[petsc-users] petsc4py problem

[Juha Jaykka]

> Looks like there is an issue with petsc4py and --with-log=0 . Try rebuilding

Yea, noticed that, too.

> --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..

I'm not sure I know what you mean by "general use" but this is for my use, so 
I'd guess not what you'd mean by "general".

Anyway, numpy and boost I can probably live without, C++ is necessary because 
of Chombo (it might be possible to tweak things to work without it); c-support 
I don't know: I thought there wouldn't be C bindings otherwise, just C++?

64-bit alignment is something I'm testing, but will probably be a good idea on 
Knights Landing.

Cheers,
Juha

> 
> 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