[petsc-users] Petsc not work in Windows-10

Qin Lu lu_qin_2000 at yahoo.com
Tue Mar 31 13:42:13 CDT 2020 

 My program has multiple files in a single directory, and there are some other dependencies. Are you talking about /petsc-3.12.4/makefile? Is there any instructions on how to compile my code using petsc makefile?
Thanks,Qin
    On Tuesday, March 31, 2020, 12:16:31 PM CDT, Satish Balay <balay at mcs.anl.gov> wrote:  
 
 Is your code a single source file?  multiple sourcefiles in a single dir? any external dependencies other than petsc?

If possible - try compiling your code with petsc makefile. Does the code run correctly this way?

Satish

On Tue, 31 Mar 2020, Qin Lu via petsc-users wrote:

>  I built and tested ex1f.F90 and ex2f.F90, both call KSPCreate(), both work well.
> My program is built using either MS Visual Studio or my own makefile. Are there any special compilation/link options required for my program in order to link with Petsc lib in Win-10?
> Thanks,Qin
>    On Tuesday, March 31, 2020, 11:51:43 AM CDT, Satish Balay <balay at mcs.anl.gov> wrote:  
>  
>  And use 'CHKERRA(ierr)' in your code to catch such failures early.
> 
> Refer to example src/ksp/ksp/examples/tutorials/ex7f.F90
> 
> >>>>>>>>>
>       call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
>       if (ierr /= 0) then
>         write(6,*)'Unable to initialize PETSc'
>         stop
>       endif
>       
>       call PetscOptionsGetInt(PETSC_NULL_OPTIONS,PETSC_NULL_CHARACTER,'-m',m,flg,ierr)
>       CHKERRA(ierr)
> <<<<<<
> 
> etc..
> 
> Satish
> 
> On Tue, 31 Mar 2020, Satish Balay via petsc-users wrote:
> 
> > Try PETSc examples with KSPCreate() - do they run correctly?
> > 
> > How do you build your code - do you use petsc formatted makefile?
> > 
> > Look for differences. Also run your code in valgrind on linux. Or you need to debug further on windows..
> > 
> > Satish
> > 
> > On Tue, 31 Mar 2020, Qin Lu via petsc-users wrote:
> > 
> > > 
> > > In the MS Visual Studio debugger, I can see there are 2 calls before KSPSetType:
> > > 
> > > call PetscInitialize(PETSC_NULL_CHARACTER,ierr)  
> > > 
> > > call KSPCreate(PETSC_COMM_WORLD,ksp_solver,ierr)
> > > 
> > > It turns out KSPCreate returns ierr=1, so it is the first Petsc call that got error.
> > > 
> > > My program in Linux (also built with Intel compilers 2018) works without problem.
> > > 
> > > Thanks,
> > > 
> > > Qin
> > > 
> > > 
> > > 
> > > 
> > > 
> > >    On Tuesday, March 31, 2020, 11:01:56 AM CDT, Satish Balay <balay at mcs.anl.gov> wrote:  
> > >  
> > >  Do PETSc examples that use KSPSetType() say src/ksp/ksp/tutorials/ex7f.F90 compile/run with this install?
> > > 
> > > Its probably best to run your code in a debugger to determine the problem.
> > > 
> > > [If your code can compile on linux - I'll also suggest running it with valgrind]
> > > 
> > > Satish
> > > 
> > > On Tue, 31 Mar 2020, Qin Lu wrote:
> > > 
> > > >  Hello,
> > > > I moved Intel-MPI libs to a directory without space, now the configuration/build of Petsc-3.12.4 worked with Intel-MPI, and test of ex2 worked well with mpiexec. However, my Fortran-90 program linked with this Petsc lib still crashed at calling KSPSetType(ksp_solver,KSPBCGS,ierr), same as what happened when using MPICH2. I suspect the issue is not in MPI, but in how Petsc is configured/built in Windows-10 using Intel compilers (the same program in Win-7 works without problem). The configuration is attached below.
> > > > 
> > > > Do you any suggestions how to proceed?
> > > > Thanks,Qin
