Re: [petsc-users] CUDA MatSetValues test

that it >> will be forced to be configured later? >> >>> On May 28, 2021, at 8:12 PM, Stefano Zampini >> <mailto:stefano.zamp...@gmail.com>> wrote: >>> >>> That branch provides a fix for MatSetValuesDevice but it never got m

Re: [petsc-users] CUDA MatSetValues test

~/petsc/src/mat/tutorials (barry/2021-05-28/robustify-cuda-gencodearch-check=) arch-robustify-cuda-gencodearch-check $ ./ex5cu terminate called after throwing an instance of 'thrust::system::system_error' what(): fill_n: failed to synchronize: cudaErrorIllegalAddress: an illegal memory

Re: [petsc-users] Collect Trajectories components

partlocal[i] = Ui[1]; > ierr = DMDAVecRestoreArray(appctx.da,U,);CHKERRQ(ierr); > ierr = VecRestoreArray(partial,);CHKERRQ(ierr); > ierr = DMRestoreLocalVector(appctx.da,);CHKERRQ(ierr); > } > > >> Il giorno 27 mag 2021, alle ore 01:15, Barry Smith > &l

Re: [petsc-users] Did CUDA break again?

it will guess by compiling for different generations but this can produce an incorrect answer. Barry > On May 28, 2021, at 7:59 AM, Mark Adams wrote: > > > > On Thu, May 27, 2021 at 11:50 PM Barry Smith <mailto:bsm...@petsc.dev>> wrote: > > Mark, > > &

Re: [petsc-users] Did CUDA break again?

gt; config = self.getChild(moduleName, keywordArgs) > File "/global/u2/m/madams/petsc/config/BuildSystem/config/framework.py", > line 302, in getChild > type = __import__(moduleName, globals(), locals(), > ['Configure']).Configure > 19:16 cgpu02 (149e269f45...)|BISECTIN

Re: [petsc-users] Collect Trajectories components

ult on the other ranks. > Should I build everything into an external function outside the main? It can be called in main, does not need to be in a different function. > > Francesco > > >> Il giorno 26 mag 2021, alle ore 16:20, Barry Smith > <mailto:bsm...@pe

Re: [petsc-users] Did CUDA break again?

major+minor); return(0); } This is what I get $ nvcc mytest.c -lcuda ~/petsc (main=) arch-main $ ./a.out 70 70 Which is exactly what it is suppose to do. Barry > On May 26, 2021, at 5:31 PM, Barry Smith wrote: > > > Yes, this code which I

Re: [petsc-users] Did CUDA break again?

Yes, this code which I guess never got hit before cudaDeviceProp dp;cudaGetDeviceProperties(, 0); printf("%d\n",10*dp.major+dp.minor);return(0);; is using the wrong property for the generation. Back to the CUDA documentation for the

Re: [petsc-users] Collect Trajectories components

Based on the error message it appears that your code is requesting different times on different MPI ranks. Is that what you intend to do? TSTrajectoryGetVecs() is listed as Collective on TS. This means all ranks must call it with the same times in the same order of operations on all ranks

Re: [petsc-users] divergence of quasi-Newton scheme (SNES)

Excellant, thanks for letting us know. > On May 25, 2021, at 5:30 PM, hg wrote: > > Thanks Barry, with -snes_qn_m 0 it gives exact convergence as -snes_type > newtonls -snes_linesearch_type basic > > Giang > > > On Tue, May 25, 2021 at 10:51 PM Barry Smit

Re: [petsc-users] divergence of quasi-Newton scheme (SNES)

Yes, with your options I would expect the first SNES iteration of QN to produce the same result as the first iteration of SNES Newton ls. I have fixed an error that crept (well actually I put it there) in where KSPSetFromOptions() was not being called with the QN and Jacobian option,

Re: [petsc-users] adding calls before and after each iteration of snes

There is also SNESMonitorSet() and SNESSetConvergenceTest(). > On May 25, 2021, at 9:25 AM, Matthew Knepley wrote: > > On Tue, May 25, 2021 at 8:41 AM hg > wrote: > Hello > > I would like to ask if it is possible to add function call before and after > each

Re: [petsc-users] Integrating SNES in FEM code

ompute the residual in. It is just a work vector you can pass in. You can pass in NULL and PETSc will create the work vector it needs internally. > > Best regards, > Saransh > > > > > > On Tue, May 25, 2021 at 10:15 AM Barry Smith <mailto:bsm...@petsc.dev>&

