Re: [petsc-dev] Bug introduced in MatGetSubmatrices()

v] Sent: Friday, January 20, 2017 8:19 PM To: Matthew Knepley Cc: Zhang, Hong; PETSc Subject: Re: [petsc-dev] Bug introduced in MatGetSubmatrices() Ok, so the problem comes from setting the flag in in the original matrix that other people have access to and can be used for other purposes by

Re: [petsc-dev] Bug introduced in MatGetSubmatrices()

OK, I removed flag MAT_SUBMAT_SINGLEIS https://bitbucket.org/petsc/petsc/commits/65b5f10fe03da0cc383d7dd0f31fadf6a7ab9abe Hong From: Barry Smith [bsm...@mcs.anl.gov] Sent: Monday, January 23, 2017 2:29 PM To: Zhang, Hong Cc: Matthew Knepley; PETSc Subject

Re: [petsc-dev] Bug introduced in MatGetSubmatrices()

_ From: Barry Smith [bsm...@mcs.anl.gov] Sent: Friday, January 20, 2017 1:11 PM To: Matthew Knepley Cc: Zhang, Hong; PETSc Subject: Re: [petsc-dev] Bug introduced in MatGetSubmatrices() > On Jan 20, 2017, at 12:45 PM, Matthew Knepley <knep...@gmail.com> wrote: > > On Fri, Jan 20, 20

Re: [petsc-dev] download problem p4est on Cori at NERSC

Feb 16, 2017 at 6:29 PM, Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> wrote: On Thu, Feb 16, 2017 at 4:49 PM, Zhang, Hong <hongzh...@anl.gov<mailto:hongzh...@anl.gov>> wrote: On cori, I tried to compile PETSc on a compute node in the interactive mode, but it did n

Re: [petsc-dev] download problem p4est on Cori at NERSC

On cori, I tried to compile PETSc on a compute node in the interactive mode, but it did not work. What worked for me is to do the following: 1. configure with --with-batch=1 to generate a binary 2. submit the binary to the queue: srun -n 1 -c 1 ./conftest-xxx 3. run the reconfigure-xxx script

Re: [petsc-dev] Bug introduced in MatGetSubmatrices()

What if a MPI process has no submatrices, how does it save the flag? case of 'SingleIS' is for ismax=1 in all processes. For PCASM, all process has ismax=1, isn't it? Hong > On Jan 22, 2017, at 8:58 PM, Zhang, Hong <hzh...@mcs.anl.gov> wrote: > > The 'saved' context is

Re: [petsc-dev] Bug introduced in MatGetSubmatrices()

We allocate array submats[] with length 'ismax+1'. When a process has ismax=0, submats[0] is still generated with a 0-dimension matrix, so 'saved context' can be attached for reuse. Hong From: Zhang, Hong Sent: Monday, January 23, 2017 10:51 AM To: Barry

Re: [petsc-dev] Bug introduced in MatGetSubmatrices()

Sorry, checking the code, we actually require user to provide 0-length IS's with ismax=1 as input in the case of (MAT_REUSE_MATRIX && !ismax). Hong ____ From: Zhang, Hong Sent: Monday, January 23, 2017 10:54 AM To: Barry Smith Cc: Matthew Knepley; PETSc

Re: [petsc-dev] Strange behaviour from TSARKIMEX

> On Nov 15, 2016, at 10:56 AM, Emil Constantinescu > wrote: > > > > On 11/15/16 7:35 AM, Stefano Zampini wrote: >> Emil, >> >> I have modifed the example code to also include the convection matrix in the >> lhs. >> >> Plain arkimex with -ts_arkimex_fully_implicit

Re: [petsc-dev] Fwd: no petsc on Edison

eCreate(A->cmap->n,aN,); Mark: can you make this change and let me know if it fix the problem? I'll check similar problems in other parallel matrix product routines. Hong From: Barry Smith [bsm...@mcs.anl.gov] Sent: Wednesday, January 11, 2017 2:55 P

Re: [petsc-dev] Fwd: no petsc on Edison

Hong From: Barry Smith [bsm...@mcs.anl.gov] Sent: Wednesday, January 11, 2017 2:55 PM To: Kong, Fande; Zhang, Hong Cc: Mark Adams; petsc-dev; David Trebotich Subject: Re: [petsc-dev] Fwd: no petsc on Edison > On Jan 11, 2017, at 2:41 PM, Kong, Fande <fande.k...@inl.gov> wrote: &g