> > > > ============./configure --with-cc='win32fe icl' --with-fc='win32fe ifort' --with-cxx='win32fe icl' --with-petsc-arch="arch-win64-release-intel-mpi" --prefix=/cygdrive/c/cygwin_cache/petsc-3.12.4-release-win-64bit-intel-mpi --with-blas-lapack-dir="/cygdrive/c/Program Files (x86)/IntelSWTools/compilers_and_libraries_2018.5.274/windows/mkl/lib/intel64" --with-mpi-include="/cygdrive/c/cygwin_cache/Intel-mpi-2019.6.166/intel64/include" --with-mpi-lib="/cygdrive/c/cygwin_cache/Intel-mpi-2019.6.166/intel64/lib/release/impi.lib"  --with-mpi-compilers=0--with-debugging=0 --useThreads=0 --with-x=0 --with-x11=0 --with-xt=0 --with-shared-libraries=0
> > > > 
> > > > 
> > > >    On Tuesday, March 31, 2020, 08:39:01 AM CDT, Satish Balay via petsc-users <petsc-users at mcs.anl.gov> wrote:  
> > > >  
> > > >  On Mon, 30 Mar 2020, Jacob Faibussowitsch wrote:
> > > > 
> > > > > >> We just cannot cope with spaces in paths. Can you use the shortened
> > > > > >> contiguous name instead of "Program File"?
> > > > > 
> > > > > FYI: Program Files or Program Files(x86) is where windows installs all of its applications (from OS or installed by user). It is best to install your MPI and other packages in root dir C:. Thats why for example MinGW installs itself in there, so it doesn’t have to deal with the space in the path.
> > > > 
> > > > No need to do this alternate install if using cygpath - as per installation instructions https://www.mcs.anl.gov/petsc/documentation/installation.html
> > > > 
> > > > Satish
> > > > 
> > > > > 
> > > > > Best regards,
> > > > > 
> > > > > Jacob Faibussowitsch
> > > > > (Jacob Fai - booss - oh - vitch)
> > > > > Cell: (312) 694-3391
> > > > > 
> > > > > > On Mar 30, 2020, at 9:18 PM, Satish Balay via petsc-users <petsc-users at mcs.anl.gov> wrote:
> > > > > > 
> > > > > > On Mon, 30 Mar 2020, Matthew Knepley wrote:
> > > > > > 
> > > > > >> On Mon, Mar 30, 2020 at 9:28 PM Qin Lu <lu_qin_2000 at yahoo.com> wrote:
> > > > > >> 
> > > > > >>> Hi,
> > > > > >>> 
> > > > > >>> I installed Intel-MPI 2019, and configured petsc-3.12.4 using
> > > > > >>> --with-mpi-dir="/cygdrive/c/Program Files
> > > > > >>> (x86)/IntelSWTools/mpi/2019.6.166/intel64", it didn't work. So I change to
> > > > > >>> use --with-mpi-include and --with-mpi-lib, still didn't work. The
> > > > > >>> config.log is attached.
> > > > > >>> 
> > > > > >>> The following is my configuration:
> > > > > >>> ===============
> > > > > >>> 
> > > > > >>> ./configure --with-cc='win32fe icl' --with-fc='win32fe ifort'
> > > > > >>> --with-cxx='win32fe icl' --with-petsc-arch="arch-win64-release-intel-mpi"
> > > > > >>> --prefix=/cygdrive/c/cygwin_cache/petsc-3.12.4-release-win-64bit-intel-mpi
> > > > > >>> --with-blas-lapack-dir="/cygdrive/c/Program Files
> > > > > >>> (x86)/IntelSWTools/compilers_and_libraries_2018.5.274/windows/mkl/lib/intel64"
> > > > > >>> --with-mpi-include="/cygdrive/c/Program Files
> > > > > >>> (x86)/IntelSWTools/mpi/2019.6.166/intel64/include" --with-mpi-lib="/cygdrive/c/Program
> > > > > >>> Files (x86)/IntelSWTools/mpi/2019.6.166/intel64/lib/impicxx.lib"  --with-
> > > > > >>> mpi-compilers=0 --with-debugging=0 --useThreads=0 --with-x=0 --with-x11=0
> > > > > >>> --with-xt=0 --with-shared-libraries=0
> > > > > >>> 
> > > > > >>> =============
> > > > > >>> 
> > > > > >>> Thanks for any suggestions.
> > > > > >>> 
> > > > > >> We just cannot cope with spaces in paths. Can you use the shortened
> > > > > >> contiguous name instead of "Program File"?
> > > > > > 
> > > > > > 
> > > > > > Yeah - the config/examples/arch-ci-mswin*.py lists paths without spaces - and https://www.mcs.anl.gov/petsc/documentation/installation.html <https://www.mcs.anl.gov/petsc/documentation/installation.html> has the instructions
> > > > > > 
> > > > > > The way to get this is: (for example)
> > > > > > 
> > > > > > balay at ps5 ~
> > > > > > $ cygpath -u `cygpath -ms '/cygdrive/C/Program Files/Microsoft MPI/Bin/mpiexec'`
> > > > > > /cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec.exe
