problem for compiling last version of fluidfft on our SGI HPC cluster. Intel compiler used and MPT for mpi. (see install.txt)
When compiling fluidfft:
make developpython setup.py develop��������CMPT ERROR: mpiexec_mpt must be used to launch all MPI applicationsMakefile:5: recipe for target 'develop' failedmake: *** [develop] Error 255
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The last time, I didn't manage to run the simulation. I got the last version of fluiddyn, recompiled and it worked.
This time, I have the last version of fluiddyn and fluidfft, and I can't compile fluidfft.
python setup.py develop��������CMPT ERROR: mpiexec_mpt must be used to launch all MPI applicationsMakefile:5: recipe for target 'develop' failedmake: *** [develop] Error 255
Is there something I don't understand? something I missed in the installation?
Regarding the install commands, just after a clone, you don't need the hg pull but it is a good idea to run hg up master instead. Just after a clone, you don't need make clean.
To debug this, we'll need to understand what is done in setup.py which is not liked by this special MPI implementation...
You can already try (without$MPI_LAUNCH and from the root directory fluidfft):
hg clone https://bitbucket.org/fluiddyn/fluiddyncd fluiddynhg up mastermake
The same as above.
hg clone https://bitbucket.org/fluiddyn/fluidfftcd fluidffthg up mastermake
The same...
python -c "from fluiddyn.util.mpi import _detect_mpi_type; print('detected mpi_type:', _detect_mpi_type())"��������CMPT ERROR: mpiexec_mpt must be used to launch all MPI applicationspython -c "from fluiddyn.util.mpi import printby0, nb_proc; printby0(nb_proc)"��������CMPT ERROR: mpiexec_mpt must be used to launch all MPI applicationspython -c "import purepymake"��������CMPT ERROR: mpiexec_mpt must be used to launch all MPI applicationspython -c "import mpi4py; print(mpi4py.__version__)"3.0.0python -c "from runpy import run_path; run_path('fluidfft/util.py')"��������CMPT ERROR: mpiexec_mpt must be used to launch all MPI applicationsmpicxx -showme:compileicpc: command line warning #10006: ignoring unknown option '-showme:compile'/usr/lib/../lib64/crt1.o: In function `_start':/home/abuild/rpmbuild/BUILD/glibc-2.19/csu/../sysdeps/x86_64/start.S:118: undefined reference to `main'mpicxx -showicpc -std=c++11 -I/appli/mpt/2.17-p11472/include -lpthread /usr/lib64/libcpuset.so.1 /usr/lib64/libbitmask.so.1 -L/appli/mpt/2.17-p11472/lib -lmpi++ -lmpi
python -c "from mpi4py import MPI"��������CMPT ERROR: mpiexec_mpt must be used to launch all MPI applications
I launch a batch in an interactive access to use $MPI_LAUNCH
qsub -I job_datarmorsetenv CC mpiccsetenv CXX mpicxxsetenv MPICC_CC iccsetenv MPICXX_CXX icpcsetenv MPI_PATH $MPI_ROOTsetenv CXXFLAGS "-std=c++11"module purgemodule load intel-cc-18 mpt/2.17 intel-cmkl-18 gcc/5.3set FLUIDPATH=fluidsimsetenv LD_LIBRARY_PATH $HOME/lib/fftw/3.3.7/lib:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $HOME/lib/hdf5/1.10.2/lib:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $HOME/.miniconda2/envs/$FLUIDPATH/lib:$LD_LIBRARY_PATHsetenv C_INCLUDE_PATH $HOME/lib/fftw/3.3.7/include:$C_INCLUDE_PATHsetenv C_INCLUDE_PATH $HOME/lib/hdf5/1.10.2/include:$C_INCLUDE_PATHsetenv C_INCLUDE_PATH $HOME/.miniconda2/envs/$FLUIDPATH/include:$C_INCLUDE_PATHconda activate $FLUIDPATHcd fluidfft$MPI_LAUNCH -n 1 python setup.py developicpc: command line warning #10006: ignoring unknown option '-showme:compile'/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crt1.o: In function `_start':/home/abuild/rpmbuild/BUILD/glibc-2.19/csu/../sysdeps/x86_64/start.S:118: undefined reference to `main'Traceback (most recent call last): File "/home1/datahome/slgentil/fluidsim/fluidfft/purepymake.py", line 95, in <module> subprocess.check_output(["mpicxx", "-showme:compile"]) File "/home1/datahome/slgentil/.miniconda2/envs/fluidsim/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/home1/datahome/slgentil/.miniconda2/envs/fluidsim/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr)subprocess.CalledProcessError: Command '['mpicxx', '-showme:compile']' returned non-zero exit status 1.During handling of the above exception, another exception