[petsc-dev] building with MKL
Mark Adams
mfadams at lbl.gov
Sun Jul 1 09:17:22 CDT 2018
On Sun, Jul 1, 2018 at 4:08 AM Karl Rupp <rupp at iue.tuwien.ac.at> wrote:
> Hi Mark,
>
> have a look at config/examples/arch-linux-knl.py, which contains on line
> 20:
> '--with-blaslapack-dir='+os.environ['MKLROOT'],
>
> It's important that you specify the BLAS library *and* the MKL include
> directory (either via --with-blaslapack-dir or via a pair of
> --with-blaslapack-include and --with-blaslapack-lib),
I think what I sent was this second option. I nuked, reconfigured and
tested again. Same thing:
> [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 Release Version 3.9.2, unknown
> [0]PETSC ERROR:
/global/u2/m/madams/petsc_install/petsc/src/snes/examples/tutorials/./ex19
on a named nid02516 by madams Sun Jul 1 07:10:33 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 793 in
/global/u2/m/madams/petsc_install/petsc/src/dm/impls/da/fdda.c
> [0]PETSC ERROR: #4 DMCreateMatrix() line 1262 in
/global/u2/m/madams/petsc_install/petsc/src/dm/interface/dm.c
> [0]PETSC ERROR: #5 SNESSetUpMatrices() line 646 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 2908 in
/global/u2/m/madams/petsc_install/petsc/src/snes/interface/snes.c
> [0]PETSC ERROR: #8 SNESSolve() line 4300 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
> [0]PETSC ERROR: PETSc Option Table entries:
> [0]PETSC ERROR: -da_refine 3
> [0]PETSC ERROR: -ksp_monitor
> [0]PETSC ERROR: -mat_type aijmkl
> [0]PETSC ERROR: -options_left
> [0]PETSC ERROR: -pc_type gamg
> [0]PETSC ERROR: -snes_monitor_short
> [0]PETSC ERROR: -snes_view
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
error message to petsc-maint at mcs.anl.gov----------
> Rank 0 [Sun Jul 1 07:10:33 2018] [c1-1c0s5n0] application called
MPI_Abort(MPI_COMM_WORLD, 86) - process 0
> srun: error: nid02516: task 0: Aborted
> srun: Terminating job step 13487457.2
> otherwise it's not
> possible to compile the aijmkl code.
>
> Best regards,
> Karli
>
>
>
>
> On 06/30/2018 09:55 PM, Mark Adams wrote:
> > It builds and runs but looks like PETSc does not register aijmkl
> matrices.
> >
> >
> > ---
> > > [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 Release Version 3.9.2, unknown
> > > [0]PETSC ERROR:
> >
> /global/u2/m/madams/petsc_install/petsc/src/snes/examples/tutorials/./ex19
> > on a named nid02516 by madams Sat Jun 30 12:48:10 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-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 793 in
> > /global/u2/m/madams/petsc_install/petsc/src/dm/impls/da/fdda.c
> > > [0]PETSC ERROR: #4 DMCreateMatrix() line 1262 in
> > /global/u2/m/madams/petsc_install/petsc/src/dm/interface/dm.c
> > > [0]PETSC ERROR: #5 SNESSetUpMatrices() line 646 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 2908 in
> > /global/u2/m/madams/petsc_install/petsc/src/snes/interface/snes.c
> > > [0]PETSC ERROR: #8 SNESSolve() line 4300 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
> > > [0]PETSC ERROR: PETSc Option Table entries:
> > > [0]PETSC ERROR: -da_refine 3
> > > [0]PETSC ERROR: -ksp_monitor
> > > [0]PETSC ERROR: -mat_type aijmkl
> > > [0]PETSC ERROR: -options_left
> > > [0]PETSC ERROR: -pc_type gamg
> > > [0]PETSC ERROR: -snes_monitor_short
> > > [0]PETSC ERROR: -snes_view
> > > [0]PETSC ERROR: ----------------End of Error Message -------se
> >
> > On Sat, Jun 30, 2018 at 3:08 PM Mark Adams <mfadams at lbl.gov
> > <mailto:mfadams at lbl.gov>> wrote:
> >
> > OK, that got further.
> >
> > On Sat, Jun 30, 2018 at 3:03 PM Mark Adams <mfadams at lbl.gov
> > <mailto:mfadams at lbl.gov>> wrote:
> >
> > Like this?
> >
> >
> >
> '--with-blaslapack-lib=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a',
> >
> >
> > On Sat, Jun 30, 2018 at 3:00 PM Mark Adams <mfadams at lbl.gov
> > <mailto:mfadams at lbl.gov>> wrote:
> >
> >
> > Specify either "--with-blaslapack-dir" or
> > "--with-blaslapack-lib --with-blaslapack-include".
> > But not both!
> >
> >
> > Get rid of the dir option, and give the full path to the
> > library.
> >
> >
> > What is the syntax for giving the full path?
> >
>
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