> > > > > > 
> > > > > > Satish
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > >> 
> > > > > >>  Thanks,
> > > > > >> 
> > > > > >>    Matt
> > > > > >> 
> > > > > >>> Regards,
> > > > > >>> 
> > > > > >>> Qin
> > > > > >>> 
> > > > > >>> 
> > > > > >>> 
> > > > > >>> 
> > > > > >>> 
> > > > > >>> On Monday, March 30, 2020, 04:15:14 PM CDT, Matthew Knepley <
> > > > > >>> knepley at gmail.com> wrote:
> > > > > >>> 
> > > > > >>> 
> > > > > >>> On Mon, Mar 30, 2020 at 4:43 PM Qin Lu via petsc-users <
> > > > > >>> petsc-users at mcs.anl.gov> wrote:
> > > > > >>> 
> > > > > >>> Hi Satish,
> > > > > >>> 
> > > > > >>> The ex2.exe works with "mpiexec -np 2" when I ran it from command line.
> > > > > >>> Then I ran "which mpiexec", it actually points to Intel-MPI instead of
> > > > > >>> MPICH2, probably because I have set the former's path in environment
> > > > > >>> variable PATH in Win-10. I will try to reinstall Intel-MPI and build Petsc
> > > > > >>> with Intel-MPI.
> > > > > >>> 
> > > > > >>> As for the crash of calling to KSPSetPCSide(ksp_solver,PC_RIGHT,ierr) in
> > > > > >>> my Fortran-90 program, do you have any idea what can be wrong? Can it be
> > > > > >>> related to MPI?
> > > > > >>> 
> > > > > >>> I tested config/examples/arch-ci-mswin-intel.py as you suggested, but got
> > > > > >>> the following output:
> > > > > >>> 
> > > > > >>> ============
> > > > > >>> python ./arch-ci-mswin-intel.py
> > > > > >>> Traceback (most recent call last):
> > > > > >>>  File "./arch-ci-mswin-intel.py", line 10, in <module>
> > > > > >>>    import configure
> > > > > >>> ImportError: No module named configure
> > > > > >>> ============
> > > > > >>> 
> > > > > >>> 
> > > > > >>> You have to run those from $PETSC_DIR.
> > > > > >>> 
> > > > > >>>  Matt
> > > > > >>> 
> > > > > >>> 
> > > > > >>> Thanks,
> > > > > >>> Qin
> > > > > >>> 
> > > > > >>> 
> > > > > >>> 
> > > > > >>> I will try to use Intel-MPI and see what will happen.
> > > > > >>> 
> > > > > >>> Thanks,
> > > > > >>> Qin
> > > > > >>> 
> > > > > >>> On Monday, March 30, 2020, 01:47:49 PM CDT, Satish Balay <
> > > > > >>> balay at mcs.anl.gov> wrote:
> > > > > >>> 
> > > > > >>> 
> > > > > >>> Please preserve cc: to the list
> > > > > >>> 
> > > > > >>>> shared libraries: disabled
> > > > > >>> 
> > > > > >>> So PETSc  is correctly built as static.
> > > > > >>> 
> > > > > >>>>> C:/Program Files/mpich2x64/bin/mpiexec.exe: error while loading shared
> > > > > >>> libraries: ?: cannot open shared object file: No such file or directory
> > > > > >>> 
> > > > > >>> So its not clear which shared library this error is referring to. But then
> > > > > >>> - this error was with petsc-3.4.2
> > > > > >>> 
> > > > > >>> You can always try to run the code manually without mpiexec - and see if
> > > > > >>> that works.
> > > > > >>> 
> > > > > >>> cd src/ksp/ksp/examples/tutorials
> > > > > >>> make ex2
> > > > > >>> ./ex2
> > > > > >>> 
> > > > > >>> Wrt MSMPI - yes its free to download
> > > > > >>> 
> > > > > >>> And PETSc does work with Intel-MPI. It might be a separate
> > > > > >>> download/install. [so I can't say if what you have is the correct install
> > > > > >>> of IntelMPI or not]
> > > > > >>> 
> > > > > >>> Check the builds we use for testing - for ex:
> > > > > >>> config/examples/arch-ci-mswin-*.py
> > > > > >>> 
> > > > > >>> Satish
> > > > > >>> 
> > > > > >>> On Mon, 30 Mar 2020, Qin Lu wrote:
> > > > > >>> 
> > > > > >>>> Hi Satish,
> > > > > >>>> The configure.log and RDict.log of  Petsc-3.12.4 build is attached.
> > > > > >>>> Is the MSMPI free to use in Windows-10?
> > > > > >>>> Does Petsc support Intel-MPI? I have it in my machine, but for some
> > > > > >>> reason I only find the /mpi/intel64/bin, but not /mpi/intel64/include
