November 2025 - petsc-users - mailman3.cels.anl.gov

Re: [petsc-users] Error in configuring PETSc with Cygwin on Windows by using MS-MPI
by Barry Smith 14 Nov '25

14 Nov '25

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(a)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(a)petsc.dev <mailto:[email protected]>> > 发送时间: 2025-11-13 23:05:05 (星期四) > 收件人: 程奔 <202321009113(a)mail.scut.edu.cn <mailto:[email protected]>> > 抄送: petsc-users <petsc-users(a)mcs.anl.gov <mailto:[email protected]>> > 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(a)mail.scut.edu.cn <mailto:[email protected]>> 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(a)mcs.anl.gov <mailto:[email protected]> >> ******************************************************************** >> 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(a)petsc.dev <mailto:[email protected]>> >> 发送时间: 2025-11-13 00:03:50 (星期四) >> 收件人: 程奔 <202321009113(a)mail.scut.edu.cn <mailto:[email protected]>> >> 抄送: PETSc <petsc-users(a)mcs.anl.gov <mailto:[email protected]>> >> 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(a)mail.scut.edu.cn <mailto:[email protected]>> 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.… . 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.… 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(a)petsc.dev <mailto:[email protected]>> >> 发送时间: 2025-11-11 23:29:01 (星期二) >> 收件人: "Matthew Knepley" <knepley(a)gmail.com <mailto:[email protected]>> >> 抄送: 程奔 <ctchengben(a)mail.scut.edu.cn <mailto:[email protected]>>, petsc-users(a)mcs.anl.gov <mailto:[email protected]> >> 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(a)gmail.com <mailto:[email protected]>> wrote: >> >> On Tue, Nov 11, 2025 at 4:44 AM 程奔 <ctchengben(a)mail.scut.edu.cn <mailto:[email protected]>> 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_uC… >> >> > > >

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Fwd: Fw: gpu cpu parallel
by Junchao Zhang 13 Nov '25

13 Nov '25

Glad to hear it works! --Junchao Zhang ---------- Forwarded message --------- From: Grace <amarantos(a)126.com> Date: Thu, Nov 13, 2025 at 9:05 PM Subject: Fw: [petsc-users] gpu cpu parallel To: junchao.zhang(a)gmail.com <junchao.zhang(a)gmail.com> Hello, Junchao, Thank you for your prompt help and the detailed solution. We have tested the approach you suggested, using the set_gpu_device wrapper script to control GPU visibility via CUDA_VISIBLE_DEVICES. It works perfectly and now correctly maps the ranks to the intended GPUs as we desired. We really appreciate your guidance in resolving this issue. Best regards, Grace Gao ---- Forwarded Message ---- >From Grant Chao<grantchao2018(a)163.com> <grantchao2018(a)163.com> Date 11/14/2025 08:40 To amarantos(a)126.com Cc Subject Fw:Re: Re: [petsc-users] gpu cpu parallel -- sent by my netease email phone version -------- Forward mail content -------- From: "Junchao Zhang" <junchao.zhang(a)gmail.com> Date: 2025-11-14 07:02:20 To: "Grant Chao" <grantchao2018(a)163.com> CC: "Barry Smith" <bsmith(a)petsc.dev>,petsc-users <petsc-users(a)mcs.anl.gov> Subject: Re: Re: [petsc-users] gpu cpu parallel Hi, Grant, I could reproduce the issue with your code. I think petsc code has some problems and I created an issue at https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/issues/1826__;!… . Though we should fix it (not sure how for now), I think a much simpler approach is to use CUDA_VISIBLE_DEVICES. For example, if you just want ranks 0, 4 to use GPUs 0, 1 respectively, you can just delete these lines in your example if (global_rank == 0) { cudaSetDevice(0); } else if (global_rank == 4) { cudaSetDevice(1); } Then, instead, just make GPUs 0, 1 visible to ranks 0, 4 respectively upfront, by $ cat set_gpu_device #!/bin/bash # select_gpu_device wrapper script export CUDA_VISIBLE_DEVICES=$((OMPI_COMM_WORLD_LOCAL_RANK/(OMPI_COMM_WORLD_LOCAL_SIZE/2))) exec $* $ mpirun -n 8 ./set_gpu_device ./ex0 [Rank 5] no computation assigned. [Rank 6] no computation assigned. [Rank 7] no computation assigned. [Rank 0] using GPU 0, [line 23]. [Rank 0] using GPU 0, [line 32] after setdevice. [Rank 1] no computation assigned. [Rank 2] no computation assigned. [Rank 3] no computation assigned. [Rank 4] using GPU 0, [line 23]. [Rank 4] using GPU 0, [line 32] after setdevice. [Rank 0] using GPU 0, [line 42] after create A. [Rank 4] using GPU 0, [line 42] after create A. [Rank 4] using GPU 0, [line 46] after set A type. [Rank 0] using GPU 0, [line 46] after set A type. [Rank 0] using GPU 0, [line 50] after MatSetUp. [Rank 4] using GPU 0, [line 50] after MatSetUp. [Rank 0] using GPU 0, [line 63] after Mat Assemble. [Rank 4] using GPU 0, [line 63] after Mat Assemble. Smallest eigenvalue = 100.000000 Smallest eigenvalue = 100.000000 Note for rank 4, GPU 0 is actually the physical GPU 1. Let me know if it works. --Junchao Zhang On Thu, Nov 13, 2025 at 11:17 AM Grant Chao <grantchao2018(a)163.com> wrote: > Junchao, > We have tried cudaSetDevice. > The test code is attached. 8 cpu and 2 gpu are used. And we create a > gpu_comm including rank 0 and rank 4. > Then we set gpu 0 to rank 0, gpu 1 to rank 1 respectively. > After MatSetType, rank 1 is mapped to gpu0 again. > > The run cmd is > mpirun -n 8 ./a.out -eps_type jd -st_ksp_type gmres -st_pc_type none > > The std out is show below, > [Rank 0] using GPU 0, [line 22]. > [Rank 1] no computation assigned. > [Rank 2] no computation assigned. > [Rank 3] no computation assigned. > [Rank 4] using GPU 0, [line 22]. > [Rank 5] no computation assigned. > [Rank 6] no computation assigned. > [Rank 7] no computation assigned. > [Rank 4] using GPU 1, [line 31] after setdevice. -------- Here set > device successfully > [Rank 0] using GPU 0, [line 31] after setdevice. > [Rank 4] using GPU 1, [line 41] after create A. > [Rank 0] using GPU 0, [line 41] after create A. > [Rank 0] using GPU 0, [line 45] after set A type. > [Rank 4] using GPU 0, [line 45] after set A type. ------ change to 0? > [Rank 4] using GPU 0, [line 49] after MatSetUp. > [Rank 0] using GPU 0, [line 49] after MatSetUp. > [Rank 4] using GPU 0, [line 62] after Mat Assemble. > [Rank 0] using GPU 0, [line 62] after Mat Assemble. > Smallest eigenvalue = 100.000000 > Smallest eigenvalue = 100.000000 > > BEST, > Grant > > > > > At 2025-11-13 05:58:05, "Junchao Zhang" <junchao.zhang(a)gmail.com> wrote: > > A common approach is to use CUDA_VISIBLE_DEVICES to manipulate MPI ranks > to GPUs mapping, see the section at > https://urldefense.us/v3/__https://docs.nersc.gov/jobs/affinity/*gpu-nodes_… > > With OpenMPI, you can use OMPI_COMM_WORLD_LOCAL_RANK in place of > SLURM_LOCALID (see > https://urldefense.us/v3/__https://docs.open-mpi.org/en/v5.0.x/tuning-apps/… ). > For example, with 8 MPI ranks and 4 GPUs per node, the following script > will map ranks 0, 1 to GPU 0, ranks 2, 3 to GPU 1. > > #!