occurred:Traceback (most recent call last): File "setup.py", line 24, in <module> from purepymake import ( File "/home1/datahome/slgentil/fluidsim/fluidfft/purepymake.py", line 101, in <module> subprocess.call(["CC", "--version"]) File "/home1/datahome/slgentil/.miniconda2/envs/fluidsim/lib/python3.6/subprocess.py", line 267, in call with Popen(*popenargs, **kwargs) as p: File "/home1/datahome/slgentil/.miniconda2/envs/fluidsim/lib/python3.6/subprocess.py", line 709, in __init__ restore_signals, start_new_session) File "/home1/datahome/slgentil/.miniconda2/envs/fluidsim/lib/python3.6/subprocess.py", line 1344, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename)FileNotFoundError: [Errno 2] No such file or directory: 'CC': 'CC'
with $MPI_LAUNCH -n 1 python setup.py develop, it goes further but failed with
... instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::numpy::functor::square, Args=<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>>]" at line 478 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::mul, Args=<<unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::numpy::functor::square, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>]" at line 58 of "fluidfft/fft2d/util_pythran.cpp" instantiation of class "__pythran_util_pythran::myfunc::type<argument_type0> [with argument_type0=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>]" at line 369 of "fluidfft/fft2d/util_pythran.cpp"error: can't copy 'build/lib.linux-x86_64-3.6/fluidfft/fft2d/util_pythran.cpython-36m-x86_64-linux-gnu.so': doesn't exist or not a regular file
ls -R buildbuild/:temp.linux-x86_64-3.6build/temp.linux-x86_64-3.6:fluidfftbuild/temp.linux-x86_64-3.6/fluidfft:fft2d fft3dbuild/temp.linux-x86_64-3.6/fluidfft/fft2d:build/temp.linux-x86_64-3.6/fluidfft/fft3d:
icpc: command line warning #10006: ignoring unknown option '-showme:compile'/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crt1.o: In function `_start':/home/abuild/rpmbuild/BUILD/glibc-2.19/csu/../sysdeps/x86_64/start.S:118: undefined reference to `main'************************************************** numpy installed: True mpi4py installed: True cython installed: True pythran installed: True mako installed: True**************************************************Parsing site.cfgfftw3: use: True dir: /home1/datahome/slgentil/lib/fftw/3.3.7 include_dir: /home1/datahome/slgentil/lib/fftw/3.3.7/include library_dir: /home1/datahome/slgentil/lib/fftw/3.3.7/libfftw3_mpi: use: True dir: /home1/datahome/slgentil/lib/fftw/3.3.7 include_dir: /home1/datahome/slgentil/lib/fftw/3.3.7/include library_dir: /home1/datahome/slgentil/lib/fftw/3.3.7/libmake_extensions: purepymake.Extension<fluidfft.fft2d.with_fftw1d>make_extensions: purepymake.Extension<fluidfft.fft2d.with_fftw2d>make_extensions: purepymake.Extension<fluidfft.fft2d.mpi_with_fftw1d>make_extensions: purepymake.Extension<fluidfft.fft3d.with_fftw3d>make_extensions: purepymake.Extension<fluidfft.fft3d.mpi_with_fftw1d>launching command:compile_single( *args=('fluidfft/fft2d/fft2dmpi_with_fftw1d.pyx',), **kwargs={'options': <Cython.Compiler.Main.CompilationOptions object at 0x2aca44f17c18>, 'full_module_name': 'fluidfft.fft2d.mpi_with_fftw1d'})/home1/datahome/slgentil/test/fluidfft/purepymake.py:109: UserWarning: Unable to find MPI compile flags.Setting mpicxx_compile_words=[] "Unable to find MPI compile flags."setup.py:169: UserWarning: When numpy uses mkl (as for example with conda), there are symbol conflicts between mkl and fftw. This can lead to a segmentation fault so we do not build the extensions using fftwmpi. "When numpy uses mkl (as for example with conda), "launching command:compile_single( *args=('fluidfft/fft3d/fft3dmpi_with_fftw1d.pyx',), **kwargs={'options': <Cython.Compiler.Main.CompilationOptions object at 0x2aca44f17be0>, 'full_module_name': 'fluidfft.fft3d.mpi_with_fftw1d'})launching command:compile_single( *args=('fluidfft/fft2d/fft2d_with_fftw2d.pyx',), **kwargs={'options': <Cython.Compiler.Main.CompilationOptions object at 0x2aca44f17ba8>, 'full_module_name': 'fluidfft.fft2d.with_fftw2d'})launching command:compile_single( *args=('fluidfft/fft3d/fft3d_with_fftw3d.pyx',), **kwargs={'options': <Cython.Compiler.Main.CompilationOptions