[petsc-users] configuration option for PETSc on cluster

Tue Apr 24 09:08:31 CDT 2018

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
>>>>>>
>>