/bin/bash > # select_gpu_device wrapper script > export > CUDA_VISIBLE_DEVICES=$((OMPI_COMM_WORLD_LOCAL_RANK/(OMPI_COMM_WORLD_LOCAL_SIZE/4))) > exec $* > > On Wed, Nov 12, 2025 at 10:20 AM Barry Smith <bsmith(a)petsc.dev> wrote: > >> >> >> On Nov 12, 2025, at 2:31 AM, Grant Chao <grantchao2018(a)163.com> wrote: >> >> >> Thank you for the suggestion. >> >> We have already tried running multiple CPU ranks with a single GPU. >> However, we observed that as the number of ranks increases, the EPS solver >> becomes significantly slower. We are not sure of the exact cause—could it >> be due to process access contention, hidden data transfers, or perhaps >> another reason? We would be very interested to hear your insight on this >> matter. >> >> To avoid this problem, we used the gpu_comm approach mentioned before. >> During testing, we noticed that the mapping between rank ID and GPU ID >> seems to be set automatically and is not user-specifiable. >> >> For example, with 4 GPUs (0-3) and 8 CPU ranks (0-7), the program binds >> ranks 0 and 4 to GPU 0, ranks 1 and 5 to GPU 1, and so on. >> >> >> >> >> We tested possible solutions, such as calling cudaSetDevice() manually to >> set rank 4 to device 1, but it did not work as expected. Ranks 0 and 4 >> still used GPU 0. >> >> We would appreciate your guidance on how to customize this mapping. Thank >> you for your support. >> >> >> So you have a single compute "node" connected to multiple GPUs? Then >> the mapping of MPI ranks to GPUs doesn't matter and changing it won't >> improve the performance. >> > >> However, we observed that as the number of ranks increases, the EPS >> solver becomes significantly slower. >> >> >> Does the number of EPS "iterations" increase? Run with one, two, four >> and eight MPI ranks (and the same number of "GPUs" (if you only have say >> four GPUs that is fine, just virtualize them so two different MPI ranks >> share one) and the option -log_view and send the output. We need to know >> what is slowing down before trying to find any cure. >> >> Barry >> >> >> >> >> >> Best wishes, >> Grant >> >> >> At 2025-11-12 11:48:47, "Junchao Zhang" <junchao.zhang(a)gmail.com>, said: >> >> Hi, Wenbo, >> I think your approach should work. But before going this extra step >> with gpu_comm, have you tried to map multiple MPI ranks (CPUs) to one GPU, >> using nvidia's multiple process service (MPS)? If MPS works well, then >> you can avoid the extra complexity. >> >> --Junchao Zhang >> >> >> On Tue, Nov 11, 2025 at 7:50 PM Wenbo Zhao <zhaowenbo.npic(a)gmail.com> >> wrote: >> >>> Dear all, >>> >>> We are trying to solve ksp using GPUs. >>> We found the example, src/ksp/ksp/tutorials/bench_kspsolve.c, in which >>> the matrix is created and assembling using COO way provided by PETSc. In >>> this example, the number of CPU is as same as the number of GPU. >>> In our case, computation of the parameters of matrix is performed on >>> CPUs. And the cost of it is expensive, which might take half of total time >>> or even more. >>> >>> We want to use more CPUs to compute parameters in parallel. And a >>> smaller communication domain (such as gpu_comm) for the CPUs corresponding >>> to the GPUs is created. The parameters are computed by all of the CPUs (in >>> MPI_COMM_WORLD). Then, the parameters are send to gpu_comm related CPUs via >>> MPI. Matrix (type of aijcusparse) is then created and assembled within >>> gpu_comm. Finally, ksp_solve is performed on GPUs. >>> >>> I’m not sure if this approach will work in practice. Are there any >>> comparable examples I can look to for guidance? >>> >>> Best, >>> Wenbo >>> >> >>