Re: [petsc-dev] Seeking current Eclipse/PETSc developer

I am always itching to add something in this section. Finally got the change to do that. Since Patrick has already added the part on how to use PETSc with other codes in Eclipse, I prepared a write-up based on my experience of indexing and building just the PETSc code. See

Re: [petsc-dev] Seeking current Eclipse/PETSc developer

o old. Maybe we should remove this paragraph. I can do it if nobody else objects. Hong (Mr.) On Sun, Jan 15, 2017 at 3:39 AM, Zhang, Hong <hongzh...@anl.gov<mailto:hongzh...@anl.gov>> wrote: I am always itching to add something in this section. Finally got the change to do that. Since

Re: [petsc-dev] Using multiple mallocs with PETSc

On Mar 9, 2017, at 8:50 PM, Barry Smith <bsm...@mcs.anl.gov<mailto:bsm...@mcs.anl.gov>> wrote: On Mar 9, 2017, at 8:29 PM, Zhang, Hong <hongzh...@anl.gov<mailto:hongzh...@anl.gov>> wrote: On Mar 9, 2017, at 7:38 PM, Barry Smith <bsm...@mcs.anl.gov<mai

Re: [petsc-dev] Using multiple mallocs with PETSc

> On Mar 9, 2017, at 7:38 PM, Barry Smith wrote: > > >> On Mar 9, 2017, at 7:18 PM, Richard Mills wrote: >> >> Hi Barry, >> >> I like the sound of this, but I think we'd need to be careful about not >> messing up data alignment if we do this.

Re: [petsc-dev] Test failures in PetscCommBuildTwoSided_Ibarrier?

GCC works great on Linux, but IMHO it is always problematic on Mac. I had a lot of trouble when using GCC on Mac for netcdf, libmesh and some other stuff. And it seems not easy to fix the problems on the library side. For example, the netcdf problem I got has existed for several years, and

Re: [petsc-dev] TSTrajectory

Hi Stefano, > On Jul 25, 2017, at 1:09 PM, Stefano Zampini > wrote: > > Is TSTrajectory and its API (in the public header petscts.h) supposed to be > used from outside a TSAdjointSolve? TSTrajectory is mainly used by TSAdjoint, but not limited to it. For example,

Re: [petsc-dev] PETSc release?

I will create a pull request today. Presumably the review process would take long for this monster, so it is fine if it cannot go in the release. Thanks, Hong (Mr.) On Jul 24, 2017, at 11:23 AM, Richard Tran Mills > wrote: On Sun, Jul 23, 2017 at 3:08

Re: [petsc-dev] TSAdjoint implementation

Sure. I already created a separate file 'tsfwdsen.c' for the forward sensitivity approach. Similarly, we can have a file `tsadjsen.c` for TSAdjoint. Hong (Mr.) > On Jul 27, 2017, at 2:31 AM, Lisandro Dalcin wrote: > > Would it be possible to create a new "tsadjoint.c" file

Re: [petsc-dev] TSTrajectory

> On Jul 26, 2017, at 9:31 AM, Lisandro Dalcin wrote: > > On 26 July 2017 at 16:34, Stefano Zampini wrote: >> >> We should come to an agreement on it, as it is used to monitoring a TSSolve >> call, and to save the trajectory, as per commit >> >

Re: [petsc-dev] TSTrajectory

hy not using ts->steps instead of ts->total_steps in TSMonitor and TSSetTrajectory? We should be really careful when modifying interface code. 2017-07-26 13:11 GMT+03:00 Stefano Zampini <stefano.zamp...@gmail.com<mailto:stefano.zamp...@gmail.com>>: 2017-07-25 22:45 GMT+03:00 Zh

Re: [petsc-dev] PETSC optimization

> > On Aug 16, 2017, at 12:01 PM, Jiyuan Li wrote: > > Dear developers, > > I am wondering if PETSC is optimized for modern intel architectures (Xeon E5, > Xeon phi, ...), We have been optimizing PETSc for KNL (2nd generation Xeon Phi). If you happen to be using KNL,

[petsc-dev] Some warnings in Master branch

The first one looks like a bug. CC-128 craycc: WARNING File = /global/u2/h/hongzh/Project/petsc/src/dm/impls/plex/plextree.c, Line = 3149 The indicated loop is not reachable from preceding code. SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unsupported discretization

Re: [petsc-dev] Some warnings in Master branch

I see these warnings only with Cray compilers. Maybe it is a false positive. Hong On Jun 5, 2017, at 11:39 AM, Matthew Knepley <knep...@gmail.com<mailto:knep...@gmail.com>> wrote: On Mon, Jun 5, 2017 at 11:29 AM, Zhang, Hong <hongzh...@anl.gov<mailto:hongzh...@anl.gov>&

Re: [petsc-dev] So PETSc's function names are restricted to 31 characters?

