[petsc-users] Error configuring with --download-ml and Intel MKL

[David Knezevic]

On Thu, Mar 26, 2015 at 6:23 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Thu, Mar 26, 2015 at 5:10 PM, David Knezevic <
> david.knezevic at akselos.com> wrote:
>
>> On Thu, Mar 26, 2015 at 4:21 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Thu, Mar 26, 2015 at 1:48 PM, David Knezevic <
>>> david.knezevic at akselos.com> 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
================================================================================
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