Re: [petsc-dev] Error creating DMPlex from CGNS file

Thanks for fixing this issue. To contribute, the standard practice is to make a fork and push there. https: //urldefense. us/v3/__https: //gitlab. com/petsc/petsc/-/forks/new__;!!G_uCfscf7eWS!dT8V-NZ0-KPA3SkO_ZJ7HqQVqnCB0IftBhmT_RQAaVE2s3mVhMzzLkDDiw1LV3RyVSXBuH5a7Dk9JZVDoAA$

Re: [petsc-dev] Matshell with PETSs solvers using GPU

ult()? If you do your own communication, you don't need to use DMGlobalToLocalBegin/End. > > Thank you, > Han > >> On Nov 4, 2022, at 9:06 AM, Jed Brown wrote: >> >> Yes, this is supported. You can use VecGetArrayAndMemType() to get access to >> device mem

Re: [petsc-dev] How to add strangers as MR reviewers?

Probably adding them as guests (or developers) would be the way to go. My guess is it's to cut down on accidental assignments, but these policies always have side-effects. Barry Smith writes: > Is there a way to add people not in some magic inner circle as an MR > reviewer? For example, I

Re: [petsc-dev] Latest Pull breaks the 'test' target

Matthew Knepley writes: > On Wed, May 24, 2023 at 6:53 AM Matthew Knepley wrote: > >> On Tue, May 23, 2023 at 9:00 PM Jed Brown wrote: >> >>> I use it that way all the time, but I can't reproduce. >>> >>> $ touch src/snes/interface/snes.c >>&g

Re: [petsc-dev] Latest Pull breaks the 'test' target

I use it that way all the time, but I can't reproduce. $ touch src/snes/interface/snes.c $ make test gs=snes_tutorials-ex5_1 CC ompi/obj/snes/interface/snes.o Using MAKEFLAGS: -j8 -l12 --jobserver-auth=fifo:/tmp/GMfifo1004133 -- gs=snes_tutorials-ex5_1 CLINKER

Re: [petsc-dev] Putting more menu items at the top of petsc.org pages (how to?)

Here's the theme option to control it. https://pydata-sphinx-theme.readthedocs.io/en/stable/user_guide/header-links.html#navigation-bar-dropdown-links "Zhang, Hong via petsc-dev" writes: > I think this is controlled by the theme we are using, which is > pydata-sphinx-theme. It seems that the

Re: [petsc-dev] Apply for Google Summer of Code 2023?

Satish Balay via petsc-dev writes: > BTW: ANL summer student application process is also in progress - and > it could be easier process [for Junchao] than google to get a student We should be more proactive about ANL summer student openings, even with suggested project ideas to work with

Re: [petsc-dev] Apply for Google Summer of Code 2023?

Thanks for proposing this. Some ideas: * DMPlex+libCEED automation * Pipelined Krylov methods using Rust async * Differentiable programming using Enzyme with PETSc Karl Rupp writes: > Dear PETSc developers, > > in order to attract students to PETSc development, I'm thinking about a > PETSc

Re: [petsc-dev] xlocal = da.getLocalVec() .. da.restoreLocalVec(xlocal) skip the restore

Barry Smith writes: >> On Feb 1, 2023, at 9:17 PM, Matthew Knepley wrote: >> >> On Wed, Feb 1, 2023 at 9:06 PM Barry Smith > > wrote: >>> >>> Hmm, When I do >>> >>>def somePythonfunction(): >>>... >>>x = da.createLocalVec() >>> >>>return

Re: [petsc-dev] PetscOptionsGetViewer() problems with multiple usage on the same object but different options databases

scOptionsGetViewer() that no one realized was there when they wrote it > (probably me :-)). > > > > > >> On Jan 22, 2023, at 1:16 PM, Jed Brown wrote: >> >> Matthew Knepley writes: >> >>> On Sun, Jan 22, 2023 at 1:06 PM Barry Smith wrote: >>>

Re: [petsc-dev] PetscOptionsGetViewer() problems with multiple usage on the same object but different options databases

Matthew Knepley writes: > On Sun, Jan 22, 2023 at 1:06 PM Barry Smith wrote: > >> >> That makes incrementally adding new options to an existing object >> difficult, since each call to setFromOptions() screws up previous calls. >> >> We already have >> >> -ksp_monitor_cancel >>

