February 2016 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] PETSc release soon, request for input on needed fixes or enhancements
by Barry Smith 28 Feb '16

28 Feb '16

> On Feb 28, 2016, at 8:55 PM, Jeff Hammond <jeff.science(a)gmail.com> wrote: > > > > On Sunday, February 28, 2016, Satish Balay <balay(a)mcs.anl.gov> wrote: > This build is using gnu compilers with MKL. And PETSc configure > doesn't guess compiler shortcuts like -mlk [or -framework Veclib] type > options.. > > Sounds like a BS design by Matt :-) There is little in this world more absurd than the inexcusable MKL link lines. > > Jeff > > > Satish > > On Sun, 28 Feb 2016, Jeff Hammond wrote: > > > On Sunday, February 28, 2016, Matthew Knepley <knepley(a)gmail.com> wrote: > > > > > On Sun, Feb 28, 2016 at 3:12 PM, Barry Smith <bsmith(a)mcs.anl.gov > > > <javascript:_e(%7B%7D,'cvml','bsmith(a)mcs.anl.gov');>> wrote: > > > > > >> > > >> Satish, > > >> > > >> Yeah, hypre totally botched its implementation of a way to check for > > >> the blas/lapack libraries. I've iterated with them several times on the > > >> basic problem but they keep patching what they do, rather then discard all > > >> their incorrect code and handle it simply as they should. > > > > > > > > > I'm sure it would have worked if they had used CMake ;) > > > > > > > > Intel compilers need only "-mkl" unless you want threaded ScaLAPACK. Works > > for both shared and static linking. > > > > I haven't tried but does "-lmkl" (plus appropriate LD_LIBRARY_PATH) not > > work with shared linking? > > > > As far as I know, static linking of MKL with non-Intel compiler is the only > > hard case for build systems. > > > > Obviously, CMake and C++11 are the only way to solve this problem :-D > > > > Jeff > > > > > > > Matt > > > > > > > > >> > > >> Barry > > >> > > >> > On Feb 28, 2016, at 3:00 PM, Satish Balay <balay(a)mcs.anl.gov > > >> <javascript:_e(%7B%7D,'cvml','balay(a)mcs.anl.gov');>> wrote: > > >> > > > >> > Executing: cd > > >> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.hypre/src > > >> && ./configure --prefix=/opt/petsc-master_debug MAKE=/bin/gmake > > >> --libdir=/opt/petsc-master_debug/lib CC="/opt/openmpi-1.10.2/bin/mpicc" > > >> CFLAGS="-fPIC -g3" CXX="/opt/openmpi-1.10.2/bin/mpicxx" CXXFLAGS="-g -fPIC" > > >> F90="/opt/openmpi-1.10.2/bin/mpif90" F90FLAGS="-fPIC -ffree-line-length-0 > > >> -g" F77="/opt/openmpi-1.10.2/bin/mpif90" FFLAGS="-fPIC -ffree-line-length-0 > > >> -g" FC="/opt/openmpi-1.10.2/bin/mpif90" FCFLAGS="-fPIC -ffree-line-length-0 > > >> -g" --with-MPI-include="/opt/openmpi-1.10.2/include" --with-MPI-lib-dirs="" > > >> --with-MPI-libs="" > > >> --with-blas-lib="-Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 > > >> -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core > > >> -lmkl_intel_thread -liomp5 -ldl -lpthread -lm > > >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi > > >> -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -lgfortran -lm -lquadmath -lm" --with-lapack-lib=" " --with-blas=no > > >> --with-lapack=no --with-fmangle-blas=one-underscore > > >> --with-fmangle-lapack=one-underscore --without-mli --without-fei > > >> --without-superlu AR="/bin/ar cr" > > >> > > > >> > checking for dgemm_ in -lm... no > > >> > checking for dgemm_ in -lquadmath... no > > >> > checking for dgemm_ in -lm... (cached) no > > >> > checking for dgemm_ in -lgfortran... no > > >> > checking for dgemm_ in -linux/4.8.5... no > > >> > checking for dgemm_ in -lm... (cached) no > > >> > checking for dgemm_ in -lgfortran... (cached) no > > >> > checking for dgemm_ in -lmpi_mpifh... no > > >> > checking for dgemm_ in -lmpi_usempi... no > > >> > checking for dgemm_ in -linux/4.8.5... (cached) no > > >> > checking for dgemm_ in -lm... (cached) no > > >> > checking for dgemm_ in -lpthread... no > > >> > checking for dgemm_ in -ldl... no > > >> > checking for dgemm_ in -liomp5... no > > >> > checking for dgemm_ in -lmkl_intel_thread... no > > >> > checking for dgemm_ in -lmkl_core... no > > >> > checking for dgemm_ in -lmkl_intel_lp64... noconfigure: error: > > >> **************** Non-linkable blas library error: > > >> *************************** > > >> > User set BLAS library path using either --with-blas-lib=<lib>, or > > >> > --with-blas-libs=<blas_lib_base_name> and > > >> --with-blas_dirs=<path-to-blas-lib>, > > >> > but -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/opt/openmpi-1.10.2/lib > > >> -L/opt/intel/composerxe/mkl/lib/intel64 -lm -lquadmath -lm -lgfortran > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lgfortran -lmpi_mpifh -lmpi_usempi > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lpthread -ldl -liomp5 > > >> -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64 > > >> -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 provided cannot be used. > > >> See "configure --help" for usage details. > > >> > > > >> ***************************************************************************************** > > >> > > > >> ******************************************************************************* > > >> > > > >> > > > >> > Hm - instead of using all the libs from --with-blas-libs in a single > > >> > link command - hypre is checking one '-llibrary' form this list at a > > >> > time? [including -linux/4.8.5 which is from a -L option] > > >> > > > >> > > > >> > '-lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core > > >> -lmkl_intel_lp64' ? > > >> > > > >> > Is hypre configure reversing the arguments it got? Its changed from > > >> > > > >> > --with-blas-lib='... -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread > > >> -liomp5 -ldl -lpthread -lm ...' > > >> > > > >> > I can reproduce this issue locally with: > > >> > > > >> > ./configure --download-hypre PETSC_ARCH=arch-hypre > > >> --with-blas-lapack-dir=/soft/com/packages/intel/15/update3/mkl > > >> --with-sowing=0 > > >> > > > >> > Satish > > >> > > > >> > On Sun, 28 Feb 2016, Eric Chamberland wrote: > > >> > > > >> >> Hi Barry, > > >> >> > > >> >> the configuration of hypre looks broken since last night...? > > >> >> > > >> >> Here is the log issued from our automatic compilation of > > >> petsc-master.tar.gz > > >> >> at 2016-02-28 02h00: > > >> >> > > >> >> > > >> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_… > > >> >> > > >> >> Everything was fine until last night... > > >> >> > > >> >> Thanks, > > >> >> > > >> >> Eric > > >> >> > > >> >> Le 2016-02-27 15:36, Barry Smith a écrit : > > >> >>> PETSc Users, > > >> >>> > > >> >>> We are planning the PETSc release 3.7 shortly. If you know of any > > >> bugs > > >> >>> that need to be fixed or enhancements added before the release > > >> please > > >> >>> let us know. > > >> >>> > > >> >>> You can think of the master branch of the PETSc repository > > >> obtainable > > >> >>> with > > >> >>> > > >> >>> git clone https://bitbucket.org/petsc/petsc petsc > > >> >>> > > >> >>> as a release candidate for 3.7. Changes for the release are listed at > > >> >>> http://www.mcs.anl.gov/petsc/documentation/changes/dev.html > > >> >>> > > >> >>> Thanks > > >> >>> > > >> >>> Barry > > >> >>> > > >> >> > > >> >> > > >> > > >> > > > > > > > > > -- > > > 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 > > > > > > > > > > > > -- > Jeff Hammond > jeff.science(a)gmail.com > http://jeffhammond.github.io/

