[petsc-users] Error in configuring PETSc with Cygwin on Windows by using MS-MPI

Barry Smith bsmith at petsc.dev
Fri Nov 14 09:45:13 CST 2025 

   The C preprocessor may be failing on the complicated gymnastics of PETSC_DEPRECATED_FUNCTION

    My conclusion is PETSc is unbuildable on the version of the Microsoft compilers you are using, and you need to upgrade to the latest Microsoft compilers.

   The Microsoft C compiler has never been properly standard-compliant (and proudly so), so it can fail on correct C code.

   Barry


> On Nov 14, 2025, at 7:18 AM, 程奔 <202321009113 at mail.scut.edu.cn> wrote:
> 
>> Hi Barry
>> 
>> 
>> 
>> Thanks for your advice.
>> I follow your advice and configure and make again.
>> 
>> /******************************************
>> ./configure --with-debugging=0 --with-cc="win32fe_cl" --with-fc=0 --with-cxx="win32fe_cl" --download-f2cblaslapack=/cygdrive/g/mypetsc/f2cblaslapack-3.8.0.q2.tar.gz --with-mpi-include=\[/cygdrive/g/MSmpi/MicrosoftSDKs/Include,/cygdrive/g/MSmpi/MicrosoftSDKs/Include/x64\] --with-mpi-lib=\[/cygdrive/g/MSmpi/MicrosoftSDKs/Lib/x64/msmpifec.lib,/cygdrive/g/MSmpi/MicrosoftSDKs/Lib/x64/msmpi.lib\] --with-mpiexec=/cygdrive/g/MSmpi/MicrosoftMPI/Bin/mpiexec --download-metis=/cygdrive/g/mypetsc/petsc-pkg-metis-69fb26dd0428.tar.gz --download-parmetis=/cygdrive/g/mypetsc/petsc-pkg-parmetis-f5e3aab04fd5.tar.gz --with-strict-petscerrorcode=0 --with-64-bit-indices -CFLAGS='-O2 -MD -wd4996' -CXXFLAGS='-O2 -MD -wd4996'
>> *******************************************/
>> 
>> 
>> It happen to be another problems when performing the make all.
>> 
>> 
>> 
>> The new configure.log and make.log is attached below.
>> 
>> Sorry for bother you so many times but I wish your can help me again.
>> 
>>  
>> Looking forward your reply!
>> 
>> sinserely,
>> Cheng.
>> 
> 
> 
> 
> -----原始邮件-----
> 发件人: "Barry Smith" <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> 发送时间: 2025-11-13 23:05:05 (星期四)
> 收件人: 程奔 <202321009113 at mail.scut.edu.cn <mailto:202321009113 at mail.scut.edu.cn>>
> 抄送: petsc-users <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> 主题: Re: [petsc-users] Error in configuring PETSc with Cygwin on Windows by using MS-MPI
> 
> 
>   Change
> 
> __attribute__((packed))
> 
> to 
> 
> /* __attribute__((packed)) */ 
> 
> in include/petscmath.h 
> 
> and run make again.
> 
> I think you should install a new version of Microsoft's compilers etc.
> 
>   Barry
> 
> 
>> On Nov 13, 2025, at 3:53 AM, 程奔 <202321009113 at mail.scut.edu.cn <mailto:202321009113 at mail.scut.edu.cn>> wrote:
>> 
>> Hi Barry
>> 
>> 
>> 
>> Thanks for your advice.
>> I use AI help me that change the file on the petsc-3.24.1/arch-mswin-c-opt/externalpackages/petsc-pkg-parmetis-f5e3aab04fd5/headers/gk_arch. 
>> 
>> 
>> The change is from: 
>> 
>> #ifdef __MSC__ 
>>   #include "ms_stdint.h"
>>   #include "ms_inttypes.h"
>>   #include "ms_stat.h"              
>> #else
>> #ifndef SUNOS
>>   #include <stdint.h>
>> #endif
>> #if !defined(WIN32) && !defined(__MINGW32__)
>>   #include <sys/resource.h>
>> #endif
>>   #include <inttypes.h>
>>   #include <sys/types.h>
>>   #include <sys/time.h>
>> #endif
>> 
>> To:
>> 
>> #if (defined(__MSC__) || defined(_MSC_VER)) && defined(_MSC_VER) && _MSC_VER < 1900
>>   #include "ms_stdint.h"
>>   #include "ms_inttypes.h"
>>   #include "ms_stat.h"
>> #else
>> #ifndef SUNOS
>>   #include <stdint.h>
>> #endif
>> #if !defined(WIN32) && !defined(__MINGW32__) && !defined(_MSC_VER)
>>   #include <sys/resource.h>
>> #endif
>>   #include <inttypes.h>
>>   #include <sys/types.h>
>> #if !defined(_MSC_VER)
>>   #include <sys/time.h>
>> #endif
>> #endif
>> 
>> 
>> 
>> Then I configure the PETSc:
>> 