> > > > > >>> subdirectory of it.
> > > > > >>>> Thanks a lot for your help.Qin
> > > > > >>>>  On Monday, March 30, 2020, 12:26:09 PM CDT, Satish Balay <
> > > > > >>> balay at mcs.anl.gov> wrote:
> > > > > >>>> 
> > > > > >>>> MPICH is unsupported - and we haven't tested with it for a long time.
> > > > > >>>> 
> > > > > >>>> And petsc-3.4.2 is from 2013 - and untested with current gen
> > > > > >>> os/compilers/libraries.
> > > > > >>>> 
> > > > > >>>> Can you send logs from Petsc-3.12.4 build [or try latest Petsc-3.13.0]?
> > > > > >>>> 
> > > > > >>>> We recommend 64bit MSMPI for windows.
> > > > > >>>> 
> > > > > >>>> Satish
> > > > > >>>> 
> > > > > >>>> On Mon, 30 Mar 2020, Qin Lu via petsc-users wrote:
> > > > > >>>> 
> > > > > >>>>> Hello,
> > > > > >>>>> I am trying to build Petsc-3.4.2 in my Windows-10 workstation using
> > > > > >>> Cygwin, with Intel-2018 compilers and MKL, and MPICH2. The
> > > > > >>> configuration/compilation/installation seem to finish without problem, but
> > > > > >>> test program (ex19) failed since it could not find a shared lib. Then I
> > > > > >>> linked the libpetsc.lib with my program (in Fortran-90), but it got run
> > > > > >>> time crash when it calls KSPSetPCSide(ksp_solver,PC_RIGHT,ierr) or other
> > > > > >>> Petsc subroutines. Note that this package was built, tested and worked well
> > > > > >>> with the same Fortran-90 program in my Windows-7 workstation.
> > > > > >>>>> 
> > > > > >>>>> Also tried Petsc-3.12.4 but got the same errors.
> > > > > >>>>> 
> > > > > >>>>> The following is my configuration:
> > > > > >>>>> 
> > > > > >>>>> 
> > > > > >>>>> ===============
> > > > > >>>>> 
> > > > > >>>>> ./configure --with-cc='win32fe icl' --with-fc='win32fe ifort'
> > > > > >>> --with-cxx='win32fe icl' --with-petsc-arch="arch-win64-release"
> > > > > >>> --prefix=/cygdrive/c/cygwin_cache/petsc-3.4.2-release-win-64bit
> > > > > >>> --with-blas-lapack-dir="/cygdrive/c/Program Files
> > > > > >>> (x86)/IntelSWTools/compilers_and_libraries_2018.5.274/windows/mkl/lib/intel64"
> > > > > >>> --with-mpi-dir="/cygdrive/c/Program Files/mpich2x64" --with-debugging=0
> > > > > >>> --useThreads=0 --with-x=0 --with-x11=0 --with-xt=0 --with-shared-libraries=0
> > > > > >>>>> 
> > > > > >>>>> ===============
> > > > > >>>>> 
> > > > > >>>>> 
> > > > > >>>>> The error message of running ex19 is:
> > > > > >>>>> 
> > > > > >>>>> 
> > > > > >>>>> =================
> > > > > >>>>> 
> > > > > >>>>> $ make PETSC_DIR=/cygdrive/c/cygwin_cache/petsc-3.4.2-debug-win-64bit
> > > > > >>> test
> > > > > >>>>> 
> > > > > >>>>> Running test examples to verify correct installation
> > > > > >>>>> 
> > > > > >>>>> Using PETSC_DIR=/cygdrive/c/cygwin_cache/petsc-3.4.2-debug-win-64bit
> > > > > >>> and PETSC_ARCH=arch-win64-debug
> > > > > >>>>> 
> > > > > >>>>> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1
> > > > > >>> MPI process
> > > > > >>>>> 
> > > > > >>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > > > >>>>> 
> > > > > >>>>> C:/Program Files/mpich2x64/bin/mpiexec.exe: error while loading shared
> > > > > >>> libraries: ?: cannot open shared object file: No such file or directory
> > > > > >>>>> 
> > > > > >>>>> =================
> > > > > >>>>> 
> > > > > >>>>> 
> > > > > >>>>> Thanks a lot for any suggestions.
> > > > > >>>>> 
> > > > > >>>>> 
> > > > > >>>>> Best Regards,
> > > > > >>>>> 
> > > > > >>>>> Qin
> > > > > >>> 
> > > > > >>>>> 
> > > > > >>>>> 
> > > > > >>>>> 
> > > > > >>>>> 
> > > > > >>>>> 
> > > > > >>> 
> > > > > >>> 
> > > > > >>> 
> > > > > >>> --
> > > > > >>> 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/ <http://www.cse.buffalo.edu/~knepley/>>
> > > > > 
> > > > > 
> > > >  
> > >  
> > 
>  
  
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