November 2022 - petsc-users - mailman3.cels.anl.gov

Re: [petsc-users] PETSc Windows Installation
by Pierre Jolivet 07 Nov '22

07 Nov '22

Please, keep the list in copy. You can get MSYS2 from https://www.msys2.org/ Then install the following packages: https://github.com/FreeFem/FreeFem-sources/tree/master/etc/jenkins/deployRe… Also install MS-MPI: https://www.microsoft.com/en-us/download/details.aspx?id=100593 Configure and compile PETSc under a MSYS2 MinGW x64 shell. Compile your code, and copy the binary. Notice in my screenshot that there are two shells, the MinGW one for building PETSc. The Microsoft (native one) for launching the binary. Thanks, Pierre > On 7 Nov 2022, at 1:53 PM, Mohammad Ali Yaqteen <mhyaqteen(a)sju.ac.kr> wrote: > > Is there a guide for it? That would be very useful! Because I have been trying a lot of things but every now and then there is a little step that is either outdated or can’t run! > > Your help will be highly appreciated > > Thanks > Ali > > From: Pierre Jolivet <pierre(a)joliv.et> > Sent: Monday, November 7, 2022 9:50 PM > To: Mohammad Ali Yaqteen <mhyaqteen(a)sju.ac.kr> > Cc: petsc-users <petsc-users(a)mcs.anl.gov> > Subject: Re: [petsc-users] PETSc Windows Installation > > Or you can use MinGW, it’s not tricky, you don’t need to change any PETSc code, and you can ship .exe for either x86_64 (mingw-w64-x86_64-gcc) or ARM (mingw-w64-clang-aarch64-clang, without MPI). > > Thanks, > Pierre > > > On 7 Nov 2022, at 1:38 PM, hamid badi <badi.hamid(a)gmail.com <mailto:[email protected]>> wrote: > > You can try gcc/clang cross-compilers, it's a little but tricky, i had to change some petsc codes but it works fine. > > Le lun. 7 nov. 2022 à 13:30, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> a écrit : > On Mon, Nov 7, 2022 at 7:11 AM Mohammad Ali Yaqteen <mhyaqteen(a)sju.ac.kr <mailto:[email protected]>> wrote: > Once I finish writing the code, the .exe file will not change. Can I make an .exe file using WSL2 and VScode? > > If you build in WSL2, it will link to system libraries. You would probably need to run in WSL2 after that. If you are planning > on running on native Windows, you likely need to build there. > > Thanks, > > Matt > > Thanks, > Ali > > From: Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> > Sent: Monday, November 7, 2022 7:13 PM > To: Mohammad Ali Yaqteen <mhyaqteen(a)sju.ac.kr <mailto:[email protected]>> > Cc: petsc-users <petsc-users(a)mcs.anl.gov <mailto:[email protected]>> > Subject: Re: [petsc-users] PETSc Windows Installation > > On Mon, Nov 7, 2022 at 12:21 AM Mohammad Ali Yaqteen <mhyaqteen(a)sju.ac.kr <mailto:[email protected]>> wrote: > I have written backend code for a software company. If WSL2 and VSCode(Linux) can be called through a command line and executed at the backend, then it will be great. But if I have to install WSL2 and other required things on every other PC that will run that software, then I think I will be at a disadvantage. What do you suggest? > > As long as you do not change the architecture and the compiler libraries are available, you can run the executable. > > Thanks, > > Matt > > Thank you > Ali > > -----Original Message----- > From: Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]>> > Sent: Monday, November 7, 2022 12:00 AM > To: Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> > Cc: Mohammad Ali Yaqteen <mhyaqteen(a)sju.ac.kr <mailto:[email protected]>>; petsc-users(a)mcs.anl.gov <mailto:[email protected]> > Subject: Re: [petsc-users] PETSc Windows Installation > > Likely the compilers are not setup correctly as per instructions. > > https://petsc.org/release/install/windows/#installation-with-microsoft-inte… > > And if you do not have a specific windows need - and only need IDE - perhaps a WSL2 (aka linux) install with VSCode(linux) might be the way to go. > > Satish > > On Sun, 6 Nov 2022, Matthew Knepley wrote: > > > We need to see configure.log to see what is going on. Can you send it? > > > > Thanks, > > > > Matt > > > > On Sun, Nov 6, 2022 at 4:29 AM Mohammad Ali Yaqteen > > <mhyaqteen(a)sju.ac.kr <mailto:[email protected]>> > > wrote: > > > > > Dear Sir/Madam, > > > > > > > > > > > > I am installing PETSc on windows but it keeps giving me unexpected errors. > > > I want to use it on MS Visual Studio or Codeblocks. When I use the > > > command on your webpage (./configure --with-cc='win32fe cl' > > > --with-fc='win32fe ifort' --with-cxx='win32fe cl' --with-mpi=0 > > > --download-fblaslapack), I get the following error message: > > > > > > > > > > > > $ ./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' > > > --with-cxx='win32fe cl' --with-mpi=0 --download-fblaslapack > > > > > > > > > ==================================================================== > > > ========================= > > > > > > Configuring PETSc to compile on your system > > > > > > > > > ==================================================================== > > > ========================= > > > > > > TESTING: checkCCompiler from > > > config.setCompilers(config/BuildSystem/config/setCompilers.py:1341)* > > > ******************************************************************** > > > ********** > > > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > > details): > > > > > > > > > -------------------------------------------------------------------- > > > ----------- > > > > > > C compiler you provided with -with-cc=win32fe cl cannot be found or > > > does not work. > > > > > > Cannot compile/link C with > > > /home/SEJONG/petsc-3.18.1/lib/petsc/bin/win32fe/win32fe cl. > > > > > > > > > > > > Kindly look into this problem! Your prompt response will highly be > > > appreciated > > > > > > > > > > > > Thank you > > > > > > Ali > > > > > > > > > > > > > -- > 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://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/> > > > -- > 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://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Manually setting PetscSF
by Nicholas Arnold-Medabalimi 07 Nov '22

