[petsc-users] configuration option for PETSc on cluster

[Satish Balay]

>>>>>>
Executing: cc  -o /tmp/petsc-tyd_Hm/config.libraries/conftest     -O /tmp/petsc-tyd_Hm/config.libraries/conftest.o  -Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lstdc++ -ldl
Possible ERROR while running linker: exit code 256
stderr:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libmkl_core.a(mkl_semaphore.o): In function `mkl_serv_load_inspector':
mkl_semaphore.c:(.text+0x123): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libmkl_core.a(dgetrs.o): In function `mkl_lapack_dgetrs':
dgetrs_gen.f:(.text+0x224): undefined reference to `mkl_blas_dtrsm'
dgetrs_gen.f:(.text+0x2b1): undefined reference to `mkl_blas_dtrsm'
dgetrs_gen.f:(.text+0x2e7): undefined reference to `mkl_lapack_dlaswp'
<<<<<<<<

For some reason the compiler is picking up static version of MKL - instead of shared libraries.

What do you have for:

ls /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/

Satish

On Tue, 24 Apr 2018, Samuel Lanthaler wrote:

> Dear Satish and Stefano,
> 
> Thank you for your answers. I believe I had initially tried to use the option
> --with-blaslapack-dir=[...], instead of specifying lib and include directly.
> But that gives me an error message:
> 
> *******************************************************************************
>          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for
> details):
> -------------------------------------------------------------------------------
> You set a value for --with-blaslapack-dir=<dir>, but
> /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl cannot be used
> *******************************************************************************
> 
> I attach the new configure.log. Do you think there is something wrong with the
> mkl version that I'm trying to use? Or is it only related to petsc?
> 
> Cheers,
> Samuel
> 
> 
> On 04/24/2018 02:55 PM, Satish Balay wrote:
> > On Tue, 24 Apr 2018, Samuel Lanthaler wrote:
> >
> >> Hi there,
> >>
> >> I was wondering if you could help me with the correct configuration of
> >> PETSc-dev version on a cluster (https://www.cscs.ch/)? I'm not sure which
> >> information would be useful to you, but basically the problem seems to be
> >> in
> >> correctly compiling it with intel compiler and the existing mkl library.
> >>
> >> The pre-installed mkl version is
> >>
> >> intel/17.0.4.196
> >>
> >> I have tried various things and finally, I got it at least to compile with
> >> the
> >> following options (options chosen in reference to the mkl link advisor...):
> >>
> >> ./configure --with-fc=ftn --with-cc=cc --with-cxx=CC --with-debugging=0
> >> --with-scalar-type=complex --download-scalapack --download-mumps=yes
> >> --download-superlu --with-batch --known-mpi-shared-libraries=1
> >> *--with-blaslapack-lib=*" ${MKLROOT}/lib/intel64/libmkl_blas95_lp64.a
> >> ${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a -Wl,--start-group
> >> ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a
> >> ${MKLROOT}/lib/intel64/libmkl_sequential.a
> >> ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl"
> >> *--with-blaslapack-include*="[/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include/intel64/lp64]"
> > Can you remove the above 2 options [--with-blaslapack-lib,
> > --with-blaslapack-include] and use:
> >
> > --with-blas-lapack-dir=${MKLROOT}
> >
> > And see if you still have this problem?
> >
> > Satish
> >
> >> --known-64-bit-blas-indices=0
> >>
> >> After compilation, when trying to compile
> >> /users/lanthale/petsc-git/src/snes/examples/tutorials/ex5f I get linking
> >> errors (attached). Would anyone be able to help me out here? I really don't
> >> have a good understanding of this.
> >>
> >> I'm attaching the configuration.log file, as well as the linking errors
> >> when
> >> trying to compile ex5f.
> >>
> >> Thank you very much in advance!
> >>
> >> Best regards,
> >> Samuel
> >>
> 
>