1 0

gpu cpu parallel
by Wenbo Zhao 13 Nov '25

13 Nov '25

Dear all, We are trying to solve ksp using GPUs. We found the example, src/ksp/ksp/tutorials/bench_kspsolve.c, in which the matrix is created and assembling using COO way provided by PETSc. In this example, the number of CPU is as same as the number of GPU. In our case, computation of the parameters of matrix is performed on CPUs. And the cost of it is expensive, which might take half of total time or even more. We want to use more CPUs to compute parameters in parallel. And a smaller communication domain (such as gpu_comm) for the CPUs corresponding to the GPUs is created. The parameters are computed by all of the CPUs (in MPI_COMM_WORLD). Then, the parameters are send to gpu_comm related CPUs via MPI. Matrix (type of aijcusparse) is then created and assembled within gpu_comm. Finally, ksp_solve is performed on GPUs. I’m not sure if this approach will work in practice. Are there any comparable examples I can look to for guidance? Best, Wenbo

4 7

How to map global vector to natural vector
by Xu, Donghui 13 Nov '25

13 Nov '25

Dear PETSc Team, I am working with petsc4py for my model. I had some experience of using PETSc in Fortran. In Fortran, I used the following subroutines: call DMPlexCreateNaturalVector(dm, natural, ierr) call DMPlexNaturalToGlobalBegin(dm,natural,X,ierr) call DMPlexNaturalToGlobalEnd(dm,natural,X,ierr) However, I found there are no such interfaces in petsc4py. Can you advise me on how to get the global vector in natural order with DMPLEX in petsc4py? Thanks, Donghui

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Re: [petsc-users] Error in configuring PETSc with Cygwin on Windows by using MS-MPI
by Barry Smith 13 Nov '25

13 Nov '25

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(a)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(a)mcs.anl.gov <mailto:[email protected]> > ******************************************************************** > 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(a)petsc.dev <mailto:[email protected]>> > 发送时间: 2025-11-13 00:03:50 (星期四) > 收件人: 程奔 <202321009113(a)mail.scut.edu.cn <mailto:[email protected]>> > 抄送: PETSc <petsc-users(a)mcs.anl.gov <mailto:[email protected]>> > 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(a)mail.scut.edu.cn <mailto:[email protected]>> 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.… . 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.… 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(a)petsc.dev <mailto:[email protected]>> > 发送时间: 2025-11-11 23:29:01 (星期二) > 收件人: "Matthew Knepley" <knepley(a)gmail.com <mailto:[email protected]>> > 抄送: 程奔 <ctchengben(a)mail.scut.edu.cn <mailto:[email protected]>>, petsc-users(a)mcs.anl.gov <mailto:[email protected]> > 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(a)gmail.com <mailto:[email protected]>> wrote: > > On Tue, Nov 11, 2025 at 4:44 AM 程奔 <ctchengben(a)mail.scut.edu.cn <mailto:[email protected]>> 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_uC… > >

1 0

Inquiry about issue when compiling with clang
by Benjamin Chapman 13 Nov '25

13 Nov '25

Hello, We are using PETSc as part of a larger project and are switching from compiling with gcc to using AOCC (clang). However, I am getting an error from my include statements stating that the data type __complex128 is an "unknown type name". The full error log is attached. I found this solution online (FreeFem - PETSc compilation error - libblas.a/liblapack.a cannot be used - FreeFEM installation - FreeFEM<https://urldefense.us/v3/__https://community.freefem.org/t/freefem-petsc-co… >), which says to comment out a line in the petscconf.h header file. Is this a safe fix or is there a more elegant way to go about this? Best, Ben

3 2

Re: [petsc-users] Error in configuring PETSc with Cygwin on Windows by using MS-MPI
by Barry Smith 12 Nov '25

12 Nov '25

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(a)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.… . 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.… <https://urldefense.us/v3/__https://bitbucket.org/petsc/pkg-parmetis/get/v4.… >.tar.gz <https://urldefense.us/v3/__https://bitbucket.org/petsc/pkg-parmetis/get/v4.… > 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(a)petsc.dev> > 发送时间: 2025-11-11 23:29:01 (星期二) > 收件人: "Matthew Knepley" <knepley(a)gmail.com> > 抄送: 程奔 <ctchengben(a)mail.scut.edu.cn>, petsc-users(a)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'] > > > >> On Nov 11, 2025, at 7:35 AM, Matthew Knepley <knepley(a)gmail.com> wrote: >> >> On Tue, Nov 11, 2025 at 4:44 AM 程奔 <ctchengben(a)mail.scut.edu.cn <mailto:[email protected]>> 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_uC… <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCf…> >

1 0

Error in configuring PETSc with Cygwin on Windows by using MS-MPI
by 程奔 11 Nov '25

11 Nov '25

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 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.