object at 0x2aca44f17b70>, 'full_module_name': 'fluidfft.fft3d.with_fftw3d'})launching command:compile_single( *args=('fluidfft/fft2d/fft2d_with_fftw1d.pyx',), **kwargs={'options': <Cython.Compiler.Main.CompilationOptions object at 0x2aca44f17b38>, 'full_module_name': 'fluidfft.fft2d.with_fftw1d'})launching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c fluidfft/fft2d/fft2dmpi_with_fftw1d.cpp -o build/temp.linux-x86_64-3.6/fluidfft/fft2d/fft2dmpi_with_fftw1d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c fluidfft/fft3d/fft3dmpi_with_fftw1d.cpp -o build/temp.linux-x86_64-3.6/fluidfft/fft3d/fft3dmpi_with_fftw1d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c fluidfft/fft2d/fft2d_with_fftw2d.cpp -o build/temp.linux-x86_64-3.6/fluidfft/fft2d/fft2d_with_fftw2d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c fluidfft/fft3d/fft3d_with_fftw3d.cpp -o build/temp.linux-x86_64-3.6/fluidfft/fft3d/fft3d_with_fftw3d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c fluidfft/fft2d/fft2d_with_fftw1d.cpp -o build/temp.linux-x86_64-3.6/fluidfft/fft2d/fft2d_with_fftw1d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/2d/fft2dmpi_with_fftw1d.cpp -o build/temp.linux-x86_64-3.6/src_cpp/2d/fft2dmpi_with_fftw1d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/2d/fft2d_with_fftw1d.cpp -o build/temp.linux-x86_64-3.6/src_cpp/2d/fft2d_with_fftw1d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/3d/base_fft3dmpi.cpp -o build/temp.linux-x86_64-3.6/src_cpp/3d/base_fft3dmpi.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/2d/base_fft2dmpi.cpp -o build/temp.linux-x86_64-3.6/src_cpp/2d/base_fft2dmpi.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/2d/base_fft2d.cpp -o build/temp.linux-x86_64-3.6/src_cpp/2d/base_fft2d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/3d/base_fft3d.cpp -o build/temp.linux-x86_64-3.6/src_cpp/3d/base_fft3d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/base/base_fft.cpp -o build/temp.linux-x86_64-3.6/src_cpp/base/base_fft.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/base/base_fftmpi.cpp -o build/temp.linux-x86_64-3.6/src_cpp/base/base_fftmpi.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/3d/fft3dmpi_with_fftw1d.cpp -o build/temp.linux-x86_64-3.6/src_cpp/3d/fft3dmpi_with_fftw1d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/3d/fft3d_with_fftw3d.cpp -o build/temp.linux-x86_64-3.6/src_cpp/3d/fft3d_with_fftw3d.olaunching command:mpicxx -pthread -fwrapv -O3 -Wall -Wno-unused-result -Wsign-compare -Wno-unused-result -Wsign-compare -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -I/home1/datahome/slgentil/.miniconda2/envs/test/include -Isrc_cy -Ifluidfft/fft2d -Ifluidfft/fft3d -Isrc_cpp/base -Isrc_cpp/3d -Isrc_cpp/2d -Iinclude -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/mpi4py/include -I/home1/datahome/slgentil/lib/fftw/3.3.7/include -c src_cpp/2d/fft2d_with_fftw2d.cpp -o build/temp.linux-x86_64-3.6/src_cpp/2d/fft2d_with_fftw2d.olaunching command:mpicxx -pthread -shared -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed build/temp.linux-x86_64-3.6/fluidfft/fft3d/fft3dmpi_with_fftw1d.o build/temp.linux-x86_64-3.6/src_cpp/3d/fft3dmpi_with_fftw1d.o build/temp.linux-x86_64-3.6/src_cpp/base/base_fft.o build/temp.linux-x86_64-3.6/src_cpp/3d/base_fft3d.o build/temp.linux-x86_64-3.6/src_cpp/base/base_fftmpi.o build/temp.linux-x86_64-3.6/src_cpp/3d/base_fft3dmpi.o -o build/lib.linux-x86_64-3.6/fluidfft/fft3d/mpi_with_fftw1d.cpython-36m-x86_64-linux-gnu.so -L/home1/datahome/slgentil/lib/fftw/3.3.7/lib -lfftw3launching command:mpicxx -pthread -shared -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed build/temp.linux-x86_64-3.6/fluidfft/fft3d/fft3d_with_fftw3d.o build/temp.linux-x86_64-3.6/src_cpp/3d/fft3d_with_fftw3d.o build/temp.linux-x86_64-3.6/src_cpp/base/base_fft.o build/temp.linux-x86_64-3.6/src_cpp/3d/base_fft3d.o -o build/lib.linux-x86_64-3.6/fluidfft/fft3d/with_fftw3d.cpython-36m-x86_64-linux-gnu.so -L/home1/datahome/slgentil/lib/fftw/3.3.7/lib -lfftw3launching command:mpicxx -pthread -shared -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed build/temp.linux-x86_64-3.6/fluidfft/fft2d/fft2dmpi_with_fftw1d.o