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 <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> wrote: On Sun, Jul 1, 2018 at 4:08 AM Karl Rupp <r...@iue.tuwien.ac.at<mailto:r...@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-ma...@mcs.anl.gov<mailto:petsc-ma...@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 > <mfad...@lbl.gov<mailto:mfad...@lbl.gov> > <mailto:mfad...@lbl.gov<mailto:mfad...@lbl.gov>>> wrote: > > OK, that got further. > > On Sat, Jun 30, 2018 at 3:03 PM Mark Adams > <mfad...@lbl.gov<mailto:mfad...@lbl.gov> > <mailto:mfad...@lbl.gov<mailto:mfad...@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 > <mfad...@lbl.gov<mailto:mfad...@lbl.gov> > <mailto:mfad...@lbl.gov<mailto:mfad...@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>