>> ./configure --with-debugging=0 --with-cc=cl --with-fc=0 --with-cxx=cl --download-f2cblaslapack=/cygdrive/g/mypetsc/f2cblaslapack-3.8.0.q2.tar.gz --with-mpi-include=\[/cygdrive/g/MSmpi/MicrosoftSDKs/Include,/cygdrive/g/MSmpi/MicrosoftSDKs/Include/x64\] --with-mpi-lib=\[/cygdrive/g/MSmpi/MicrosoftSDKs/Lib/x64/msmpifec.lib,/cygdrive/g/MSmpi/MicrosoftSDKs/Lib/x64/msmpi.lib\] --with-mpiexec=/cygdrive/g/MSmpi/MicrosoftMPI/Bin/mpiexec --download-metis=/cygdrive/g/mypetsc/petsc-pkg-metis-69fb26dd0428.tar.gz --download-parmetis=/cygdrive/g/mypetsc/petsc-pkg-parmetis-f5e3aab04fd5.tar.gz --with-strict-petscerrorcode=0 --with-64-bit-indices
>> 
>> It seems good, but then I make it
>> 
>> it  have the error:
>> 
>> 
>> 
>> make[3]: *** [gmakefile:211: arch-mswin-c-opt/obj/src/sys/objects/device/interface/mark_dcontext.o] Error 2
>> make[3]: Leaving directory '/cygdrive/g/mypetsc/petsc-3.24.1'
>> make[2]: *** [/cygdrive/g/mypetsc/petsc-3.24.1/lib/petsc/conf/rules_doc.mk:5: libs] Error 2
>> make[2]: Leaving directory '/cygdrive/g/mypetsc/petsc-3.24.1'
>> **************************ERROR*************************************
>>   Error during compile, check arch-mswin-c-opt/lib/petsc/conf/make.log
>>   Send it and arch-mswin-c-opt/lib/petsc/conf/configure.log to petsc-maint at mcs.anl.gov <mailto:petsc-maint at mcs.anl.gov>
>> ********************************************************************
>> make[1]: *** [makefile:44: all] Error 1
>> make: *** [GNUmakefile:9: all] Error 2
>> 
>> 
>> The new configure.log and make.log is attached below.
>> 
>> I don't know if it is caused by the change I made or the other problems.
>> 
>> 
>> 
>> So I ask for your help again.  
>> Looking forward your reply!
>> 
>> 
>> sinserely,
>> Cheng.
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -----原始邮件-----
>> 发件人: "Barry Smith" <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
>> 发送时间: 2025-11-13 00:03:50 (星期四)
>> 收件人: 程奔 <202321009113 at mail.scut.edu.cn <mailto:202321009113 at mail.scut.edu.cn>>
>> 抄送: PETSc <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
>> 主题: Re: [petsc-users] Error in configuring PETSc with Cygwin on Windows by using MS-MPI
>> 
>> G:\VisualStudio2022\VC\Tools\MSVC\14.37.32822\include\stdint.h(37): error C2371: 'int_fast16_t': redefinition; different basic types
>> G:\mypetsc\petsc-3.24.1\arch-mswin-c-opt\externalpackages\petsc-pkg-parmetis-f5e3aab04fd5\headers\ms_stdint.h(80): note: see declaration of 'int_fast16_t'
>> G:\VisualStudio2022\VC\Tools\MSVC\14.37.32822\include\stdint.h(41): error C2371: 'uint_fast16_t': redefinition; different basic types
>> G:\mypetsc\petsc-3.24.1\arch-mswin-c-opt\externalpackages\petsc-pkg-parmetis-f5e3aab04fd5\headers\ms_stdint.h(84): note: see declaration of 'uint_fast16_t'
>> G:\VisualStudio2022\VC\Tools\MSVC\14.37.32822\include\stdint.h(49): warning C4005: 'INT8_MIN': macro redefinition
>> G:\mypetsc\petsc-3.24.1\arch-mswin-c-opt\externalpackages\petsc-pkg-parmetis-f5e3aab04fd5\headers\ms_stdint.h(107): note: see previous definition of 'INT8_MIN'
>> 
>> Parmetis has its own definitions for many C standard types, etc in headers\ms_stdint.h that duplicate what is available in stdint.h on Unix systems. Normally, this gets included when __MSC_ is defined instead of stdint.h (in gk_arch.h).
>> 
>> But for some reason, with your system it appears that Microsoft's stdint.h is also getting included; presumably brought in through some other system include file since it is only included in one place.
>> 
>> $ git grep stdint.h
>> headers/gk_arch.h:  #include "ms_stdint.h"
>> headers/gk_arch.h:  #include <stdint.h>
>> headers/ms_inttypes.h:#include "ms_stdint.h"
>> headers/ms_stdint.h:// ISO C9x  compliant stdint.h for Microsoft Visual Studio
>> 
>> You have a fairly old VisualStudio, 2022. Can you upgrade to the latest? Let us know if this resolves the problem.
>> 
>> Barry
>> 
>> 
>> 
>> 
>>  
>> 
>> 
>> 
>> 
>> 
