Send configure.log from the failed configure
> On Apr 1, 2015, at 10:29 PM, David Knezevic <[email protected]>
> wrote:
>
> On Thu, Mar 26, 2015 at 6:23 PM, Matthew Knepley <[email protected]> wrote:
> On Thu, Mar 26, 2015 at 5:10 PM, David Knezevic <[email protected]>
> wrote:
> On Thu, Mar 26, 2015 at 4:21 PM, Matthew Knepley <[email protected]> wrote:
> On Thu, Mar 26, 2015 at 1:48 PM, David Knezevic <[email protected]>
> wrote:
> Hi all,
>
> I'm trying to configure PETSc using Intel's MKL and with --download-ml. Here
> is my configure line:
>
> ./configure
> --with-blas-lapack-dir=/opt/intel/composer_xe_2015/mkl/lib/intel64
> --download-ml
>
> I get an error when ML does "checking for dgemm". The configure.log is
> attached. I was wondering if anyone has any suggestions about how I can get
> this to work?
>
> We will need $PETSC_ARCH/externalpackages/ml-*/config.log to see where their
> test failed.
>
>
> I've attached this file.
>
> I do not understand the error:
>
> configure:10865: mpicxx -o conftest -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -g -O0 -fPIC
> -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -I/usr/lib/openmpi/include
> -I/usr/lib/openmpi/include/openmpi -g -O2 -I/usr/lib/openmpi/include
> -I/usr/lib/openmpi/include/openmpi conftest.cpp
> -Wl,-rpath,/opt/intel/composer_xe_2015/mkl/lib/intel64
> -L/opt/intel/composer_xe_2015/mkl/lib/intel64 -lmkl_intel_lp64
> -lmkl_sequential -lmkl_core -lpthread -lm -Wl,-rpath,/usr/lib/openmpi/lib
> -L/usr/lib/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8
> -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
> -L/lib/x86_64-linux-gnu -lmpi_f90 -lmpi_f77 -lgfortran -lm
> -Wl,-rpath,/usr/lib/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8
> -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
> -lgfortran -lm -lquadmath -lm -L/usr//lib -L/usr/lib/openmpi/lib
> -L/usr/lib/gcc/x86_64-linux-gnu/4.8
> -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu
> -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu
> -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib
> -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lmpi_f90 -lmpi_f77 -lmpi -ldl
> -lhwloc -lgfortran -lm -lquadmath -lpthread >&5
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `logf'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `atan2'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `sin'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `fabs'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `exp'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `cos'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `sqrt'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_intel_lp64.so: undefined
> reference to `log'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `pow'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `log10'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `ceil'
> /opt/intel/composer_xe_2015/mkl/lib/intel64/libmkl_core.so: undefined
> reference to `expf'
> collect2: error: ld returned 1 exit status
>
> Clearly these symbols should be in -lm, which is in the link line, and it
> linked when we tried in our configure. Can
> you run this link line manually and figure out what is wrong?
>
>
> I didn't get to the bottom of this issue with ML+MKL yet, but I have another
> case that's more pressing right now, and I was wondering if you might be able
> to help me out with it. The configuration I'm trying is as follows:
>
> ./configure --with-scalar-type=complex --with-clanguage=cxx --download-metis
> --download-parmetis --download-superlu_dist
> --with-blas-lapack-dir=/path/to/mkl
>
> So I'm still trying to use MKL for the time being (though I certainly
> appreciate your input about the drawbacks of this!), along with SuperLU_dist
> in complex mode. This configuration fails for me. I don't see any
> configuration log file in $PETSC_ARCH/externalpackages/SuperLU_DIST, is it
> supposed to be there somewhere?
>
> The error in the PETSc configure.log is pasted below. Interestingly if I
> configure in real mode (by removing "--with-scalar-type=complex
> --with-clanguage=cxx") then it works fine.
>
> If anyone has any suggestions about what I might be able to do to fix this,
> that'd be most appreciated.
>
> Thanks!
> David
>
>
> *******************************************************************************
> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
> details):
> -------------------------------------------------------------------------------
> Downloaded superlu_dist could not be used. Please check install in
> /home/dknez/software/petsc-3.5.2/arch-linux2-cxx-debug
> *******************************************************************************
> File "./config/configure.py", line 272, in petsc_configure
> framework.configure(out = sys.stdout)
> File
> "/home/dknez/software/petsc-3.5.2/config/BuildSystem/config/framework.py",
> line 935, in configure
> child.configure()
> File
> "/home/dknez/software/petsc-3.5.2/config/BuildSystem/config/package.py", line
> 606, in configure
> self.executeTest(self.configureLibrary)
> File "/home/dknez/software/petsc-3.5.2/config/BuildSystem/config/base.py",
> line 126, in executeTest
> ret = test(*args,**kargs)
> File
> "/home/dknez/software/petsc-3.5.2/config/BuildSystem/config/package.py", line
> 536, in configureLibrary
> for location, directory, lib, incl in self.generateGuesses():
> File
> "/home/dknez/software/petsc-3.5.2/config/BuildSystem/config/package.py", line
> 273, in generateGuesses
> raise RuntimeError('Downloaded '+self.package+' could not be used. Please
> check install in '+d+'\n')
> ================================================================================
> Finishing Configure Run at Wed Apr 1 23:09:45 2015
> ================================================================================
>
>
>