Re: [petsc-users] Integrating SNES in FEM code

TSC_NULL, solpetsc); > > // Print the norm of residual: > double normres; > VecNorm(residualpetsc, NORM_2, ); > std::cout << "L2 norm of the residual is : " << normres << std::endl; > > //Set the solution to all the fields: >

Re: [petsc-users] Help needed with MUMPS solver

Please run with -ksp_error_if_not_converged and send all the output Barry > On May 23, 2021, at 10:16 AM, Karl Yang wrote: > > Hello, > > I am using MUMPS direct solver for my project. I used the following options > for solving my problem and it works in most cases. But for some cases

Re: [petsc-users] nghosts in 'DMMoabLoadFromFile'

Probably. It is not documented unfortunately, but does seem to related to the how many ghost layers are needed. Barry > On May 20, 2021, at 11:25 AM, Bhamidipati, Vikram > wrote: > > Hello, > > I am in the process of updating PetSc versions and I see that > ‘DMMoabLoadFromFile’

Re: [petsc-users] Code hangs when calling PetscIntView (MPI, fortran)

You can also have the processes with no values print an array of length zero. Like if (rank3 == PROC_ROW) then ! IF mpi PROCESS OWNS THIS ROW THEN .. .. else NO_A_ENTRIES = 0 call PetscIntView(NO_A_ENTRIES,JALOC(1:NO_A_ENTRIES), & &

Re: [petsc-users] Using SNES to solve Non linear elasticity, passing matrix to form function

> ierr = MatSeqAIJGetArray(ptr->K,);CHKERRQ(ierr); > ierr = MatGetLocalSize(ptr->K,,); CHKERRQ(ierr); > for(i=0;i { > for(j=0;j { > v = *(Kc + (i*n+j)); > ierr = MatSetValues(Kloc,1,,1,,,INSERT_VALUES);CHKERRQ(ierr); > } > } > I don't understand

Re: [petsc-users] configure error

> < 1.50024 > < 3.01563 > < Process [1] > < 4.67798 > < 7. > < 0 SNES Function norm 5.414682427127e+00 > < 1 SNES Function norm 2.952582418265e-01 > < 2 SNES Function norm 4.502293658739e-04 > < 3 SNES Function norm 1.389665806646e-09 > < Number of SNES itera

Re: [petsc-users] Efficient FFTShift-implementation for vectors/matrices

I found a variety of things on the web, below. I don't understand this but for the even case it seems one simply modifies the input matrix before the FFT http://www.fftw.org/faq/section3.html#centerorigin https://stackoverflow.com/questions/5915125/fftshift-ifftshift-c-c-source-code

Re: [petsc-users] configure error

Could still be a gencode arch issue. Is it possible that Kokkos was built with the 80 arch and when you reran configure with 70 it did not rebuild Kokkos because it didn't know it needed to? Sorry, but this may require another rm -rf arch* and running ./configure again.

Re: [petsc-users] configure error

> [cgpu11:39927] [23] > > /global/u2/m/madams/petsc/src/snes/tutorials/./ex19[0x4021ba] > > [cgpu11:39927] *** End of error message *** > > srun: error: cgpu11: task 0: Aborted > > srun: Terminating job step 1921749.6 > /global/homes/m/madams/petsc/src/snes/tut

Re: [petsc-users] configure error

SNESSolve+0x821)[0x2c146ed1] > > [cgpu11:39927] [21] > > /global/u2/m/madams/petsc/src/snes/tutorials/./ex19[0x401a69] > > [cgpu11:39927] [22] /lib64/libc.so.6(__libc_start_main+0xea)[0x2aab1295df8a] > > [cgpu11:39927] [23] > > /global/u2/m/madams/petsc

Re: [petsc-users] configure error

it and arch-cori-gpu-opt-kokkos-gcc/lib/petsc/conf/configure.log to > petsc-ma...@mcs.anl.gov <mailto:petsc-ma...@mcs.anl.gov> > > gmake[1]: *** [makefile:40: all] Error 1 > make: *** [GNUmakefile:9: all] Error

Re: [petsc-users] configure error

Bitbucket is off-line. Do you need fortran stubs at this moment? If not use --with-fortran-interface=0 > On May 15, 2021, at 2:51 PM, Mark Adams wrote: > > I can build a non-kokkos PETSc here (Cori/GPU) but I get this error with > Kokkos. > Any suggestions? > Thanks, > Mark > >

Re: [petsc-users] Questions on matrix-free GMRES implementation

re blocks (ranks) you use". > somehow I did not see a big difference in my non-linear residual when I use > 1, 2, 3 cpus in this case. I can try a different case and check. > > Thanks, > Feng > > From: Barry Smith mailto:bsm...@petsc.dev>> > Sent: 12

Re: [petsc-users] Questions on matrix-free GMRES implementation

> mailto:snails...@hotmail.com>> > Sent: 28 March 2021 22:05 > To: Barry Smith mailto:bsm...@petsc.dev>> > Cc: petsc-users@mcs.anl.gov <mailto:petsc-users@mcs.anl.gov> > mailto:petsc-users@mcs.anl.gov>> > Subject: Re: [petsc-users] Questions on matrix-free G

Re: [petsc-users] Binary format in real vs. complex scalar type configurations

> On May 11, 2021, at 3:08 PM, Frederico Teixeira wrote: > > Hi Pierre, > > Thanks for your tip. > I don't have access to MATLAB. Would Octave also work? Or Python? Yes, they should both be fine. All you need to is split the matrix into the 2 matrices in Octave or Python and then save

Re: [petsc-users] Integrating SNES in FEM code

solver to start with. I'll get back to you guys if I have any questions. > > Cheers, > Saransh > > On Sat, May 8, 2021 at 5:18 AM Barry Smith <mailto:bsm...@petsc.dev>> wrote: > Saransh, > > I've add some code for SNESSetPicard() in the PETSc branch

Re: [petsc-users] Integrating SNES in FEM code

Saransh, I've add some code for SNESSetPicard() in the PETSc branch barry/2021-05-06/add-snes-picard-mf see also https://gitlab.com/petsc/petsc/-/merge_requests/3962 that will make your coding much easier. With this branch you can provide code that computes A(x), using

Re: [petsc-users] Error in installation of petsc4py

PETSc folks who know a little bit about Windows Python, Does the Microsoft Python environment work with the standard Python setup tools? It seems like it should but ... Is the following error coming from the generic use of setup.py on Windows or is it somehow specific to PETSc's use

Re: [petsc-users] Equivalent function call for -mg_levels_ksp_type & -mg_levels_pc_type

Milan, The simplest way is to use PetscOptionsSetValue() in the code to set the options. If you have multiple solvers you can use PetscObjectSetOptionsPrefix() to use different prefixes for each solver and control them separately. The number of levels and the solvers at each

Re: [petsc-users] MatDestroy problem with multiple matrices and SUPERLU_DIST

en F-series > <https://www.marin.nl/news/working-paper-on-the-design-of-the-wageningen-f-series> > > > > From: Barry Smith mailto:bsm...@petsc.dev>> > Sent: Sunday, May 2, 2021 6:30 PM > To: Deij-van Rijswijk, Menno mailto:m.d...@marin.nl>> &

Re: [petsc-users] Parallel TS for ODE

/impls/da/dareg.c > [1]PETSC ERROR: #3 DMSetUp() line 787 in > /home/fbrarda/petsc/src/dm/interface/dm.c > [1]PETSC ERROR: #4 main() line 232 in test_ic.c > [1]PETSC ERROR: No PETSc Option Table entries > [1]PETSC ERROR: End of Error Message ---send entire error >

Re: [petsc-users] Parallel TS for ODE

; const PetscScalar *x; >>>>> >>>>> PetscFunctionBeginUser; >>>>> ierr = MatGetOwnershipRange(B,,NULL);CHKERRQ(ierr); >>>>> ierr = VecGetArrayRead(X,);CHKERRQ(ierr); >>>>> if (my

Re: [petsc-users] MatDestroy problem with multiple matrices and SUPERLU_DIST

(in > /home/mdeij/install-gnu/extLibs/lib/libpetsc.so.3.14.5) > ==1026905== If you believe this happened as a result of a stack > ==1026905== overflow in your program's main thread (unlikely but > ==1026905== possible), you can try to increase the size of the > ==1026905== main

Re: [petsc-users] Can I assign different local number of row and column to the parallel matrix in different process?

basically the stencil width s and type of boundary conditions determine the ghosting. You cannot use another ghosting. But global indexing has nothing to do with ghosting and any process can use any global indices it would like and the Mat/Vec handle the needed communication. Barry >

Re: [petsc-users] Mat-Mat element wise multiplication

> On Apr 25, 2021, at 12:09 PM, Rui Silva wrote: > > I am writing to you, to ask if there is any simple way to perform > element-wise multiplication of 2 mpiaij matrices in Petsc? You can imitate MatAXPY_SeqAIJ() on each of the two parts of the MPIAIJ matrix. > Furthermore is there

Re: [petsc-users] Can I assign different local number of row and column to the parallel matrix in different process?

