[petsc-users] petsc4py problem

[Satish Balay]

well if you are using numpy, boost from your code - you can always do
that.

'--with-numpy=1 --with-boost=1' suggests that you want petsc to use
these externalpackages. But PETSc doesn't provide interface to these
packages [they are provides to satisfy dependencies of some
externalpackages - for eg: '--downlaod-boost --download-trilinos']

So when so many unneeded options are listed - its not clear if you
really were seeking this functionality [which doesn't exist] or trying
out a generic build by enabling all possible options.

memalign is a property of compiler - and configure attempts to detect
thisvalue .  Not sure what you would get by changing this
value. [other than test if something in petsc breaks with it or not -
esp when it doesn't match the compiler behavior..]

And you have lots of options enabled - so it wasn't clear if you
actually needed them.. [like --with-log=0 --with-pic=1 LDFLAGS="-lgfortran -g" --LIBS=- lgfortran]

Satish

On Mon, 16 May 2016, Barry Smith wrote:

>   
>   You should be able to build PETSc with C and use it from Chombo even though Chombo is built in C++. You shouldn't need --with-c-support --with-clanguage=C++
> 
>   Barry
> 
> > On May 16, 2016, at 11:11 PM, Juha Jaykka <juhaj at iki.fi> wrote:
> > 
> >> 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
> > 
> 
>