[petsc-users] configuration option for PETSc on cluster

Tue Apr 24 09:14:21 CDT 2018

Sorry I should have clarified - its a configure option.

Satish

On Tue, 24 Apr 2018, Samuel Lanthaler wrote:

> Sorry, I'm confused: Can I add this somehow when doing the ./configure? Or do
> you mean to add it when compiling ex5f with the configuration I had initially?
> 
> Cheers,
> Samuel
> 
> 
> On 04/24/2018 04:03 PM, Satish Balay wrote:
> > 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
> >>>>>>
> >>
> 
> 
> 