[petsc-users] PETSC on Cray Hazelhen

Vaz, Guilherme G.Vaz at marin.nl
Tue Jun 13 08:34:41 CDT 2017 

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<mailto:G.Vaz at marin.nl> | www.marin.nl<http://www.marin.nl>

[LinkedIn]<https://www.linkedin.com/company/marin> [YouTube] <http://www.youtube.com/marinmultimedia>  [Twitter] <https://twitter.com/MARIN_nieuws>  [Facebook] <https://www.facebook.com/marin.wageningen>
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________________________________
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<mailto: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/academic/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<tel:+31%20317%20493%20325> | M +31 621 13 11 97 | G.Vaz at marin.nl<mailto:G.Vaz at marin.nl> | www.marin.nl<http://www.marin.nl>

[LinkedIn]<https://www.linkedin.com/company/marin> [YouTube] <http://www.youtube.com/marinmultimedia>  [Twitter] <https://twitter.com/MARIN_nieuws>  [Facebook] <https://www.facebook.com/marin.wageningen>
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--
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/


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