build/temp.linux-x86_64-3.6/src_cpp/2d/fft2dmpi_with_fftw1d.o build/temp.linux-x86_64-3.6/src_cpp/base/base_fft.o build/temp.linux-x86_64-3.6/src_cpp/2d/base_fft2d.o build/temp.linux-x86_64-3.6/src_cpp/base/base_fftmpi.o build/temp.linux-x86_64-3.6/src_cpp/2d/base_fft2dmpi.o -o build/lib.linux-x86_64-3.6/fluidfft/fft2d/mpi_with_fftw1d.cpython-36m-x86_64-linux-gnu.so -L/home1/datahome/slgentil/lib/fftw/3.3.7/lib -lfftw3launching command:mpicxx -pthread -shared -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed build/temp.linux-x86_64-3.6/fluidfft/fft2d/fft2d_with_fftw2d.o build/temp.linux-x86_64-3.6/src_cpp/2d/fft2d_with_fftw2d.o build/temp.linux-x86_64-3.6/src_cpp/base/base_fft.o build/temp.linux-x86_64-3.6/src_cpp/2d/base_fft2d.o -o build/lib.linux-x86_64-3.6/fluidfft/fft2d/with_fftw2d.cpython-36m-x86_64-linux-gnu.so -L/home1/datahome/slgentil/lib/fftw/3.3.7/lib -lfftw3launching command:mpicxx -pthread -shared -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed -L/home1/datahome/slgentil/.miniconda2/envs/test/lib -Wl,-rpath=/home1/datahome/slgentil/.miniconda2/envs/test/lib,--no-as-needed build/temp.linux-x86_64-3.6/fluidfft/fft2d/fft2d_with_fftw1d.o build/temp.linux-x86_64-3.6/src_cpp/2d/fft2d_with_fftw1d.o build/temp.linux-x86_64-3.6/src_cpp/base/base_fft.o build/temp.linux-x86_64-3.6/src_cpp/2d/base_fft2d.o -o build/lib.linux-x86_64-3.6/fluidfft/fft2d/with_fftw1d.cpython-36m-x86_64-linux-gnu.so -L/home1/datahome/slgentil/lib/fftw/3.3.7/lib -lfftw3running developrunning egg_infocreating fluidfft.egg-infowriting fluidfft.egg-info/PKG-INFOwriting dependency_links to fluidfft.egg-info/dependency_links.txtwriting entry points to fluidfft.egg-info/entry_points.txtwriting requirements to fluidfft.egg-info/requires.txtwriting top-level names to fluidfft.egg-info/top_level.txtwriting manifest file 'fluidfft.egg-info/SOURCES.txt'reading manifest file 'fluidfft.egg-info/SOURCES.txt'reading manifest template 'MANIFEST.in'writing manifest file 'fluidfft.egg-info/SOURCES.txt'running build_extbuilding 'fluidfft.fft2d.util_pythran' extensionmpicxx: fluidfft/fft2d/util_pythran.cppbuilding 'fluidfft.fft3d.util_pythran' extensionmpicxx: fluidfft/fft3d/util_pythran.cppmodule: Command not found.module: Command not found.In file included from fluidfft/fft3d/util_pythran.cpp(13):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1178): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<4, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 761 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^In file included from fluidfft/fft3d/util_pythran.cpp(13):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1226): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<5, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 816 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_gexpr.hpp(768): error: expression preceding parentheses of apparent call must have (pointer-to-) function type -> decltype(std::declval<value_type>()(s...)); ^ detected during: instantiation of class "<unnamed>::pythonic::types::numpy_gexpr<Arg, S...> [with Arg=<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>>>, S=<<unnamed>::pythonic::types::normalized_slice>]" at line 633 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::mul, Args=<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>>>, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>>]" at line 478 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::add, Args=<<unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>>, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>, <unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>>, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>>]" at line 478 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::add, Args=<<unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::add, <unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, <unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>, <unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, <unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>, <unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, <unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>]" at