On Mon, Sep 1, 2014 at 3:22 AM, Åsmund Ervik <asmund.er...@ntnu.no> wrote:
> Hi, > > When I try to configure PETSc with HDF5 by using "--download-hdf5", I > get a very long error message from PETSc compiling HDF5 (see attached > error-down-hdf5.tar.gz) which boils down to > > h5tools_str.c: In function 'h5tools_str_indent': > h5tools_str.c:635:1: error: expected expression before '/' token > > This happens both with PETSc 3.5.1 and 3.4.5. It appears this was an > error in HDF5 version 1.8.10, cf. > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=711777 > > > Subsequently I installed HDF5 v. 1.8.12 using my OS package manager and > then tried to configure with "--with-hdf5 > --with-hdf5-dir=/path/to/system/hdf5" using PETSc 3.5.1. This time both > configure and make were successful, but "make test" fails with loads of > undefined references to PETSc HDF5 stuff (see below). configure.log and > make.log attached also for this case (error-with-hdf5.tar.gz) > It did not build src/sys/classes/viewer/impls/hdf5/, clearly from the log. However, it should have. We have been trying to understand why Make behaves in a bad way after configuration failure. It should go away with make clean and another make. Jed, here is another case of this make bug. Thanks, Matt > > If you need any more info, just ask :) > > Regards, > Åsmund > > > Using PETSC_DIR=/opt/petsc/optim_gfortran and PETSC_ARCH=linux > *******************Error detected during compile or > link!******************* > See http://www.mcs.anl.gov/petsc/documentation/faq.html > /opt/petsc/optim_gfortran/src/snes/examples/tutorials ex19 > > ********************************************************************************* > /opt/petsc/optim_gfortran/linux/bin/mpicc -o ex19.o -c -fPIC -Wall > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O3 > -march=native -I/opt/petsc/optim_gfortran/include > -I/opt/petsc/optim_gfortran/linux/include -I/usr/include `pwd`/ex19.c > /opt/petsc/optim_gfortran/linux/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -O3 -march=native -o ex19 > ex19.o -Wl,-rpath,/opt/petsc/optim_gfortran/linux/lib > -L/opt/petsc/optim_gfortran/linux/lib -lpetsc > -Wl,-rpath,/opt/petsc/optim_gfortran/linux/lib -lHYPRE > -Wl,-rpath,/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.0 > -L/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.0 -lmpichcxx -lstdc++ > -lsuperlu_4.3 -lflapack -lfblas -lparmetis -lmetis -lX11 -lpthread -lssl > -lcrypto -Wl,-rpath,/usr/lib -L/usr/lib -lhdf5_hl -lhdf5 -lm -lmpichf90 > -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpichcxx -lstdc++ -ldl > -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5GetFileId' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5PushGroup' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5PopGroup' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerCreate_HDF5' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5ReadAttribute' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5WriteAttribute' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5SetTimestep' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PETSC_VIEWER_HDF5_' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5HasAttribute' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5GetTimestep' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5GetGroup' > collect2: error: ld returned 1 exit status > makefile:108: recipe for target 'ex19' failed > make[3]: [ex19] Error 1 (ignored) > /usr/bin/rm -f ex19.o > *******************Error detected during compile or > link!******************* > See http://www.mcs.anl.gov/petsc/documentation/faq.html > /opt/petsc/optim_gfortran/src/snes/examples/tutorials ex5f > ********************************************************* > /opt/petsc/optim_gfortran/linux/bin/mpif90 -c -fPIC -Wall > -Wno-unused-variable -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > -march=native -fno-protect-parens -fstack-arrays > -I/opt/petsc/optim_gfortran/include > -I/opt/petsc/optim_gfortran/linux/include -I/usr/include -o ex5f.o > ex5f.F > /opt/petsc/optim_gfortran/linux/bin/mpif90 -fPIC -Wall > -Wno-unused-variable -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > -march=native -fno-protect-parens -fstack-arrays -o ex5f ex5f.o > -Wl,-rpath,/opt/petsc/optim_gfortran/linux/lib > -L/opt/petsc/optim_gfortran/linux/lib -lpetsc > -Wl,-rpath,/opt/petsc/optim_gfortran/linux/lib -lHYPRE > -Wl,-rpath,/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.0 > -L/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.0 -lmpichcxx -lstdc++ > -lsuperlu_4.3 -lflapack -lfblas -lparmetis -lmetis -lX11 -lpthread -lssl > -lcrypto -Wl,-rpath,/usr/lib -L/usr/lib -lhdf5_hl -lhdf5 -lm -lmpichf90 > -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpichcxx -lstdc++ -ldl > -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5GetFileId' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5PushGroup' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5PopGroup' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerCreate_HDF5' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5ReadAttribute' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5WriteAttribute' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5SetTimestep' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PETSC_VIEWER_HDF5_' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5HasAttribute' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5GetTimestep' > /opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to > `PetscViewerHDF5GetGroup' > collect2: error: ld returned 1 exit status > makefile:50: recipe for target 'ex5f' failed > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener