[petsc-dev] building with MKL
Mark Adams
mfadams at lbl.gov
Sun Jul 1 12:11:34 CDT 2018
On Sun, Jul 1, 2018 at 12:49 PM Victor Eijkhout <eijkhout at tacc.utexas.edu>
wrote:
> My petsc installation work with
>
>
> --with-blaslapack-dir=/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl
>
Yea, this is the first thing that I tried. I get configure failures that it
can not find libmkl_intel.a. I have libmkl_intel_thread.a and a few others.
Thanks,
>
> 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> wrote:
>
>
>
> 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?
>> >
>>
> <configure.log>
>
>
>
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