Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

s/local/spack/software/gcc-7.5.0/cuda-10.1.243-v4ymjqcrr7f72qfiuzsstuy5jiajbuey/lib64/stubs > -lcudart -lcufft -lcublas -lcusparse -lcusolver -lcurand -lcuda > > > You can see the `stubs` directory is not in rpath. We took a lot of > effort to achieve that. You need to double check the reason. > &g

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

to search for "stubs" since the system might have the correct ones in other places. Should not I do a batch compiling? Thanks, Fande On Wed, Jan 26, 2022 at 1:49 PM Fande Kong wrote: > Yes, please see the attached file. > > Fande > > On Wed, Jan 26, 2022 at 11:4

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

gt;> -L/apps/local/spack/software/gcc-7.5.0/cuda-10.1.243-v4ymjqcrr7f72qfiuzsstuy5jiajbuey/lib64/stubs >> -lcuda >> >> good does not. >> >> Try removing the stubs directory and -lcuda from the bad >> $PETSC_ARCH/lib/petsc/conf/variables and likely the bad will start working. >&g

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

gt; $PETSC_ARCH/lib/petsc/conf/variables and likely the bad will start working. > It seems I still got the same issue after removing stubs directory and -lcuda. Thanks, Fande > > Barry > > I never liked the stubs stuff. > > On Jan 25, 2022, at 11:29 PM, Fande Kong wrote: &

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

2021 + Config: fix CUDA library and header dirs :04 04 187c86055adb80f53c1d0565a704fec43a96 ea1efd7f594fd5e8df54170bc1bc7b00f35e4d5f M config Started from this commit, and GPU did not work for me on our HPC Thanks, Fande On Tue, Jan 25, 2022 at 7:18 PM Fande Kong wrote: > >

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

> (Jacob Fai - booss - oh - vitch) > > On Jan 21, 2022, at 12:01, Fande Kong wrote: > > Thanks Jacob, > > On Thu, Jan 20, 2022 at 6:25 PM Jacob Faibussowitsch > wrote: > >> Segfault is caused by the following check at >> src/sys/objects/device/impls/cupm/cupmdevic

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

possible to run a solve > that doesn't use a GPU in PETSC_ARCH that supports GPUs, regardless of > whether a GPU is actually present. > > Fande Kong writes: > > > I spoke too soon. It seems that we have trouble creating cuda/kokkos vecs > > now. Got Segmentation

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

e/sawtooth/moosegpu/scripts/../libmesh/installed/include/libmesh/petsc_vector.h:693 On Thu, Jan 20, 2022 at 1:09 PM Fande Kong wrote: > Thanks, Jed, > > This worked! > > Fande > > On Wed, Jan 19, 2022 at 11:03 PM Jed Brown wrote: > >> Fande Kong writes: >

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

Thanks, Jed, This worked! Fande On Wed, Jan 19, 2022 at 11:03 PM Jed Brown wrote: > Fande Kong writes: > > > On Wed, Jan 19, 2022 at 11:39 AM Jacob Faibussowitsch < > jacob@gmail.com> > > wrote: > > > >> Are you running on login nodes or

Re: [petsc-users] Does mpiaijkok intend to support 64-bit integers?

Thanks, Mark, PETSc-main has no issue. Fande On Thu, Jan 20, 2022 at 9:14 AM Fande Kong wrote: > > > On Thu, Jan 20, 2022 at 6:49 AM Mark Adams wrote: > >> Humm, I was not able to reproduce this on my Mac. Trying Crusher now. >> Are you using main? or even a rec

Re: [petsc-users] Does mpiaijkok intend to support 64-bit integers?

in mpiaijkok. > > Thanks, > Mark > > On Thu, Jan 20, 2022 at 12:12 AM Fande Kong wrote: > >> Hi All, >> >> It seems that mpiaijkok does not support 64-bit integers at this time. Do >> we have any motivation for this? Or Is it just a bug? >> >

[petsc-users] Does mpiaijkok intend to support 64-bit integers?

