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

[Barry Smith]

 Send configure.log from the failed configure

> On Apr 1, 2015, at 10:29 PM, David Knezevic <david.knezevic at akselos.com> wrote:
> 
> 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
> ================================================================================
> 
> 
>