Does PETSc build faster at 38,000 feet? On Sep 22, 2017, at 8:47 PM, Richard Tran Mills > wrote: Certainly! Being 38,000 feet in the air is no barrier to PETSc development! --Richard On Fri, Sep 22, 2017 at 6:44 PM, Smith, Barry F.

Re: [petsc-dev] (no subject)

Great news! According to their papers, MLSVM works only in serial. I am not sure what is stopping them using PETSc in parallel. Btw, are there any other cases that use PETSc for machine learning? Hong (Mr.) > On Sep 21, 2017, at 1:02 PM, Barry Smith wrote: > > > From:

Re: [petsc-dev] TS Terminology

On Oct 20, 2017, at 11:34 AM, Jed Brown > wrote: Matthew Knepley > writes: On Fri, Oct 20, 2017 at 11:58 AM, Emil Constantinescu > wrote: On 10/20/17

Re: [petsc-dev] TS Terminology

> On Oct 20, 2017, at 3:15 PM, Jed Brown <j...@jedbrown.org> wrote: > > "Zhang, Hong" <hongzh...@anl.gov> writes: > >> Another confusion which is not related to this topic is the usage of the >> word "DAE". >> I d

Re: [petsc-dev] Proposed changes to TS API

On May 10, 2018, at 4:12 PM, Jed Brown <j...@jedbrown.org<mailto:j...@jedbrown.org>> wrote: "Zhang, Hong" <hongzh...@anl.gov<mailto:hongzh...@anl.gov>> writes: Dear PETSc folks, Current TS APIs (IFunction/IJacobian+RHSFunction/RHSJacobian) were designed for

Re: [petsc-dev] Proposed changes to TS API

Brown <j...@jedbrown.org<mailto:j...@jedbrown.org>> wrote: "Zhang, Hong" <hongzh...@anl.gov<mailto:hongzh...@anl.gov>> writes: Dear PETSc folks, Current TS APIs (IFunction/IJacobian+RHSFunction/RHSJacobian) were designed for the fully implicit formulation F(t,U,Udot

Re: [petsc-dev] Proposed changes to TS API

On May 11, 2018, at 1:01 PM, Lisandro Dalcin > wrote: On Fri, 11 May 2018 at 19:34, Jed Brown > wrote: "Smith, Barry F." > writes: I assemble the combined

[petsc-dev] Proposed changes to TS API

Dear PETSc folks, Current TS APIs (IFunction/IJacobian+RHSFunction/RHSJacobian) were designed for the fully implicit formulation F(t,U,Udot) = G(t,U). Shampine's paper

Re: [petsc-dev] running test harness under batch system

rs are all available and working on the >> compute nodes, correct? >> >> Thanks >> >> Barry >> >> Do the compilers work on the compute nodes of theta? >> >> >> >>> On Jun 25, 2018, at 12:03 PM, Zhang, Hong wrote:

Re: [petsc-dev] running test harness under batch system

Yes, it is possible. I have run the test harness on cori submitting the following script #!/bin/bash -l #SBATCH -N 1 #Use 1 nodes #SBATCH -t 02:00:00 #Set time limit #SBATCH -p regular #Submit to the regular 'partition' #SBATCH -C knl,quad,cache #Use

Re: [petsc-dev] plans for preconditioners for SeqSELL

Hi Richard, MatConvert_Basic() does not work for most cases when converting AIJ to SELL because SELL may require padding and being preallocated based on the nonzeros per row. See the correct conversion in

Re: [petsc-dev] plans for preconditioners for SeqSELL

L work properly with a block size > 1? I don't think we need more code. Thanks, Hong (Mr.) --Richard On Mon, Jun 25, 2018 at 2:04 PM, Zhang, Hong mailto:hongzh...@anl.gov>> wrote: Hi Richard, MatConvert_Basic() does not work for most cases when converting AIJ to SELL because SELL may r

Re: [petsc-dev] plans for preconditioners for SeqSELL

> On Feb 12, 2018, at 8:36 AM, Jed Brown wrote: > > Karl Rupp writes: > >> Hi Stefano, >> >>> Is there any plan to write code for native ILU/ICC etc for SeqSELL, at >>> least to have BJACOBI in parallel? >> >> (imho) ILU/ICC is a pain to do with

Re: [petsc-dev] plans for preconditioners for SeqSELL

Hi Stefano, On Feb 13, 2018, at 5:40 AM, Stefano Zampini > wrote: Richard, what are the performances you get with MATSELL in PFLOTRAN? For PFLOTRAN and many other examples, the SELL-based MatMult is usually 2X faster than AIJ

Re: [petsc-dev] any script to extract data from "-log_view"?

