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 ================================================================================