Yes; but note that for square matrices using n == m almost always makes sense, otherwise the input vector to the matrix-vector product will have a different layout than the output vector. Code code is difficult to manage. > On Apr 23, 2021, at 9:29 PM, 王 杰 wrote: > > hello, > > I use

Re: [petsc-users] Kokkos error at NERSC

unsigned short() const" > function "__half::operator int() const" > function "__half::operator unsigned int() const" > function "__half::operator long long() const" > function "__half::operator unsigned l

Re: [petsc-users] Kokkos error at NERSC

In kokkos-kernels.py comment out #self.includes = ['KokkosBlas.hpp','KokkosSparse_CrsMatrix.hpp'] I don't know why this didn't hit has a long long time ago. > On Apr 24, 2021, at 8:21 AM, Mark Adams wrote: > > I don't see this in kokkos-kernels.py. > I seem to get past

Re: [petsc-users] Adding a CUDA library

./configure other arguments LIBS="-lxxx" This should work. Send configure.log to petsc-ma...@mcs.anl.gov > On Apr 23, 2021, at 6:33 PM, Mark Adams wrote: > > How would I add a CUDA library that is in the CUDA library directory? That is > just add

Re: [petsc-users] MatDestroy problem with multiple matrices and SUPERLU_DIST

ompany/marin> > <http://www.youtube.com/marinmultimedia> > <https://twitter.com/MARIN_nieuws> > <https://www.facebook.com/marin.wageningen> > MARIN news: Report magazine 131: read now and register for future editions > <https://www.marin.nl/news/report-m

Re: [petsc-users] VecLoad from HDF5 file

ViewerStep is clear. > On Apr 23, 2021, at 11:21 AM, Hapla Vaclav wrote: > > > >> On 23 Apr 2021, at 00:58, Barry Smith > <mailto:bsm...@petsc.dev>> wrote: >> >> >>Can a Vec have multiple sequence numbers? You have a Tao

Re: [petsc-users] MatDestroy problem with multiple matrices and SUPERLU_DIST

Please send a code that reproduces the problem. I cannot reproduce it. It is absolutely expected to work, but there may be an untested corner case you have hit on. The comment /* This allows reusing the Superlu_DIST communicator and grid when only a single SuperLU_DIST matrix is

Re: [petsc-users] VecLoad from HDF5 file

t; trim(restartname), ierr); CHKERRA(ierr) >>> >>> call >>> PetscViewerHDF5SetTimestep(hdf5Viewer, 20, ierr); CHKERRA(ierr) >>> >>> call >>> PetscViewerHDF5PushGroup(hdf5Viewer, >>> "/fields", ierr); CHKERRA(ierr) >>>

Re: [petsc-users] MatDestroy problem with multiple matrices and SUPERLU_DIST

Hmm, I thought this was a problem that was resolved a while ago. I will try to reproduce it. Barry > On Apr 21, 2021, at 10:01 AM, Xiaoye S. Li wrote: > > When you have two matrices, I think you should create two separate > communicators, i.e., two superlu grids, > > Sherry Li > >

Re: [petsc-users] PCFIELDSPLIT with BoomerAMG preconditioning on a Schur Complement

Schur complements are generally dense, unless your original matrix has specific structure that you know of, it is unlikely hypre AMG will work well on the Schur complement. Barry > On Apr 20, 2021, at 5:26 PM, Matthew Knepley wrote: > > On Tue, Apr 20, 2021 at 4:33 PM Jorti, Zakariae

Re: [petsc-users] Preconditioner for stokes flow with mixed boundary conditions.

