Stefano/Mathew,
Do I need all this :-)? And I dont want a debug version, just an optimized release version. Thus I understand the -g -O0 flags for debug, but the rest I am not sure what is for debug and for a release version. Sorry... I am also kind of confused on the shared libraries issue, '--known-mpi-shared-libraries=0', '--with-shared-libraries=1', on the static vs dynamic linking (I thought in XC-40 we had to compile everything statically, --LDFLAGS=-dynamic and on the FFFLAG: --FFLAGS=-mkl=sequential -g -O0 -lstdc++ Is this to be used with Intel MKL libraries? Thanks for the help, you both. 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 | [email protected]<mailto:[email protected]> | 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> 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: Stefano Zampini <[email protected]> Sent: Tuesday, June 13, 2017 3:42 PM To: Vaz, Guilherme Cc: Matthew Knepley; PETSc Subject: Re: [petsc-users] PETSC on Cray Hazelhen 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 <[email protected]<mailto:[email protected]>>: 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 | [email protected]<mailto:[email protected]> | 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> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 | [email protected]<mailto:[email protected]> | 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> 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
