[petsc-users] configuration option for PETSc on cluster
Samuel Lanthaler
s.lanthaler at gmail.com
Tue Apr 24 11:23:12 CDT 2018
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
>>>>>>>>
>>
>>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: make.log
Type: text/x-log
Size: 86371 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20180424/059172c6/attachment-0002.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: configure.log
Type: text/x-log
Size: 14667608 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20180424/059172c6/attachment-0003.bin>
More information about the petsc-users
mailing list