Here is an updated (python3 and a few other new features) version of Jed's script. https://github.com/caidao22/petscplot Hong (Mr.) On Aug 8, 2018, at 10:51 PM, Jed Brown mailto:j...@jedbrown.org>> wrote: Fande Kong mailto:fdkong...@gmail.com>> writes: Hi all, If we are going to do a

Re: [petsc-dev] TSBASICSYMPLECTIC

A few related discussions can be found at https://bitbucket.org/petsc/petsc/pull-requests/1108/rename-bsi-to-symplectic/diff In addition, what we have in PETSc now is "Basic Symplectic Integrators" as introduced in Ernst Hairer's article https://www.unige.ch/~hairer/poly_geoint/week2.pdf .

Re: [petsc-dev] upcoming release and testing

Hi Satish, I have just updated the dev changes in the branch hongzh/update-dev. Regards, Hong (Mr.) > On Apr 2, 2018, at 12:18 PM, Satish Balay wrote: > > All, > > It would be good if > http://www.mcs.anl.gov/petsc/documentation/changes/dev.html is cheked and > updated

Re: [petsc-dev] plans for preconditioners for SeqSELL

Hi Karli, Thank you for offering help to clean up. I have no objection. We have thought about subclassing long before. As Barry suggested, an ideal solution is to make a base class (XAIJ ?) for AIJ, BAIJ, SBAIJ, and SELL. The base class will have diagonal and off diagonal parts without binding

Re: [petsc-dev] MUMPS silent errors

Junchao: Hong, The user's example code reads a matrix, calls KSPSolve, then over. From his log_view file, I saw long MatLUFactorNum time and short MatSolve time. Now I know that is because MatSolve was skipped. Thanks. This is intended. Hong From: Zhang

Re: [petsc-dev] MUMPS silent errors

Junchao : When matrix factorization fails, we diver error message back to user and skip MatSolve. Can you reproduce this problem and I'll take a look at it? What is embarrassing is the user sent me beautiful -log_view outputs and began doing performance comparison. The whole thing is

Re: [petsc-dev] How to know MatSolve() was successful?

Junchao : I learned users should call KSPGetConvergedReason to check if a KSPSolve was successful. But if users directly call MatSolve() or MatMatSolve etc, how can they know it was successful? I see in MatSolve_MUMPS, it first checks factor errors. If there is, it sets the solution to

Re: [petsc-dev] Segmentation faults in MatMatMult & MatTransposeMatMult

Replace ierr = MatSetType(A, MATMPIAIJ);CHKERRQ(ierr); to ierr = MatSetType(A, MATAIJ);CHKERRQ(ierr); Replace ierr = MatSetType(B, MATMPIDENSE)i;CHKERRQ(ierr); to ierr = MatSetType(B, MATDENSE)i;CHKERRQ(ierr); Then add MatSeqAIJSetPreallocation() MatSeqDenseSetPreallocation() Hong On Mon, Jan

Re: [petsc-dev] [petsc-users] Bad memory scaling with PETSc 3.10

Myriam, - PETSc 3.6.4 (reference) - PETSc 3.10.4 without specific options - PETSc 3.10.4 with the three scalability options you mentionned What are the 'three scalability options' here? What is "MaxMemRSS", the max memory used by a single core? How many cores do you start with? Do you have

Re: [petsc-dev] How long?

Is linux kernel maintainable and extendable? Does anyone want to reimplement linux in Julia? Hong (Mr.) > On Mar 11, 2019, at 9:28 PM, Smith, Barry F. via petsc-dev > wrote: > > > PETSc source code is becoming an unmaintainable, unextendable monstrosity. > How long until Julia is mature

Re: [petsc-dev] [petsc-users] Bad memory scaling with PETSc 3.10

Fande, The images are very interesting and helpful. How did you get these images? Petsc PtAP uses 753MB for PtAPSymbolic and only 116MB for PtAPNumeric, while hypre uses 215MB -- it seems hypre does not implement symbolic PtAP. When I implement PtAP, my focus was on numeric part because it was

Re: [petsc-dev] New implementation of PtAP based on all-at-once algorithm

I would suggest Fande add this new implementation into petsc. What is the algorithm? I'll try to see if I can further reduce memory consumption of the current symbolic PtAP when I get time. Hong On Fri, Apr 12, 2019 at 8:27 AM Mark Adams via petsc-dev mailto:petsc-dev@mcs.anl.gov>> wrote: On

Re: [petsc-dev] moving from BitBucket to GitLab

If it is mainly because of CI, why don't we host petsc on GitHub and use the GitLab CI? https://about.gitlab.com/solutions/github/ GitHub has been the biggest social network for developers. Changing a utility is easy to me, but changing a social network isn't. Thanks, Hong (Mr.) On Jun 15,

Re: [petsc-dev] Is bitbucket less responsive than it use to be?

