Error when building with intel mkl 7.21

[Brad Aagaard]

Ben-

Matt's suggestion of not using shared libraries may work, but it looks to me 
like PETSc is trying to link 64-bit PETSc libraries against 32-bit MKL 
libraries (note the directory 32 in the MKL path). I don't know the layout of 
the MKL tree but you probably need to adjust your configuration line to make 
sure PETSc finds the 64-bit MKL libraries (assuming you have them).

Brad

On Friday 08 December 2006 9:19 am, Matthew Knepley wrote:
> Your MKL is incompatible with shared libraries on 64-bit machines because
> it was compiled without -fPIC. You need to configure with --with-shared=0.
>
>    Matt
>
> On 12/8/06, Ben Tay <zonexo at gmail.com> wrote:
> > Hi,
> >
> > I tried to build the libraries on my school's em64t machines which is
> > supposed to be faster. The compilers are intel cc,fc ver 9. mkl is
> > 7.21.I'm trying to build a shared library. My command is
> >
> > ./config/configure.py --with-vendor-compilers=intel
> > --with-blas-lapack-dir=/opt/intel/mkl721/ --with-mpi=0
> > --with-x=0 --with-shared
> >
> > during compilation, I can get the following error msg:
> >
> > making shared libraries in
> > /lsftmp/g0306332/petsc-2.3.2-p7//lib/linux64-nompi-shared
> > building libpetsc.so
> > building libpetscvec.so
> > building libpetscmat.so
> > ld:
> > /usr/local/intel/mkl721cluster/lib/32/libmkl_lapack.a(dgetrf_omp.o):
> > relocation R_X86_64_PC32 against
> > `_mkl_lapack_dgetrf_omp_271__par_loop0' can not be used
> > when making a shared object; recompile with -fPIC
> > ld: final link failed: Bad value
> > make[2]: [shared_linux] Error 1 (ignored)
> > building libpetscdm.so
> > building libpetscksp.so
> > ld:
> > /usr/local/intel/mkl721cluster/lib/32/libmkl_lapack.a(dgeqrf_omp.o):
> > relocation R_X86_64_PC32 against
> > `_mkl_lapack_dgeqrf_301__par_loop0' can not be used when
> > making a shared object; recompile with -fPIC
> > ld: final link failed: Bad value
> > make[2]: [shared_linux] Error 1 (ignored)
> > building libpetscsnes.so
> > building libpetscts.so
> > building libpetsccontrib.so
> >
> > The examples ran ok though. However, when I try to run my own code (which
> > worked on another server), I get the following error msg:
> >
> > petsc_sub.o(.text+0xcb): In function `petsc_solver':
> > /nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:46: undefined
> > reference to `matcreateseqaij_'
> > petsc_sub.o(.text+0x150):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:52
> >: undefined reference to `kspcreate_'
> > petsc_sub.o(.text+0x657):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:10
> >5: undefined reference to `matsetvalues_'
> > petsc_sub.o(.text+0x73e):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:11
> >0: undefined reference to `matsetvalues_'
> > petsc_sub.o(.text+0x823):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:11
> >5: undefined reference to `matsetvalues_'
> > petsc_sub.o(.text+0x90a):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:12
> >0: undefined reference to `matsetvalues_'
> > petsc_sub.o(.text+0xa01):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:12
> >5: undefined reference to `matsetvalues_'
> > petsc_sub.o(.text+0xafa):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:13
> >0: more undefined references to `matsetvalues_' follow
> > petsc_sub.o(.text+0x3501): In function `petsc_solver':
> > /nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:402:
> > undefined reference to `matassemblybegin_'
> > petsc_sub.o(.text+0x3526):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:4
> >03: undefined reference to `matassemblyend_'
> > petsc_sub.o(.text+0x356d):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:4
> >05: undefined reference to `kspsetoperators_'
> > petsc_sub.o(.text+0x3595):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:4
> >07: undefined reference to `kspgetpc_'
> > petsc_sub.o(.text+0x35e4):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:4
> >11: undefined reference to `kspsettype_'
> > petsc_sub.o(.text+0x3633):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:4
> >16: undefined reference to `pcsettype_'
> > petsc_sub.o(.text+0x364e):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:4
> >19: undefined reference to `kspsetfromoptions_'
> > petsc_sub.o(.text+0x36ad):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:4
> >25: undefined reference to `kspsettolerances_'
> > petsc_sub.o(.text+0x36e2):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:4
> >27: undefined reference to `kspsolve_'
> > petsc_sub.o(.text+0x3704):/nfs/home/enduser/g0306332/ns2d_c/petsc_sub.F:4
> >29: undefined reference to `kspgetconvergedreason_'
> > /tmp/ifortuYcl1b.o(.text+0x8f2e): In function `ns2d_c':
> > /nfs/home/enduser/g0306332/ns2d_c/ns2d_c.f90:825: undefined
> > reference to `matdestroy_'
> > /tmp/ifortuYcl1b.o(.text+0x8f4c):/nfs/home/enduser/g0306332/ns2d_c/ns2d_c
> >.f90:827: undefined reference to `kspdestroy_'
> > make: *** [a.out] Error 1
> >
> > It happens when I'm trying to link all the files together. compiling
> > petsc_sub.F has no problem and I am using the same option as for the
> > examples. Also if I use the downloaded blas/lapack instead of mkl, there
> > is also no problem so I guess the problem is from mkl...
> >
> > Hope someone can help. Thank you.