[petsc-dev] building with MKL

[Smith, Barry F.]

  This library does not have the function mkl_set_num_thread() hence PETSc concludes it is not MKL and doesn't check for the various MKL specific information.  Yet the single file does appear to have a complete copy of BLAS/LAPACK. 

   Barry


> On Jul 1, 2018, at 4:12 PM, Mark Adams <mfadams at lbl.gov> wrote:
> 
> This is the alternative approach setting the lib and include. This builds but PETSc has not configured with MKL so I get this run time error:
> 
> > lid velocity = 0.0204082, prandtl # = 1., grashof # = 1.
> > [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> > [0]PETSC ERROR: Unknown type. Check for miss-spelling or missing package: http://www.mcs.anl.gov/petsc/documentation/installation.html#external
> > [0]PETSC ERROR: Unknown Mat type given: aijmkl
> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > [0]PETSC ERROR: Petsc Development GIT revision: v3.9.2-825-g3a11c7608d  GIT Date: 2018-07-01 06:15:09 +0200
> > [0]PETSC ERROR: /global/u2/m/madams/petsc_install/petsc/src/snes/examples/tutorials/./ex19 on a  named nid02516 by madams Sun Jul  1 14:11:09 2018
> > [0]PETSC ERROR: Configure options --known-level1-dcache-size=32768 --known-level1-dcache-linesize=64 --known-level1-dcache-assoc=8 --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-memcmp-ok=1 --known-sizeof-MPI_Comm=4 --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --known-mpi-int64_t=1 --known-mpi-c-double-complex=1 --known-has-attribute-aligned=1 --with-cc=cc --with-cxx=CC --with-fc=ftn COPTFLAGS="  -g -O0 -hcpu=mic-knl -qopenmp-simd" CXXOPTFLAGS="-g -O0 -hcpu=mic-knl -qopenmp-simd" FOPTFLAGS="  -g -O0 -hcpu=mic-knl -qopenmp-simd" --download-metis=1 --with-hypre-dir=/global/homes/m/madams/tmp/hypre-2.14.0 --download-parmetis=1 --with-blaslapack-lib=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a --with-blaslapack-include=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/include --with-debugging=1 --with-mpiexec=srun --with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 --with-64-bit-indices=1 PETSC_ARCH=arch-cori-knl-dbg64-intel-omp --with-openmp=1 --download-p4est=0 --with-x=0 --prefix=/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp PETSC_DIR=/global/homes/m/madams/petsc_install/petsc
> > [0]PETSC ERROR: #1 MatSetType() line 61 in /global/u2/m/madams/petsc_install/petsc/src/mat/interface/matreg.c
> > [0]PETSC ERROR: #2 MatSetFromOptions() line 229 in /global/u2/m/madams/petsc_install/petsc/src/mat/utils/gcreate.c
> > [0]PETSC ERROR: #3 DMCreateMatrix_DA() line 892 in /global/u2/m/madams/petsc_install/petsc/src/dm/impls/da/fdda.c
> > [0]PETSC ERROR: #4 DMCreateMatrix() line 1266 in /global/u2/m/madams/petsc_install/petsc/src/dm/interface/dm.c
> > [0]PETSC ERROR: #5 SNESSetUpMatrices() line 647 in /global/u2/m/madams/petsc_install/petsc/src/snes/interface/snes.c
> > [0]PETSC ERROR: #6 SNESSetUp_NEWTONLS() line 296 in /global/u2/m/madams/petsc_install/petsc/src/snes/impls/ls/ls.c
> > [0]PETSC ERROR: #7 SNESSetUp() line 2941 in /global/u2/m/madams/petsc_install/petsc/src/snes/interface/snes.c
> > [0]PETSC ERROR: #8 SNESSolve() line 4338 in /global/u2/m/madams/petsc_install/petsc/src/snes/interface/snes.c
> > [0]PETSC ERROR: #9 main() line 161 in /global/homes/m/madams/petsc_install/petsc/src/snes/examples/tutorials/ex19.c
> 
> 
> On Sun, Jul 1, 2018 at 2:59 PM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
> 
>    Mark,
> 
>     You need to send the full configure.log (it if doesn't fit for petsc-dev, better to send it to petsc-maint that doesn't mind big attachments.
> 
>    Barry
> 
> 
> > On Jul 1, 2018, at 1:49 PM, Mark Adams <mfadams at lbl.gov> wrote:
> > 
> > 
> > 
> > On Sun, Jul 1, 2018 at 1:43 PM Victor Eijkhout <eijkhout at tacc.utexas.edu> wrote:
> > 
> > 
> >> On Jul 1, 2018, at 12:30 PM, Jeff Hammond <jeff.science at gmail.com> wrote:
> >> 
> >> If you really want to do this, then replace COMMON with CORE to specialize for SKX. There’s not point to using COMMON if you’ve got the MIC path already.
> >> 
> > 
> > We advocate CORE on our userguides, but the Intel compiler crashes reliably with that in certain cases. I think in particular Intel has never figured out how complex numbers work. If the compiler crashes it’s always on the petsc complex mode. I think I have submitted tickets about that, so maybe it’s fixed in update 3.
> > 
> > I have also seen cases where CORE gives numerical problems and replacing by COMMON fixed them. Sorry, that was a user ticket and having solved it I didn’t bother to submit an Intel support ticket.
> > 
> > I have unconfirmed reports of numerical problems. I will try your flags if I can reproduce them. Any other tricks that you used to get MKL/PETSc to work?
> > 
> > Also, PETSc is having problems finding libs. I get this error that it can not find -blas and I see that there is a libmkl_blas95_ilp64.a and libmkl_blas95_lp64.a, but no libblas.a.
> > 
> > I'm stuck, any help would be appreciated,
> > 
> > Thanks,
> > Mark
> > 
> > Executing: cc  -o /tmp/petsc-WPf2VB/config.libraries/conftest     -g -O0 -hcpu=mic-knl -qopenmp-simd -fopenmp /tmp/petsc-WPf2VB/config.libraries/conftest.o  -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 -L/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64 -lblas -lstdc++ -ldl 
> > Possible ERROR while running linker: exit code 256
> > stderr:
> > /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lblas
> >                     Popping language C
> >               Unknown name mangling in BLAS/LAPACK
> > **** Configure header /tmp/petsc-WPf2VB/confdefs.h ****
> > #if !defined(INCLUDED_UNKNOWN)
> >  
> > 
> > The support website is a nightmare anyway, so I’m not overly motivated to submit support tickets in the first place.
> > 
> > Victor.
> 
> <configure.log>