You might consider a discretization that replaces the direct 4th order discretization with a coupled set of second order discretions and then using PCFIELDSPLIT to organize appropriate algebraic multigrid on the 2nd order discretions. The thing is traditional linear iterative solvers are

Re: [petsc-users] Nesting splits based on IS

en I think the software stack is not well designed or defined. I fear we cannot make such a cartoon currently. Barry > On Apr 18, 2021, at 8:54 AM, Matthew Knepley wrote: > > On Sat, Apr 17, 2021 at 6:13 PM Barry Smith <mailto:bsm...@petsc.dev>> wrote: > > So you wou

Re: [petsc-users] Nesting splits based on IS

So you would like to be able to create three IS in your code and attach them with names to the PC. Then have -pc_fieldsplit_XXX_fields be able to utilize the attached IS by name and use them to define the blocks. This is all doable and could be added to PCFIELDSPLIT without too much

Re: [petsc-users] AMPERE80

valgrind first and I think NVIDIA has a "valgrind" for GPUs; then start in debugger. You could also back off on the aggressive optimization and see if that changes the behavior. > On Apr 16, 2021, at 9:24 AM, Matthew Knepley wrote: > > Can you get a stack trace? > > Matt > > On

Re: [petsc-users] Can't compile code after upgrading to VS2017 and Intel One API + PETSc 3.15

Please send configure.log and make.log and the results of "make check" so we have the details on the build process. > No rule to make target > '/cygdrive/d/Lib/petsc-3.15.0_win64_impi_vs2017/share/petsc/examples/src/ksp/ksp/tutorials/lib/petsc/conf/test'. > Stop. > Looks funny; it does

Re: [petsc-users] GAMG preconditioning

Please send -log_view for the ilu and GAMG case. Barry > On Apr 12, 2021, at 10:34 AM, Milan Pelletier via petsc-users > wrote: > > Dear all, > > I am currently trying to use PETSc with CG solver and GAMG preconditioner. > I have started with the following set of parameters: >

Re: [petsc-users] BoomerAMG Hypre options

> Regards > > Sthavishtha > > > > > > > On Mon, Apr 12, 2021 at 4:36 AM Barry Smith <mailto:bsm...@petsc.dev>> wrote: > > 0 SNES Function norm 6.145506780035e-04 > 0 KSP Residual norm 2.013603254316e+41 > >

Re: [petsc-users] BoomerAMG Hypre options

BoomerAMG will never simply solve the resulting linear system. Mixing elliptic and hyperbolic equations into a linear system and then trying a "black-box" solver will never work. > On Apr 11, 2021, at 11:35 PM, sthavishtha bhopalam > wrote: > > I am solving the isothermal form of the

Re: [petsc-users] BoomerAMG Hypre options

0 SNES Function norm 6.145506780035e-04 0 KSP Residual norm 2.013603254316e+41 My guess is that your matrix has zeros or essentially zeros on some diagonal entries, this could be breaking Relax down symmetric-SOR/Jacobi Relax upsymmetric-SOR/Jacobi

Re: [petsc-users] Newbie question: Strange failure when calling PetscIntView from slepc application

I have submitted a MR that adds a Fortran interface for these functions so it will automatically error at compile time if you do not include the appropriate arguments. Barry > On Apr 9, 2021, at 5:35 AM, dazza simplythebest wrote: > > Dear Pierre and Stefano, >

Re: [petsc-users] Undefined reference in PETSc 3.13+ with old MPI version

Depending on the network you can remove the ./configure options --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 and use instead --with-cc=icc --with-cxx=icpc and--with-fc=ifort --download-openmpi Barry > On Apr 10, 2021, at 12:18 PM, Danyang Su wrote: > > Dear PETSc developers and

Re: [petsc-users] Running SNES in parallel

Your FormFunction is not doing any communication of x values, thus the function evaluation can only use local values (same with the Jacobian). So these functions cannot be correct. If you look at the DMDA version you will see DMGlobalToLocal() that manages the communication inside

Re: [petsc-users] VecLoad from HDF5 file

Matt, Is there anyway to provide this "extra meta-data" inside the generated HDF file? Then when a fresh viewer opens the file it uses this meta-data to know that the file contains "time-steps" and allows processing of them? The simplest thing would be to have the viewer generate an

Re: [petsc-users] correction to previous email

That does seem like a great deal of memory per timestep. We need a bit more information to help you. Which TSTrajectory are you using? Have you built PETSc with --download-revolve? Are you trying to save the entire trajectory for post-processing or just enough to run with TSAdjoint

