[petsc-users] PETSC on Cray Hazelhen
Stefano Zampini
stefano.zampini at gmail.com
Tue Jun 13 08:42:59 CDT 2017
Guilherme,
here is my debug configuration (with shared libraries) in PETSc on a XC40
'--CFLAGS=-mkl=sequential -g -O0 ',
'--CXXFLAGS=-mkl=sequential -g -O0 ',
'--FFLAGS=-mkl=sequential -g -O0 -lstdc++',
'--LDFLAGS=-dynamic',
'--download-metis-cmake-arguments=-DCMAKE_C_COMPILER_FORCED=1',
'--download-metis=1',
'--download-parmetis-cmake-arguments=-DCMAKE_C_COMPILER_FORCED=1',
'--download-parmetis=1',
'--known-bits-per-byte=8',
'--known-has-attribute-aligned=1',
'--known-level1-dcache-assoc=8',
'--known-level1-dcache-linesize=64',
'--known-level1-dcache-size=32768',
'--known-memcmp-ok=1',
'--known-mpi-c-double-complex=1',
'--known-mpi-int64_t=1',
'--known-mpi-long-double=1',
'--known-mpi-shared-libraries=0',
'--known-sdot-returns-double=0',
'--known-sizeof-MPI_Comm=4',
'--known-sizeof-MPI_Fint=4',
'--known-sizeof-char=1',
'--known-sizeof-double=8',
'--known-sizeof-float=4',
'--known-sizeof-int=4',
'--known-sizeof-long-long=8',
'--known-sizeof-long=8',
'--known-sizeof-short=2',
'--known-sizeof-size_t=8',
'--known-sizeof-void-p=8',
'--known-snrm2-returns-double=0',
'--with-ar=ar',
'--with-batch=1',
'--with-cc=/opt/cray/craype/2.4.2/bin/cc',
'--with-clib-autodetect=0',
'--with-cmake=/home/zampins/local/bin/cmake',
'--with-cxx=/opt/cray/craype/2.4.2/bin/CC',
'--with-cxxlib-autodetect=0',
'--with-debugging=1',
'--with-dependencies=0',
'--with-etags=0',
'--with-fc=/opt/cray/craype/2.4.2/bin/ftn',
'--with-fortran-datatypes=0',
'--with-fortran-interfaces=0',
'--with-fortranlib-autodetect=0',
'--with-pthread=0',
'--with-ranlib=ranlib',
'--with-scalar-type=real',
'--with-shared-ld=ar',
'--with-shared-libraries=1',
'PETSC_ARCH=arch-intel-debug',
2017-06-13 15:34 GMT+02:00 Vaz, Guilherme <G.Vaz at marin.nl>:
> Dear Matthew,
>
>
> Thanks. It went further, but now I get:
> TESTING: configureMPIEXEC from config.packages.MPI(/zhome/
> academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/Libs/build/
> petsc-3.7.5/config/BuildSystem/config/packages/MPI.py:143)
> ************************************************************
> *******************
> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
> details):
> ------------------------------------------------------------
> -------------------
> Must give a default value for known-mpi-shared-libraries since executables
> cannot be run
> ************************************************************
> *******************
>
> Last lines from the log:
> File "./config/configure.py", line 405, in petsc_configure
> framework.configure(out = sys.stdout)
> File "/zhome/academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/
> Libs/build/petsc-3.7.5/config/BuildSystem/config/framework.py", line
> 1090, in configure
> self.processChildren()
> File "/zhome/academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/
> Libs/build/petsc-3.7.5/config/BuildSystem/config/framework.py", line
> 1079, in processChildren
> self.serialEvaluation(self.childGraph)
> File "/zhome/academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/
> Libs/build/petsc-3.7.5/config/BuildSystem/config/framework.py", line
> 1060, in serialEvaluation
> child.configure()
> File "/zhome/academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/
> Libs/build/petsc-3.7.5/config/BuildSystem/config/package.py", line 791,
> in configure
> self.executeTest(self.checkSharedLibrary)
> File "/zhome/academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/
> Libs/build/petsc-3.7.5/config/BuildSystem/config/base.py", line 126, in
> executeTest
> ret = test(*args,**kargs)
> File "/zhome/academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/
> Libs/build/petsc-3.7.5/config/BuildSystem/config/packages/MPI.py", line
> 135, in checkSharedLibrary
> self.shared = self.libraries.checkShared('#include
> <mpi.h>\n','MPI_Init','MPI_Initialized','MPI_Finalize',checkLink =
> self.checkPackageLink,libraries = self.lib, defaultArg =
> 'known-mpi-shared-libraries', ex
> ecutor = self.mpiexec)
> File "/zhome/academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/
> Libs/build/petsc-3.7.5/config/BuildSystem/config/libraries.py", line 471,
> in checkShared
> if self.checkRun(defaultIncludes, body, defaultArg = defaultArg,
> executor = executor):
> File "/zhome/academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/
> Libs/build/petsc-3.7.5/config/BuildSystem/config/base.py", line 628, in
> checkRun
> (output, returnCode) = self.outputRun(includes, body, cleanup,
> defaultArg, executor)
> File "/zhome/academic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/
> Libs/build/petsc-3.7.5/config/BuildSystem/config/base.py", line 598, in
> outputRun
> raise ConfigureSetupError('Must give a default value for
> '+defaultOutputArg+' since executables cannot be run')
>
> Any ideas? Something related with
> --with-shared-libraries=0 \
> --with-batch=1 \
> The first I set because it was in the cray example, and the second
> because aprun (the mpiexec of Cray) is not available in the frontend.
