[petsc-users] Fail to Configure petsc-3.6.1

[Jed Brown]

Rongliang Chen <rongliang.chan at gmail.com> writes:

> Hi Jed,
>
> Thanks for your reply.
>
> I checked the netcdf and hdf5's config.log and could not find any 
> possible solutions. Can you help me check these two files again? The two 
> files are attached. Thanks.

It looks to me like libhdf5.a needs to be linked with -ldl, which partly
defeats the intent of static linking.  PETSc folks, do we blame this on
HDF5 with --disable-shared not being a truly static build?  Should we
pass LDLIBS=-ldl so that NetCDF can link?

This likely all works if you use shared libraries.  (I can't believe
this is still a debate in 2015.)

configure:16585: mpicc -o conftest -g3 -O0 -I/home/rlchen/soft/petsc-3.6.1/64bit-debug/include  conftest.c -lhdf5  -lm -Wl,-rpath,/home/rlchen/soft/petsc-3.6.1/64bit-debug/lib -L/home/rlchen/soft/petsc-3.6.1/64bit-debug/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz >&5
/home/rlchen/soft/petsc-3.6.1/64bit-debug/lib/libhdf5.a(H5PL.o): In function `H5PL__open':
/home/rlchen/soft/petsc-3.6.1/64bit-debug/externalpackages/hdf5-1.8.12/src/H5PL.c:535: undefined reference to `dlopen'
/home/rlchen/soft/petsc-3.6.1/64bit-debug/externalpackages/hdf5-1.8.12/src/H5PL.c:536: undefined reference to `dlerror'
/home/rlchen/soft/petsc-3.6.1/64bit-debug/externalpackages/hdf5-1.8.12/src/H5PL.c:544: undefined reference to `dlsym'
/home/rlchen/soft/petsc-3.6.1/64bit-debug/lib/libhdf5.a(H5PL.o): In function `H5PL__search_table':
/home/rlchen/soft/petsc-3.6.1/64bit-debug/externalpackages/hdf5-1.8.12/src/H5PL.c:627: undefined reference to `dlsym'
/home/rlchen/soft/petsc-3.6.1/64bit-debug/lib/libhdf5.a(H5PL.o): In function `H5PL__close':
/home/rlchen/soft/petsc-3.6.1/64bit-debug/externalpackages/hdf5-1.8.12/src/H5PL.c:661: undefined reference to `dlclose'
collect2: error: ld returned 1 exit status
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