[petsc-users] configuration option for PETSc on cluster

Tue Apr 24 09:03:04 CDT 2018

Ok - I do see: libmkl_intel_lp64.so libmkl_sequential.so libmkl_core.so - these should
be the ones that get picked up.

I do not know why 'cc' is picking up static libraries instead of the
shared ones. Perhaps it needs an extra option

'LDFLAGS=-dynamic'

Satish

On Tue, 24 Apr 2018, Samuel Lanthaler wrote:

> Dear Satish,
> 
> I get the following when doing the ls:
> 
> [lanthale at daint103 mkl]$ ls
> /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/
> libmkl_ao_worker.so             libmkl_blacs_sgimpt_lp64.so
> libmkl_intel_lp64.a        libmkl_sequential.so
> libmkl_avx2.so                  libmkl_blas95_ilp64.a libmkl_intel_lp64.so
> libmkl_tbb_thread.a
> libmkl_avx512_mic.so            libmkl_blas95_lp64.a libmkl_intel_thread.a
> libmkl_tbb_thread.so
> libmkl_avx512.so                libmkl_cdft_core.a libmkl_intel_thread.so
> libmkl_vml_avx2.so
> libmkl_avx.so                   libmkl_cdft_core.so libmkl_lapack95_ilp64.a
> libmkl_vml_avx512_mic.so
> libmkl_blacs_intelmpi_ilp64.a   libmkl_core.a libmkl_lapack95_lp64.a
> libmkl_vml_avx512.so
> libmkl_blacs_intelmpi_ilp64.so  libmkl_core.so libmkl_mc3.so
> libmkl_vml_avx.so
> libmkl_blacs_intelmpi_lp64.a    libmkl_def.so libmkl_mc.so
> libmkl_vml_cmpt.so
> libmkl_blacs_intelmpi_lp64.so   libmkl_gf_ilp64.a libmkl_pgi_thread.a
> libmkl_vml_def.so
> libmkl_blacs_openmpi_ilp64.a    libmkl_gf_ilp64.so libmkl_pgi_thread.so
> libmkl_vml_mc2.so
> libmkl_blacs_openmpi_ilp64.so   libmkl_gf_lp64.a libmkl_rt.so
> libmkl_vml_mc3.so
> libmkl_blacs_openmpi_lp64.a     libmkl_gf_lp64.so libmkl_scalapack_ilp64.a
> libmkl_vml_mc.so
> libmkl_blacs_openmpi_lp64.so    libmkl_gnu_thread.a libmkl_scalapack_ilp64.so
> locale
> libmkl_blacs_sgimpt_ilp64.a     libmkl_gnu_thread.so libmkl_scalapack_lp64.a
> libmkl_blacs_sgimpt_ilp64.so    libmkl_intel_ilp64.a libmkl_scalapack_lp64.so
> libmkl_blacs_sgimpt_lp64.a      libmkl_intel_ilp64.so libmkl_sequential.a
> 
> 
> Cheers,
> Samuel
> 
> On 04/24/2018 03:50 PM, Satish Balay wrote:
> > 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
> >>>>
> >>
> 
> 