5 4

Two SNES on the same DM not working
by Samuele Ferri 07 Nov '25

07 Nov '25

Dear petsc users, in petsc version 3.24, I'm trying to create two snes over the same DM, but with different functions and jacobians. Despite making different calls to SNESSetFunction it happens the second snes uses the same function of the first. Can you help me finding the problem, please? Here below there is a minimal working example showing the issue: static char help[] = "Test SNES.\n"; #include <petscsys.h> #include <petscdmda.h> #include <petscsnes.h> PetscErrorCode Jac_1(SNES snes, Vec x, Mat J, Mat B, void *){ PetscFunctionBegin; printf("Jac 1\n"); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode Function_1(SNES snes, Vec x, Vec f, void *){ PetscFunctionBegin; printf("Function 1\n"); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode Jac_2(SNES snes, Vec x, Mat J, Mat B, void *){ PetscFunctionBegin; printf("Jac 2\n"); PetscFunctionReturn(PETSC_SUCCESS); } PetscErrorCode Function_2(SNES snes, Vec x, Vec f, void *){ PetscFunctionBegin; printf("Function 2\n"); PetscFunctionReturn(PETSC_SUCCESS); } int main(int argc, char **argv) { PetscFunctionBeginUser; PetscCall(PetscInitialize(&argc, &argv, NULL, help)); DM dm; PetscCall(DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, 100, 1, 1, NULL, &dm)); PetscCall(DMSetFromOptions(dm)); PetscCall(DMSetUp(dm)); SNES snes1, snes2; Vec r1,r2; Mat J1, J2; PetscCall(DMCreateGlobalVector(dm, &r1)); PetscCall(DMCreateGlobalVector(dm, &r2)) PetscCall(DMCreateMatrix(dm, &J1)); PetscCall(DMCreateMatrix(dm, &J2)); PetscCall(SNESCreate(PETSC_COMM_WORLD, &snes1)); PetscCall(SNESCreate(PETSC_COMM_WORLD, &snes2)); PetscCall(SNESSetType(snes1, SNESNEWTONLS)); PetscCall(SNESSetType(snes2, SNESNEWTONLS)); PetscCall(SNESSetFromOptions(snes1)); PetscCall(SNESSetFromOptions(snes2)); PetscCall(SNESSetFunction(snes1, r1, Function_1, NULL)); PetscCall(SNESSetFunction(snes2, r2, Function_2, NULL)); PetscCall(SNESSetJacobian(snes1, J1, J1, Jac_1, NULL)); PetscCall(SNESSetJacobian(snes2, J2, J2, Jac_2, NULL)); PetscCall(SNESSetDM(snes1, dm)); PetscCall(SNESSetDM(snes2, dm)); PetscCall(SNESSolve(snes1, NULL, NULL)); PetscCall(SNESSolve(snes2, NULL, NULL)); printf("snes1 %p; snes2 %p\n", snes1, snes2); SNESFunctionFn *p; PetscCall(SNESGetFunction(snes1, NULL, &p, NULL)); printf("snes1: pointer %p, true function %p\n", *p, Function_1); PetscCall(SNESGetFunction(snes2, NULL, &p, NULL)); printf("snes2: pointer %p, true function %p\n", *p, Function_2); PetscCall(PetscFinalize()); PetscFunctionReturn(PETSC_SUCCESS); }

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Fortran program compilation hangs with new PETSc version
by Hom Nath Gharti 06 Nov '25

06 Nov '25

I compiled the latest version of PETSc (3.24.1) and attempted to compile my package, which uses Fortran and MPI. But the compilation of my package hangs forever. I tried it on a different cluster with the same behaviour. The compilation precisely hangs when linking to the PETSc program. It seems to be entering into some sort of infinite loop. This problem did not happen with PETSc 3.22.4. I tried with GCC versions 11 and 12. Any advice would be greatly appreciated. Best, Hom Nath

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