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Re: [petsc-dev] PETSc release soon, request for input on needed fixes or enhancements
by Jeff Hammond 28 Feb '16

28 Feb '16

On Sunday, February 28, 2016, Satish Balay <balay(a)mcs.anl.gov> wrote: > This build is using gnu compilers with MKL. And PETSc configure > doesn't guess compiler shortcuts like -mlk [or -framework Veclib] type > options.. Sounds like a BS design by Matt :-) Jeff > > Satish > > On Sun, 28 Feb 2016, Jeff Hammond wrote: > > > On Sunday, February 28, 2016, Matthew Knepley <knepley(a)gmail.com > <javascript:;>> wrote: > > > > > On Sun, Feb 28, 2016 at 3:12 PM, Barry Smith <bsmith(a)mcs.anl.gov > <javascript:;> > > > <javascript:_e(%7B%7D,'cvml','bsmith(a)mcs.anl.gov <javascript:;>');>> > wrote: > > > > > >> > > >> Satish, > > >> > > >> Yeah, hypre totally botched its implementation of a way to check > for > > >> the blas/lapack libraries. I've iterated with them several times on > the > > >> basic problem but they keep patching what they do, rather then > discard all > > >> their incorrect code and handle it simply as they should. > > > > > > > > > I'm sure it would have worked if they had used CMake ;) > > > > > > > > Intel compilers need only "-mkl" unless you want threaded ScaLAPACK. > Works > > for both shared and static linking. > > > > I haven't tried but does "-lmkl" (plus appropriate LD_LIBRARY_PATH) not > > work with shared linking? > > > > As far as I know, static linking of MKL with non-Intel compiler is the > only > > hard case for build systems. > > > > Obviously, CMake and C++11 are the only way to solve this problem :-D > > > > Jeff > > > > > > > Matt > > > > > > > > >> > > >> Barry > > >> > > >> > On Feb 28, 2016, at 3:00 PM, Satish Balay <balay(a)mcs.anl.gov > <javascript:;> > > >> <javascript:_e(%7B%7D,'cvml','balay(a)mcs.anl.gov <javascript:;>');>> > wrote: > > >> > > > >> > Executing: cd > > >> > /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.hypre/src > > >> && ./configure --prefix=/opt/petsc-master_debug MAKE=/bin/gmake > > >> --libdir=/opt/petsc-master_debug/lib > CC="/opt/openmpi-1.10.2/bin/mpicc" > > >> CFLAGS="-fPIC -g3" CXX="/opt/openmpi-1.10.2/bin/mpicxx" CXXFLAGS="-g > -fPIC" > > >> F90="/opt/openmpi-1.10.2/bin/mpif90" F90FLAGS="-fPIC > -ffree-line-length-0 > > >> -g" F77="/opt/openmpi-1.10.2/bin/mpif90" FFLAGS="-fPIC > -ffree-line-length-0 > > >> -g" FC="/opt/openmpi-1.10.2/bin/mpif90" FCFLAGS="-fPIC > -ffree-line-length-0 > > >> -g" --with-MPI-include="/opt/openmpi-1.10.2/include" > --with-MPI-lib-dirs="" > > >> --with-MPI-libs="" > > >> --with-blas-lib="-Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 > > >> -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core > > >> -lmkl_intel_thread -liomp5 -ldl -lpthread -lm > > >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > -lmpi_usempi > > >> -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -lgfortran -lm -lquadmath -lm" --with-lapack-lib=" " --with-blas=no > > >> --with-lapack=no --with-fmangle-blas=one-underscore > > >> --with-fmangle-lapack=one-underscore --without-mli --without-fei > > >> --without-superlu AR="/bin/ar cr" > > >> > > > >> > checking for dgemm_ in -lm... no > > >> > checking for dgemm_ in -lquadmath... no > > >> > checking for dgemm_ in -lm... (cached) no > > >> > checking for dgemm_ in -lgfortran... no > > >> > checking for dgemm_ in -linux/4.8.5... no > > >> > checking for dgemm_ in -lm... (cached) no > > >> > checking for dgemm_ in -lgfortran... (cached) no > > >> > checking for dgemm_ in -lmpi_mpifh... no > > >> > checking for dgemm_ in -lmpi_usempi... no > > >> > checking for dgemm_ in -linux/4.8.5... (cached) no > > >> > checking for dgemm_ in -lm... (cached) no > > >> > checking for dgemm_ in -lpthread... no > > >> > checking for dgemm_ in -ldl... no > > >> > checking for dgemm_ in -liomp5... no > > >> > checking for dgemm_ in -lmkl_intel_thread... no > > >> > checking for dgemm_ in -lmkl_core... no > > >> > checking for dgemm_ in -lmkl_intel_lp64... noconfigure: error: > > >> **************** Non-linkable blas library error: > > >> *************************** > > >> > User set BLAS library path using either --with-blas-lib=<lib>, > or > > >> > --with-blas-libs=<blas_lib_base_name> and > > >> --with-blas_dirs=<path-to-blas-lib>, > > >> > but -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/opt/openmpi-1.10.2/lib > > >> -L/opt/intel/composerxe/mkl/lib/intel64 -lm -lquadmath -lm -lgfortran > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lgfortran -lmpi_mpifh > -lmpi_usempi > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > > >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lpthread -ldl -liomp5 > > >> -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64 > > >> -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 provided cannot be > used. > > >> See "configure --help" for usage details. > > >> > > > >> > ***************************************************************************************** > > >> > > > >> > ******************************************************************************* > > >> > > > >> > > > >> > Hm - instead of using all the libs from --with-blas-libs in a single > > >> > link command - hypre is checking one '-llibrary' form this list at a > > >> > time? [including -linux/4.8.5 which is from a -L option] > > >> > > > >> > > > >> > '-lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core > > >> -lmkl_intel_lp64' ? > > >> > > > >> > Is hypre configure reversing the arguments it got? Its changed from > > >> > > > >> > --with-blas-lib='... -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread > > >> -liomp5 -ldl -lpthread -lm ...' > > >> > > > >> > I can reproduce this issue locally with: > > >> > > > >> > ./configure --download-hypre PETSC_ARCH=arch-hypre > > >> --with-blas-lapack-dir=/soft/com/packages/intel/15/update3/mkl > > >> --with-sowing=0 > > >> > > > >> > Satish > > >> > > > >> > On Sun, 28 Feb 2016, Eric Chamberland wrote: > > >> > > > >> >> Hi Barry, > > >> >> > > >> >> the configuration of hypre looks broken since last night...? > > >> >> > > >> >> Here is the log issued from our automatic compilation of > > >> petsc-master.tar.gz > > >> >> at 2016-02-28 02h00: > > >> >> > > >> >> > > >> > http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_… > > >> >> > > >> >> Everything was fine until last night... > > >> >> > > >> >> Thanks, > > >> >> > > >> >> Eric > > >> >> > > >> >> Le 2016-02-27 15:36, Barry Smith a écrit : > > >> >>> PETSc Users, > > >> >>> > > >> >>> We are planning the PETSc release 3.7 shortly. If you know of > any > > >> bugs > > >> >>> that need to be fixed or enhancements added before the release > > >> please > > >> >>> let us know. > > >> >>> > > >> >>> You can think of the master branch of the PETSc repository > > >> obtainable > > >> >>> with > > >> >>> > > >> >>> git clone https://bitbucket.org/petsc/petsc petsc > > >> >>> > > >> >>> as a release candidate for 3.7. Changes for the release are > listed at > > >> >>> http://www.mcs.anl.gov/petsc/documentation/changes/dev.html > > >> >>> > > >> >>> Thanks > > >> >>> > > >> >>> Barry > > >> >>> > > >> >> > > >> >> > > >> > > >> > > > > > > > > > -- > > > 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 > > > > > > > > > > -- Jeff Hammond jeff.science(a)gmail.com http://jeffhammond.github.io/