Re: [petsc-users] Parallel TS for ODE

> On Apr 1, 2021, at 9:17 PM, Zhang, Hong via petsc-users > wrote: > > > >> On Mar 31, 2021, at 2:53 AM, Francesco Brarda >> wrote: >> >> Hi everyone! >> >> I am trying to solve a system of 3 ODEs (a basic SIR model) with TS. >> Sequentially works pretty well, but I need to switch it

Re: [petsc-users] Kokkos OMP on Summit

petsc/-/commits/adams/landau-gpu-opt> > On Thu, Apr 1, 2021 at 4:34 PM Barry Smith <mailto:bsm...@petsc.dev>> wrote: > > Mark, this branch should resolve the problem. > > barry/2021-04-01/fix-threadsafety-error-check/release > > https://gitlab.com/petsc/petsc/-/

Re: [petsc-users] Kokkos OMP on Summit

Mark, this branch should resolve the problem. barry/2021-04-01/fix-threadsafety-error-check/release https://gitlab.com/petsc/petsc/-/merge_requests/3802 > On Apr 1, 2021, at 12:28 PM, Mark Adams wrote: > > I am getting this fail with

[petsc-users] PETSc 3.15 release

Ali Reza Khaz'ali Alp Dener Barry Smith Blaise Bourdin Connor Ward Damian Marek Ed Bueler Emil Constantinescu Eric Chamberland Fande Kong Hong Zhang Jacob Faibussowitsch Jed Brown Jonathan Lambrechts Jose Roman Junchao Zhang Kaushik Kulkarni Koki Sagiyama Lawrence Mitchell Lisandro

Re: [petsc-users] Local Discontinuous Galerkin with PETSc TS

everything but the implementation looks very straightforward with RK. Barry > On Mar 27, 2021, at 11:39 AM, Matthew Knepley wrote: > > On Fri, Mar 26, 2021 at 8:20 PM Barry Smith <mailto:bsm...@petsc.dev>> wrote: > >What is SLATE in this context? > > SL

Re: [petsc-users] Local Discontinuous Galerkin with PETSc TS

his formulation would be > > > > dF/dU = [[M, 0, 0], > > [0, M, 0], > > [H'(p1), H'(p2), \sigma*M]] > > > > where M is a mass matrix, H'(p1) is the jacobian of H(p1, p2) w.r.t. p1 and > H'(p2), the jacobian of H(p1, p2) w.r.

Re: [petsc-users] Questions on matrix-free GMRES implementation

g the "new" ordering then it will reflect the same function evaluation and matrix free operators so should be ok. Barry > > Thanks, > Feng > > From: Barry Smith mailto:bsm...@petsc.dev>> > Sent: 25 March 2021 0:03 > To: feng wang mailto:snails...@ho

Re: [petsc-users] Questions on matrix-free GMRES implementation

your distributed data and use it for the rest of the run. You might use the object from AOCreate to do the renumbering for you. Barry > Thanks, > Feng > > From: Barry Smith mailto:bsm...@petsc.dev>> > Sent: 22 March 2021 1:28 > To: feng wang mailto:snails...@hotmail.c

Re: [petsc-users] MUMPS failure

integers, what else could go wrong. > -sanjay > > PS: I am not advocating this as a great idea, but I am curious if there or > other obscure compiler level things that could go wrong. > > > On 3/22/21 8:53 PM, Barry Smith wrote: >> >> >>> On Mar 22

Re: [petsc-users] MUMPS failure

> On Mar 22, 2021, at 3:24 PM, Junchao Zhang wrote: > > > > > On Mon, Mar 22, 2021 at 1:39 PM Barry Smith <mailto:bsm...@petsc.dev>> wrote: > >Version of PETSc and MUMPS? We fixed a bug in MUMPs a couple years ago > that produced error messages as

Re: [petsc-users] Local Discontinuous Galerkin with PETSc TS

u_t = G(u) I don't see why you won't just compute any needed u_x from the given u and then you can use any explicit or implicit TS solver trivially. For implicit methods it can automatically compute the Jacobian of G for you or you can provide it directly. Explicit methods will just use

Re: [petsc-users] PF+Navier stokes

Singular systems come up in solving PDEs almost always due to issues related to boundary conditions. For example all Neumann (natural) boundary conditions can produce singular systems. Direct factorizations generically will eventually hit a zero pivot in such cases and there is no

