[petsc-dev] building with MKL

Sun Jul 1 16:12:47 CDT 2018

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.
>
>
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