line 328 of "fluidfft/fft3d/util_pythran.cpp" instantiation of class "__pythran_util_pythran::divfft_from_vecfft::type<argument_type0, argument_type1, argument_type2, argument_type3, argument_type4, argument_type5> [with argument_type0=<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type1=<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type2=<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type3=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type4=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type5=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>]" at line 733 of "fluidfft/fft3d/util_pythran.cpp"module: Command not found.module: Command not found.In file included from fluidfft/fft3d/util_pythran.cpp(13):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1178): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<4, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 761 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^In file included from fluidfft/fft3d/util_pythran.cpp(13):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1226): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<5, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 816 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_gexpr.hpp(768): error: expression preceding parentheses of apparent call must have (pointer-to-) function type -> decltype(std::declval<value_type>()(s...)); ^ detected during: instantiation of class "<unnamed>::pythonic::types::numpy_gexpr<Arg, S...> [with Arg=<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>>>, S=<<unnamed>::pythonic::types::normalized_slice>]" at line 633 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::mul, Args=<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>>>, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>>]" at line 478 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::add, Args=<<unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>>, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>, <unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>>, <unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>>]" at line 478 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::add, Args=<<unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::add, <unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, <unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>, <unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, <unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>, <unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::operator_::functor::mul, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, <unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>>>]" at line 328 of "fluidfft/fft3d/util_pythran.cpp" instantiation of class "__pythran_util_pythran::divfft_from_vecfft::type<argument_type0, argument_type1, argument_type2, argument_type3, argument_type4, argument_type5> [with argument_type0=<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type1=<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type2=<unnamed>::pythonic::types::ndarray<std::complex<double>, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type3=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type4=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>, argument_type5=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long, long>>]" at line 733 of "fluidfft/fft3d/util_pythran.cpp"module: Command not found.module: Command not found.In file included from fluidfft/fft2d/util_pythran.cpp(16):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1178): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<4, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 761 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^In file included from fluidfft/fft2d/util_pythran.cpp(16):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1226): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<5, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 816 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_gexpr.hpp(768): error: expression preceding parentheses of apparent call must have (pointer-to-) function type -> decltype(std::declval<value_type>()(s...)); ^ detected during: instantiation of class "<unnamed>::pythonic::types::numpy_gexpr<Arg, S...