[petsc-users] configuration option for PETSc on cluster
Satish Balay
balay at mcs.anl.gov
Tue Apr 24 11:33:57 CDT 2018
Hm - I'm not sure why configure didn't try and set -fPIC compiler options.
Workarround is:
CFLAGS=-fPIC FFLAGS=-fPICC CXXFLAGS=-fPIC
or alternatively - you can disable sharedlibraries
--with-shared-libraries=0
Satish
On Tue, 24 Apr 2018, Samuel Lanthaler wrote:
> Dear Satish,
>
> As you suggested, the configure appears to work with
>
> ./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-dir=${MKLROOT} --known-64-bit-blas-indices=0
> --LDFLAGS="-dynamic"
>
> However, after doing the reconfigure, I tried to compile using make, and ran
> into trouble with CLINKER:
>
> [...]
> CC arch-complex/obj/sys/classes/draw/impls/x/xops.o
> CLINKER arch-complex/lib/libpetsc.so.3.09.0
> Warning:
> -dynamic was already seen on command line, overriding with -shared.
> /usr/bin/ld: arch-complex/obj/sys/fsrc/somefort.o: relocation R_X86_64_32
> against `petscfortran5_' can not be used when making a shared object;
> recompile with -fPIC
> arch-complex/obj/sys/fsrc/somefort.o: error adding symbols: Bad value
> [...]
> **************************ERROR*************************************
> Error during compile, check arch-complex/lib/petsc/conf/make.log
> Send it and arch-complex/lib/petsc/conf/configure.log to
> petsc-maint at mcs.anl.gov
> ********************************************************************
> makefile:30: recipe for target 'all' failed
> make: *** [all] Error 1
>
> Any ideas? Again, I'm attaching the .log files.
>
>
>
> On 04/24/2018 04:14 PM, Satish Balay wrote:
> > Sorry I should have clarified - its a configure option.
> >
> > Satish
> >
> > On Tue, 24 Apr 2018, Samuel Lanthaler wrote:
> >
> >> Sorry, I'm confused: Can I add this somehow when doing the ./configure? Or
> >> do
> >> you mean to add it when compiling ex5f with the configuration I had
> >> initially?
> >>
> >> Cheers,
> >> Samuel
> >>
> >>
> >> On 04/24/2018 04:03 PM, Satish Balay wrote:
> >>> Ok - I do see: libmkl_intel_lp64.so libmkl_sequential.so libmkl_core.so -
> >>> these should
> >>> be the ones that get picked up.
> >>>
> >>> I do not know why 'cc' is picking up static libraries instead of the
> >>> shared ones. Perhaps it needs an extra option
> >>>
> >>> 'LDFLAGS=-dynamic'
> >>>
> >>> Satish
> >>>
> >>> On Tue, 24 Apr 2018, Samuel Lanthaler wrote:
> >>>
> >>>> Dear Satish,
> >>>>
> >>>> I get the following when doing the ls:
> >>>>
> >>>> [lanthale at daint103 mkl]$ 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
> >>>>>>>>
> >>
> >>
>
>
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