[petsc-users] Configure/make with "--download-hdf5" or "--with-hdf5-dir=" crashes

[Matthew Knepley]

On Mon, Sep 1, 2014 at 3:22 AM, Åsmund Ervik <asmund.ervik at 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
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