Re: [petsc-dev] New Object and Function Development

Brandon Denton writes: > Good Morning, > > For the past few years, I have been working to integrate CAD into PETSc. > Over this time, I've worked with Dr. Knepley to enable PETSc to open and > utilize STEP, IGES, EGADS and EGADSlite files. We've also worked to expose > the geometry's parameters

Re: [petsc-dev] bad cpu/MPI performance problem

nroots=-1 is like a collective setup_called=false flag, except that this SF is always in that not-set-up state for serial runs. I don't think that's a bug per so, though perhaps you'd like it to be conveyed differently. Barry Smith writes: >There is a bug in the routine

Re: [petsc-dev] Matshell with PETSs solvers using GPU

Yes, this is supported. You can use VecGetArrayAndMemType() to get access to device memory. You'll often use DMGlobalToLocalBegin/End() or VecScatter to communicate, but that will use GPU-aware MPI if your Vec is a device vector. Han Tran writes: > Hi, > > I am aware that PETSc recently

Re: [petsc-dev] PETSc 3.18.1 undefined reference

Indeed, if you configure PETSc with CGNS, you must provide an MPI-enabled CGNS. I'm sad that they chose to package this way. Do you think PETSc should do something different other than documenting this? "Antonio T. sagitter" writes: > 'cgp_close()' is in MPI CGNS only. > > Thank you > >

Re: [petsc-dev] Potential memory leak in PETSc - hypre interface when using Euclid

I think you mean 2.25 versus 2.26, and we can use --download-hypre-commit=origin/v2.26.0 to test if the Euclid issue is fixed (likely no because Euclid hasn't seen much activity this release cycle). Pierre Jolivet writes: > Please do note that we are currently stuck with version 2.15.0 > They

Re: [petsc-dev] Potential memory leak in PETSc - hypre interface when using Euclid

I did this for one step and ten steps, then compared the output using meld. $ PPROF_PATH=/usr/bin/pprof HEAPCHECK=normal LD_PRELOAD=/usr/lib/libtcmalloc.so mpich-clang/tests/ts/tutorials/ex15 -da_grid_x 20 -da_grid_y 20 -boundary 0 -ts_max_steps 20 -Jtype 1 -ts_monitor -pc_type hypre

Re: [petsc-dev] PetscLogEventRegister() is problematic since it must be call in exactly the same order on all ranks

With shared libraries, you can use __attribute__((constructor)) to run when the shared library is loaded, though this is problematic with static libraries. In libCEED, we adopted a strategy using weak symbols to register everything (including optional dependencies) without needing any feature

Re: [petsc-dev] Fwd: Pending configuration of custom domain docs.petsc.org

I agree. I removed the domain from readthedocs.org so it should step complaining now. Satish Balay via petsc-dev writes: > Hm - we don't use readthedocs anymore. > > And I see docs.petsc.org is getting redirected to https://petsc.org/release/ > > So I guess perhaps we don't need to update

Re: [petsc-dev] tests coverage

We should report coverage to GitLab, in which case it'll annotate the diff. For example, this MR shows a red mark on this line that isn't covered by the tests, versus green marks for the covered changes.

Re: [petsc-dev] How to update tests output

make test search=... REPLACE=1 see `make help-test` for more Blaise Bourdin writes: > Silly question, but I can’t find the answer in my notes or on the petsc > developer pages: How do I automatically update the output of a series of > tests without running them all by hand, one at a time? >

Re: [petsc-dev] GPU performance of MatSOR()

rallelism on GPUs but at the cost of multiple phases and slower >> convergence rates. Unless someone already has one coded for CUDA or Kokkos >> it would take a good amount of code to produce one that offers (but does >> not necessarily guarantee) reasonable performance

Re: [petsc-dev] PETSc future starting as a new design layer that runs on top of PETSc 3?