07 Nov '22

Hi Petsc Users, I am working on setting up the star forest to connect my meshes on different processors. For a 2-processor example, I have set up a dmplex object and read in the coordinates nodes and cell2node charts on each one. But right now they are independent effectively. For simplicity lets just say each process has 4 cells. [image: image.png] I'm trying to build the star forest that sets the edge between the two partitions. (see fig) To my understanding, I do this using PetscSFSetGraph. I choose either 9-10 on rank 0 or 1-2 on rank 1 to be the "roots". For simplicity lets say the 1-2 on rank 1 are roots. (also for the rest of the discussion I'm switching 1 and 2 to be 0 and 1 and 9 and 10 to be 8 9 ) (the figure is 1 indexed but for the code below it will be 0) So on rank 0 I would set nleaves=2 nroots= 8+c1 (graph is only cells and verts so its 8 verts plus the cell count(c1) remote[0].rank=1 remote[0].index=0+(cell count on rank1) leaf[0]=8+c1 remote[1].rank=1 remote[1].index=0+(cell count on rank1) leaf[1]=9+c1 and on rank 1 we would set nroots= ncells+nverts nleaves=0 Since its all roots I don't think I need to set anything else? PetscSFSetGraph(sf,nroots,nleaves,leaves,PETSC_COPY_VALUES,remote,PETSC_COPY_VALUES) I am certain I am making a mistake somewhere since I get an error when I then call PetscSFSetup. I am working in C++ right now but this is just testing out before implementation in fortran which is why I am using PETSC_COPY. Any help and clarification would be appreciated. Sincerely Nicholas -- Nicholas Arnold-Medabalimi Ph.D. Candidate Computational Aeroscience Lab University of Michigan

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Error configuring external packages
by Hom Nath Gharti 07 Nov '22

07 Nov '22

Dear all, I am trying to compile the latest version, but I am getting the following error: ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error configuring METIS with CMake ******************************************************************************* When I remove this package from the configure option, I get the same error for other packages. Is there something wrong with my configure command or compilers? Attached is the configure log file. Best, Hom Nath

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Dof ordering in DMPlexVecGet/Set/RestoreClosure
by Blaise Bourdin 07 Nov '22

07 Nov '22

Hi, How are degree of freedom ordered in calls to DMPlexVec[Set/Get/Restore]Closure? Given a FE mesh and a section for P2-Lagrange elements (i.e. 1 dof per vertex and edge), I was naively assuming that the “local” vector would contain dof at vertices then edges (in this order), since it matches the section ordering, but it looks like I get edges then vertices… Here is my section (my mesh has 8 cells, 16 edges, and 9 vertices) PetscSection Object: U 1 MPI process type not yet set 1 fields field 0 with 1 components Process 0: ( 0) dim 0 offset 0 ( 1) dim 0 offset 0 ( 2) dim 0 offset 0 ( 3) dim 0 offset 0 ( 4) dim 0 offset 0 ( 5) dim 0 offset 0 ( 6) dim 0 offset 0 ( 7) dim 0 offset 0 ( 8) dim 1 offset 0 ( 9) dim 1 offset 1 ( 10) dim 1 offset 2 ( 11) dim 1 offset 3 ( 12) dim 1 offset 4 ( 13) dim 1 offset 5 ( 14) dim 1 offset 6 ( 15) dim 1 offset 7 ( 16) dim 1 offset 8 ( 17) dim 1 offset 9 ( 18) dim 1 offset 10 ( 19) dim 1 offset 11 ( 20) dim 1 offset 12 ( 21) dim 1 offset 13 ( 22) dim 1 offset 14 ( 23) dim 1 offset 15 ( 24) dim 1 offset 16 ( 25) dim 1 offset 17 ( 26) dim 1 offset 18 ( 27) dim 1 offset 19 ( 28) dim 1 offset 20 ( 29) dim 1 offset 21 ( 30) dim 1 offset 22 ( 31) dim 1 offset 23 ( 32) dim 1 offset 24 Start from the following local vector: Vec Object: U 1 MPI process type: seq 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. Call PetscCallA(DMPlexVecGetClosure(dmU,sectionU,U,0_Ki,UArray,ierr)) and get the following for Array: 10.000000000000000 11.000000000000000 12.000000000000000 1.0000000000000000 2.0000000000000000 3.0000000000000000 Is this ordering predictable and documented somewhere? Is it ordered by stratum? Regards, Blaise — Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1) Professor, Department of Mathematics & Statistics Hamilton Hall room 409A, McMaster University 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada https://www.math.mcmaster.ca/bourdin | +1 (905) 525 9140 ext. 27243

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Petsc Documentation
by Palmer, Bruce J 07 Nov '22

07 Nov '22

Hi, The new Petsc documentation pages don't seem to have a search function. Would it be possible to add one? I was looking around for the documentation on PetscPrintf and couldn't find it, even on the single index of all petsc man pages. Bruce Palmer Computer Scientist Pacific Northwest National Laboratory (509) 375-3899

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petsc crash with float128
by Gong Ding 07 Nov '22

07 Nov '22

Dear petsc developer, The petsc linear solver crash with following report [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [1]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [1]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [1]PETSC ERROR: The line numbers in the error traceback are not always exact. [1]PETSC ERROR: #1 MatLUFactorNumeric_SeqAIJ_Inode() at /usr/local/petsc-3.18.0/src/mat/impls/aij/seq/inode.c:1259 [1]PETSC ERROR: #2 MatLUFactorNumeric() at /usr/local/petsc-3.18.0/src/mat/interface/matrix.c:3200 [1]PETSC ERROR: #3 PCSetUp_LU() at /usr/local/petsc-3.18.0/src/ksp/pc/impls/factor/lu/lu.c:120 [1]PETSC ERROR: #4 PCSetUp() at /usr/local/petsc-3.18.0/src/ksp/pc/interface/precon.c:994 [1]PETSC ERROR: #5 KSPSetUp() at /usr/local/petsc-3.18.0/src/ksp/ksp/interface/itfunc.c:406 [1]PETSC ERROR: #6 PCSetUpOnBlocks_ASM() at /usr/local/petsc-3.18.0/src/ksp/pc/impls/asm/asm.c:417 [1]PETSC ERROR: #7 PCSetUpOnBlocks() at /usr/local/petsc-3.18.0/src/ksp/pc/interface/precon.c:1027 [1]PETSC ERROR: #8 KSPSetUpOnBlocks() at /usr/local/petsc-3.18.0/src/ksp/ksp/interface/itfunc.c:219 [1]PETSC ERROR: #9 KSPSolve_Private() at /usr/local/petsc-3.18.0/src/ksp/ksp/interface/itfunc.c:826 [1]PETSC ERROR: #10 KSPSolve() at /usr/local/petsc-3.18.0/src/ksp/ksp/interface/itfunc.c:1071 [1]PETSC ERROR: #11 SNESSolve_NEWTONLS() at /usr/local/petsc-3.18.0/src/snes/impls/ls/ls.c:210 [1]PETSC ERROR: #12 SNESSolve() at /usr/local/petsc-3.18.0/src/snes/interface/snes.c:4689 The petsc is configured by export PETSC_ARCH=arch-linux2-float128-gcc export MPICH_CC=gcc export MPICH_CXX=g++ export MPICH_F77=gfortran export MPICH_F90=gfortran python3 configure --with-precision=__float128 --download-f2cblaslapack=1 --with-debugging=yes --with-x=0 --with-pic=1 --with-mpi-dir=/usr/local/mpich-3.4.2/ COPTFLAGS="-O3 -mavx2" CXXOPTFLAGS="-O3 -mavx2" FOPTFLAGS="-O3 -mavx2" --force make and run with 8 mpi process. The linear solver is set as ierr = KSPSetType (ksp, (char*) KSPBCGSL); assert(!ierr); ierr = PCSetType (pc, (char*) PCASM); assert(!ierr); ierr = set_petsc_option("-sub_ksp_type","preonly"); assert(!ierr); ierr = set_petsc_option("-sub_pc_type","lu"); assert(!ierr); ierr = set_petsc_option("-sub_pc_factor_reuse_fill","1"); assert(!ierr); ierr = set_petsc_option("-sub_pc_factor_reuse_ordering","1"); assert(!ierr); ierr = set_petsc_option("-sub_pc_factor_shift_type","NONZERO"); assert(!ierr); if remove set_petsc_option("-sub_pc_factor_reuse_ordering","1"); it seems the crash will not happen. (Not fully tested) Hope this bug can be fixed. Gong Ding

