[petsc-users] petsc+chombo

[Juha Jaykka]

Dear Barry,

Please find the configure.log at http://www.iki.fi/~juhaj/configure.log.

On a more general level, I wonder if the chombo-petsc interoperability is 
documented anywhere? I grepped through the examples and came up blank.

Cheers,
Juha

On Thursday 01 Oct 2015 09:53:26 Barry Smith wrote:
>   We absolutely NEED configure.log to help you.
> 
>   Barry
> 
> > On Oct 1, 2015, at 9:24 AM, Juha Jaykka <juhaj at iki.fi> wrote:
> > 
> > Hi list,
> > 
> > I'm trying to compile PETSc 3.6 with --download-chombo, but keep failing.
> > It seems to me the chombo build system is not told to link in
> > libgfortran.so, but no matter how I try to convince PETSc to add that, it
> > won't. How should this be used, please?
> > 
> > The full configure line is
> > 
> > ./configure --prefix=/home/juhaj/progs+3.6/petsc --with-shared-libraries
> > --
> > with-debugging=0 \
> > 
> >          --useThreads 0 --with-clanguage=C++ --with-c-support \
> >          --with-fortran-interfaces=1 \
> >          --with-mpi=1 --with-mpi-shared=1 \
> > 	  
> > 	  --with-blas-lapack-include=/usr/include/openblas --with-blas-
> > 
> > lib=/usr/lib/openblas-base/libblas.so --with-lapack-lib=/usr/lib/openblas-
> > base/liblapack.so \
> > 
> >          --with-scalapack=1 --with-scalapack-include=/usr/include \
> >          --with-scalapack-lib=/usr/lib/libscalapack-openmpi.so \
> >          --with-mumps=0 \
> > 	  
> > 	  --with-suitesparse=0 \
> > 	  
> >          --with-spooles=1 --with-spooles-include=/usr/include/spooles \
> >          --with-spooles-lib=/usr/lib/libspooles.so \
> >          --with-hypre=1 --with-hypre-include=/usr/include --with-hypre-
> > 
> > lib=/usr/lib/libHYPRE_IJ_mv-2.8.0b.so \
> > 
> >          --with-fftw=1 --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-hdf5=1 --with-hdf5-include=/usr/include/hdf5/openmpi
> >          --with-
> > 
> > hdf5-lib=/usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so \
> > 
> > 	  --CXX_LINKER_FLAGS="-Wl,--no-as-needed -lgfortran" --LDFLAGS="-
> > 
> > lgfortran -g" --LIBS="-lgfortran" \
> > 
> > 	  --with-clean=1 --with-memalign=64 --with-log=0 --with-valgrind=1 \
> > 	  --with-afterimage=1 --with-afterimage-
> > 
> > include=/usr/include/libAfterImage --with-afterimage-lib=/usr/lib/x86_64-
> > linux-gnu/libAfterImage.so \
> > 
> > 	  --with-boost=1 \
> > 	  --with-netcdf=1 --with-netcdf-include=/usr/include/ --with-netcdf-
> > 
> > lib=/usr/lib/libnetcdf.so \
> > 
> > 	  --with-triangle=0 \
> > 	  --with-numpy=1 \
> > 	  --with-hwloc=1  --with-external-packages-
> > 
> > dir=/home/juhaj/progs+3.6/automatic-downloads \
> > 
> > 	  --with-parmetis=0 --with-metis=0 \
> > 	  --with-tetgen=0 \
> > 	  --with-scalar-type=real --with-pic=1 --with-gnu-compilers=1 --with-
> > 
> > openmp=1 \
> > 
> > 	  --with-64-bit-indices \
> > 	  --download-chombo
> > 
> > and the final error in configure is
> > 
> > /bin/csh -f -c "mpicxx -g
> > o/2d.Linux.64.mpicxx.mpif90.DEBUG/testFourthOrderFillPatch.o   -
> > L/home/juhaj/progs+3.6/automatic-downloads/arch-linux2-cxx-
> > opt/Chombo/lib/test/AMRTimeDependent/../.. -
> > lamrtimedependent2d.Linux.64.mpicxx.mpif90.DEBUG -
> > lamrtools2d.Linux.64.mpicxx.mpif90.DEBUG -
> > lboxtools2d.Linux.64.mpicxx.mpif90.DEBUG -
> > lbasetools2d.Linux.64.mpicxx.mpif90.DEBUG 
> > -Wl,-rpath,/usr/lib/x86_64-linux- gnu -L/usr/lib/x86_64-linux-gnu
> > -lhdf5_openmpi     -Wl,-
> > rpath,/usr/lib/openblas-base -L/usr/lib/openblas-base -llapack -Wl,-
> > rpath,/usr/lib/openblas-base -L/usr/lib/openblas-base -lblas  -o
> > testFourthOrderFillPatch2d.Linux.64.mpicxx.mpif90.DEBUG.ex |&  awk -f
> > /home/juhaj/progs+3.6/automatic-downloads/arch-linux2-cxx-
> > opt/Chombo/lib/test/AMRTimeDependent/../../mk/tempnam.awk"
> > /usr/bin/ld: /home/juhaj/progs+3.6/automatic-downloads/arch-linux2-cxx-
> > opt/Chombo/lib/test/AMRTimeDependent/../../libamrtools2d.Linux.64.mpicxx.m
> > pif90.DEBUG.a(CFLeastSquares.o): undefined reference to symbol
> > '_gfortran_transfer_integer_write@@GFORTRAN_1.4'
> > /usr/lib/x86_64-linux-gnu/libgfortran.so.3: error adding symbols: DSO
> > missing from command line
> > collect2: error: ld returned 1 exit status
> > 
> > 
> > 
> > Cheers,
> > Juha
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 819 bytes
Desc: This is a digitally signed message part.
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20151002/9662e594/attachment.pgp>