Vote for GitHub +1. We would have almost moved to GitHub early last year. But I was not sure what stopped the transition. Hong On May 14, 2019, at 10:51 AM, Fande Kong via petsc-dev mailto:petsc-dev@mcs.anl.gov>> wrote: Any difficulty to switch over to GitHub? I like GitHub better than

Re: [petsc-dev] Broken MatMatMult_MPIAIJ_MPIDense

Barry : We would like avoid allocating a huge array for the matrix and then having the user place on top of it. In the new paradigm there could be options called on the resulting C of MatMatGetProduct() that would take effect before the C is fully formed to prevent the allocating and

Re: [petsc-dev] Broken MatMatMult_MPIAIJ_MPIDense

Barry: As a hack for this release could you have the Numeric portion of the multiply routines check if the symbolic data is there and if not just call the symbolic an attach the needed data? You might need to have a utility function that does all the symbolic part except the allocation of

Re: [petsc-dev] Broken MatMatMult_MPIAIJ_MPIDense

Yes, we should allow users to provide their own matrix array. We use MatDensePlaceArray() to plug an array into matrix C before MatMatMult(). If we cannot do this, we will have to copy from the internal array of the result C to our array. Would the following sequence work? MatMatMultSymbolic()

Re: [petsc-dev] Broken MatMatMult_MPIAIJ_MPIDense

Thanks, Pierre On 23 Sep 2019, at 6:02 PM, Zhang, Hong mailto:hzh...@mcs.anl.gov>> wrote: Barry: As a hack for this release could you have the Numeric portion of the multiply routines check if the symbolic data is there and if not just call the symbolic an attach the needed data? Yo

Re: [petsc-dev] Broken MatMatMult_MPIAIJ_MPIDense

I'll check it tomorrow. Hong On Sun, Sep 22, 2019 at 1:04 AM Pierre Jolivet via petsc-dev mailto:petsc-dev@mcs.anl.gov>> wrote: Jed, I’m not sure how easy it is to put more than a few lines of code on GitLab, so I’ll just send the (tiny) source here, as a follow-up of our discussion

Re: [petsc-dev] "participants" on gitlab

problem you > mention below. Unfortunately, I think that reduces incentive to review, > and we're always stressed for reviewing resources. > > "Zhang, Hong via petsc-dev" writes: > >> How is the list of participants determined when a MR is created on gitlab? &g

[petsc-dev] "participants" on gitlab

How is the list of participants determined when a MR is created on gitlab? It seems to include everybody by default. Is there any way to shorten the list? Ideally only the participants involved in the particular MR should be picked. Note that currently there is a huge gap between the

Re: [petsc-dev] AVX kernels, old gcc, still broken

Hi Lisandro, Can you please check if the following patch fixes the problem? I will create a MR. diff --git a/src/mat/impls/aij/seq/aijperm/aijperm.c b/src/mat/impls/aij/seq/aijperm/aijperm.c index 577dfc6713..568535117a 100644 --- a/src/mat/impls/aij/seq/aijperm/aijperm.c +++

Re: [petsc-dev] People spent tim doing this

It is hard to understand where the speedup comes. What is the difference between "manner 1" and "manner 2”? Btw, we don’t provide “ELL” format in PETSc. We provide “SELL”, which should be more SIMD-friendly than the column-ELL proposed in the paper. Hong On Oct 10, 2019, at 8:16 PM, Matthew

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

On Feb 8, 2020, at 5:03 PM, Matthew Knepley mailto:knep...@gmail.com>> wrote: On Sat, Feb 8, 2020 at 4:34 PM Zhang, Hong via petsc-dev mailto:petsc-dev@mcs.anl.gov>> wrote: I did some further investigation. The overhead persists for both the PETSc shared library and the st

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

On Feb 12, 2020, at 11:09 AM, Matthew Knepley mailto:knep...@gmail.com>> wrote: On Wed, Feb 12, 2020 at 11:06 AM Zhang, Hong via petsc-dev mailto:petsc-dev@mcs.anl.gov>> wrote: Sorry for the long post. Here are replies I have got from OLCF so far. We still don’t know how to solve