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Re: [petsc-dev] PETSc release soon, request for input on needed fixes or enhancements
by Satish Balay 28 Feb '16

28 Feb '16

This build is using gnu compilers with MKL. And PETSc configure doesn't guess compiler shortcuts like -mlk [or -framework Veclib] type options.. Satish On Sun, 28 Feb 2016, Jeff Hammond wrote: > On Sunday, February 28, 2016, Matthew Knepley <knepley(a)gmail.com> wrote: > > > On Sun, Feb 28, 2016 at 3:12 PM, Barry Smith <bsmith(a)mcs.anl.gov > > <javascript:_e(%7B%7D,'cvml','bsmith(a)mcs.anl.gov');>> wrote: > > > >> > >> Satish, > >> > >> Yeah, hypre totally botched its implementation of a way to check for > >> the blas/lapack libraries. I've iterated with them several times on the > >> basic problem but they keep patching what they do, rather then discard all > >> their incorrect code and handle it simply as they should. > > > > > > I'm sure it would have worked if they had used CMake ;) > > > > > Intel compilers need only "-mkl" unless you want threaded ScaLAPACK. Works > for both shared and static linking. > > I haven't tried but does "-lmkl" (plus appropriate LD_LIBRARY_PATH) not > work with shared linking? > > As far as I know, static linking of MKL with non-Intel compiler is the only > hard case for build systems. > > Obviously, CMake and C++11 are the only way to solve this problem :-D > > Jeff > > > > Matt > > > > > >> > >> Barry > >> > >> > On Feb 28, 2016, at 3:00 PM, Satish Balay <balay(a)mcs.anl.gov > >> <javascript:_e(%7B%7D,'cvml','balay(a)mcs.anl.gov');>> wrote: > >> > > >> > Executing: cd > >> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.hypre/src > >> && ./configure --prefix=/opt/petsc-master_debug MAKE=/bin/gmake > >> --libdir=/opt/petsc-master_debug/lib CC="/opt/openmpi-1.10.2/bin/mpicc" > >> CFLAGS="-fPIC -g3" CXX="/opt/openmpi-1.10.2/bin/mpicxx" CXXFLAGS="-g -fPIC" > >> F90="/opt/openmpi-1.10.2/bin/mpif90" F90FLAGS="-fPIC -ffree-line-length-0 > >> -g" F77="/opt/openmpi-1.10.2/bin/mpif90" FFLAGS="-fPIC -ffree-line-length-0 > >> -g" FC="/opt/openmpi-1.10.2/bin/mpif90" FCFLAGS="-fPIC -ffree-line-length-0 > >> -g" --with-MPI-include="/opt/openmpi-1.10.2/include" --with-MPI-lib-dirs="" > >> --with-MPI-libs="" > >> --with-blas-lib="-Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 > >> -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core > >> -lmkl_intel_thread -liomp5 -ldl -lpthread -lm > >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > >> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > >> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > >> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > >> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > >> -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi > >> -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > >> -lgfortran -lm -lquadmath -lm" --with-lapack-lib=" " --with-blas=no > >> --with-lapack=no --with-fmangle-blas=one-underscore > >> --with-fmangle-lapack=one-underscore --without-mli --without-fei > >> --without-superlu AR="/bin/ar cr" > >> > > >> > checking for dgemm_ in -lm... no > >> > checking for dgemm_ in -lquadmath... no > >> > checking for dgemm_ in -lm... (cached) no > >> > checking for dgemm_ in -lgfortran... no > >> > checking for dgemm_ in -linux/4.8.5... no > >> > checking for dgemm_ in -lm... (cached) no > >> > checking for dgemm_ in -lgfortran... (cached) no > >> > checking for dgemm_ in -lmpi_mpifh... no > >> > checking for dgemm_ in -lmpi_usempi... no > >> > checking for dgemm_ in -linux/4.8.5... (cached) no > >> > checking for dgemm_ in -lm... (cached) no > >> > checking for dgemm_ in -lpthread... no > >> > checking for dgemm_ in -ldl... no > >> > checking for dgemm_ in -liomp5... no > >> > checking for dgemm_ in -lmkl_intel_thread... no > >> > checking for dgemm_ in -lmkl_core... no > >> > checking for dgemm_ in -lmkl_intel_lp64... noconfigure: error: > >> **************** Non-linkable blas library error: > >> *************************** > >> > User set BLAS library path using either --with-blas-lib=<lib>, or > >> > --with-blas-libs=<blas_lib_base_name> and > >> --with-blas_dirs=<path-to-blas-lib>, > >> > but -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > >> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > >> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > >> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > >> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/opt/openmpi-1.10.2/lib > >> -L/opt/intel/composerxe/mkl/lib/intel64 -lm -lquadmath -lm -lgfortran > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lgfortran -lmpi_mpifh -lmpi_usempi > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lpthread -ldl -liomp5 > >> -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64 > >> -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 provided cannot be used. > >> See "configure --help" for usage details. > >> > > >> ***************************************************************************************** > >> > > >> ******************************************************************************* > >> > > >> > > >> > Hm - instead of using all the libs from --with-blas-libs in a single > >> > link command - hypre is checking one '-llibrary' form this list at a > >> > time? [including -linux/4.8.5 which is from a -L option] > >> > > >> > > >> > '-lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core > >> -lmkl_intel_lp64' ? > >> > > >> > Is hypre configure reversing the arguments it got? Its changed from > >> > > >> > --with-blas-lib='... -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread > >> -liomp5 -ldl -lpthread -lm ...' > >> > > >> > I can reproduce this issue locally with: > >> > > >> > ./configure --download-hypre PETSC_ARCH=arch-hypre > >> --with-blas-lapack-dir=/soft/com/packages/intel/15/update3/mkl > >> --with-sowing=0 > >> > > >> > Satish > >> > > >> > On Sun, 28 Feb 2016, Eric Chamberland wrote: > >> > > >> >> Hi Barry, > >> >> > >> >> the configuration of hypre looks broken since last night...? > >> >> > >> >> Here is the log issued from our automatic compilation of > >> petsc-master.tar.gz > >> >> at 2016-02-28 02h00: > >> >> > >> >> > >> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_… > >> >> > >> >> Everything was fine until last night... > >> >> > >> >> Thanks, > >> >> > >> >> Eric > >> >> > >> >> Le 2016-02-27 15:36, Barry Smith a écrit : > >> >>> PETSc Users, > >> >>> > >> >>> We are planning the PETSc release 3.7 shortly. If you know of any > >> bugs > >> >>> that need to be fixed or enhancements added before the release > >> please > >> >>> let us know. > >> >>> > >> >>> You can think of the master branch of the PETSc repository > >> obtainable > >> >>> with > >> >>> > >> >>> git clone https://bitbucket.org/petsc/petsc petsc > >> >>> > >> >>> as a release candidate for 3.7. Changes for the release are listed at > >> >>> http://www.mcs.anl.gov/petsc/documentation/changes/dev.html > >> >>> > >> >>> Thanks > >> >>> > >> >>> Barry > >> >>> > >> >> > >> >> > >> > >> > > > > > > -- > > 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 > > > > >

