[petsc-dev] PETSc release soon, request for input on needed fixes or enhancements

Barry Smith bsmith at mcs.anl.gov
Sun Feb 28 15:12:07 CST 2016 

  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 at 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_0200.log
>> 
>> 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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