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

ith, Barry F. mailto:bsm...@mcs.anl.gov>> wrote: gprof or some similar tool? On Feb 10, 2020, at 11:18 AM, Zhang, Hong via petsc-dev mailto:petsc-dev@mcs.anl.gov>> wrote: -cuda_initialize 0 does not make any difference. Actually this issue has nothing to do with PetscInitialize(). I

[petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

Hi all, Previously I have noticed that the first call to a CUDA function such as cudaMalloc and cudaFree in PETSc takes a long time (7.5 seconds) on summit. Then I prepared a simple example as attached to help OCLF reproduce the problem. It turned out that the problem was caused by PETSc. The

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

Statically linked excitable works fine. The dynamic linker is probably broken. Hong On Feb 7, 2020, at 12:53 PM, Matthew Knepley mailto:knep...@gmail.com>> wrote: On Fri, Feb 7, 2020 at 1:23 PM Zhang, Hong via petsc-dev mailto:petsc-dev@mcs.anl.gov>> wrote: Hi all, Previously I

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

Note that the overhead was triggered by the first call to a CUDA function. So it seems that the first CUDA function triggered loading petsc so (if petsc so is linked), which is slow on the summit file system. Hong On Feb 7, 2020, at 2:54 PM, Zhang, Hong via petsc-dev mailto:petsc-dev

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

ur libraries > in a different place than /autofs/nccs-svm1_home1 > > > >> On Feb 7, 2020, at 3:09 PM, Zhang, Hong wrote: >> >> Note that the overhead was triggered by the first call to a CUDA function. >> So it seems that the first CUDA function trigg

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

.anl.gov>> wrote: ldd -o on the executable of both linkings of your code. My guess is that without PETSc it is linking the static version of the needed libraries and with PETSc the shared. And, in typical fashion, the shared libraries are off on some super slow file syst

Re: [petsc-dev] [petsc-users] Matrix-free method in PETSc

DMDA and MatShell are among the least documented in PETSc. But they are extremely useful at least to me. Hopefully I will try to get my TS+MatShell+DMDA example into master early next month. Hong On Feb 18, 2020, at 9:10 PM, Smith, Barry F. via petsc-dev mailto:petsc-dev@mcs.anl.gov>> wrote:

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

le by hand? PETSc was built into a static lib. Then both of the two example were built with the static lib. Hong > > Barry > > >> On Feb 12, 2020, at 7:29 PM, Zhang, Hong wrote: >> >> >> >>> On Feb 12, 2020, at 5:11 PM, Smith, Barry F. wrote:

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

) (s2 - s1)) / CLOCKS_PER_SEC,((double) (s3 - s2)) / CLOCKS_PER_SEC); ierr = PetscFinalize(); return ierr; } Hong On Feb 7, 2020, at 3:09 PM, Zhang, Hong mailto:hongzh...@anl.gov>> wrote: Note that the overhead was triggered by the first call to a CUDA function. So it seems that the first CUDA fu

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

; think some MPI compilers insert their own version. >> >> Todd. >> >>> On Feb 12, 2020, at 11:38 AM, Zhang, Hong via petsc-dev >>> wrote: >>> >>> >>> >>>> On Feb 12, 2020, at 11:09 AM, Matthew Knepley wrote: >>

Re: [petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit

As I mentioned, have you tried -cuda_initialize 0? Also, PetscCUDAInitialize contains ierr = PetscCUBLASInitializeHandle();CHKERRQ(ierr); ierr = PetscCUSOLVERDnInitializeHandle();CHKERRQ(ierr); Have you tried to comment out them and test again? --Junchao Zhang On Sat, Feb 8, 2020 at 5:22 PM Zhang, Ho

Re: [petsc-dev] MATOP_MAT_MULT

Pierre, MatMatMult_xxx() is removed from MatOps table. MatMatMult() is replaced by MatProductCreate() MatProductSetType(,MATPRODUCT_AB) MatProductSetFromOptions() MatProductSymbolic() MatProductNumeric() Where/when do you need query a single matrix for its product operation? Hong

Re: [petsc-dev] MATOP_MAT_MULT

Jose, >> I also now just tested some previously PETSC_VERSION_LT(3,13,0) running code >> with C=A*B, Dense=Nest*Dense, all previously allocated prior to a call to >> MatMatMult and scall = MAT_REUSE_MATRIX. >> Sadly, it’s now broken. It is my fault for not having a test for this in >>

