Cray machines can be used with shared libraries, it’s not like the earlier versions of BG/Q
Yes, you need almost all of this. If you run with configure with the option —with-batch=1, will then generate something like the one I have sent you. —with-shared-libraries is a PETSc configuration, i.e. you will create libpetsc.so —LDFLAGS=-dynamic is used to link dynamically a PETSc executable —known-mpi-shared-libraries=0 will use a statically linked MPI You can remove the first two options listed above if you would like to have a static version of PETSC. You may want to refine the options for optimized builds, i.e. add your favorite COPTFLAGS and remove —with-debugging=1 Another thing you can do. Load any of the PETSc modules on the XC40, and then look at the file $PETSC_DIR/include/petscconfiginfo.h > On Jun 13, 2017, at 4:01 PM, Vaz, Guilherme <[email protected]> wrote: > > 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/> > > <image067d96.PNG> <https://www.linkedin.com/company/marin> <image0c3f53.PNG> > <http://www.youtube.com/marinmultimedia> <image887afd.PNG> > <https://twitter.com/MARIN_nieuws> <image2a2a45.PNG> > <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] > <mailto:[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/> > > <image628296.PNG> <https://www.linkedin.com/company/marin> <imagecdd6dd.PNG> > <http://www.youtube.com/marinmultimedia> <imageae7ad3.PNG> > <https://twitter.com/MARIN_nieuws> <image9aa6ed.PNG> > <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/> > > <imageb0ee12.PNG> <https://www.linkedin.com/company/marin> <imaged8f08c.PNG> > <http://www.youtube.com/marinmultimedia> <imagedacd80.PNG> > <https://twitter.com/MARIN_nieuws> <image1bd020.PNG> > <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/ <http://www.caam.rice.edu/~mk51/> > > > > -- > Stefano
