[petsc-users] petsc on windows

Thu Aug 29 17:46:47 CDT 2019

After I removed following lines inin config/BuildSystem/config/package.py,
configuration finished without error.
 self.executeTest(self.checkDependencies)
 self.executeTest(self.configureLibrary)
 self.executeTest(self.checkSharedLibrary)

I then add my mpi wrapper to ${PTESTC_ARCH}/lib/petsc/conf/petscvariables:
PCC_LINKER_FLAGS =    -MD -wd4996 -Z7
/home/xianzhongg/dev/star/lib/win64/intel18.3vc14/lib/StarMpiWrapper.lib

On Thu, Aug 29, 2019 at 3:28 PM Balay, Satish <balay at mcs.anl.gov> wrote:

> On Thu, 29 Aug 2019, Sam Guo via petsc-users wrote:
>
> > I can link when I add my wrapper to
> > PCC_LINKER_FLAGS =    -MD -wd4996 -Z7
> > /home/xianzhongg/dev/star/lib/win64/intel18.3vc14/lib/StarMpiWrapper.lib
>
> I don't understand what you mean here. Add PCC_LINKER_FLAGS to where? This
> is a variable in configure generated makefile
>
> Since PETSc is not built [as configure failed] - there should be no
> configure generated makefiles.
>
> > (I don't understand why configure does not include my wrapper)
>
> Well the compiler gives the error below. Can you try to compile
> manually [i.e without PETSc or any petsc makefiles] a simple MPI code
> - say cpi.c from MPICH and see if it works?  [and copy/paste the log
> from this compile attempt.
>
> Satish
>
> >
> >
> > On Thu, Aug 29, 2019 at 1:28 PM Matthew Knepley <knepley at gmail.com>
> wrote:
> >
> > > On Thu, Aug 29, 2019 at 4:02 PM Sam Guo <sam.guo at cd-adapco.com> wrote:
> > >
> > >> Thanks for the quick response. Attached please find the configure.log
> > >> containing the configure error.
> > >>
> > >
> > > Executing: /home/xianzhongg/petsc-3.11.3/lib/petsc/bin/win32fe/win32fe
> cl
> > > -c -o /tmp/petsc-6DsCEk/config.libraries/conftest.o
> > > -I/tmp/petsc-6DsCEk/config.compilers
> > > -I/tmp/petsc-6DsCEk/config.setCompilers
> > > -I/tmp/petsc-6DsCEk/config.utilities.closure
> > > -I/tmp/petsc-6DsCEk/config.headers
> > > -I/tmp/petsc-6DsCEk/config.utilities.cacheDetails
> > > -I/tmp/petsc-6DsCEk/config.types -I/tmp/petsc-6DsCEk/config.atomics
> > > -I/tmp/petsc-6DsCEk/config.functions
> > > -I/tmp/petsc-6DsCEk/config.utilities.featureTestMacros
> > > -I/tmp/petsc-6DsCEk/config.utilities.missing
> > > -I/tmp/petsc-6DsCEk/PETSc.options.scalarTypes
> > > -I/tmp/petsc-6DsCEk/config.libraries  -MD -wd4996 -Z7
> > >  /tmp/petsc-6DsCEk/config.libraries/conftest.c
> > > stdout: conftest.c
> > > Successful compile:
> > > Source:
> > > #include "confdefs.h"
> > > #include "conffix.h"
> > > /* Override any gcc2 internal prototype to avoid an error. */
> > > char MPI_Init();
> > > static void _check_MPI_Init() { MPI_Init(); }
> > > char MPI_Comm_create();
> > > static void _check_MPI_Comm_create() { MPI_Comm_create(); }
> > >
> > > int main() {
> > > _check_MPI_Init();
> > > _check_MPI_Comm_create();;
> > >   return 0;
> > > }
> > > Executing: /home/xianzhongg/petsc-3.11.3/lib/petsc/bin/win32fe/win32fe
> cl
> > >  -o /tmp/petsc-6DsCEk/config.libraries/conftest.exe    -MD -wd4996 -Z7
> > > /tmp/petsc-6DsCEk/config.libraries/conftest.o
> > >
> /home/xianzhongg/dev/star/lib/win64/intel18.3vc14/lib/StarMpiWrapper.lib
> > > Ws2_32.lib
> > > stdout:
> > > LINK : C:\cygwin64\tmp\PE81BA~1\CONFIG~1.LIB\conftest.exe not found or
> not
> > > built by the last incremental link; performing full link
> > > conftest.obj : error LNK2019: unresolved external symbol MPI_Init
> > > referenced in function _check_MPI_Init
> > > conftest.obj : error LNK2019: unresolved external symbol
> MPI_Comm_create
> > > referenced in function _check_MPI_Comm_create
> > > C:\cygwin64\tmp\PE81BA~1\CONFIG~1.LIB\conftest.exe : fatal error
> LNK1120:
> > > 2 unresolved externals
> > > Possible ERROR while running linker: exit code 2
> > > stdout:
> > > LINK : C:\cygwin64\tmp\PE81BA~1\CONFIG~1.LIB\conftest.exe not found or
> not
> > > built by the last incremental link; performing full link
> > > conftest.obj : error LNK2019: unresolved external symbol MPI_Init
> > > referenced in function _check_MPI_Init
> > > conftest.obj : error LNK2019: unresolved external symbol
> MPI_Comm_create
> > > referenced in function _check_MPI_Comm_create