Re: [petsc-dev] MATOP_MAT_MULT

e know if you have better solution. See ex109.c and ex195.c for tests. Hong From: Pierre Jolivet Sent: Saturday, April 25, 2020 11:45 AM To: Zhang, Hong Cc: Jose E. Roman ; Stefano Zampini ; petsc-dev ; Smith, Barry F. Subject: Re: [petsc-dev] MATOP_MAT_MULT Hong

Re: [petsc-dev] MATOP_MAT_MULT

, (including basic implementation) or NULL. Let me know your suggestions. I'll list all of you as reviewer. Hong From: Jose E. Roman Sent: Wednesday, April 22, 2020 9:07 AM To: Stefano Zampini Cc: Zhang, Hong ; Pierre Jolivet ; petsc-dev Subject: Re: [petsc-dev

Re: [petsc-dev] MATOP_MAT_MULT

>vmm && flg) { MatProductSymbolic(Wmat); MatProductNumeric(Wmat); } else { MatDestroy(Wmat); ... } Hong From: Jose E. Roman Sent: Tuesday, April 21, 2020 11:21 AM To: Pierre Jolivet Cc: Zhang, Hong ; petsc-dev Subject: Re: [petsc-dev] MATOP_M

Re: [petsc-dev] MATOP_MAT_MULT

() with seqsbaij and dense matrices, a detailed error message will be out from MatProductSetFromOptions() (or MatMatMult() if you use the wrapper). I'll discuss Jose's usage in next email. Hong From: Pierre Jolivet Sent: Tuesday, April 21, 2020 10:53 AM To: Zhang, Hong Cc

Re: [petsc-dev] MATOP_MAT_MULT

Jose, I'll check and fix them. I have to do it in master, is ok? Hong From: Pierre Jolivet Sent: Wednesday, April 22, 2020 3:08 PM To: Zhang, Hong Cc: Jose E. Roman ; Stefano Zampini ; petsc-dev ; Smith, Barry F. Subject: Re: [petsc-dev] MATOP_MAT_MULT Hong

Re: [petsc-dev] MATOP_MAT_MULT

needed features are maintained. Report to me -- I'll do my best to provided needed support. Hong From: Pierre Jolivet mailto:pierre.joli...@enseeiht.fr>> Sent: Tuesday, April 21, 2020 10:53 AM To: Zhang, Hong mailto:hzh...@mcs.anl.gov>> Cc: petsc-dev

Re: [petsc-dev] MATOP_MAT_MULT

I'll try to do it in maint. Hong From: Jose E. Roman Sent: Thursday, April 23, 2020 2:36 AM To: Pierre Jolivet Cc: Zhang, Hong ; Stefano Zampini ; petsc-dev ; Smith, Barry F. Subject: Re: [petsc-dev] MATOP_MAT_MULT I agree with Pierre. However, if the fix

Re: [petsc-dev] MATOP_MAT_MULT

eration(C,MATOP_PRODUCTSYMBOLIC,); if (flg) { MatProductSymbolic(C); ... } else { MatDestroy(); ... } Either you take care of this bug report, or let me know your thoughts about how to fix this bug. Hong ____ From: Zhang, Hong Sent: Saturday, April 25, 202

Re: [petsc-dev] Question about Binary-IO in READ mode with POSIX APIs

On Mar 16, 2020, at 12:12 PM, Lisandro Dalcin mailto:dalc...@gmail.com>> wrote: On Mon, 16 Mar 2020 at 16:35, Jed Brown mailto:j...@jedbrown.org>> wrote: Lisandro Dalcin mailto:dalc...@gmail.com>> writes: > Currently, binary viewers using POSIX file descriptors with READ mode open > the

Re: [petsc-dev] MATOP_MAT_MULT

Stefano, How about you work on this issue? Hong From: Stefano Zampini Sent: Wednesday, May 6, 2020 2:09 AM To: Zhang, Hong Cc: Pierre Jolivet ; Jose E. Roman ; petsc-dev ; Smith, Barry F. Subject: Re: [petsc-dev] MATOP_MAT_MULT Hong If the product

[petsc-dev] Statistics on the popularity of PETSc

Someone asks about the number of PETSc users. Do we have relevant info? Hong

Re: [petsc-dev] Statistics on the popularity of PETSc

brew info petsc … install: 142 (30 days), 436 (90 days), 1,554 (365 days) install-on-request: 140 (30 days), 412 (90 days), 1,450 (365 days) Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) Cell: (312) 694-3391 On Sep 10, 2020, at 16:29, Zhang, Hong via petsc-dev mailto:petsc-dev

