[petsc-users] petsc+chombo

[Juha Jaykka]

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.mpif90.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
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