Re: [petsc-users] funny link error

> On Mar 22, 2021, at 12:19 PM, Matthew Knepley wrote: > > On Mon, Mar 22, 2021 at 12:16 PM Scott Kruger > wrote: > > The short answer is $PETSC_INSTALL_DIR/lib/pkgconfig/PETSc.pc > > Attached is a PETSc CMake snippet that should show you how to use > pkg-config. >

Re: [petsc-users] MUMPS failure

Version of PETSc and MUMPS? We fixed a bug in MUMPs a couple years ago that produced error messages as below. Please confirm you are using the latest PETSc and MUMPS. You can run your production version with the option -malloc_debug ; this will slow it down a bit but if there is memory

Re: [petsc-users] Questions on matrix-free GMRES implementation

es, you can use Get/Restore but the input vector x will need to be, as noted above, scattered into a haloed version to get all the entries you will need to do the local part of the product. > Thanks, > Feng > > From: Barry Smith mailto:bsm...@petsc.dev>> > Sent: 12 March 2021 2

Re: [petsc-users] error message

Sam, You can pass a simple C function to PetscPushErrorHandler() that prints the top message and then immediately aborts to get the effect you want. But I agree with Dave you lose a lot of useful information by producing such a simple error message. Barry > On Mar 16, 2021, at 5:43

Re: [petsc-users] Questions on matrix-free GMRES implementation

ample MatAssemblyBegin(petsc_A_mf,...) MatAssemblyEnd(petsc_A_mf,...) KSPSolve() > > From: Matthew Knepley > Sent: 12 March 2021 15:08 > To: feng wang > Cc: Barry Smith ; petsc-users@mcs.anl.gov > > Subject: Re: [petsc-users] Questions on matrix-free GMRES i

Re: [petsc-users] Block unstructured grid

If it is not a BAIJ matrix, perhaps a figure of the matrix (for some small b and N) might help us understand the structure. We understand vector valued (non-scalar) PDEs and have worked with cases of 1000s of entries at each grid point but don't understand the index notation you are using

Re: [petsc-users] Questions on matrix-free GMRES implementation

Feng, The first thing to check is that for each linear solve that involves a new operator (values in the base vector) the MFFD matrix knows it is using a new operator. The easiest way is to call MatMFFDSetBase() before each solve that involves a new operator (new values in the base

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

gt; Your branch works very well. Thanks for your help!!! > > Could you merge it to upstream? > > Fande > > On Wed, Mar 10, 2021 at 6:30 PM Barry Smith <mailto:bsm...@petsc.dev>> wrote: > > Fande, > > Before send the files I requested in my last e

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

s Framework(config.base.Configure, > > > > script.LanguageProcessor): > > > > lines = [s for s in lines if s.find('Load a valid targeting module > > > > or > > > > set CRAY_CPU_TARGET') < 0] > > > > # pgi dumps filename on s

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

> > > > @@ -504,6 +504,8 @@ class Framework(config.base.Configure, > > > > script.LanguageProcessor): > > > > lines = [s for s in lines if s.find('Load a valid targeting module > > > > or > > > > set CRAY_CPU_TARGET') < 0] > >

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

quot;, referenced from: > implicit entry/start for main executable > ld: symbol(s) not found for architecture x86_64 > clang-11: error: linker command failed with exit code 1 (use -v to see > invocation) > Rejected C compiler flag -fPIC because it was not compatible wi

Re: [petsc-users] Exhausted all shared linker guesses. Could not determine how to create a shared library!

Fande, I see you are using CONDA, this can cause issues since it sticks all kinds of things into the environment. PETSc tries to remove some of them but perhaps not enough. If you run printenv you will see all the mess it is dumping in. Can you trying the same build without CONDA

Re: [petsc-users] DMPlex in Firedrake: scaling of mesh distribution

Mark, Thanks for the numbers. Extremely problematic. DMPlexDistribute takes 88 percent of the total run time, SFBcastOpEnd takes 80 percent. Probably Matt is right, PetscSF is flooding the network which it cannot handle. IMHO fixing PetscSF would be a far better route than

Re: [petsc-users] DMPlex in Firedrake: scaling of mesh distribution

mat/tests/ex13.c creates a sequential AIJ matrix, converts it to the same format, reorders it and then prints it and the reordering in ASCII. Each of these steps is sequential and takes place on each rank. The prints are ASCII stdout on the ranks. ierr =

Re: [petsc-users] DMPlex in Firedrake: scaling of mesh distribution

Alexei, Sorry to hear about your difficulties with the mesh distribution step. Based on the figures you included, the extreme difficulties occur on the Oak Ridge Summit system? But on the Argonne Theta system though the distribution time goes up it does not dominate the computation?