Jacob, would you consider VTK to be "Modern C++"? It was designed in the 90s and I think C++11 isn't widely used (architecturally) since it was first allowed a few years ago. I feel like changing languages (or adopting a second essential implementation language) is a significant complexity

Re: [petsc-dev] GPU performance of MatSOR()

Unfortunately, MatSOR is a really bad operation for GPUs. We can make it use sparse triangular primitives from cuSPARSE, but those run on GPU at about 20x slower than MatMult with the same sparse matrix. So unless MatSOR reduces iteration count by 20x compared to your next-best preconditioning

Re: [petsc-dev] PETSc future starting as a new design layer that runs on top of PETSc 3?

cult to provide multiple language APIs that properly > utilize each language's object oriented features automatically from one given > starting language? Without a lot of thought and effort. > > > >> On Jul 27, 2022, at 3:12 PM, Jed Brown wrote: >> >> I expect

Re: [petsc-dev] PETSc future starting as a new design layer that runs on top of PETSc 3?

hoice today >> and for the foreseeable future. And it could become even more important on >> tomorrow’s heterogeneous hardware architectures. >> >> On Tue, Jul 26, 2022 at 11:09 AM Barry Smith wrote: >>> >>> >>>> On Jul 26, 2022, at 11:30 AM

Re: [petsc-dev] PETSc future starting as a new design layer that runs on top of PETSc 3?

These ownership patterns need to be addressed for reliable interfaces in any language, the compiler just forces you to do it (or use the unsafe escape hatch) in Rust. I think it's necessary in any incremental porting effort for "old" code to call "new" code, due to the nature of our

Re: [petsc-dev] PETSc future starting as a new design layer that runs on top of PETSc 3?

I have to put in a good word for Rust. There are many parallels in capability with modern C++, but the compiler enforces many good practices (and guarantees safety), compiler error and warning messages are really useful, and the tooling is phenomenal on multiple fronts, from packaging to

Re: [petsc-dev] Problem with unnamed side sets in DMPlexCreateExodus

David Andrs writes: > Hi Matt! > > On Jun 26, 2022, at 10:39, Matthew Knepley wrote: >> >> On Sun, Jun 26, 2022 at 8:31 AM David Andrs > > wrote: >> Hi Jed! >> >> I have been thinking about this and I think more correct would be not to >> create the label with an

Re: [petsc-dev] Fortran binding for VecGetValuesSection

Sorry about our late reply. Isn't VecGetValues similar? Note that VecGetValuesSection currently leaks a mutable pointer and really shouldn't exist like this without a matching VecRestoreValuesSection. PetscCall(VecGetArray(v, )); *values = [s->atlasOff[p]]; PetscCall(VecRestoreArray(v,

Re: [petsc-dev] Problem with unnamed side sets in DMPlexCreateExodus

Do you think this is more correct than just using "Face Sets", which gives you a numbered index? There is curently some inconsistency between file formats in whether various sets show up as stand-alone labels or values under Face Sets. And there's this lingering issue to have a way to name

Re: [petsc-dev] Upgrade to Gitlab Open source project must be done ASAP?

Note this from the FAQ: Can I also use this license for projects that aren't open source, or to host private projects? No. You may use the GitLab license you receive from the GitLab for Open Source Program only for the

Re: [petsc-dev] Upgrade to Gitlab Open source project must be done ASAP?

I think it's just links and screenshots. Barry Smith writes: > Crap, do you have any documents you used in the submission process so I can > reuse them? > > >> On Jun 20, 2022, at 3:41 PM, Jed Brown wrote: >> >> I submitted in February and never heard b

Re: [petsc-dev] Upgrade to Gitlab Open source project must be done ASAP?

I submitted in February and never heard back. Feel free to submit again. Barry Smith writes: > Benefits of the GitLab for Open Source Program apply to a namespace. To > qualify, every project in an applicant’s namespace must carry an OSI-approved > open source license. > > Again, GitLab when

Re: [petsc-dev] Another SSP method

You'll want to use the low-storage form. It's discussed in Ketcheson's paper; the method was originally discovered by Kraaijevanger 1991 and rediscovered by Spiter and Ruuth 2002. Note that the effective SSP coefficient is 0.302 while Ketcheson's rk104 has effective coefficient 0.6. As a

Re: [petsc-dev] Gmsh files - PETSc label names and values for physical groups

See -dm_plex_gmsh_use_regions. https://gitlab.com/petsc/petsc/-/issues/689#note_837942276 There are a couple issues. One is that a number of functions take a label and a list of values. For example, we have meshes of a bunch of sand grains (e.g., segmented from CT images), where each grain is