1 0

Re: [petsc-dev] PETSc release soon, request for input on needed fixes or enhancements
by Jeff Hammond 28 Feb '16

28 Feb '16

On Sunday, February 28, 2016, Matthew Knepley <knepley(a)gmail.com> wrote: > On Sun, Feb 28, 2016 at 3:12 PM, Barry Smith <bsmith(a)mcs.anl.gov > <javascript:_e(%7B%7D,'cvml','bsmith(a)mcs.anl.gov');>> wrote: > >> >> Satish, >> >> Yeah, hypre totally botched its implementation of a way to check for >> the blas/lapack libraries. I've iterated with them several times on the >> basic problem but they keep patching what they do, rather then discard all >> their incorrect code and handle it simply as they should. > > > I'm sure it would have worked if they had used CMake ;) > > Intel compilers need only "-mkl" unless you want threaded ScaLAPACK. Works for both shared and static linking. I haven't tried but does "-lmkl" (plus appropriate LD_LIBRARY_PATH) not work with shared linking? As far as I know, static linking of MKL with non-Intel compiler is the only hard case for build systems. Obviously, CMake and C++11 are the only way to solve this problem :-D Jeff > Matt > > >> >> Barry >> >> > On Feb 28, 2016, at 3:00 PM, Satish Balay <balay(a)mcs.anl.gov >> <javascript:_e(%7B%7D,'cvml','balay(a)mcs.anl.gov');>> wrote: >> > >> > Executing: cd >> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.hypre/src >> && ./configure --prefix=/opt/petsc-master_debug MAKE=/bin/gmake >> --libdir=/opt/petsc-master_debug/lib CC="/opt/openmpi-1.10.2/bin/mpicc" >> CFLAGS="-fPIC -g3" CXX="/opt/openmpi-1.10.2/bin/mpicxx" CXXFLAGS="-g -fPIC" >> F90="/opt/openmpi-1.10.2/bin/mpif90" F90FLAGS="-fPIC -ffree-line-length-0 >> -g" F77="/opt/openmpi-1.10.2/bin/mpif90" FFLAGS="-fPIC -ffree-line-length-0 >> -g" FC="/opt/openmpi-1.10.2/bin/mpif90" FCFLAGS="-fPIC -ffree-line-length-0 >> -g" --with-MPI-include="/opt/openmpi-1.10.2/include" --with-MPI-lib-dirs="" >> --with-MPI-libs="" >> --with-blas-lib="-Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 >> -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core >> -lmkl_intel_thread -liomp5 -ldl -lpthread -lm >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 >> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 >> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 >> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 >> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 >> -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi >> -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 >> -lgfortran -lm -lquadmath -lm" --with-lapack-lib=" " --with-blas=no >> --with-lapack=no --with-fmangle-blas=one-underscore >> --with-fmangle-lapack=one-underscore --without-mli --without-fei >> --without-superlu AR="/bin/ar cr" >> > >> > checking for dgemm_ in -lm... no >> > checking for dgemm_ in -lquadmath... no >> > checking for dgemm_ in -lm... (cached) no >> > checking for dgemm_ in -lgfortran... no >> > checking for dgemm_ in -linux/4.8.5... no >> > checking for dgemm_ in -lm... (cached) no >> > checking for dgemm_ in -lgfortran... (cached) no >> > checking for dgemm_ in -lmpi_mpifh... no >> > checking for dgemm_ in -lmpi_usempi... no >> > checking for dgemm_ in -linux/4.8.5... (cached) no >> > checking for dgemm_ in -lm... (cached) no >> > checking for dgemm_ in -lpthread... no >> > checking for dgemm_ in -ldl... no >> > checking for dgemm_ in -liomp5... no >> > checking for dgemm_ in -lmkl_intel_thread... no >> > checking for dgemm_ in -lmkl_core... no >> > checking for dgemm_ in -lmkl_intel_lp64... noconfigure: error: >> **************** Non-linkable blas library error: >> *************************** >> > User set BLAS library path using either --with-blas-lib=<lib>, or >> > --with-blas-libs=<blas_lib_base_name> and >> --with-blas_dirs=<path-to-blas-lib>, >> > but -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 >> -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 >> -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 >> -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 >> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/opt/openmpi-1.10.2/lib >> -L/opt/intel/composerxe/mkl/lib/intel64 -lm -lquadmath -lm -lgfortran >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lgfortran -lmpi_mpifh -lmpi_usempi >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 >> -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 >> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 >> -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lpthread -ldl -liomp5 >> -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64 >> -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 provided cannot be used. >> See "configure --help" for usage details. >> > >> ***************************************************************************************** >> > >> ******************************************************************************* >> > >> > >> > Hm - instead of using all the libs from --with-blas-libs in a single >> > link command - hypre is checking one '-llibrary' form this list at a >> > time? [including -linux/4.8.5 which is from a -L option] >> > >> > >> > '-lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core >> -lmkl_intel_lp64' ? >> > >> > Is hypre configure reversing the arguments it got? Its changed from >> > >> > --with-blas-lib='... -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread >> -liomp5 -ldl -lpthread -lm ...' >> > >> > I can reproduce this issue locally with: >> > >> > ./configure --download-hypre PETSC_ARCH=arch-hypre >> --with-blas-lapack-dir=/soft/com/packages/intel/15/update3/mkl >> --with-sowing=0 >> > >> > Satish >> > >> > On Sun, 28 Feb 2016, Eric Chamberland wrote: >> > >> >> Hi Barry, >> >> >> >> the configuration of hypre looks broken since last night...? >> >> >> >> Here is the log issued from our automatic compilation of >> petsc-master.tar.gz >> >> at 2016-02-28 02h00: >> >> >> >> >> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_… >> >> >> >> Everything was fine until last night... >> >> >> >> Thanks, >> >> >> >> Eric >> >> >> >> Le 2016-02-27 15:36, Barry Smith a écrit : >> >>> PETSc Users, >> >>> >> >>> We are planning the PETSc release 3.7 shortly. If you know of any >> bugs >> >>> that need to be fixed or enhancements added before the release >> please >> >>> let us know. >> >>> >> >>> You can think of the master branch of the PETSc repository >> obtainable >> >>> with >> >>> >> >>> git clone https://bitbucket.org/petsc/petsc petsc >> >>> >> >>> as a release candidate for 3.7. Changes for the release are listed at >> >>> http://www.mcs.anl.gov/petsc/documentation/changes/dev.html >> >>> >> >>> Thanks >> >>> >> >>> Barry >> >>> >> >> >> >> >> >> > > > -- > 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 > -- Jeff Hammond jeff.science(a)gmail.com http://jeffhammond.github.io/

1 0

Re: [petsc-dev] PETSc release soon, request for input on needed fixes or enhancements
by Matthew Knepley 28 Feb '16

