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

Thu Nov 13 09:05:05 CST 2025

  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> 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!fxWXWboQRNUYFGMA0mW58ZDCE6A4aGfOZvzcj0EG2lHsj_174DkztA-YDWKfPXg9WJxjRkZ13WsNy2TXkQuzMkw$ . 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!fxWXWboQRNUYFGMA0mW58ZDCE6A4aGfOZvzcj0EG2lHsj_174DkztA-YDWKfPXg9WJxjRkZ13WsNy2TXPQoo3R0$  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!fxWXWboQRNUYFGMA0mW58ZDCE6A4aGfOZvzcj0EG2lHsj_174DkztA-YDWKfPXg9WJxjRkZ13WsNy2TXA-nTYTc$ 
> 
> 

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