>
> Thanks,
>
> Guilherme V.
>
> dr. ir. Guilherme Vaz | CFD Research Coordinator / Senior CFD Researcher |
> Research & Development
> MARIN | T +31 317 49 33 25 | M +31 621 13 11 97 | G.Vaz at marin.nl |
> www.marin.nl
>
> [image: LinkedIn] <https://www.linkedin.com/company/marin> [image:
> YouTube] <http://www.youtube.com/marinmultimedia> [image: Twitter]
> <https://twitter.com/MARIN_nieuws> [image: Facebook]
> <https://www.facebook.com/marin.wageningen>
> MARIN news: MARIN deelt onderzoek tijdens R&D Seminar, 21 juni 2017
> <http://www.marin.nl/web/News/News-items/MARIN-deelt-onderzoek-tijdens-RD-Seminar-21-juni-2017.htm>
>
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Tuesday, June 13, 2017 2:34 PM
> *To:* Vaz, Guilherme
> *Cc:* PETSc
> *Subject:* Re: [petsc-users] PETSC on Cray Hazelhen
>
> On Tue, Jun 13, 2017 at 3:48 AM, Vaz, Guilherme <G.Vaz at marin.nl> wrote:
>
>> Dear all,
>>
>> I am trying to install PETSC on a Cray XC40 system (Hazelhen) with the
>> usual Cray wrappers for Intel compilers, with some chosen external packages
>> and MKL libraries.
>>
>> I read some threads in the mailing list about this, and I tried the
>> petsc-3.7.5/config/examples/arch-cray-xt6-pkgs-opt.py configuration options.
>> After trying this (please abstract from my own env vars),
>> CONFOPTS="--prefix=$PETSC_INSTALL_DIR \
>> --with-cc=cc \
>> --with-cxx=CC \
>> --with-fc=ftn \
>> --with-clib-autodetect=0 \
>> --with-cxxlib-autodetect=0 \
>> --with-fortranlib-autodetect=0 \
>> --COPTFLAGS=-fast -mp \
>> --CXXOPTFLAGS=-fast -mp \
>> --FOPTFLAGS=-fast -mp \
>> --with-shared-libraries=0 \
>> --with-batch=1 \
>> --with-x=0 \
>> --with-mpe=0 \
>> --with-debugging=0 \
>> --download-superlu_dist=$SOURCE_DIR/$SUPERLU_SOURCE_FILE \
>> --with-blas-lapack-dir=$BLASDIR \
>> --download-parmetis=$SOURCE_DIR/$PARMETIS_SOURCE_FILE \
>> --download-metis=$SOURCE_DIR/$METIS_SOURCE_FILE \
>> --with-external-packages-dir=$INSTALL_DIR \
>> --with-ssl=0 "
>>
>>
>> I get the following error:
>>
>>
>> TESTING: checkFortranLinkingCxx from config.compilers(/zhome/academ
>> ic/HLRS/pri/iprguvaz/ReFRESCO/Dev/trunk/Libs/build/petsc-3.
>> 7.5/config/BuildSystem/config/compilers.py:1097)
>> ************************************************************
>> *******************
>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
>> details):
>> ------------------------------------------------------------
>> -------------------
>> Fortran could not successfully link C++ objects
>> ************************************************************
>> *******************
>>
>> Does it ring a bell? Any tips?
>>
>
> You turned off autodetection, so it will not find libstdc++. That either
> has to be put in LIBS, or I would recommend
>
> --with-cxx=0
>
> since nothing you have there requires C++.
>
> Thanks,
>
> Matt
>
>
>> Thanks,
>> Guilherme V.
>>
>> dr. ir. Guilherme Vaz | CFD Research Coordinator / Senior CFD Researcher |
>> Research & Development
>> MARIN | T +31 317 49 33 25 <+31%20317%20493%20325> | M +31 621 13 11 97
>> | G.Vaz at marin.nl | www.marin.nl
>>
>> [image: LinkedIn] <https://www.linkedin.com/company/marin> [image:
>> YouTube] <http://www.youtube.com/marinmultimedia> [image: Twitter]
>> <https://twitter.com/MARIN_nieuws> [image: Facebook]
>> <https://www.facebook.com/marin.wageningen>
>> MARIN news: Maritime Safety seminar, September 12, Singapore
>> <http://www.marin.nl/web/News/News-items/Maritime-Safety-seminar-September-12-Singapore.htm>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> http://www.caam.rice.edu/~mk51/
>
>
--
Stefano
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