28 Feb '16

On Sun, Feb 28, 2016 at 3:12 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > Satish, > > Yeah, hypre totally botched its implementation of a way to check for > the blas/lapack libraries. I've iterated with them several times on the > basic problem but they keep patching what they do, rather then discard all > their incorrect code and handle it simply as they should. I'm sure it would have worked if they had used CMake ;) Matt > > Barry > > > On Feb 28, 2016, at 3:00 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > > Executing: cd > /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.hypre/src > && ./configure --prefix=/opt/petsc-master_debug MAKE=/bin/gmake > --libdir=/opt/petsc-master_debug/lib CC="/opt/openmpi-1.10.2/bin/mpicc" > CFLAGS="-fPIC -g3" CXX="/opt/openmpi-1.10.2/bin/mpicxx" CXXFLAGS="-g -fPIC" > F90="/opt/openmpi-1.10.2/bin/mpif90" F90FLAGS="-fPIC -ffree-line-length-0 > -g" F77="/opt/openmpi-1.10.2/bin/mpif90" FFLAGS="-fPIC -ffree-line-length-0 > -g" FC="/opt/openmpi-1.10.2/bin/mpif90" FCFLAGS="-fPIC -ffree-line-length-0 > -g" --with-MPI-include="/opt/openmpi-1.10.2/include" --with-MPI-lib-dirs="" > --with-MPI-libs="" > --with-blas-lib="-Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 > -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core > -lmkl_intel_thread -liomp5 -ldl -lpthread -lm > -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib > -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi > -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib > -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > -lgfortran -lm -lquadmath -lm" --with-lapack-lib=" " --with-blas=no > --with-lapack=no --with-fmangle-blas=one-underscore > --with-fmangle-lapack=one-underscore --without-mli --without-fei > --without-superlu AR="/bin/ar cr" > > > > checking for dgemm_ in -lm... no > > checking for dgemm_ in -lquadmath... no > > checking for dgemm_ in -lm... (cached) no > > checking for dgemm_ in -lgfortran... no > > checking for dgemm_ in -linux/4.8.5... no > > checking for dgemm_ in -lm... (cached) no > > checking for dgemm_ in -lgfortran... (cached) no > > checking for dgemm_ in -lmpi_mpifh... no > > checking for dgemm_ in -lmpi_usempi... no > > checking for dgemm_ in -linux/4.8.5... (cached) no > > checking for dgemm_ in -lm... (cached) no > > checking for dgemm_ in -lpthread... no > > checking for dgemm_ in -ldl... no > > checking for dgemm_ in -liomp5... no > > checking for dgemm_ in -lmkl_intel_thread... no > > checking for dgemm_ in -lmkl_core... no > > checking for dgemm_ in -lmkl_intel_lp64... noconfigure: error: > **************** Non-linkable blas library error: > *************************** > > User set BLAS library path using either --with-blas-lib=<lib>, or > > --with-blas-libs=<blas_lib_base_name> and > --with-blas_dirs=<path-to-blas-lib>, > > but -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/opt/openmpi-1.10.2/lib > -L/opt/intel/composerxe/mkl/lib/intel64 -lm -lquadmath -lm -lgfortran > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lgfortran -lmpi_mpifh -lmpi_usempi > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 > -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 > -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 > -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lpthread -ldl -liomp5 > -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64 > -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 provided cannot be used. > See "configure --help" for usage details. > > > ***************************************************************************************** > > > ******************************************************************************* > > > > > > Hm - instead of using all the libs from --with-blas-libs in a single > > link command - hypre is checking one '-llibrary' form this list at a > > time? [including -linux/4.8.5 which is from a -L option] > > > > > > '-lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core > -lmkl_intel_lp64' ? > > > > Is hypre configure reversing the arguments it got? Its changed from > > > > --with-blas-lib='... -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread > -liomp5 -ldl -lpthread -lm ...' > > > > I can reproduce this issue locally with: > > > > ./configure --download-hypre PETSC_ARCH=arch-hypre > --with-blas-lapack-dir=/soft/com/packages/intel/15/update3/mkl > --with-sowing=0 > > > > Satish > > > > On Sun, 28 Feb 2016, Eric Chamberland wrote: > > > >> Hi Barry, > >> > >> the configuration of hypre looks broken since last night...? > >> > >> Here is the log issued from our automatic compilation of > petsc-master.tar.gz > >> at 2016-02-28 02h00: > >> > >> > http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_… > >> > >> Everything was fine until last night... > >> > >> Thanks, > >> > >> Eric > >> > >> Le 2016-02-27 15:36, Barry Smith a écrit : > >>> PETSc Users, > >>> > >>> We are planning the PETSc release 3.7 shortly. If you know of any > bugs > >>> that need to be fixed or enhancements added before the release > please > >>> let us know. > >>> > >>> You can think of the master branch of the PETSc repository > obtainable > >>> with > >>> > >>> git clone https://bitbucket.org/petsc/petsc petsc > >>> > >>> as a release candidate for 3.7. Changes for the release are listed at > >>> http://www.mcs.anl.gov/petsc/documentation/changes/dev.html > >>> > >>> Thanks > >>> > >>> Barry > >>> > >> > >> > > -- 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

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Re: [petsc-dev] PETSc release soon, request for input on needed fixes or enhancements
by Barry Smith 28 Feb '16

28 Feb '16

Satish, Yeah, hypre totally botched its implementation of a way to check for the blas/lapack libraries. I've iterated with them several times on the basic problem but they keep patching what they do, rather then discard all their incorrect code and handle it simply as they should. Barry > On Feb 28, 2016, at 3:00 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > Executing: cd /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.hypre/src && ./configure --prefix=/opt/petsc-master_debug MAKE=/bin/gmake --libdir=/opt/petsc-master_debug/lib CC="/opt/openmpi-1.10.2/bin/mpicc" CFLAGS="-fPIC -g3" CXX="/opt/openmpi-1.10.2/bin/mpicxx" CXXFLAGS="-g -fPIC" F90="/opt/openmpi-1.10.2/bin/mpif90" F90FLAGS="-fPIC -ffree-line-length-0 -g" F77="/opt/openmpi-1.10.2/bin/mpif90" FFLAGS="-fPIC -ffree-line-length-0 -g" FC="/opt/openmpi-1.10.2/bin/mpif90" FCFLAGS="-fPIC -ffree-line-length-0 -g" --with-MPI-include="/opt/openmpi-1.10.2/include" --with-MPI-lib-dirs="" --with-MPI-libs="" --with-blas-lib="-Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lgfortran -lm -lquadmath -lm" --with-lapack-lib=" " --with-blas=no --with-lapack=no --with-fmangle-blas=one-underscore --with-fmangle-lapack=one-underscore --without-mli --without-fei --without-superlu AR="/bin/ar cr" > > checking for dgemm_ in -lm... no > checking for dgemm_ in -lquadmath... no > checking for dgemm_ in -lm... (cached) no > checking for dgemm_ in -lgfortran... no > checking for dgemm_ in -linux/4.8.5... no > checking for dgemm_ in -lm... (cached) no > checking for dgemm_ in -lgfortran... (cached) no > checking for dgemm_ in -lmpi_mpifh... no > checking for dgemm_ in -lmpi_usempi... no > checking for dgemm_ in -linux/4.8.5... (cached) no > checking for dgemm_ in -lm... (cached) no > checking for dgemm_ in -lpthread... no > checking for dgemm_ in -ldl... no > checking for dgemm_ in -liomp5... no > checking for dgemm_ in -lmkl_intel_thread... no > checking for dgemm_ in -lmkl_core... no > checking for dgemm_ in -lmkl_intel_lp64... noconfigure: error: **************** Non-linkable blas library error: *************************** > User set BLAS library path using either --with-blas-lib=<lib>, or > --with-blas-libs=<blas_lib_base_name> and --with-blas_dirs=<path-to-blas-lib>, > but -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/opt/openmpi-1.10.2/lib -L/opt/intel/composerxe/mkl/lib/intel64 -lm -lquadmath -lm -lgfortran -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lgfortran -lmpi_mpifh -lmpi_usempi -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64 -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 provided cannot be used. See "configure --help" for usage details. > ***************************************************************************************** > ******************************************************************************* > > > Hm - instead of using all the libs from --with-blas-libs in a single > link command - hypre is checking one '-llibrary' form this list at a > time? [including -linux/4.8.5 which is from a -L option] > > > '-lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64' ? > > Is hypre configure reversing the arguments it got? Its changed from > > --with-blas-lib='... -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm ...' > > I can reproduce this issue locally with: > > ./configure --download-hypre PETSC_ARCH=arch-hypre --with-blas-lapack-dir=/soft/com/packages/intel/15/update3/mkl --with-sowing=0 > > Satish > > On Sun, 28 Feb 2016, Eric Chamberland wrote: > >> Hi Barry, >> >> the configuration of hypre looks broken since last night...? >> >> Here is the log issued from our automatic compilation of petsc-master.tar.gz >> at 2016-02-28 02h00: >> >> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_… >> >> Everything was fine until last night... >> >> Thanks, >> >> Eric >> >> Le 2016-02-27 15:36, Barry Smith a écrit : >>> PETSc Users, >>> >>> We are planning the PETSc release 3.7 shortly. If you know of any bugs >>> that need to be fixed or enhancements added before the release please >>> let us know. >>> >>> You can think of the master branch of the PETSc repository obtainable >>> with >>> >>> git clone https://bitbucket.org/petsc/petsc petsc >>> >>> as a release candidate for 3.7. Changes for the release are listed at >>> http://www.mcs.anl.gov/petsc/documentation/changes/dev.html >>> >>> Thanks >>> >>> Barry >>> >> >>