Re: [petsc-dev] C++ and hypre long long int vs PETSc int64_t for 64 bit integer builds

C/C++ integer hierarchy was a mistake, with the language-specified types overlapping and the size-specific (int64_t) being typedefs. So long is "different" from long long even if they're both 64-bit signed integers. I think they should test that sizeof(HYPRE_Int) == sizeof(PetscInt), but not

[petsc-dev] PETSc support for Ukraine

Dear PETSc community, The DOE Office of Science has offered to supplement current projects to support collaboration and hosting of students, postdoctoral researchers, and scientists who have been impacted by the conflict in Ukraine. This can include support via European universities. Details

Re: [petsc-dev] PetscUse/TryMethod

Sundials, for example. PETSc is still relatively low in the software stack. If everyone is making biannual releases for ECP, then we'd need a topological sort on dependencies and PETSc would need to release (or at least freeze) early, e.g., January or February, so other packages have time to

Re: [petsc-dev] PETSc amg solver with gpu seems run slowly

be large for 3D problems) >>>>> * Now hypre's mesh setup is definitely better that GAMG's and AMGx is >>>>> out of this world. >>>>> - AMGx is the result of a serious development effort by NVIDIA about >>>>> 15 years ago with many 1

Re: [petsc-dev] Current status of using streams within PETSc

Note that operations that don't have communication (like VecAXPY and VecPointwiseMult) are already non-blocking on streams. (A recent Thrust update helped us recover what had silently become blocking in a previous release.) For multi-rank, operations like MatMult require communication and MPI

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

s > actually not allocate the nonzeros and just stores the nonzero structure. But > if this is not the case then of course I just duplicate the matrix. > > Thanks for the feedback. > >> Gesendet: Donnerstag, den 03.02.2022 um 03:09 Uhr >> Von: "Jed Brown" >> A

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

Marius Buerkle writes: > Thanks for they reply. Yes the example works, this is how I was doing it > before. But the matrix is rather big and i need a matrix with the same > structure at various points in my code. So it was convenient to create the > matrix with preallocate, destroy it after

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

Stefano Zampini writes: > Il giorno mar 1 feb 2022 alle ore 18:34 Jed Brown ha > scritto: > >> Patrick Sanan writes: >> >> > Am Di., 1. Feb. 2022 um 16:20 Uhr schrieb Jed Brown : >> > >> >> Patrick Sanan writes: >>

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

Patrick Sanan writes: > Am Di., 1. Feb. 2022 um 16:20 Uhr schrieb Jed Brown : > >> Patrick Sanan writes: >> >> > Sorry about the delay on this. I can reproduce. >> > >> > This regression appears to be a result of this optimization: >> >

Re: [petsc-dev] [petsc-users] MatPreallocatorPreallocate segfault with PETSC 3.16

Patrick Sanan writes: > Sorry about the delay on this. I can reproduce. > > This regression appears to be a result of this optimization: > https://gitlab.com/petsc/petsc/-/merge_requests/4273 Thanks for tracking this down. Is there a reason to prefer preallocating twice ierr =

Re: [petsc-dev] Kokkos/Crusher perforance

Barry Smith writes: >> What is the command line option to turn >> PetscLogGpuTimeBegin/PetscLogGpuTimeEnd into a no-op even when -log_view is >> on? I know it'll mess up attribution, but it'll still tell us how long the >> solve took. > > We don't have an API for this yet. It is slightly

Re: [petsc-dev] Kokkos/Crusher perforance

Barry Smith writes: >> On Jan 25, 2022, at 11:55 AM, Jed Brown wrote: >> >> Barry Smith writes: >> >>> Thanks Mark, far more interesting. I've improved the formatting to make it >>> easier to read (and fixed width font for email reading) &

Re: [petsc-dev] Kokkos/Crusher perforance

Barry Smith writes: > Thanks Mark, far more interesting. I've improved the formatting to make it > easier to read (and fixed width font for email reading) > > * Can you do same run with say 10 iterations of Jacobi PC? > > * PCApply performance (looks like GAMG) is terrible! Problems too

Re: [petsc-dev] Kokkos/Crusher perforance

Mark Adams writes: > adding Suyash, > > I found the/a problem. Using ex56, which has a crappy decomposition, using > one MPI process/GPU is much faster than using 8 (64 total). (I am looking > at ex13 to see how much of this is due to the decomposition) > If you only use 8 processes it seems

Re: [petsc-dev] Kokkos/Crusher perforance

Barry Smith writes: > We should make it easy to turn off the logging and synchronizations (from > PetscLogGpu) for everything Vec and below, and everything Mat and below to > remove all the synchronizations needed for the low level timing. I think we > can do that by having PetscLogGpu

Re: [petsc-dev] Kokkos/Crusher perforance

Barry Smith writes: > Norm, AXPY, pointwisemult roughly the same. These are where I think we need to start. The bandwidth they are achieving is supposed to be possible with just one chiplet. Mark, can we compare with Spock?

Re: [petsc-dev] Kokkos/Crusher perforance

Barry Smith via petsc-dev writes: > The PetscLogGpuTimeBegin()/End was written by Hong so it works with events > to get a GPU timing, it is not suppose to include the CPU kernel launch times > or the time to move the scalar arguments to the GPU. It may not be perfect > but it is the best we

Re: [petsc-dev] Kokkos/Crusher perforance

e > myself in any brand new serious benchmarking studies in my current lifetime, > doing one correctly is a massive undertaking IMHO. > >> On Jan 22, 2022, at 6:43 PM, Jed Brown wrote: >> >> This isn't so much more or less work, but work in more useful places. Maybe

Re: [petsc-dev] Kokkos/Crusher perforance

h is why PETSc has its hacked-up ones). I submit a properly performance > study is a full-time job and everyone always has those. > >> On Jan 22, 2022, at 2:11 PM, Jed Brown wrote: >> >> Barry Smith writes: >> >>>> On Jan 22, 2022, at 12:15 PM, Jed Brow

Re: [petsc-dev] Kokkos/Crusher perforance

We could create a communicator for the MPI ranks in the first shared-memory node, then enumerate their mapping (NUMA and core affinity, and what GPUs they see). Barry Smith writes: > I suggested years ago that -log_view automatically print useful information > about the GPU setup (when

Re: [petsc-dev] Kokkos/Crusher perforance

Barry Smith writes: >> On Jan 22, 2022, at 12:15 PM, Jed Brown wrote: >> Barry, when you did the tech reports, did you make an example to reproduce >> on other architectures? Like, run this one example (it'll run all the >> benchmarks across different sizes)

Re: [petsc-dev] Kokkos/Crusher perforance

Mark Adams writes: > On Sat, Jan 22, 2022 at 12:29 PM Jed Brown wrote: > >> Mark Adams writes: >> >> >> >> >> >> >> >> >> > VecPointwiseMult 402 1.0 2.9605e-01 3.6 1.05e+08 1.0 0.0e+00 >> 0.0e+00 >> >> 0

Re: [petsc-dev] Kokkos/Crusher perforance

Mark Adams writes: >> >> >> >> > VecPointwiseMult 402 1.0 2.9605e-01 3.6 1.05e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 5 1 0 0 0 22515 70608 0 0.00e+000 >> 0.00e+00 100 >> > VecScatterBegin 400 1.0 1.6791e-01 6.0 0.00e+00 0.0 3.7e+05 1.6e+04 >> 0.0e+00 0 0 62

Re: [petsc-dev] Kokkos/Crusher perforance

Mark Adams writes: > as far as streams, does it know to run on the GPU? You don't specify > something like -G 1 here for GPUs. I think you just get them all. No, this isn't GPU code. BabelStream is a common STREAM suite for different programming models, though I think it doesn't support MPI

Re: [petsc-dev] Kokkos/Crusher perforance

Mark Adams writes: > On Fri, Jan 21, 2022 at 9:55 PM Barry Smith wrote: > >> >> Interesting, Is this with all native Kokkos kernels or do some kokkos >> kernels use rocm? >> > > Ah, good question. I often run with tpl=0 but I did not specify here on > Crusher. In looking at the log files I see

Re: [petsc-dev] Gitlab workflow discussion with GitLab developers

When applying suggestions, it should offer to "instant fixup" (apply it to some prior commit in this branch, but not in any other branches). That instant fixup should highlight commits that changed nearby lines. When you make an inline comment and the author changes those lines of code, it now