>> On Nov 12, 2025, at 5:29 AM, 程奔 <202321009113 at mail.scut.edu.cn <mailto:202321009113 at mail.scut.edu.cn>> wrote:
>> 
>> Hi Barry
>> Thanks for your reply.
>> I check the package parmetis,and the "petsc-pkg-parmetis-45100eac9301.tar.gz" is form https://urldefense.us/v3/__https://bitbucket.org/petsc/pkg-parmetis/get/v4.0.3.tar.gz__;!!G_uCfscf7eWS!dCHHyY-VxDm-ywDHjCTx7TuexZfZSpNvZITmJoKuqThj3NRnYxGB_lEcLPxzGRFkPS8_uyJCqoS_NU4txpTE0xQ$ . So I made a mistake about the package.
>> Then I download the package form https://urldefense.us/v3/__https://bitbucket.org/petsc/pkg-parmetis/get/v4.0.3-p9.tar.gz__;!!G_uCfscf7eWS!dCHHyY-VxDm-ywDHjCTx7TuexZfZSpNvZITmJoKuqThj3NRnYxGB_lEcLPxzGRFkPS8_uyJCqoS_NU4twjES1lo$  and it is "petsc-pkg-parmetis-f5e3aab04fd5.tar.gz" 
>> 
>> 
>> Then the compiler option in configuration is:
>> ./configure --with-debugging=0 --with-cc=cl --with-fc=0 --with-cxx=cl --download-f2cblaslapack=/cygdrive/g/mypetsc/f2cblaslapack-3.8.0.q2.tar.gz --with-mpi-include=\[/cygdrive/g/MSmpi/MicrosoftSDKs/Include,/cygdrive/g/MSmpi/MicrosoftSDKs/Include/x64\] --with-mpi-lib=\[/cygdrive/g/MSmpi/MicrosoftSDKs/Lib/x64/msmpifec.lib,/cygdrive/g/MSmpi/MicrosoftSDKs/Lib/x64/msmpi.lib\] --with-mpiexec=/cygdrive/g/MSmpi/MicrosoftMPI/Bin/mpiexec --download-metis=/cygdrive/g/mypetsc/petsc-pkg-metis-69fb26dd0428.tar.gz --download-parmetis=/cygdrive/g/mypetsc/petsc-pkg-parmetis-f5e3aab04fd5.tar.gz --with-strict-petscerrorcode=0 --with-64-bit-indices
>> 
>> but it still have the same error:
>> *********************************************************************************************
>> =============================================================================================
>> =============================================================================================
>>                 Configuring PARMETIS with CMake; this may take several minutes
>> =============================================================================================
>> =============================================================================================
>>                Compiling and installing PARMETIS; this may take several minutes
>> =============================================================================================
>> 
>> 
>> *********************************************************************************************
>>            UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
>> ---------------------------------------------------------------------------------------------
>>                                Error running make on  PARMETIS
>> 
>> 
>> *********************************************************************************************
>> 
>> 
>> The new configure.log is attached below.
>> So I ask for your help again.  
>> Looking forward your reply!
>> 
>> 
>> sinserely,
>> Cheng.
>> 
>> 
>> 
>> 
>> -----原始邮件-----
>> 发件人: "Barry Smith" <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
>> 发送时间: 2025-11-11 23:29:01 (星期二)
>> 收件人: "Matthew Knepley" <knepley at gmail.com <mailto:knepley at gmail.com>>
>> 抄送: 程奔 <ctchengben at mail.scut.edu.cn <mailto:ctchengben at mail.scut.edu.cn>>, petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>
>> 主题: Re: [petsc-users] Error in configuring PETSc with Cygwin on Windows by using MS-MPI
>> 
>> 
>>   Where/how did you obtain /cygdrive/g/mypetsc/petsc-pkg-parmetis-45100eac9301.tar.gz ? Was it from PETSc ./configure?
>> 
>>     self.version          = '4.0.3'
>>     self.versionname      = 'PARMETIS_MAJOR_VERSION.PARMETIS_MINOR_VERSION.PARMETIS_SUBMINOR_VERSION'
>>     self.gitcommit         = 'v'+self.version+'-p9'
>>     self.download          = ['git://https://bitbucket.org/petsc/pkg-parmetis.git','https://bitbucket.org/petsc/pkg-parmetis/get/'+self.gitcommit+'.tar.gz <git://https//bitbucket.org/petsc/pkg-parmetis.git','https://bitbucket.org/petsc/pkg-parmetis/get/'+self.gitcommit+'.tar.gz>']
