[petsc-users] petsc under cygwin
Povolotskyi, Mykhailo
mpovolot at purdue.edu
Fri Dec 6 09:21:24 CST 2019
Hi Satish,
I have installed cygwin yesterday, and this is the output I have:
cygcheck.exe -f /usr/bin/mpicxx
openmpi-3.1.3-1
mpicxx -show
g++ -fexceptions -L/usr/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal -lm
-lgdi32
As you can see, my installation for some reasons requires libmpi_cxx.
Do you have an idea how can this be solved?
Michael.
On 12/6/2019 9:04 AM, Balay, Satish wrote:
> Its likely my cygwin is slightly old [as its not updated in the past few months].
>
> balay at ps5 ~/petsc
> $ cygcheck.exe -f /usr/bin/mpicxx
> openmpi-3.1.3-1
>
> Satish
>
> On Fri, 6 Dec 2019, Balay, Satish wrote:
>
>> 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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