1 0

Re: [petsc-dev] PETSc release soon, request for input on needed fixes or enhancements
by Satish Balay 28 Feb '16

28 Feb '16

Executing: cd /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.hypre/src && ./configure --prefix=/opt/petsc-master_debug MAKE=/bin/gmake --libdir=/opt/petsc-master_debug/lib CC="/opt/openmpi-1.10.2/bin/mpicc" CFLAGS="-fPIC -g3" CXX="/opt/openmpi-1.10.2/bin/mpicxx" CXXFLAGS="-g -fPIC" F90="/opt/openmpi-1.10.2/bin/mpif90" F90FLAGS="-fPIC -ffree-line-length-0 -g" F77="/opt/openmpi-1.10.2/bin/mpif90" FFLAGS="-fPIC -ffree-line-length-0 -g" FC="/opt/openmpi-1.10.2/bin/mpif90" FCFLAGS="-fPIC -ffree-line-length-0 -g" --with-MPI-include="/opt/openmpi-1.10.2/include" --with-MPI-lib-dirs="" --with-MPI-libs="" --with-blas-lib="-Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lgfortran -lm -lquadmath -lm" --with-lapack-lib=" " --with-blas=no --with-lapack=no --with-fmangle-blas=one-underscore --with-fmangle-lapack=one-underscore --without-mli --without-fei --without-superlu AR="/bin/ar cr" checking for dgemm_ in -lm... no checking for dgemm_ in -lquadmath... no checking for dgemm_ in -lm... (cached) no checking for dgemm_ in -lgfortran... no checking for dgemm_ in -linux/4.8.5... no checking for dgemm_ in -lm... (cached) no checking for dgemm_ in -lgfortran... (cached) no checking for dgemm_ in -lmpi_mpifh... no checking for dgemm_ in -lmpi_usempi... no checking for dgemm_ in -linux/4.8.5... (cached) no checking for dgemm_ in -lm... (cached) no checking for dgemm_ in -lpthread... no checking for dgemm_ in -ldl... no checking for dgemm_ in -liomp5... no checking for dgemm_ in -lmkl_intel_thread... no checking for dgemm_ in -lmkl_core... no checking for dgemm_ in -lmkl_intel_lp64... noconfigure: error: **************** Non-linkable blas library error: *************************** User set BLAS library path using either --with-blas-lib=<lib>, or --with-blas-libs=<blas_lib_base_name> and --with-blas_dirs=<path-to-blas-lib>, but -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/opt/openmpi-1.10.2/lib -L/opt/intel/composerxe/mkl/lib/intel64 -lm -lquadmath -lm -lgfortran -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lgfortran -lmpi_mpifh -lmpi_usempi -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64 -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 provided cannot be used. See "configure --help" for usage details. ***************************************************************************************** ******************************************************************************* Hm - instead of using all the libs from --with-blas-libs in a single link command - hypre is checking one '-llibrary' form this list at a time? [including -linux/4.8.5 which is from a -L option] '-lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64' ? Is hypre configure reversing the arguments it got? Its changed from --with-blas-lib='... -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm ...' I can reproduce this issue locally with: ./configure --download-hypre PETSC_ARCH=arch-hypre --with-blas-lapack-dir=/soft/com/packages/intel/15/update3/mkl --with-sowing=0 Satish On Sun, 28 Feb 2016, Eric Chamberland wrote: > Hi Barry, > > the configuration of hypre looks broken since last night...? > > Here is the log issued from our automatic compilation of petsc-master.tar.gz > at 2016-02-28 02h00: > > http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_… > > Everything was fine until last night... > > Thanks, > > Eric > > Le 2016-02-27 15:36, Barry Smith a écrit : > > PETSc Users, > > > > We are planning the PETSc release 3.7 shortly. If you know of any bugs > > that need to be fixed or enhancements added before the release please > > let us know. > > > > You can think of the master branch of the PETSc repository obtainable > > with > > > > git clone https://bitbucket.org/petsc/petsc petsc > > > > as a release candidate for 3.7. Changes for the release are listed at > > http://www.mcs.anl.gov/petsc/documentation/changes/dev.html > > > > Thanks > > > > Barry > > > >

1 0

Re: [petsc-dev] hypre unable to handle blas/lapack library in newest release candidate
by Barry Smith 28 Feb '16