>> 
>> 
>> 
>> On Nov 11, 2025, at 7:35 AM, Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>> wrote:
>> 
>> On Tue, Nov 11, 2025 at 4:44 AM 程奔 <ctchengben at mail.scut.edu.cn <mailto:ctchengben at mail.scut.edu.cn>> wrote:
>> Hello,
>> Recently I try to install PETSc with Cygwin since I'd like to use PETSc with Visual Studio on Windows10 plateform.For the sake of clarity, I firstly list the softwares/packages used below:
>> 1. PETSc: version 3.14.1
>> 2. VS: version 2022 
>> 3. MS MPI: download Microsoft MPI v10.1.2
>> 4. Cygwin
>> 
>> Quick question: Have you considered installing on WSL? I have had much better luck with that on Windows.
>> 
>> This seems to be an incompatibility of ParMetis Windows support and your version:
>> 
>> G:\VisualStudio2022\VC\Tools\MSVC\14.37.32822\include\stdint.h(37): error C2371: 'int_fast16_t': redefinition; different basic types^M
>> G:\mypetsc\petsc-3.24.1\arch-mswin-c-opt\externalpackages\petsc-pkg-parmetis-f5e3aab04fd5\headers\ms_stdint.h(80): note: see declaration of 'int_fast16_t'^M
>> G:\VisualStudio2022\VC\Tools\MSVC\14.37.32822\include\stdint.h(41): error C2371: 'uint_fast16_t': redefinition; different basic types^M
>> G:\mypetsc\petsc-3.24.1\arch-mswin-c-opt\externalpackages\petsc-pkg-parmetis-f5e3aab04fd5\headers\ms_stdint.h(84): note: see declaration of 'uint_fast16_t'^M 
>> 
>>   Thanks,
>> 
>>      Matt
>> 
>> And the compiler option in configuration is:
>> ./configure --with-debugging=0 --with-cc=cl --with-fc=0 --with-cxx=cl 
>> --download-f2cblaslapack=/cygdrive/g/mypetsc/f2cblaslapack-3.8.0.q2.tar.gz 
>> --with-mpi-include=\[/cygdrive/g/MSmpi/MicrosoftSDKs/Include,/cygdrive/g/MSmpi/MicrosoftSDKs/Include/x64\] 
>> --with-mpi-lib=\[/cygdrive/g/MSmpi/MicrosoftSDKs/Lib/x64/msmpifec.lib,/cygdrive/g/MSmpi/MicrosoftSDKs/Lib/x64/msmpi.lib\] 
>> --with-mpiexec=/cygdrive/g/MSmpi/MicrosoftMPI/Bin/mpiexec 
>> --download-metis=/cygdrive/g/mypetsc/petsc-pkg-metis-69fb26dd0428.tar.gz 
>> --download-parmetis=/cygdrive/g/mypetsc/petsc-pkg-parmetis-45100eac9301.tar.gz 
>> --with-strict-petscerrorcode=0 --with-64-bit-indices --download-hdf5=/cygdrive/g/mypetsc/hdf5-1.14.3-p1.tar.bz2
>> 
>> 
>> 
>> 
>> 
>> 
>> but there return an error:
>> *********************************************************************************************
>> =============================================================================================
>> =============================================================================================
>>                 Configuring PARMETIS with CMake; this may take several minutes
>> =============================================================================================
>> =============================================================================================
>>                Compiling and installing PARMETIS; this may take several minutes
>> =============================================================================================
>> 
>> 
>> *********************************************************************************************
>>            UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
>> ---------------------------------------------------------------------------------------------
>>                                Error running make on  PARMETIS
>> 
>> 
>> *********************************************************************************************
>> 
>> 
>> The configure.log is attached below.
>> So I write this email to report my problem and ask for your help.  
>> Looking forward your reply!
>> 
>> 
>> sinserely,
>> Cheng.
>> 
>> 
>> -- 
>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dCHHyY-VxDm-ywDHjCTx7TuexZfZSpNvZITmJoKuqThj3NRnYxGB_lEcLPxzGRFkPS8_uyJCqoS_NU4tpGoejyM$ 
>> 
>> 
> 
> 
> 

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