Re: [petsc-users] What about user-functions containing OpenMP ?

So long as 1) you configure PETSc with --with-openmp 2) your pragma loops inside the functions inside RHSFunction do not touch PETSc objects directly (PETSc arrays like from VecGetArray() or DMDAVecGetArray() are fine you can access them) or make PETSc calls then this is fine. But how

Re: [petsc-users] PETSC installation on Cray

Please try the following. Make four files as below then compile each with cc -c -o test.o test1.c again for test2.c etc Send all the output. test1.c #include test2.c #define _BSD_SOURCE #include test3.c #define _DEFAULT_SOURCE #include test4.c #define _GNU_SOURCE

Re: [petsc-users] Caught signal number 11 SEGV

start_in_debugger noxterm -debugger_nodes 3 Use -start_in_debugger noxterm -debugger_nodes 0 when not opening windows for each debugger it is best to have the first rank associated with the tty as the debugger node > On Feb 23, 2021, at 3:46 PM, Francesco Brarda > wrote: > > Using the

Re: [petsc-users] Explicit linking to OpenMP results in performance drop and wrong results

> On Feb 18, 2021, at 6:10 AM, Matthew Knepley wrote: > > On Thu, Feb 18, 2021 at 3:09 AM Roland Richter > wrote: > Hei, > > that was the reason for increased run times. When removing #pragma omp > parallel for, my loop took ~18 seconds. When changing it to

Re: [petsc-users] An issue about pipelined CG and Gropp's CG

the result and info into attachment, please > check it. > > > > > > Thanks, > > Gang > > > > -原始邮件- > 发件人:"Barry Smith" > 发送时间:2021-02-18 10:52:11 (星期四) > 收件人: "赵刚" > 抄送: PETSc > 主题: Re: [petsc-users] An issue about pip

Re: [petsc-users] insufficient virtual memory?

PETSc gets almost all its memory using the C malloc system calls so it is unlikely that this Fortran error message comes from PETSc code. My guess is that you have some Fortran arrays declared somewhere in your code that are large and require memory that is not available. Barry > On

Re: [petsc-users] An issue about pipelined CG and Gropp's CG

Put the performance output into > attachment, please check it. > > > > Thanks, > Gang > > > -原始邮件- > 发件人: "Barry Smith" > 发送时间: 2021-02-18 09:17:17 (星期四) > 收件人: "赵刚" > 抄送: PETSc > 主题: Re: [petsc-users] An issue about pipelined CG a

Re: [petsc-users] An issue about pipelined CG and Gropp's CG

> On Feb 17, 2021, at 6:47 PM, 赵刚 wrote: > > Dear PETSc team, > > I am interested in pipelined CG (-ksp_type pipecg) and Gropp's CG (-ksp_type > groppcg), it is expected that this iterative method with pipelined has > advantages over traditional CG in the case of multiple processes. So I'd

Re: [petsc-users] makefile for building application with petsc

Swarnava, sddft.h is not a PETSc include file, nor is it used by PETSc so I think the issue is not directly to PETSc it is related to where sddft is on the machine and how it is found by your makefile. Barry > On Feb 15, 2021, at 7:47 PM, Swarnava Ghosh wrote: > > Dear Petsc developers

Re: [petsc-users] using preconditioner with SLEPc

ing it > correctly? > I wrote a small standalone example based on ex9.py from slepc4py, where i > tried to use an operator. > > best wishes > Florian > > On Sat, Feb 13, 2021 at 7:15 PM Barry Smith <mailto:bsm...@petsc.dev>> wrote: > > >> On Feb 13,

Re: [petsc-users] using preconditioner with SLEPc

lement? > > This is what Barry’s suggestion is implementing. Don’t know why it doesn’t > work with your Python operator though. > > Thanks, > Pierre > >> best wishes >> Florian >> >> >> On Sat, Feb 13, 2021 at 4:19 AM Barry Smith >

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