28 Feb '16

hypre folks, One of our users was unable to build with your new hypre release candidate: output below. It looks like your configure is still trying to check --with-blas-lib= entries one at a time to find the blas routines. This won't work because, for example, with MKL to use blas/lapack you must link against a very specific list of libraries in the correct order. Hence checking one library at a time won't work. You need to treat the entire --with-blas-lib= information as a single blob you pass to the linker. Underneath your ./configure output I show the PETSc configure output where it does find the blas/lapack routines. Barry Error running configure on HYPRE: Could not execute "cd /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.hypre/src && ./configure --prefix=/opt/petsc-master_debug MAKE=/bin/gmake --libdir=/opt/petsc-master_debug/lib CC="/opt/openmpi-1.10.2/bin/mpicc" CFLAGS="-fPIC -g3" CXX="/opt/openmpi-1.10.2/bin/mpicxx" CXXFLAGS="-g -fPIC" F90="/opt/openmpi-1.10.2/bin/mpif90" F90FLAGS="-fPIC -ffree-line-length-0 -g" F77="/opt/openmpi-1.10.2/bin/mpif90" FFLAGS="-fPIC -ffree-line-length-0 -g" FC="/opt/openmpi-1.10.2/bin/mpif90" FCFLAGS="-fPIC -ffree-line-length-0 -g" --with-MPI-include="/opt/openmpi-1.10.2/include" --with-MPI-lib-dirs="" --with-MPI-libs="" --with-blas-lib="-Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lgfortran -lm -lquadmath -lm" --with-lapack-lib=" " --with-blas=no --with-lapack=no --with-fmangle-blas=one-underscore --with-fmangle-lapack=one-underscore --without-mli --without-fei --without-superlu AR="/bin/ar cr"": checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking whether /bin/gmake sets $(MAKE)... yes checking for ranlib... ranlib checking for gcc... /opt/openmpi-1.10.2/bin/mpicc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /opt/openmpi-1.10.2/bin/mpicc accepts -g... yes checking for /opt/openmpi-1.10.2/bin/mpicc option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether /opt/openmpi-1.10.2/bin/mpicxx accepts -g... yes checking whether we are using the GNU Fortran compiler... yes checking whether /opt/openmpi-1.10.2/bin/mpif90 accepts -g... yes checking how to get verbose linking output from /opt/openmpi-1.10.2/bin/mpif90... -v checking for Fortran libraries of /opt/openmpi-1.10.2/bin/mpif90... -L/opt/openmpi-1.10.2/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/../compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for MPI_Init... yes checking for mpi.h... yes checking for MPI_Comm_f2c... yes checking how to run the C preprocessor... /opt/openmpi-1.10.2/bin/mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether MPI_Comm_f2c is a macro... no checking for cabs in -lm... yes checking for dgemm_ in -lm... no checking for dgemm_ in -lquadmath... no checking for dgemm_ in -lm... (cached) no checking for dgemm_ in -lgfortran... no checking for dgemm_ in -linux/4.8.5... no checking for dgemm_ in -lm... (cached) no checking for dgemm_ in -lgfortran... (cached) no checking for dgemm_ in -lmpi_mpifh... no checking for dgemm_ in -lmpi_usempi... no checking for dgemm_ in -linux/4.8.5... (cached) no checking for dgemm_ in -lm... (cached) no checking for dgemm_ in -lpthread... no checking for dgemm_ in -ldl... no checking for dgemm_ in -liomp5... no checking for dgemm_ in -lmkl_intel_thread... no checking for dgemm_ in -lmkl_core... no checking for dgemm_ in -lmkl_intel_lp64... noconfigure: error: **************** Non-linkable blas library error: *************************** User set BLAS library path using either --with-blas-lib=<lib>, or --with-blas-libs=<blas_lib_base_name> and --with-blas_dirs=<path-to-blas-lib>, but -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/opt/openmpi-1.10.2/lib -L/opt/intel/composerxe/mkl/lib/intel64 -lm -lquadmath -lm -lgfortran -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lgfortran -lmpi_mpifh -lmpi_usempi -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/openmpi-1.10.2/lib -lm -lpthread -ldl -liomp5 -lmkl_intel_thread -lmkl_core -lmkl_intel_lp64 -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 provided cannot be used. See "configure --help" for usage details. TEST configureLibrary from config.packages.BlasLapack(/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/config/BuildSystem/config/packages/BlasLapack.py:337) TESTING: configureLibrary from config.packages.BlasLapack(/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/config/BuildSystem/config/packages/BlasLapack.py:337) Looking for BLAS/LAPACK in user specified directory: /opt/intel/composerxe/mkl/lib/intel64 Files and directorys in that directory: ['libmkl_blacs_sgimpt_ilp64.a', 'libmkl_blacs_ilp64.a', 'libmkl_core.so', 'libmkl_gf_lp64.a', 'libmkl_blacs_intelmpi_lp64.a', 'libmkl_blacs_intelmpi_lp64.so', 'libmkl_scalapack_lp64.a', 'libmkl_vml_mc3.so', 'libmkl_intel_thread.so', 'libmkl_vml_avx512.so', 'libmkl_avx.so', 'libmkl_blacs_intelmpi_ilp64.a', 'libmkl_def.so', 'libmkl_mc3.so', 'libmkl_intel_ilp64.a', 'libmkl_avx512_mic.so', 'libmkl_lapack95_ilp64.a', 'libmkl_blas95_ilp64.a', 'libmkl_lapack95_lp64.a', 'libmkl_avx2.so', 'libmkl_gf_lp64.so', 'libmkl_cdft_core.so', 'libmkl_vml_avx.so', 'libmkl_gnu_thread.so', 'libmkl_vml_avx512_mic.so', 'libmkl_cdft_core.a', 'libmkl_scalapack_ilp64.so', 'libmkl_vml_def.so', 'libmkl_gf_ilp64.a', 'libmkl_vml_avx2.so', 'libmkl_avx512.so', 'libmkl_vml_mc2.so', 'libmkl_blacs_openmpi_ilp64.a', 'libmkl_blas95_lp64.a', 'libmkl_sequential.a', 'libmkl_mc.so', 'libmkl_blacs_lp64.a', 'libmkl_blacs_openmpi_lp64.a', 'libmkl_intel_lp64.a', 'libmkl_gnu_thread.a', 'libmkl_gf_ilp64.so', 'libmkl_blacs_intelmpi_ilp64.so', 'libmkl_vml_cmpt.so', 'libmkl_intel_lp64.so', 'libmkl_scalapack_ilp64.a', 'locale', 'libmkl_intel_ilp64.so', 'libmkl_core.a', 'libmkl_rt.so', 'libmkl_scalapack_lp64.so', 'libmkl_intel_thread.a', 'libmkl_blacs_sgimpt_lp64.a', 'libmkl_sequential.so', 'libmkl_vml_mc.so'] =============================================================================== BLASLAPACK: Looking for Multithreaded MKL for Pardiso =============================================================================== MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/lib/64 MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/lib/ia64 MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/lib/em64t MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/lib/intel64 MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/64 MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/ia64 MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/em64t MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/intel64 MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/lib/32 MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/lib/ia32 MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/32 MKL Path not found.. skipping: /opt/intel/composerxe/mkl/lib/intel64/ia32 ================================================================================ Checking for a functional BLAS and LAPACK in User specified MKL-Pardiso Intel-Linux64 ================================================================================ TEST checkLib from config.packages.BlasLapack(/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/config/BuildSystem/config/packages/BlasLapack.py:106) TESTING: checkLib from config.packages.BlasLapack(/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/config/BuildSystem/config/packages/BlasLapack.py:106) Checking for BLAS and LAPACK symbols Checking for functions [ddot_] in library ['/opt/intel/composerxe/mkl/lib/intel64/libmkl_intel_lp64.a', 'mkl_core', 'mkl_intel_thread', 'iomp5', 'dl', 'pthread', 'm'] ['-Wl,-rpath,/opt/openmpi-1.10.2/lib', '-L/opt/openmpi-1.10.2/lib', '-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64', '-L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64', '-L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64', '-L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4', '-L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4', '-lmpi_usempi', '-lmpi_mpifh', '-lgfortran', '-lm', '-Wl,-rpath,/opt/openmpi-1.10.2/lib', '-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4', '-lgfortran', '-lm', '-lquadmath', '-lm'] Pushing language C Executing: /opt/openmpi-1.10.2/bin/mpicc -c -o /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest.o -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.closure -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.compilers -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.setCompilers -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.headers -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.cacheDetails -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.atomics -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.featureTestMacros -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.functions -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.missing -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.packages.MPI -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.types -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.packages.pthread -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/PETSc.options.scalarTypes -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char ddot_(); static void _check_ddot_() { ddot_(); } int main() { _check_ddot_();; return 0; } Pushing language C Popping language C Executing: /opt/openmpi-1.10.2/bin/mpicc -o /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest.o -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lgfortran -lm -lquadmath -lm -lrt -lm -lz -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -ldl -Wl,-rpath,/opt/openmpi-1.10.2/lib -lmpi -lgcc_s -lpthread -ldl Defined "HAVE_LIBMKL_INTEL_LP64" to "1" Defined "HAVE_LIBMKL_CORE" to "1" Defined "HAVE_LIBMKL_INTEL_THREAD" to "1" Defined "HAVE_LIBIOMP5" to "1" Defined "HAVE_LIBDL" to "1" Defined "HAVE_LIBPTHREAD" to "1" Defined "HAVE_LIBM" to "1" Popping language C Checking for functions [dgetrs_] in library ['/opt/intel/composerxe/mkl/lib/intel64/libmkl_intel_lp64.a', 'mkl_core', 'mkl_intel_thread', 'iomp5', 'dl', 'pthread', 'm'] ['-Wl,-rpath,/opt/openmpi-1.10.2/lib', '-L/opt/openmpi-1.10.2/lib', '-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64', '-L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64', '-L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64', '-L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4', '-L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4', '-lmpi_usempi', '-lmpi_mpifh', '-lgfortran', '-lm', '-Wl,-rpath,/opt/openmpi-1.10.2/lib', '-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4', '-lgfortran', '-lm', '-lquadmath', '-lm'] Pushing language C Executing: /opt/openmpi-1.10.2/bin/mpicc -c -o /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest.o -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.closure -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.compilers -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.setCompilers -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.headers -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.cacheDetails -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.atomics -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.featureTestMacros -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.functions -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.missing -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.packages.MPI -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.types -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.packages.pthread -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/PETSc.options.scalarTypes -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dgetrs_(); static void _check_dgetrs_() { dgetrs_(); } int main() { _check_dgetrs_();; return 0; } Pushing language C Popping language C Executing: /opt/openmpi-1.10.2/bin/mpicc -o /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest.o -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lgfortran -lm -lquadmath -lm -lrt -lm -lz -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -ldl -Wl,-rpath,/opt/openmpi-1.10.2/lib -lmpi -lgcc_s -lpthread -ldl Defined "HAVE_LIBMKL_INTEL_LP64" to "1" Defined "HAVE_LIBMKL_CORE" to "1" Defined "HAVE_LIBMKL_INTEL_THREAD" to "1" Defined "HAVE_LIBIOMP5" to "1" Defined "HAVE_LIBDL" to "1" Defined "HAVE_LIBPTHREAD" to "1" Defined "HAVE_LIBM" to "1" Popping language C Checking for functions [dgeev_] in library ['/opt/intel/composerxe/mkl/lib/intel64/libmkl_intel_lp64.a', 'mkl_core', 'mkl_intel_thread', 'iomp5', 'dl', 'pthread', 'm'] ['-Wl,-rpath,/opt/openmpi-1.10.2/lib', '-L/opt/openmpi-1.10.2/lib', '-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64', '-L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64', '-L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64', '-L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4', '-L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4', '-lmpi_usempi', '-lmpi_mpifh', '-lgfortran', '-lm', '-Wl,-rpath,/opt/openmpi-1.10.2/lib', '-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64', '-Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4', '-lgfortran', '-lm', '-lquadmath', '-lm'] Pushing language C Executing: /opt/openmpi-1.10.2/bin/mpicc -c -o /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest.o -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.closure -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.compilers -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.setCompilers -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.headers -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.cacheDetails -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.atomics -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.featureTestMacros -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.functions -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.utilities.missing -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.packages.MPI -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.types -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.packages.pthread -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/PETSc.options.scalarTypes -I/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dgeev_(); static void _check_dgeev_() { dgeev_(); } int main() { _check_dgeev_();; return 0; } Pushing language C Popping language C Executing: /opt/openmpi-1.10.2/bin/mpicc -o /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/tmp/petsc-V3Vr9D/config.libraries/conftest.o -Wl,-rpath,/opt/intel/composerxe/mkl/lib/intel64 -L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lmpi_usempi -lmpi_mpifh -lgfortran -lm -Wl,-rpath,/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -lgfortran -lm -lquadmath -lm -lrt -lm -lz -Wl,-rpath,/opt/openmpi-1.10.2/lib -L/opt/openmpi-1.10.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/ipp/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/compiler/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64 -Wl,-rpath,/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -L/opt/intel/composer_xe_2015.2.164/tbb/lib/intel64/gcc4.4 -ldl -Wl,-rpath,/opt/openmpi-1.10.2/lib -lmpi -lgcc_s -lpthread -ldl Defined "HAVE_LIBMKL_INTEL_LP64" to "1" Defined "HAVE_LIBMKL_CORE" to "1" Defined "HAVE_LIBMKL_INTEL_THREAD" to "1" Defined "HAVE_LIBIOMP5" to "1" Defined "HAVE_LIBDL" to "1" Defined "HAVE_LIBPTHREAD" to "1" Defined "HAVE_LIBM" to "1" Popping language C Found Fortran mangling on BLAS/LAPACK which is underscore Defined "BLASLAPACK_UNDERSCORE" to "1" > On Feb 28, 2016, at 2:08 PM, Eric Chamberland <Eric.Chamberland(a)giref.ulaval.ca> wrote: > > Hi Barry, > > the configuration of hypre looks broken since last night...? > > Here is the log issued from our automatic compilation of petsc-master.tar.gz at 2016-02-28 02h00: > > http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_… > > Everything was fine until last night... > > Thanks, > > Eric > > Le 2016-02-27 15:36, Barry Smith a écrit : >> PETSc Users, >> >> We are planning the PETSc release 3.7 shortly. If you know of any bugs that need to be fixed or enhancements added before the release please let us know. >> >> You can think of the master branch of the PETSc repository obtainable with >> >> git clone https://bitbucket.org/petsc/petsc petsc >> >> as a release candidate for 3.7. Changes for the release are listed at http://www.mcs.anl.gov/petsc/documentation/changes/dev.html >> >> Thanks >> >> Barry >> >

