[petsc-users] petsc4py problem

[Satish Balay]

Looks like there is an issue with petsc4py and --with-log=0 . Try rebuilding without this option.

Are you sure you really need petsc with these options?

--with-numpy=1 --with-boost=1 --with-c-support --with-clanguage=C++
--with-memalign=64 etc don't really make sense to me for a general use install..

And most externalpackages are not tested with --with-64-bit-indices

Satish

On Mon, 16 May 2016, Juha Jaykka wrote:

> Dear list,
> 
> I cannot get petsc4py 3.7 to work. I have petsc compiled with a bunch of 
> options to suit my needs (sorry for the un-escaped line breaks):
> 
> --COPTFLAGS="-Ofast " --CXXOPTFLAGS="-Ofast " --CXX_LINKER_FLAGS="-Wl,--no-as-
> needed -lgfortran" --FOPTFLAGS="-Ofast " --LDFLAGS="-lgfortran -g" --LIBS=-
> lgfortran --download-chombo=yes --download-sprng=no --
> prefix=/home/juhaj/progs+3.7/petsc --with-64-bit-indices --with-afterimage-
> include=/usr/include/libAfterImage --with-afterimage-lib=/usr/lib/x86_64-
> linux-gnu/libAfterImage.so --with-afterimage=1 --with-blas-lapack-
> include=/usr/include/openblas --with-blas-lib=/usr/lib/openblas-
> base/libblas.so --with-boost=1 --with-c-support --with-clanguage=C++ --with-
> debugging=0 --with-external-packages-dir=/home/juhaj/progs+3.7/automatic-
> downloads --with-fftw-include=/usr/include --with-fftw-lib="[/usr/lib/x86_64-
> linux-gnu/libfftw3.so,/usr/lib/x86_64-linux-gnu/libfftw3_mpi.so]" --with-
> fftw=1 --with-fortran-interfaces=1 --with-gnu-compilers=1 --with-hdf5-
> include=/usr/include/hdf5/openmpi --with-hdf5-lib=/usr/lib/x86_64-linux-
> gnu/libhdf5_openmpi.so --with-hdf5=1 --with-hwloc=1 --with-hypre-
> include=/usr/include --with-hypre-lib=/usr/lib/libHYPRE_IJ_mv-2.8.0b.so --
> with-hypre=1 --with-lapack-lib=/usr/lib/openblas-base/liblapack.so --with-
> log=0 --with-memalign=64 --with-metis=0 --with-mpi-shared=1 --with-mpi=1 --
> with-mumps=0 --with-netcdf-include=/usr/include/ --with-netcdf-
> lib=/usr/lib/libnetcdf.so --with-netcdf=1 --with-numpy=1 --with-openmp=1 --
> with-parmetis=0 --with-pic=1 --with-scalapack-include=/usr/include --with-
> scalapack-lib=/usr/lib/libscalapack-openmpi.so --with-scalapack=1 --with-
> scalar-type=real --with-shared-libraries --with-spooles-
> include=/usr/include/spooles --with-spooles-lib=/usr/lib/libspooles.so --with-
> spooles=1 --with-suitesparse=0 --with-tetgen=0 --with-triangle=0 --with-
> valgrind=1
> 
> and after installing petsc, pip install petsc4py fails with
> 
> http://paste.debian.net/686482/
> 
> I don't really know where to start looking for the problem. Any idea how to 
> fix this?
> 
> Cheers,
> Juha
> 
>