[petsc-users] petsc on windows

Balay, Satish balay at mcs.anl.gov
Fri Aug 30 13:34:01 CDT 2019 

Thanks for the update.

Yes - having the wrong variant of libpetsc.dll in PATH can cause problems.

Satish

On Fri, 30 Aug 2019, Sam Guo via petsc-users wrote:

> Thanks a lot for your help. It is my pilot error: I have both serial
> version and parallel version of petstc. It turns out serial version is
> always loaded. Now parallel petstc is working.
> 
> On Thu, Aug 29, 2019 at 5:51 PM Balay, Satish <balay at mcs.anl.gov> wrote:
> 
> > On MS-Windows - you need the location of the DLLs in PATH
> >
> > Or use --with-shared-libraries=0
> >
> > Satish
> >
> > On Thu, 29 Aug 2019, Sam Guo via petsc-users wrote:
> >
> > > 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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