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Re: [petsc-dev] PETSc release soon, request for input on needed fixes or enhancements
by Eric Chamberland 28 Feb '16

28 Feb '16

Hi Barry, the configuration of hypre looks broken since last night...? Here is the log issued from our automatic compilation of petsc-master.tar.gz at 2016-02-28 02h00: http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/configure_20160228_… Everything was fine until last night... Thanks, Eric Le 2016-02-27 15:36, Barry Smith a ï¿½crit : > PETSc Users, > > We are planning the PETSc release 3.7 shortly. If you know of any bugs that need to be fixed or enhancements added before the release please let us know. > > You can think of the master branch of the PETSc repository obtainable with > > git clone https://bitbucket.org/petsc/petsc petsc > > as a release candidate for 3.7. Changes for the release are listed at http://www.mcs.anl.gov/petsc/documentation/changes/dev.html > > Thanks > > Barry >

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Re: [petsc-dev] Not possible to do a VecPlaceArray for veccusp
by Jeff Hammond 28 Feb '16

28 Feb '16

On Sunday, February 28, 2016, Karl Rupp <rupp(a)iue.tuwien.ac.at> wrote: > Hi, > > I like the idea of having separate VECCUDA and VECVIENNACL, because it is >> possible to implement VECCUDA without dependence on a C++ compiler (only >> the CUDA compiler). >> > > I don't understand this part. NVCC also requires a C++ host compiler and > is fairly picky about the supported compilers. > > > If you want, we can prepare a rough initial implementation of VECCUDA in >> the next days, and we can later discuss what to keep/discard. >> > > Any contributions are welcome :-) > > > Karl: regarding the time constraints, our idea is to present something at >> a conference this summer, and deadlines are approaching. >> > > Ok, this is on fairly short notice considering the changes required. I > recommend to start with copying the CUSP sources and migrate it over to > VECCUDA by replacing any use of cusp::array1d to a raw CUDA handle. > Operations from CUSP should be replaced by CUBLAS calls. > > It's hard to imagine any performance benefit from this unless CUSP sucks. What am I missing? Jeff > Best regards, > Karli > > > > >>>>> If there is interest we can help in adding this stuff. >>>>> >>>> >>>> What are your time constraints? >>>> >>>> Best regards, >>>> Karli >>>> >>>> >>>> >>> -- >>> Dominic Meiser >>> Tech-X Corporation - 5621 Arapahoe Avenue - Boulder, CO 80303 >>> >> >> > -- Jeff Hammond jeff.science(a)gmail.com http://jeffhammond.github.io/

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