[petsc-dev] Error on Fugaku

Mark Adams mfadams at lbl.gov
Wed Apr 14 15:58:17 CDT 2021 

Satish, I get this error.

I wonder if this syntax is wrong:

    '--download-kokkos-cmake-arguments=-DCMAKE_BUILD_TYPE=Release
-DBUILD_TESTING=OFF -DKokkos_ENABLE_LIBDL=OFF -DKokkos_ENABLE_OPENMP=ON
-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON',


=============================================================================================
                              Configuring KOKKOS with cmake; this may take
several minutes

=============================================================================================

Executing: /usr/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/home/ra010009/a04199/petsc/arch-arm
-DCMAKE_INSTALL_NAME_DIR:STRING="/home/ra010009/a04199/petsc/arch-arm/lib"
-DCMAKE_INSTALL_LIBDIR:STRING="lib" -DCMAKE_VERBOSE_MAKEFILE=1
-DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER="mpifcc"
-DMPI_C_COMPILER="mpifcc" -DCMAKE_AR=/usr/bin/ar
-DCMAKE_RANLIB=/usr/bin/ranlib -DCMAKE_C_FLAGS:STRING="-fPIC -Kfast,openmp
-fopenmp" -DCMAKE_C_FLAGS_DEBUG:STRING="-fPIC -Kfast,openmp -fopenmp"
-DCMAKE_C_FLAGS_RELEASE:STRING="-fPIC -Kfast,openmp -fopenmp"
-DCMAKE_CXX_COMPILER="mpiFCC" -DMPI_CXX_COMPILER="mpiFCC"
-DCMAKE_CXX_FLAGS:STRING="-Kfast,openmp -fopenmp -fPIC -fopenmp"
-DCMAKE_CXX_FLAGS_DEBUG:STRING="-Kfast,openmp -fopenmp -fPIC -fopenmp"
-DCMAKE_CXX_FLAGS_RELEASE:STRING="-Kfast,openmp -fopenmp -fPIC -fopenmp"
-DCMAKE_Fortran_COMPILER="mpifrt" -DMPI_Fortran_COMPILER="mpifrt"
-DCMAKE_Fortran_FLAGS:STRING="-fPIC -O -fopenmp"
-DCMAKE_Fortran_FLAGS_DEBUG:STRING="-fPIC -O -fopenmp"
-DCMAKE_Fortran_FLAGS_RELEASE:STRING="-fPIC -O -fopenmp"
-DCMAKE_EXE_LINKER_FLAGS:STRING=" -fopenmp" -DBUILD_SHARED_LIBS:BOOL=ON
-DUSE_XSDK_DEFAULTS=YES -DXSDK_ENABLE_DEBUG=NO
-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON
-DCMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=ON -DKokkos_ENABLE_MPI=ON
-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_OPENMP=ON
-DCMAKE_CXX_STANDARD="14" -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=OFF
-DKokkos_ENABLE_LIBDL=OFF -DKokkos_ENABLE_OPENMP=ON
-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON
stdout:
-- Setting default Kokkos CXX standard to 14
-- The CXX compiler identification is Fujitsu
-- Check for working CXX compiler: /opt/FJSVxtclanga/tcsds-1.2.31/bin/mpiFCC
-- Check for working CXX compiler:
/opt/FJSVxtclanga/tcsds-1.2.31/bin/mpiFCC -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- The project name is: Kokkos
-- Configuring incomplete, errors occurred!
See also
"/vol0004/ra010009/a04199/petsc/arch-arm/externalpackages/git.kokkos/petsc-build/CMakeFiles/CMakeOutput.log".
                    Error configuring KOKKOS with cmake Could not execute
"['/usr/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/home/ra010009/a04199/petsc/arch-arm
-DCMAKE_INSTALL_NAME_DIR:STRING="/home/ra010009/a04199/petsc/arch-arm/lib"
-DCMAKE_INSTALL_LIBDIR:STRING="lib" -DCMAKE_VERBOSE_MAKEFILE=1
-DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER="mpifcc"
-DMPI_C_COMPILER="mpifcc" -DCMAKE_AR=/usr/bin/ar
-DCMAKE_RANLIB=/usr/bin/ranlib -DCMAKE_C_FLAGS:STRING="-fPIC -Kfast,openmp
-fopenmp" -DCMAKE_C_FLAGS_DEBUG:STRING="-fPIC -Kfast,openmp -fopenmp"
-DCMAKE_C_FLAGS_RELEASE:STRING="-fPIC -Kfast,openmp -fopenmp"
-DCMAKE_CXX_COMPILER="mpiFCC" -DMPI_CXX_COMPILER="mpiFCC"
-DCMAKE_CXX_FLAGS:STRING="-Kfast,openmp -fopenmp -fPIC -fopenmp"
-DCMAKE_CXX_FLAGS_DEBUG:STRING="-Kfast,openmp -fopenmp -fPIC -fopenmp"
-DCMAKE_CXX_FLAGS_RELEASE:STRING="-Kfast,openmp -fopenmp -fPIC -fopenmp"
-DCMAKE_Fortran_COMPILER="mpifrt" -DMPI_Fortran_COMPILER="mpifrt"
-DCMAKE_Fortran_FLAGS:STRING="-fPIC -O -fopenmp"
-DCMAKE_Fortran_FLAGS_DEBUG:STRING="-fPIC -O -fopenmp"
-DCMAKE_Fortran_FLAGS_RELEASE:STRING="-fPIC -O -fopenmp"
-DCMAKE_EXE_LINKER_FLAGS:STRING=" -fopenmp" -DBUILD_SHARED_LIBS:BOOL=ON
-DUSE_XSDK_DEFAULTS=YES -DXSDK_ENABLE_DEBUG=NO
-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON
-DCMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=ON -DKokkos_ENABLE_MPI=ON
-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_OPENMP=ON
-DCMAKE_CXX_STANDARD="14" -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=OFF
-DKokkos_ENABLE_LIBDL=OFF -DKokkos_ENABLE_OPENMP=ON
-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON']":
-- Setting default Kokkos CXX standard to 14
-- The CXX compiler identification is Fujitsu
-- Check for working CXX compiler: /opt/FJSVxtclanga/tcsds-1.2.31/bin/mpiFCC
-- Check for working CXX compiler:
/opt/FJSVxtclanga/tcsds-1.2.31/bin/mpiFCC -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- The project name is: Kokkos
-- Configuring incomplete, errors occurred!
See also
"/vol0004/ra010009/a04199/petsc/arch-arm/externalpackages/git.kokkos/petsc-build/CMakeFiles/CMakeOutput.log".CMake
Error at cmake/kokkos_compiler_id.cmake:129 (STRING):

