Re: [petsc-users] petsc on windows
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 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 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
> 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
> > >> wrote:
> > >> >
> > >> > > On Thu, Aug 29, 2019 at 4:02 PM Sam Guo
> > >> 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;
> > >> > > }
> > >> > >
Re: [petsc-users] petsc on windows
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 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
> wrote:
> >
> > > On Thu, Aug 29, 2019 at 4:02 PM Sam Guo 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,
Re: [petsc-users] petsc on windows
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 why configure does not include my wrapper)
On Thu, Aug 29, 2019 at 1:28 PM Matthew Knepley wrote:
> On Thu, Aug 29, 2019 at 4:02 PM Sam Guo 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
>> wrote:
>>
>>> On Thu, Aug 29, 2019 at 3:33 PM Sam Guo via petsc-users <
>>> petsc-users@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):
>>>>
>>>> -
Re: [petsc-users] petsc on windows
Thanks for the quick response. Attached please find the configure.log
containing the configure error.
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 wrote:
> On Thu, Aug 29, 2019 at 3:33 PM Sam Guo via petsc-users <
> petsc-users@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/>
>
configure.log
Description: Binary data
[petsc-users] petsc on windows
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
***
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.
I am wondering if you could give me some tips how to debug this problem.
BR,
Sam
