openmpi or I get mpi.h not found.

It appears Miguel used a system install of FFTW but I am using the version built during installation. Therefore, I suspect my FFTW_PATH is OK. Hence, I have no idea what to try next.

Also, I have tried using my system install of FFTW (same location as Miguel) but the install script keeps reverting to the dedalus version and I can't see how to prevent that.

Basically, I don't care how we fix it. All I want is a working install of dedalus.

Many thanks,
Steve

[Jeffrey S. Oishi]

Hi Steve,

What version of openmpi are you using? You can find out by doing 

$ mpirun --version

This problem is known to occur with older versions of openMPI. What machine are you trying to install this on? 

Jeff

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[snb...@york.ac.uk]

Hi Jeff,

Thank you for your help by email. I'm just posting our correspondence here to help others in the future. (I thought the emails would appear here automatically but apparently not.)

ME:
> This is on my personal laptop. I've got openmpi v1.6.5. This is the latest
> version available in my Linux distro's repos (I'm overdue an upgrade!).
>
> Currently trying again from scratch with option activated to get dedalus to
> install openmpi... Ah, it just finished with a nice message saying dedalus is
> ready.

YOU:
> Awesome! Don't hesitate to hit up the list if you have any further questions!