> > > C:\cygwin64\tmp\PE81BA~1\CONFIG~1.LIB\conftest.exe : fatal error
> LNK1120:
> > > 2 unresolved externals
> > >
> > > The link is definitely failing. Does it work if you do it by hand?
> > >
> > >   Thanks,
> > >
> > >      Matt
> > >
> > >
> > >> Regarding our dup, our wrapper does support it. In fact, everything
> works
> > >> fine on Linux. I suspect on windows, PETSc picks the system mpi.h
> somehow.
> > >> I am investigating it.
> > >>
> > >> Thanks,
> > >> Sam
> > >>
> > >> On Thu, Aug 29, 2019 at 3:39 PM Matthew Knepley <knepley at gmail.com>
> > >> wrote:
> > >>
> > >>> On Thu, Aug 29, 2019 at 3:33 PM Sam Guo via petsc-users <
> > >>> petsc-users at mcs.anl.gov> wrote:
> > >>>
> > >>>> Dear PETSc dev team,
> > >>>>    I am looking some tips porting petsc to windows. We have our mpi
> > >>>> wrapper (so we can switch different mpi). I configure petsc using
> > >>>> --with-mpi-lib and --with-mpi-include
> > >>>>  ./configure --with-cc="win32fe cl" --with-fc=0
> > >>>> --download-f2cblaslapack
> > >>>>
> --with-mpi-lib=/home/xianzhongg/dev/star/lib/win64/intel18.3vc14/lib/StarMpiWrapper.lib
> > >>>> --with-mpi-include=/home/xianzhongg/dev/star/base/src/mpi/include
> > >>>> --with-shared-libaries=1
> > >>>>
> > >>>> But I got error
> > >>>>
> > >>>>
> ===============================================================================
> > >>>>              Configuring PETSc to compile on your system
> > >>>>
> > >>>>
> ===============================================================================
> > >>>> TESTING: check from
> > >>>> config.libraries(config/BuildSystem/config/libraries.py:154)
> > >>>>
> *******************************************************************************
> > >>>>          UNABLE to CONFIGURE with GIVEN OPTIONS    (see
> configure.log
> > >>>> for details):
> > >>>>
> > >>>>
> -------------------------------------------------------------------------------
> > >>>>
> --with-mpi-lib=['/home/xianzhongg/dev/star/lib/win64/intel18.3vc14/lib/StarMpiWrapper.lib']
> > >>>> and
> > >>>>
> --with-mpi-include=['/home/xianzhongg/dev/star/base/src/mpi/include']
> > >>>> did not work
> > >>>>
> > >>>>
> *******************************************************************************
> > >>>>
> > >>>
> > >>> Your MPI wrapper should pass the tests here. Send the configure.log
> > >>>
> > >>>
> > >>>> To fix the configuration error,  in
> > >>>> config/BuildSystem/config/package.py, I removed
> > >>>>  self.executeTest(self.checkDependencies)
> > >>>>  self.executeTest(self.configureLibrary)
> > >>>>  self.executeTest(self.checkSharedLibrary)
> > >>>>
> > >>>> To link, I add my mpi wrapper
> > >>>> to ${PTESTC_ARCH}/lib/petsc/conf/petscvariables:
> > >>>> PCC_LINKER_FLAGS =    -MD -wd4996 -Z7
> > >>>>
> /home/xianzhongg/dev/star/lib/win64/intel18.3vc14/lib/StarMpiWrapper.lib
> > >>>>
> > >>>> I got libpetstc.dll and libpetstc.lib. When I try to test it inside
> our
> > >>>> code, PETSc somehow crates a duplicate of communicator with only 1
> MPI
> > >>>> process and PETSC_COMM_WORLD is set to 2. If I set PETSC_COMM_WORLD
> to 1
> > >>>> (our MPI_COMM_WORLD), PETSc is hanging.
> > >>>>
> > >>>
> > >>> We do dup the communicator on entry. Shouldn't that be supported by
> your
> > >>> wrapper?
> > >>>
> > >>>   Thanks,
> > >>>
> > >>>      Matt
> > >>>
> > >>>
> > >>>> I am wondering if you could give me some tips how to debug this
> problem.
> > >>>>
> > >>>> BR,
> > >>>> Sam
> > >>>>
> > >>>
> > >>>
> > >>> --
> > >>> What most experimenters take for granted before they begin their
> > >>> experiments is infinitely more interesting than any results to which
> their
> > >>> experiments lead.
> > >>> -- Norbert Wiener
> > >>>
> > >>> https://www.cse.buffalo.edu/~knepley/
> > >>> <http://www.cse.buffalo.edu/~knepley/>
> > >>>
> > >>
> > >
> > > --
> > > What most experimenters take for granted before they begin their
> > > experiments is infinitely more interesting than any results to which
> their
> > > experiments lead.
> > > -- Norbert Wiener
> > >
> > > https://www.cse.buffalo.edu/~knepley/
> > > <http://www.cse.buffalo.edu/~knepley/>
> > >
> >
>
>
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