Re: [petsc-dev] user makefile

tions/21338718/using-petsc-on-makefile-within-my-user-defined-makefile > ) > > Maybe just a FAQ "Adding PETSc to a user Makefile" and you could just have > a link to Victor's page (and have him update the include path line) > > > On Thu, Jan 13, 2022 at 11:15 PM

Re: [petsc-dev] user makefile

No makefile is needed to build foo from foo.c. $ make -f $PETSC_DIR/share/petsc/Makefile.user foo In the example below, you don't have to write the recipe (the ${CLINKER} line). It's enough to write foo: foo.o baz.o Matthew Knepley writes: > foo: foo .o > ${CLINKER} -o $@ $^

Re: [petsc-dev] Questions around benchmarking and data loading with PETSc

Junchao Zhang writes: > I expected TACO was better since its website says "It uses novel compiler > techniques to get performance competitive with hand-optimized kernels" The TACO generated code is basically the same, modulo cosmetic partitioning into groups of 32 rows. #pragma omp parallel

Re: [petsc-dev] PETSc GPU example

Fande, let me know if you'd like to run the libCEED hyperelasticity solver on GPUs. It's matrix-free p-multigrid (assembling only the coarse problem). It uses DMPlex for mesh management. Mark Adams writes: > Also Fande, > > If you are _not_ using NVIDIA with the MPS system, then you should

Re: [petsc-dev] mpi_comm_create_group()

Adrian Croucher writes: > On 12/3/21 5:31 PM, Jed Brown wrote: >> You'd need more calls in case of overlap (so MPI_Comm_create_group is more >> natural), but non-participating ranks is easy. >> >>| A process may supply the color value MPI_UNDEFINED, in whi

Re: [petsc-dev] mpi_comm_create_group()

Adrian Croucher writes: > On 12/3/21 12:09 PM, Jed Brown wrote: >> Many find MPI_Comm_split() to be a more convenient interface. > Yes, I don't think that will work for my case though, as my groups may > overlap, and some processes may not be in any group. You'd need mor

Re: [petsc-dev] mpi_comm_create_group()

Adrian Croucher writes: > hi > > This question is not strictly PETSc-related but I figure you guys are > probably most likely to know the answer. > > I need to do some simple computations involving only a small subset of > the parallel processes in my simulation. > > From reading the MPI

Re: [petsc-dev] DMPLEX cannot support two different edges for the same two vertices, hence DMPLEX cannot?

Matthew Knepley writes: > On Wed, Dec 1, 2021 at 5:17 PM Abhyankar, Shrirang G < > shrirang.abhyan...@pnnl.gov> wrote: > >> “You can certainly have many fields on a given edge, but I don't know >> what it would mean to have two edges since no topological query could tell >> the difference.” >>

Re: [petsc-dev] DMPLEX with VecGhost

Yeah, I think that's about true. Should the interface for this be to set a flag before creating fields (and perhaps that flag can become true by default at some point)? Barry Smith writes: > Seems like it should be possible to simply "rewrite" the cython code into > PETSc C. > > Barry >

Re: [petsc-dev] Anyone run STREAMS on an Apple M1 system?

nks, presumably we'll see the new Mac's there in a few days. BTW: the > old streams benchmark page should point to this site; google is worthless. > > I get 24 on my Intel MacBook Pro and it also saturates with 1 core. > > Barry > > >> On Oct 18, 2021, at 4:48 PM, Jed Brown

Re: [petsc-dev] Anyone run STREAMS on an Apple M1 system?

I don't have one, but this suggests it gets about 40 GB/s and can be saturated by a single core. I believe it uses two channels of LPDDR4X-4266, which has a theoretical peak of 68 GB/s. https://browser.geekbench.com/v3/cpu/8931693 The press release claims up to 400 GB/s on the Max using DDR5.