Hi All, It seems that mpiaijkok does not support 64-bit integers at this time. Do we have any motivation for this? Or Is it just a bug? Thanks, Fande petsc/src/mat/impls/aij/mpi/kokkos/mpiaijkok.kokkos.cxx(306): error: a value of type "MatColumnIndexType *" cannot be assigned to an entity of

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

ic error > code (cudaErrorStubLibrary) for it. > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > > On Jan 19, 2022, at 12:07, Fande Kong wrote: > > Thanks, Jacob, and Junchao > > The log was attached. I am using Sawtooth at INL > https:

[petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

Hi All, Upgraded PETSc from 3.16.1 to the current main branch. I suddenly got the following error message: 2d_diffusion]$ ../../../moose_test-dbg -i 2d_diffusion_test.i -use_gpu_aware_mpi 0 -gpu_mat_type aijcusparse -gpu_vec_type cuda -log_view [0]PETSC ERROR: - Error

Re: [petsc-users] Downloaded superlu_dist could not be used. Please check install in $PREFIX

> On Tue, 18 Jan 2022, Xiaoye S. Li wrote: > > > There was a merge error in the master branch. I fixed it today. Not sure > > whether that's causing your problem. Can you try now? > > > > Sherry > > > > On Mon, Jan 17, 2022 at 11:55 AM Fande Kong wrote: &

Re: [petsc-users] Finite difference approximation of Jacobian

This is something I almost started a while ago. https://gitlab.com/petsc/petsc/-/issues/852 It would be a very interesting addition to us. Fande > On Jan 12, 2022, at 12:04 AM, Barry Smith wrote: > >  > Why does it need to handle values? > >> On Jan 12, 2022, at 12:43 AM, Jed Brown

Re: [petsc-users] Error running make on MUMPS

On Thu, Nov 11, 2021 at 1:59 PM Matthew Knepley wrote: > On Thu, Nov 11, 2021 at 3:44 PM Fande Kong wrote: > >> Thanks Matt, >> >> I understand completely, the actual error should be >> >> " >> ln -s libHYPRE_parcsr_ls-2.20.0.so libHYPRE_parcsr_ls

Re: [petsc-users] Error running make on MUMPS

.so", and then second try would see that ‘libHYPRE_parcsr_ls.so" already existed. Thanks, Fande On Thu, Nov 11, 2021 at 1:29 PM Matthew Knepley wrote: > On Thu, Nov 11, 2021 at 3:25 PM Fande Kong wrote: > >> Thanks, Satish >> >> "--with-make-np=1&

Re: [petsc-users] Error running make on MUMPS

> > Barry > > > On Nov 9, 2021, at 6:10 PM, Fande Kong wrote: > > Hi All, > > We encountered a configuration error when running the PETSc > configuration on a HPC system. Went through the log file, but could not > find much. The log file was attached. > > Any thoughts? > > Thanks for your help, as always. > > Fande > > > > > > > > > >

Re: [petsc-users] MatZeroRows changes my sparsity pattern

"if (a->keepnonzeropattern)" branch does not change ilen so that A->ops->assemblyend will be fine. It would help if you made sure that elements have been inserted for these rows before you call MatZeroRows. However, I am not sure it is necessary to call A->ops->assemblyend if we already require

Re: [petsc-users] MUMPS failure

There are some statements from MUMPS user manual http://mumps.enseeiht.fr/doc/userguide_5.3.5.pdf " A full 64-bit integer version can be obtained compiling MUMPS with C preprocessing flag -DINTSIZE64 and Fortran compiler option -i8, -fdefault-integer-8 or something equivalent depending on your

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

3-10/handle-pie-flag-conda/release *and send its > configure.log if it fails. > >Thanks > > Barry > > > On Mar 10, 2021, at 5:59 PM, Fande Kong wrote: > > Do not know what the fix should look like, but this works for me > > > @staticmethod > @@

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

output.find('argument unused') >= 0 or output.find('not supported') >= 0 or # When checking for the existence of 'attribute' output.find('is unsupported and will be skipped') >= 0 or Thanks, Fande On Wed, Mar 10, 2021 at 4:21 PM Fande Kong wrote: > > > On