Re: [petsc-dev] PDIPDM questions

Pierre, ex1.c is a toy test inherited from previous experimental pdipm. We simply sent centralised data to all other processes to test pdipm. It is not intended for performance. We should add more tests. Current pdipm is not fully developed yet, especially its linear solver may fail to handle

Re: [petsc-dev] TAOPDIPM

Pierre, We have fixed this bug in petsc-release (maint branch). Thanks for you report. Hong From: petsc-dev on behalf of Pierre Jolivet Sent: Wednesday, August 5, 2020 2:10 AM To: Abhyankar, Shrirang G Cc: PETSc Subject: Re: [petsc-dev] TAOPDIPM Sorry for

Re: [petsc-dev] sm_70

On Sep 25, 2020, at 8:09 PM, Barry Smith mailto:bsm...@petsc.dev>> wrote: Configure by default should find out the available GPU and build for that sm_* it should not require the user to set this (how the heck is the user going to know what to set?) If I remember correctly there is a

Re: [petsc-dev] problem with MatSeqAIJCUSPARSEILUAnalysisAndCopyToGPU

On Dec 22, 2020, at 3:38 PM, Mark Adams mailto:mfad...@lbl.gov>> wrote: I am MPI serial LU solving a smallish matrix (2D, Q3, 8K equations) on a Summit node (42 P9 cores, 6 V100 GPUs) using cuSparse and Kokkos kernels. The cuSparse performance is terrible. I solve the same TS problem in MPI

Re: [petsc-dev] Can I call PetscSectionAddDof(s, p, ndof) at a shred 'p' by more than one processors?

, 2020 1:56 PM To: Lawrence Mitchell Cc: Zhang, Hong ; petsc-dev Subject: Re: [petsc-dev] Can I call PetscSectionAddDof(s, p, ndof) at a shred 'p' by more than one processors? On Wed, Nov 18, 2020 at 2:19 PM Lawrence Mitchell mailto:we...@gmx.li>> wrote: > On 18 Nov 2020, at 15:26, Zh

[petsc-dev] Can I call PetscSectionAddDof(s, p, ndof) at a shred 'p' by more than one processors?

Matt or Jed, Can I call PetscSectionAddDof(s,p,ndof) at a shred 'p' by more than one processors? For example, if (rank == 0) { PetscSectionAddDof(s,p,1) ; } else if (rank == 1) { PetscSectionAddDof(s,p,2) ; } Then, at shared 'p', section 's' has dof=3? I did a test, and got an error

Re: [petsc-dev] About parallel of ILU

Just in case you want to try the exact algorithm you attached, it can be used in PETSc with -pc_type hypre -pc_hypre_type euclid Hong (Mr.) > On Jan 12, 2021, at 8:42 AM, Chen Gang <569615...@qq.com> wrote: > >  > Dear Professor, > > I'm writing about this mail about the ILU algorithm in

Re: [petsc-dev] obscure changes in TSGetStages_Theta

Done. Please check https://gitlab.com/petsc/petsc/-/merge_requests/3583 Sorry for any disturbance it caused. It was for the convenience of the adjoint implementation. The stages returned by TSGetStages_Theta currently do not reflect the true stages associated with these methods. The endpoint

Re: [petsc-dev] obscure changes in TSGetStages_Theta

lly do not need a RestoreStages if you use a scratch Vec stages[2]; in TS_theta, and pass it back with TSGetStages_Theta. I understand PETSc philosophy is that every Get should have a Restore method, but is this really necessary for TSGetStages? Il giorno sab 23 gen 2021 alle ore 21:05 Zhang

Re: [petsc-dev] "Search" does not work in the testing system?

make PETSC_DIR=/Users/kongf/projects/moose4/petsc PETSC_ARCH=arch-darwin-c-debug -f gmakefile test search='snes_tutorials-ex1_*' or make PETSC_DIR=/Users/kongf/projects/moose4/petsc PETSC_ARCH=arch-darwin-c-debug -f gmakefile test globsearch='snes_tutorials-ex1_*’ Hong (Mr.) > On Jan 27,

Re: [petsc-dev] DMNetwork static sizing

Shri, You designed this approach. Is it intended or out of implementation convenience at the time? Hong From: petsc-dev on behalf of Matthew Knepley Sent: Monday, April 5, 2021 5:47 AM To: PETSc Subject: [petsc-dev] DMNetwork static sizing Dowe really need a

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

On Mar 12, 2021, at 5:25 PM, Barry Smith mailto:bsm...@petsc.dev>> wrote: Jed, Thanks for the insight. Maybe Hong and his Ellpack format? Or his independent set algorithm? These two features are currently functional on NVIDIA GPUs. Neither needs extensive development or

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