> [with Arg=<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>, S=<<unnamed>::pythonic::types::normalized_slice>]" at line 633 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::numpy::functor::square, Args=<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>>]" at line 478 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::mul, Args=<<unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::numpy::functor::square, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>]" at line 58 of "fluidfft/fft2d/util_pythran.cpp" instantiation of class "__pythran_util_pythran::myfunc::type<argument_type0> [with argument_type0=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>]" at line 369 of "fluidfft/fft2d/util_pythran.cpp"module: Command not found.module: Command not found.In file included from fluidfft/fft2d/util_pythran.cpp(16):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1178): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<4, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 761 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^In file included from fluidfft/fft2d/util_pythran.cpp(16):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1226): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<5, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 816 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_gexpr.hpp(768): error: expression preceding parentheses of apparent call must have (pointer-to-) function type -> decltype(std::declval<value_type>()(s...)); ^ detected during: instantiation of class "<unnamed>::pythonic::types::numpy_gexpr<Arg, S...> [with Arg=<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>, S=<<unnamed>::pythonic::types::normalized_slice>]" at line 633 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::numpy::functor::square, Args=<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>>]" at line 478 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::mul, Args=<<unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::numpy::functor::square, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>]" at line 58 of "fluidfft/fft2d/util_pythran.cpp" instantiation of class "__pythran_util_pythran::myfunc::type<argument_type0> [with argument_type0=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>]" at line 369 of "fluidfft/fft2d/util_pythran.cpp"copying build/lib.linux-x86_64-3.6/fluidfft/fft2d/with_fftw1d.cpython-36m-x86_64-linux-gnu.so -> fluidfft/fft2dcopying build/lib.linux-x86_64-3.6/fluidfft/fft2d/with_fftw2d.cpython-36m-x86_64-linux-gnu.so -> fluidfft/fft2dcopying build/lib.linux-x86_64-3.6/fluidfft/fft2d/mpi_with_fftw1d.cpython-36m-x86_64-linux-gnu.so -> fluidfft/fft2dcopying build/lib.linux-x86_64-3.6/fluidfft/fft3d/with_fftw3d.cpython-36m-x86_64-linux-gnu.so -> fluidfft/fft3dcopying build/lib.linux-x86_64-3.6/fluidfft/fft3d/mpi_with_fftw1d.cpython-36m-x86_64-linux-gnu.so -> fluidfft/fft3dmodule: Command not found.module: Command not found.icc: command line warning #10006: ignoring unknown option '-Wno-unused-result'/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/interval.py:90: RuntimeWarning: invalid value encountered in double_scalars return Interval(self.low + other.low, self.high + other.high)error: can't copy 'build/lib.linux-x86_64-3.6/fluidfft/fft2d/util_pythran.cpython-36m-x86_64-linux-gnu.so': doesn't exist or not a regular file
I use gcc 5.3
pythran fluidfft/fft2d/util_pythran.py -v
running build_extnew_compiler returns <class 'distutils.unixccompiler.UnixCCompiler'>building 'util_pythran' extensionC compiler: mpicxx -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPICcreating /tmp/tmpk3e3y2qa/tmpcompile options: '-DENABLE_PYTHON_MODULE -D__PYTHRAN__=3 -DENABLE_PYTHON_MODULE -D__PYTHRAN__=3 -DPYTHRAN_BLAS_BLAS -DPYTHRAN_BLAS_BLAS -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/patch -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/patch -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -c'extra options: '-std=c++11 -fno-math-errno -w -fvisibility=hidden -fno-wrapv -std=c++11 -fno-math-errno -w -fvisibility=hidden -fno-wrapv'mpicxx: /tmp/tmpe765yepv.cppexec_command(['mpicxx', '-Wno-unused-result', '-Wsign-compare', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-m64', '-fPIC', '-m64', '-fPIC', '-fPIC', '-DENABLE_PYTHON_MODULE', '-D__PYTHRAN__=3', '-DENABLE_PYTHON_MODULE', '-D__PYTHRAN__=3', '-DPYTHRAN_BLAS_BLAS', '-DPYTHRAN_BLAS_BLAS', '-I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran', '-I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran', '-I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/patch', '-I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include', '-I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/patch', '-I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include', '-I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m', '-c', '/tmp/tmpe765yepv.cpp', '-o', '/tmp/tmpk3e3y2qa/tmp/tmpe765yepv.o', '-std=c++11', '-fno-math-errno', '-w', '-fvisibility=hidden', '-fno-wrapv', '-std=c++11', '-fno-math-errno', '-w', '-fvisibility=hidden', '-fno-wrapv'],)Retaining cwd: /home1/datahome/slgentil/test/fluidfft_preserve_environment([])_update_environment(...)module: Command not found.module: Command not found.In file included from /tmp/tmpe765yepv.cpp(19):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1178): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<4, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 761 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^In file included from /tmp/tmpe765yepv.cpp(19):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1226): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<5, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 816 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_gexpr.hpp(768): error: expression preceding parentheses of apparent call must have (pointer-to-) function type -> decltype(std::declval<value_type>()(s...)); ^ detected during: instantiation of class "<unnamed>::pythonic::types::numpy_gexpr<Arg, S...> [with Arg=<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>, S=<<unnamed>::pythonic::types::normalized_slice>]" at line 633 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::numpy::functor::square, Args=<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>>]" at line 478 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::mul, Args=<<unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::numpy::functor::square, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>]" at line 58 of "/tmp/tmpe765yepv.cpp" instantiation of class "__pythran_util_pythran::myfunc::type<argument_type0> [with argument_type0=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>]" at line 369 of "/tmp/tmpe765yepv.cpp"_update_environment(...)/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/interval.py:90: RuntimeWarning: invalid value encountered in double_scalars return Interval(self.low + other.low, self.high + other.high)module: Command not found.module: Command not found.icc: command line warning #10006: ignoring unknown option '-Wno-unused-result'[33mWARNING [0m [34mCompilation error, trying hard to find its origin...[0m[33mWARNING [0m [34mNop, I'm going to flood you with C++ errors![0m[31mCRITICAL[0m [34mCover me Jack. Jack? Jaaaaack!!!!E: error: Command "mpicxx -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -m64 -fPIC -m64 -fPIC -fPIC -DENABLE_PYTHON_MODULE -D__PYTHRAN__=3 -DENABLE_PYTHON_MODULE -D__PYTHRAN__=3 -DPYTHRAN_BLAS_BLAS -DPYTHRAN_BLAS_BLAS -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/patch -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/patch -I/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/numpy/core/include -I/home1/datahome/slgentil/.miniconda2/envs/test/include/python3.6m -c /tmp/tmpe765yepv.cpp -o /tmp/tmpk3e3y2qa/tmp/tmpe765yepv.o -std=c++11 -fno-math-errno -w -fvisibility=hidden -fno-wrapv -std=c++11 -fno-math-errno -w -fvisibility=hidden -fno-wrapv" failed with exit status 2[0mmodule: Command not found.module: Command not found.In file included from /tmp/tmpe765yepv.cpp(19):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1178): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<4, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 