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

c/lib -lmpi -lpmpi" > MPI can not generate an executable because we took out "-pie". Thanks, Fande > > etc.. [don't know if you really need LDFLAGS options] > > Satish > > On Wed, 10 Mar 2021, Fande Kong wrote: > > > I guess it was encoded in mpic

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

Rejecting C linker flag -dynamiclib -single_module due to > > ld: warning: -pie being ignored. It is only used when linking a main > executable > > This is the correct link command for the Mac but it is being rejected due > to the warning message. > Could we somehow sk

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

testpetsc/lib > -L/Users/kongf/miniconda3/envs/testpetsc/lib > > Does conda compiler pick up '-pie' from this env variable? If so - perhaps > its easier to just modify it? > > Or is it encoded in mpicc wrapper? [mpicc -show] > > Satish > > On Wed, 10 Mar 2021, Fande Kong

Re: [petsc-users] PetscAllreduceBarrierCheck is valgrind clean?

> > Barry > > > > > > > On Jan 13, 2021, at 12:32 PM, Fande Kong wrote: > > > > Hi All, > > > > I ran valgrind with mvapich-2.3.5 for a moose simulation. The > motivation was that we have a few non-deterministic parallel simulati

[petsc-users] PetscAllreduceBarrierCheck is valgrind clean?

Hi All, I ran valgrind with mvapich-2.3.5 for a moose simulation. The motivation was that we have a few non-deterministic parallel simulations in moose. I want to check if we have any memory issues. I got some complaints from PetscAllreduceBarrierCheck Thanks, Fande ==98001== 88 (24

Re: [petsc-users] counter->tag = *maxval - 128

ot easy to debug. Thanks, Fande > > Barry > > > > On Jan 12, 2021, at 10:41 AM, Fande Kong wrote: > > Hi All, > > I am curious about why we subtract 128 from the max value of tag? Can we > directly use the max tag value? > > Thanks, > > Fande, &

[petsc-users] counter->tag = *maxval - 128

Hi All, I am curious about why we subtract 128 from the max value of tag? Can we directly use the max tag value? Thanks, Fande, PetscErrorCode PetscCommGetNewTag(MPI_Comm comm,PetscMPIInt *tag) { PetscErrorCode ierr; PetscCommCounter *counter; PetscMPIInt *maxval,flg;

Re: [petsc-users] valgrind with petscmpiexec

n Dec 15, 2020, at 1:23 AM, Barry Smith wrote: > > > > > > > > > No idea. Perhaps petscmpiexec could be modified so it only ran > valgrind on the first 10 ranks? Not clear how to do that. Or valgrind > should get a MR that removes this small arbitrary limitation on t

[petsc-users] valgrind with petscmpiexec

Hi All, I tried to use valgrind to check if the simulation is valgrind clean because I saw some random communication fails during the simulation. I tried this command-line petscmpiexec -valgrind -n 576 ../../../moose-app-oprof -i input.i -log_view -snes_view But I got the following error

[petsc-users] -snes_no_convergence_test was removed from PETSc?

Hi All, I can not find the actual implementation for that. And " -snes_no_convergence_test" does not impact anything for me. Thanks, Fande,

Re: [petsc-users] EPSMonitorSet

Oh, cool. Thanks, Jose, I will try that. Fande, On Mon, Aug 31, 2020 at 11:11 AM Jose E. Roman wrote: > Call EPSMonitorCancel() before EPSMonitorSet(). > Jose > > > > El 31 ago 2020, a las 18:33, Fande Kong escribió: > > > > Hi All, > > > >

[petsc-users] EPSMonitorSet

Hi All, There is a statement on API EPSMonitorSet: "Sets an ADDITIONAL function to be called at every iteration to monitor the error estimates for each requested eigenpair." I was wondering how to replace SLEPc EPS monitors instead of adding one? I want to use my monitor only. Thanks, Fande,

Re: [petsc-users] Using edge-weights for partitioning

I agreed, Barry. A year ago, I enabled edge-weights and vertex weights for only ParMETIS and PTScotch. I did not do the same thing for Chaco, Party, etc. It is straightforward to do that, and I could add an MR if needed. Thanks, Fande, On Sun, Aug 30, 2020 at 4:20 PM Barry Smith wrote: > >