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PETSc Windows Installation
by Mohammad Ali Yaqteen 07 Nov '22

07 Nov '22

Dear Sir/Madam, I am installing PETSc on windows but it keeps giving me unexpected errors. I want to use it on MS Visual Studio or Codeblocks. When I use the command on your webpage (./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' --with-cxx='win32fe cl' --with-mpi=0 --download-fblaslapack), I get the following error message: $ ./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' --with-cxx='win32fe cl' --with-mpi=0 --download-fblaslapack ============================================================================================= Configuring PETSc to compile on your system ============================================================================================= TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:1341)******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- C compiler you provided with -with-cc=win32fe cl cannot be found or does not work. Cannot compile/link C with /home/SEJONG/petsc-3.18.1/lib/petsc/bin/win32fe/win32fe cl. Kindly look into this problem! Your prompt response will highly be appreciated Thank you Ali

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Determining maximum number of columns in sparse matrix
by Alexander Lindsay 06 Nov '22

06 Nov '22

We sometimes overallocate our sparsity pattern. Matrix assembly will squeeze out allocations that we never added into/set. Is there a convenient way to determine the size of the densest row post-assembly? I know that we could iterate over rows and call `MatGetRow` and figure it out that way. But I'm wondering if there is a better way? Alex

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On the usage of MatSetValuesBlocked
by Edoardo alinovi 05 Nov '22

05 Nov '22

Hello Jed/Barry/Petsc friends I am trying to assemble a block matrix with 3x3 in 2D and 4x4 blocks in 3D coming from the fully coupled NS equation. I am not sure I am understanding the example provided here: https://petsc.org/main/docs/manualpages/Mat/MatSetValuesBlocked/ The description says that " *v -* a logically two-dimensional array of values", while in the example is passed as a 1D array. Should I pass a 2D array like v(1:nComp,1:nComp) or an array v(1:nComp*nComp) to MatSetValuesBlocked (I am using fortran that's why I start form 1 in my arrays) ? Are *idxm *and *idxn *the global index of each block right? I guess PETSc will correctly assign each block row and column as it knows the matrix has a given structure. Thank you as always!

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Installing Triangle for PETSc by not using --download
by Mike Michell 04 Nov '22

04 Nov '22

Hi, I need to install PETSc and its dependencies to a linux system, which does not allow git clone from online. Thus I need to install all the dependencies by having their source files. First I downloaded and installed all the dependencies by relying on PETSc on my local linux (which means I used --download=triangle), then tar all of them, and brought them to the cluster. There is an issue with Triangle. I can do make (or cmake using the CMakeList file that Triangle 1.6 provides, although PETSc --download provides Triangle 1.3) and can get "libtriangle.a". But during the PETSc configure step, it fails with the error message below: {$Triangle_Home}/build/libtriangle.a(triangle.c.o): In function `poolinit': triangle.c:(.text+0x15aa): undefined reference to `PetscTrMalloc' {$Triangle_Home}/build/libtriangle.a(triangle.c.o): In function `pooldeinit': triangle.c:(.text+0x1708): undefined reference to `PetscTrFree' ... It seems that I need to let Triangle know that it will be used by PETSc to enable those functions when I install Triangle. Is this correct understanding? If so, how can I configure, install, and link Triangle with PETSc? I have seen some PETSc related commands in configure.py in the root directory of Triangle downloaded by PETSc, but it is not clear how this python script is related or can be used by user like me. Thanks, Mike

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