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 <[email protected]> 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 > > > >