Re: [petsc-users] Disable PETSC_HAVE_CLOSURE

est with a C compiler and it gets included in > C++ source. > > Fande Kong writes: > > > Hi All, > > > > We (moose team) hit an error message when compiling PETSc, recently. The > > error is related to "PETSC_HAVE_CLOSURE." Everything runs well if I am >

[petsc-users] Disable PETSC_HAVE_CLOSURE

Hi All, We (moose team) hit an error message when compiling PETSc, recently. The error is related to "PETSC_HAVE_CLOSURE." Everything runs well if I am going to turn this flag off by making the following changes: git diff diff --git a/config/BuildSystem/config/utilities/closure.py

Re: [petsc-users] ParMETIS vs. CHACO when no partitioning is made

For this particular case (one subdoanin), it may be easy to fix in petsc. We could create a partitioning index filled with zeros. Fande, On Mon, Aug 17, 2020 at 5:04 PM Fande Kong wrote: > IIRC, Chaco does not produce an arbitrary number of subdomains. The number > needs to be li

Re: [petsc-users] ParMETIS vs. CHACO when no partitioning is made

IIRC, Chaco does not produce an arbitrary number of subdomains. The number needs to be like 2^n. ParMETIS and PTScotch are much better, and they are production-level code. If there is no particular reason, I would like to suggest staying with ParMETIS and PTScotch. Thanks, Fande, On Fri, Aug

Re: [petsc-users] Only print converged reason when not converged

One alternative is to support a plugable KSP/SNESReasonView system. We then could hook up KSP/SNESReasonView_MOOSE. We could call our views from SNES/KSP"done"Solve as well if such a system is not affordable. What are the final functions we should call, where we guarantee SNES/KSP is already

Re: [petsc-users] Tough to reproduce petsctablefind error

e sense. >> >> *Chris Hewson* >> Senior Reservoir Simulation Engineer >> ResFrac >> +1.587.575.9792 >> >> >> On Mon, Jul 20, 2020 at 12:41 PM Mark Adams wrote: >> >>> >>> >>> On Mon, Jul 20, 2020 at 2:36 PM Fande Kong

Re: [petsc-users] Tough to reproduce petsctablefind error

The most frustrating part is that the issue is not reproducible. Fande, On Mon, Jul 20, 2020 at 12:36 PM Fande Kong wrote: > Hi Mark, > > Just to be clear, I do not think it is related to GAMG or PtAP. It is a > communication issue: > > Reran the same code, and I just go

Re: [petsc-users] Tough to reproduce petsctablefind error

ng GAMG. > > Chris: It sounds like you just have one matrix that you give to MUMPS. You > seem to be creating a matrix in the middle of your run. Are you doing > dynamic adaptivity? > > I think we generate unique tags for each operation but it sounds like > maybe a message is getting

Re: [petsc-users] Tough to reproduce petsctablefind error

ize integers do you use? > We are using 64-bit via "--with-64-bit-indices" I am trying to catch the cause of this issue by running more simulations with different configurations. Thanks, Fande, Thanks, > Mark > > On Mon, Jul 20, 2020 at 1:17 AM Fande Kong

Re: [petsc-users] Tough to reproduce petsctablefind error

Fande Kong wrote: > I am not entirely sure what is happening, but we encountered similar > issues recently. It was not reproducible. It might occur at different > stages, and errors could be weird other than "ctable stuff." Our code was > Valgrind clean since every PR in moo

Re: [petsc-users] Tough to reproduce petsctablefind error

I am not entirely sure what is happening, but we encountered similar issues recently. It was not reproducible. It might occur at different stages, and errors could be weird other than "ctable stuff." Our code was Valgrind clean since every PR in moose needs to go through rigorous Valgrind checks

[petsc-users] VecAssemblyEnd_MPI_BTS

Hi All, I was doing a large-scale simulation using 12288 cores and had the following error. The code ran fine using less than 12288 cores. Any quick suggestions to track down this issue? Thanks, Fande, [3342]PETSC ERROR: - Error Message