*  STRING sub-command REPLACE requires at least four arguments.*Call Stack
(most recent call first):
  cmake/kokkos_tribits.cmake:174 (INCLUDE)
  CMakeLists.txt:166 (KOKKOS_SETUP_BUILD_ENVIRONMENT)

On Wed, Apr 14, 2021 at 3:34 PM Satish Balay <balay at mcs.anl.gov> wrote:

> Additional kokkos cmake arguments can be passed in via
> --download-kokkos-cmake-arguments=string option.
>
> Satish
>
> On Wed, 14 Apr 2021, Mark Adams wrote:
>
> > Satish,
> >
> > For the fujitsu compiler OMP is -Kopenmp.
> >
> > Sarat (cc'ed) tells me that he built Kokkos with:
> >
> > cmake -DCMAKE_BUILD_TYPE=Release \
> >     -DCMAKE_INSTALL_PREFIX=${KOKKOS_SRC_DIR}/install \
> >     -DBUILD_TESTING=OFF \
> >     -DKokkos_ENABLE_LIBDL=OFF \
> >     -DKokkos_ENABLE_OPENMP=ON \
> >     -DKokkos_ENABLE_SERIAL=ON \
> >     -DKokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON \
> >     ..
> >
> > How might I make this happen in PETSc?
> >
> > Thanks,
> > Mark
> >
> >
> > On Wed, Apr 14, 2021 at 2:44 PM Satish Balay <balay at mcs.anl.gov> wrote:
> >
> > > On Wed, 14 Apr 2021, Mark Adams wrote:
> > >
> > > > I have this building now.
> > > > Do you know anything about OpenMP?
> > > > I can add --with-openmp
> > > > That should get Kokkos to be made with OpenMP.
> > > > Should PETSc deal with the compilers correctly?
> > >
> > > Well it tries the following compiler options for openmp.
> > >
> > >     oflags = ["-fopenmp", # Gnu
> > >               "-qsmp=omp",# IBM XL C/C++
> > >               "-h omp",   # Cray. Must come after XL because XL
> interprets
> > > this option as meaning "-soname omp"
> > >               "-mp",      # Portland Group
> > >               "-Qopenmp", # Intel windows
> > >               "-openmp",  # Intel
> > >               "-xopenmp", # Sun
> > >               "+Oopenmp", # HP
> > >               "/openmp"   # Microsoft Visual Studio
> > >               ]
> > >
> > > I don't know what the flag for fugaku compiler is.
> > >
> > > Satish
> > >
> > >
> > > > Thanks,
> > > > Mark
> > > >
> > > > On Wed, Apr 14, 2021 at 1:45 PM Mark Adams <mfadams at lbl.gov> wrote:
> > > >
> > > > > Thanks,
> > > > > If you feel inspired you could try Kokkos :||
> > > > > I am in a parking lot waiting for my daughter but can try this
> when I
> > > get
> > > > > home,
> > > > > Thanks again,
> > > > > Mark
> > > > >
> > > > > On Wed, Apr 14, 2021 at 1:33 PM Satish Balay <balay at mcs.anl.gov>
> > > wrote:
> > > > >
> > > > >> I think I allocated a single node - and did the build on it.
> > > > >>
> > > > >> Now I'm getting an error - don't know what changed..
