[petsc-dev] building with MKL
Victor Eijkhout
eijkhout at tacc.utexas.edu
Sun Jul 1 11:49:26 CDT 2018
My petsc installation work with
--with-blaslapack-dir=/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
FWIW
and that seems to be the only thing, but just in case:
Starting configure run at Mon, 30 Apr 2018 15:05:30 +0000
Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-x=0 -with-pic --with-make-np=12 --with-packages-dir=/admin/build/admin/rpms/s\
tampede2/SOURCES/petsc-packages/externalpackages-3.9 --with-external-packages-dir=/admin/build/admin/rpms/stampede2/SOURCES/petsc-packages/externalpackages-3.9 --with-mpi-com\
pilers=1 --with-mpi-include=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/include --with-mpi-lib=/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/int\
el64/lib/release_mt/libmpi.so --with-scalar-type=real --with-shared-libraries=1 --with-precision=double --with-chaco=1 --download-chaco --with-hypre=1 --download-hypre --with\
-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-plapack=1 --download-plapack --with-spai=1 --download-spai --with-sundials=1 --download-sundials --with\
-hdf5=1 --with-hdf5-dir=/opt/apps/intel17/impi17_0/phdf5/1.8.16/x86_64 --with-mumps=1 --download-mumps --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis -\
-with-scalapack=1 --download-scalapack --with-blacs=1 --download-blacs --with-spooles=1 --download-spooles --with-suitesparse=1 --download-suitesparse --with-superlu_dist=1 -\
-download-superlu_dist --with-superlu=1 --download-superlu --with-parmetis=1 --download-parmetis --with-metis=1 --download-metis --with-zoltan=1 --download-zoltan=1 --downloa\
d-ptscotch=1 --with-debugging=no --with-blaslapack-dir=/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl COPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,COMMON-AVX512 -O2 -g" FOPT\
FLAGS="-xCORE-AVX2 -axMIC-AVX512,COMMON-AVX512 -O2 -g" CXXOPTFLAGS="-xCORE-AVX2 -axMIC-AVX512,COMMON-AVX512 -O2 -g”
Victor.
On Jul 1, 2018, at 9:17 AM, Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>> wrote:
On Sun, Jul 1, 2018 at 4:08 AM Karl Rupp <rupp at iue.tuwien.ac.at<mailto: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<mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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?
>
<configure.log>
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