761 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^In file included from /tmp/tmpe765yepv.cpp(19):/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/types/ndarray.hpp(1226): error: declaration is incompatible with "auto <unnamed>::pythonic::types::__ndarray::getattr<5, <unnamed>::pythonic::types::numpy_texpr<E>>::operator()(const <unnamed>::pythonic::types::numpy_texpr<E> &)->decltype((<expression>))" (declared at line 816 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/ndarray.hpp") operator()(types::numpy_texpr<E> const &a) -> decltype( ^/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_gexpr.hpp(768): error: expression preceding parentheses of apparent call must have (pointer-to-) function type -> decltype(std::declval<value_type>()(s...)); ^ detected during: instantiation of class "<unnamed>::pythonic::types::numpy_gexpr<Arg, S...> [with Arg=<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>, S=<<unnamed>::pythonic::types::normalized_slice>]" at line 633 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::numpy::functor::square, Args=<<unnamed>::pythonic::types::numpy_iexpr<<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>>]" at line 478 of "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/pythonic/include/types/numpy_expr.hpp" instantiation of class "<unnamed>::pythonic::types::numpy_expr<Op, Args...> [with Op=<unnamed>::pythonic::operator_::functor::mul, Args=<<unnamed>::pythonic::types::numpy_expr<<unnamed>::pythonic::numpy::functor::square, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>, <unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>>]" at line 58 of "/tmp/tmpe765yepv.cpp" instantiation of class "__pythran_util_pythran::myfunc::type<argument_type0> [with argument_type0=<unnamed>::pythonic::types::ndarray<double, <unnamed>::pythonic::types::pshape<long, long>>]" at line 369 of "/tmp/tmpe765yepv.cpp"
I tried without defining CC and CXX and I got a different error
Using /home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packagesFinished processing dependencies for fluidfft==0.2.6/home1/datahome/slgentil/test/fluidfft/purepymake.py:109: UserWarning: Unable to find MPI compile flags.Setting mpicxx_compile_words=[] "Unable to find MPI compile flags."setup.py:169: UserWarning: When numpy uses mkl (as for example with conda), there are symbol conflicts between mkl and fftw. This can lead to a segmentation fault so we do not build the extensions using fftwmpi. "When numpy uses mkl (as for example with conda), "/home1/datahome/slgentil/.miniconda2/envs/test/lib/python3.6/site-packages/pythran/interval.py:90: RuntimeWarning: invalid value encountered in double_scalars return Interval(self.low + other.low, self.high + other.high)
These are only warnings. It seems to me that it works and that you can try to use fluidfft and fluidsim.
As written in one of these warnings, MKL is not compatible with fftw3_mpi (not my fault), so if you want to use fft using fftw3_mpi, you shouldn't use numpy linked with MKL. This isssue is explained in the documentation (https://fluidfft.readthedocs.io/en/latest/install.html)
When MPI type is not detected, it is sufficient to set the environment variable as export FLUIDDYN_FORCE_MPI=1.
Bug fluidfft: command to get the compile flag for mpicxx with Intel compiler (fixed)
In my humble opinion, it might be benificial for the user to set compile flags (via site.cfg), rather implementing something universal.
Pythran priority to chose the compiler
I am not 100% sure what the problem is but as I understand you can set MPICXX for the Cython extensions and the [environ] to override the CXX environment variable for pythran. i.e. your site.cfg should look like:
...[environ]MPICXX=mpicxx## From fluidsim site.cfg## To modify compiler used to build Pythran extensions (or alternatively,## set ~/.pythranrc. A word of caution --- the pythranrc approach may result in## race condition for setting and unsetting compilers for pythran > 0.8.6):## This happens when extensions are built in parallel.CXX=clang++ # or g++
The logic that Serge had for CXX > .pythranrc was that environment variables are more temporary than config files, and it makes sense.