[petsc-users] petsc under cygwin

Balay, Satish balay at mcs.anl.gov
Fri Dec 6 07:58:48 CST 2019


Are you sure this is cygwin from OpenMPI? I don't see it refer to -lmpi_cxx

balay at ps5 ~/petsc
$ which mpicxx
/usr/bin/mpicxx

balay at ps5 ~/petsc
$ mpicxx -show
g++ -L/usr/lib -lmpi -lopen-rte -lopen-pal -lm -lgdi32 -lz

Here is what I get with cygwin/openmpi,lapack,blas

Satish

-------

balay at ps5 ~/petsc
$ ./configure --with-scalar-type=real --with-x=0 --with-hdf5 --download-hdf5=1 --with-single-library=1 --with-shared-libraries=0 --with-log=0 --with-clanguage=C++ --with-cxx-d
ialect=C++11 --CXXFLAGS="-fopenmp -fPIC" --CFLAGS="-fopenmp -fPIC" --with-fortran=0 --FFLAGS="-fopenmp -fPIC" --with-64-bit-indices=0 --with-debugging=0 --with-cc=mpicc --with
-fc=mpif77 --with-cxx=mpicxx COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-fortran-kernels=0
===============================================================================
             Configuring PETSc to compile on your system                       
===============================================================================
===============================================================================                                                                                                       WARNING -with-clanguage=C++ is a developer feature and is *not* required for regular usage of PETSc either from C or C++                                                  ===============================================================================                                                                                                 ===============================================================================                                                                                                       Trying to download git://https://bitbucket.org/petsc/pkg-sowing.git for SOWING                                                                                            ===============================================================================                                                                                                 ===============================================================================                                                                                                       Running configure on SOWING; this may take several minutes                                                                                                                ===============================================================================                                                                                                 ===============================================================================                                                                                                       Running make on SOWING; this may take several minutes                                                                                                                     ===============================================================================                                                                                                 ===============================================================================                                                                                                       Running make install on SOWING; this may take several minutes                                                                                                             ===============================================================================                                                                                                 ===============================================================================                                                                                                       Trying to download https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz for HDF5                                                   ===============================================================================                                                                                                 ===============================================================================                                                                                                       Running configure on HDF5; this may take several minutes                                                                                                                  ===============================================================================                                                                                                 ===============================================================================                                                                                                       Running make on HDF5; this may take several minutes                                                                                                                       ===============================================================================                                                                                                 ===============================================================================                                                                                                       Running make install on HDF5; this may take several minutes                                                                                                               ===============================================================================                                                                                                 Compilers:                                                                                                                                                                      
  C Compiler:         mpicc -fopenmp -fPIC -O3 
    Version: gcc (GCC) 7.4.0
  C++ Compiler:       mpicxx -fopenmp -fPIC -O3   
    Version: g++ (GCC) 7.4.0
  Fortran Compiler:   mpif77 -fopenmp -fPIC -O3  
    Version: GNU Fortran (GCC) 7.4.0
Linkers:
  Static linker:   /usr/bin/ar cr
  Dynamic linker:   /usr/bin/ar  
  Libraries linked against:   -lgdi32 -luser32 -ladvapi32 -lkernel32 -lquadmath -lstdc++ -ldl 
make:
  Version:  4.2
  /usr/bin/make
BlasLapack:
  Library:  -llapack -lblas
  uses 4 byte integers
MPI:
  Version:  3
  Mpiexec: mpiexec --oversubscribe
  OMPI_VERSION: 3.1.3
pthread:
hdf5:
  Version:  1.10.5
  Includes: -I/home/balay/petsc/arch-mswin-cxx-opt/include
  Library:  -Wl,-rpath,/home/balay/petsc/arch-mswin-cxx-opt/lib -L/home/balay/petsc/arch-mswin-cxx-opt/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5
cmake:
  Version:  3.14.5
  /usr/bin/cmake
sowing:
  Version:  1.1.25
  /home/balay/petsc/arch-mswin-cxx-opt/bin/bfort
  Language used to compile PETSc: Cxx
PETSc:
  PETSC_ARCH: arch-mswin-cxx-opt
  PETSC_DIR: /home/balay/petsc
  Scalar type: real
  Precision: double
  Support for __float128
  Integer size: 4 bytes
  shared libraries: disabled
  Memory alignment from malloc(): 16 bytes
xxx=========================================================================xxx
 Configure stage complete. Now build PETSc libraries with:
   make PETSC_DIR=/home/balay/petsc PETSC_ARCH=arch-mswin-cxx-opt all
xxx=========================================================================xxx
                                                                                                                                                                                
balay at ps5 ~/petsc
$ 






On Fri, 6 Dec 2019, Povolotskyi, Mykhailo wrote:

> I checked:
> 
> I cannot build C++ programs with MPI, but I can build and run C programs 
> with MPI.
> 
> I have -with-log=0 because there is an overhead if many small objects 
> are created, which is my case.
> 
> As for the fortran, I will remove  --with-fortran=0
> 
> On 12/5/2019 11:53 PM, Smith, Barry F. wrote:
> >    Can you actually build and run C++ programs with the MPI?
> >
> > Executing: mpicxx  -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe   -fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o
> > Possible ERROR while running linker: exit code 1
> > stderr:
> > /usr/lib/gcc/x86_64-pc-cygwin/7.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lmpi_cxx
> > collect2: error: ld returned 1 exit status
> >            Error testing C++ compiler: Cannot compile/link Cxx with mpicxx.
> >              MPI installation mpicxx is likely incorrect.
> >    Use --with-mpi-dir to indicate an alternate MPI.
> >
> > Also you have  --with-fortran=0
> >
> > but --download-fblaslapack  and FOPTFLAGS=-O3
> >
> > and why do you have --with-log=0   it costs no overhead if you do not use it and is always useful for tracking performance.
> >
> >    Barry
> >
> >
> >> On Dec 5, 2019, at 9:19 PM, Povolotskyi, Mykhailo <mpovolot at purdue.edu> wrote:
> >>
> >> Dear Petsc support team,
> >>
> >> for some reasons I have to build petsc under Windows.
> >>
> >> I have installed Cygwin with GNU compilers and OpenMPI.
> >>
> >> Unfortunately, the configuration fails with the following message:
> >>
> >> TESTING: checkCxxCompiler from
> >> config.setCompilers(config/BuildSystem/config/setCompilers.py:814)
> >> *******************************************************************************
> >>           UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log
> >> for details):
> >> -------------------------------------------------------------------------------
> >> C++ compiler you provided with -with-cxx=mpicxx does not work.
> >> Cannot compile/link Cxx with mpicxx.
> >>
> >> I'm attaching the *.log file.
> >>
> >> Please advise,
> >>
> >> Michael.
> >>
> >> <configure.log>
> 


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