Re: [petsc-dev] Question about the fully implicit Runge-Kutta methods (TS)

Matthew Knepley writes: > On Tue, Oct 5, 2021 at 12:42 AM Wang Jingyuan > wrote: > >> Dear Sir or Madam, >> >> I am a student of the University of Macau, I am trying to learn PETSc and >> I have two questions about the TSIRK. >> >> 1.PETSc 3.16.0 adds “irk" for the TSType and it offers many

Re: [petsc-dev] NVIDIA licensing

On Mon, Sep 6, 2021, at 7:16 PM, Barry Smith wrote: > > * We should also add some text to LICENSE indicating certain files have > additional copyrights indicated at the top of the individual file.* > ** Copyright is held by hundreds of individuals and organizations. I'm not a fan of having

Re: [petsc-dev] VecGetArrayAndMemType

https://gitlab.com/petsc/petsc/-/commit/d7dd068b66a8daa3a37c9e1556b34bd8def54922 On Thu, Jun 24, 2021, at 11:40 AM, Mark Adams wrote: > How does one view a commit on gitlab? > I would like to look at d7dd068b66a8daa3a37c9e1556b34bd8def54922 > > On Thu, Jun 24, 2021 at 9:58 AM Mark Adams wrote:

Re: [petsc-dev] links from manual pages to users manual

Patrick Sanan writes: >> Am 26.05.2021 um 18:39 schrieb Jed Brown : >> >> Patrick Sanan mailto:patrick.sa...@gmail.com>> >> writes: >> >>>> Am 25.05.2021 um 22:58 schrieb Barry Smith : >>>> >>>> >>>>

Re: [petsc-dev] links from manual pages to users manual

Patrick Sanan writes: >> Am 25.05.2021 um 22:58 schrieb Barry Smith : >> >> >> Now that the users manual is html and we can properly link into it, it >> would be great to have links from the manual pages to appropriate locations >> in the users manual. For example SNESSetFunction.html

Re: [petsc-dev] git worktree

I don't follow the advantage over lightweight clones, such as: $ git clone --branch=release --reference petsc gitlab:petsc/petsc petsc-release Cloning into 'petsc-release'... remote: Enumerating objects: 261, done. remote: Counting objects: 100% (261/261), done. remote: Compressing objects: 100%

Re: [petsc-dev] empty space on left side of website pages

t's on > the front page - in the interests of simplicity and focusing on getting the > build stable, I haven't been focusing on it, but there is still discussion to > be had about whether and how to make a prettier front/landing page. > >> Am 26.04.2021 um 21:05 schrieb Jed Brown : >

Re: [petsc-dev] empty space on left side of website pages

The sphinx-pydata-theme has great mobile support and lots of development energy behind it. I don't want to switch themes again based on a sidebar sizing concern. If the sidebar width is super important, we can adjust the CSS. The standard CSS has this, which I think is what we'd want to adjust.

Re: [petsc-dev] how do people manage projects that require two or more PETSc branches

One option is to work on the throw-away combined branch as above, keep your commits for the two topics distinct, then cherry-pick out into the separate topic branches. If you are committing in the topics and respinning the throw-away branch, I would recommend rerere, so you don't have to

Re: [petsc-dev] [petsc-users] [EXTERNAL] Re: Question about periodic conditions

Matthew Knepley writes: > We use it to identify that the mesh is periodic and in what directions, and > use the length if we have to figure out the coordinates. > >> Jed may argue that he wants you to retain the far point and use L2G to >> eliminate it, but that sounds like a lot more work. >>

Re: [petsc-dev] Tag name v3.15

Satish Balay via petsc-dev writes: > On Wed, 31 Mar 2021, Lisandro Dalcin wrote: > >> On Wed, 31 Mar 2021 at 18:07, Satish Balay wrote: >> >> > And we just use 2 level workflow, and have branches for each of the >> > 'releases' [as we move from one to the other] >> > >> >> Maybe I'm not

Re: [petsc-dev] Tag name v3.15

Satish Balay via petsc-dev writes: > > https://semver.org/ > > Given a version number MAJOR.MINOR.PATCH, increment the: > > MAJOR version when you make incompatible API changes, > MINOR version when you add functionality in a backwards compatible > manner, and > PATCH version

Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1

Matthew Knepley writes: >> PetscSectionSetUp currently calculates offsets by walking the points in >> order. I'd like to be able to walk them in a different ordering, perhaps >> specified via an IS permutation, which could be computed using >> MATORDERINGRCM or directly via BFS of a closure

Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1

Matthew Knepley writes: > On Fri, Mar 19, 2021 at 2:21 PM Jed Brown wrote: > >> Matthew Knepley writes: >> >> >> Notice how the permutations are contained within the vertices {0, ..., >> 8}, >> >> edges {9, ..., 24}, and cells {25, ..., 32}. I

Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1

Matthew Knepley writes: >> Notice how the permutations are contained within the vertices {0, ..., 8}, >> edges {9, ..., 24}, and cells {25, ..., 32}. I would like to get rid of >> that restriction, but you've said it would have significant non-local >> consequences so I haven't tried. >> > >

Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1

Lawrence Mitchell writes: >> On 19 Mar 2021, at 14:21, Jed Brown wrote: >> >> Notice how the permutations are contained within the vertices {0, ..., 8}, >> edges {9, ..., 24}, and cells {25, ..., 32}. I would like to get rid of that >> restriction, but you've

Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1

Matthew Knepley writes: > On Fri, Mar 19, 2021 at 7:30 AM Lawrence Mitchell wrote: > >> > On 19 Mar 2021, at 03:51, Jed Brown wrote: >> > >> > It's a notable weakness of DMPlex that it does not apply such an >> ordering of dofs and I've complained to Mat

Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1

Note that this is specific to the node numbering, and that node numbering tends to produce poor results even for MatMult due to poor cache reuse of the vector. It's good practice after partitioning to use a locality-preserving ordering of dofs on a process (e.g., RCM if you use MatOrdering).

Re: [petsc-dev] Argonne GPU Virtual Hackathon - Accepted

Barry Smith writes: >> On Mar 12, 2021, at 6:58 PM, Jed Brown wrote: >> >> Barry Smith writes: >> >>> I think we should start porting the PetscFE infrastructure, numerical >>> integrations, vector and matrix assembly to GPUs soon. It i

Re: [petsc-dev] Argonne GPU Virtual Hackathon - Accepted

Barry Smith writes: > I think we should start porting the PetscFE infrastructure, numerical > integrations, vector and matrix assembly to GPUs soon. It is dog slow on CPUs > and should be able to deliver higher performance on GPUs. IMO, this comes via interfaces to libCEED, not rolling

Re: [petsc-dev] Argonne GPU Virtual Hackathon - Accepted

writes: > Jed, > > Thanks for the insight. > > Maybe Hong and his Ellpack format? Or his independent set algorithm? > > Maybe Stefano and his COO matrix assembly on GPUs? > > Others? > > Barry > > >> On Mar 12, 2021, at 4:37 P

Re: [petsc-dev] Fwd: Argonne GPU Virtual Hackathon - Accepted

I helped with one of these a couple years ago. It's important to go in with a well-defined problem and mini-app. If "PETSc" is the topic, then you should start with a representative benchmark problem that runs in no more than a couple minutes. It could be two problems, one that we think is good

Re: [petsc-dev] Are pipelines down?

Says the pipeline was canceled. The branch comes from a fork so it should need approval to run. https://gitlab.com/petsc/petsc/-/merge_requests/3707 Matthew Knepley writes: > https://gitlab.com/danfinn/petsc/-/pipelines/269297070 > > Thanks, > > Matt > > -- > What most experimenters

Re: [petsc-dev] plan to transition to new documentation and webpages?

The one value-add that comes from ReadTheDocs is its version switcher, which we'd need to do ourselves. I've been using this strategy (for stand-alone preview) on a different project and it's working great. We can decide how to merge it (i.e., where the doc job should run).

Re: [petsc-dev] Commit squashing in MR

If you're in Emacs, Magit (https://github.com/magit/magit) is excellent for much the same things, and works over remote (i.e., I'm editing "ssh:thathost:path/to/file.c" and invoke magit). There's also a (partial) magit clone for vscode.

Re: [petsc-dev] Case TS005062693 - XLF: ICE in xlfentry compiling a module with 358 subroutines

I wonder if gfortran has a similar "bug" but larger capacity that would explain why it's so much more expensive to compile the Fortran interface files than to compile all of PETSc. Barry Smith writes: >PETSc stacks the Fortran modules in the same way it stacks the C include > files. So

Re: [petsc-dev] Commit squashing in MR

Satish Balay via petsc-dev writes: > On Wed, 3 Mar 2021, Blaise A Bourdin wrote: > >> Hi, >> >> This is not technically a petsc question. >> It would be great to have a short section in the PETSc integration workflow >> document explaining how to squash commits in a MR for git-impaired >>

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