> > > > >>
> > > > >> login6$ pjsub --interact -L "node=1" -L "rscunit=rscunit_ft01" -L
> > > > >> "rscgrp=eap-int" -L "elapse=1:00:00" --sparam "wait-time=600"
> > > > >> [ERR.] PJM 0059 pjsub rscgrp=eap-int is disabled.
> > > > >>
> > > > >> Ok - the following worked..
> > > > >>
> > > > >> login6$ pjsub --interact -L "node=1" -L "rscunit=rscunit_ft01" -L
> > > > >> "elapse=1:00:00" --sparam "wait-time=600"
> > > > >> [INFO] PJM 0000 pjsub Job 6301572 submitted.
> > > > >> [INFO] PJM 0081 .connected.
> > > > >> [INFO] PJM 0082 pjsub Interactive job 6301572 started.
> > > > >> [a04201 at j31-3110s petsc]$
> > > > >>
> > > > >> Ok - trying this build now.
> > > > >>
> > > > >> [a04201 at j31-3110s petsc]$ cat
> > > > >> ~/petsc.save/arch-arm/lib/petsc/conf/reconfigure-arch-arm.py
> > > > >> #!/usr/bin/python3
> > > > >> if __name__ == '__main__':
> > > > >>   import sys
> > > > >>   import os
> > > > >>   sys.path.insert(0, os.path.abspath('config'))
> > > > >>   import configure
> > > > >>   configure_options = [
> > > > >>     '--with-blaslapack-lib=-lfjlapack',
> > > > >>     '--with-debugging=0',
> > > > >>     'CC=mpifcc',
> > > > >>     'CXX=mpiFCC',
> > > > >>     'FC=mpifrt',
> > > > >>     'PETSC_ARCH=arch-arm',
> > > > >>   ]
> > > > >>   configure.petsc_configure(configure_options)
> > > > >> [a04201 at j31-3110s petsc]$
> > > > >> ~/petsc.save/arch-arm/lib/petsc/conf/reconfigure-arch-arm.py
> > > > >> --download-p4est --download-zlib
> > > > >> <snip>
> > > > >> p4est:
> > > > >>   Includes: -I/vol0004/ra010009/a04201/petsc/arch-arm/include
> > > > >>   Library:  -Wl,-rpath,/vol0004/ra010009/a04201/petsc/arch-arm/lib
> > > > >> -L/vol0004/ra010009/a04201/petsc/arch-arm/lib -lp4est -lsc
> > > > >>
> > > > >> Ok - this worked for me.
> > > > >>
> > > > >> Satish
> > > > >>
> > > > >> On Wed, 14 Apr 2021, Mark Adams wrote:
> > > > >>
> > > > >> > Do you recall what nodes you use to build on a "compute" node,
> to
> > > avoid
> > > > >> > cross compilation?
> > > > >> >
> > > > >> > On Wed, Apr 14, 2021 at 12:08 PM Satish Balay <
> balay at mcs.anl.gov>
> > > > >> wrote:
> > > > >> >
> > > > >> > > looks like p4est cannot be cross-compiled.
> > > > >> > >
> > > > >> > > Satish
> > > > >> > >
> > > > >> > > On Wed, 14 Apr 2021, Mark Adams wrote:
> > > > >> > >
> > > > >> > > > I get this error with p4est on Fugaku.
> > > > >> > > > It is a Fortran error. Odd.
> > > > >> > > > Mark
> > > > >> > > >
> > > > >> > >
> > > > >> > >
> > > > >> >
> > > > >>
> > > > >>
> > > >
> > >
> > >
> >
>
>
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