[petsc-users] petsc on windows

Sam Guo sam.guo at cd-adapco.com
Thu Aug 29 17:57:49 CDT 2019 

When I use intel mpi, configuration, compile and test all work fine but I
cannot use dll in my application.

On Thu, Aug 29, 2019 at 3:46 PM Sam Guo <sam.guo at cd-adapco.com> wrote:

> 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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