Re: [petsc-users] Make stream

Thanks, Jed, It is fascinating. I will try to check if I can do anything to have this kind of improvement as well. Thanks, Fande, On Fri, Jun 12, 2020 at 7:43 PM Jed Brown wrote: > Jed Brown writes: > > > Fande Kong writes: > > > >>> There's a lot more to A

Re: [petsc-users] Make stream

Thanks, Jed, On Tue, Jun 9, 2020 at 3:19 PM Jed Brown wrote: > Fande Kong writes: > > > Hi All, > > > > I am trying to interpret the results from "make stream" on two compute > > nodes, where each node has 48 cores. > > > > If my calculatio

Re: [petsc-users] Make stream

bit higher speedup > >Jacobian evaluations often have higher arithmetic intensity but they > may have MatSetValues() which is slow because no arithmetic intensity just > memory motion > Got it. Thanks, Fande, > >Barry > > > > On Jun 9, 2020, at 3:43 PM,

[petsc-users] Make stream

Hi All, I am trying to interpret the results from "make stream" on two compute nodes, where each node has 48 cores. If my calculations are memory bandwidth limited, such as AMG, MatVec, GMRES, etc.. The best speedup I could get is 16.6938 if I start from one core?? The speedup for function

Re: [petsc-users] SuperLU + GPUs

Hi Mark, This should help: -pc_factor_mat_solver_type superlu_dist Thanks, Fande > On Apr 19, 2020, at 9:41 AM, Mark Adams wrote: > >  >> >> >> > > --download-superlu --download-superlu_dist >> >> You are installing with both superlu and superlu_dist. To verify - remove >> superlu

Re: [petsc-users] AIJ vs BAIJ when using ILU factorization

bs=4. What happens if you try aij with > '-matload_block_size 1 -mat_no_inode true'? > Hong > > ------ > *From:* petsc-users on behalf of Fande > Kong > *Sent:* Monday, March 30, 2020 12:25 PM > *To:* PETSc users list > *Subject:* [pets

Re: [petsc-users] How to set an initial guess for TS

Thanks Jed, I will try and let you know, Thanks again! Fande, On Fri, Apr 3, 2020 at 4:29 PM Jed Brown wrote: > Oh, you just want an initial guess for SNES? Does it work to pull out the > SNES and SNESSetComputeInitialGuess? > > Fande Kong writes: > > > No. I am w

Re: [petsc-users] How to set an initial guess for TS

, Fande, On Fri, Apr 3, 2020 at 1:10 PM Jed Brown wrote: > This sounds like you're talking about a starting procedure for a DAE (or > near-singular ODE)? > > Fande Kong writes: > > > Hi All, > > > > TSSetSolution will set an initial condition for the current TSSol

[petsc-users] How to set an initial guess for TS

Hi All, TSSetSolution will set an initial condition for the current TSSolve(). What should I do if I want to set an initial guess for the current solution that is different from the initial condition? The initial guess is supposed to be really close to the current solution, and then will

[petsc-users] AIJ vs BAIJ when using ILU factorization

Hi All, There is a system of equations arising from the discretization of 3D incompressible Navier-Stoke equations using a finite element method. 4 unknowns are placed on each mesh point, and then there is a 4x4 saddle point block on each mesh vertex. I was thinking to solve the linear equations

Re: [petsc-users] Poor speed up for KSP example 45

In case someone wants to learn more about the hierarchical partitioning algorithm. Here is a reference https://arxiv.org/pdf/1809.02666.pdf Thanks Fande > On Mar 25, 2020, at 5:18 PM, Mark Adams wrote: > >  > > >> On Wed, Mar 25, 2020 at 6:40

Re: [petsc-users] Poor speed up for KSP example 45

On Wed, Mar 25, 2020 at 12:18 PM Mark Adams wrote: > Also, a better test is see where streams pretty much saturates, then run > that many processors per node and do the same test by increasing the nodes. > This will tell you how well your network communication is doing. > > But this result has a

Re: [petsc-users] Rebuilding libmesh

HI Lin, Do you have a home-brew installed MPI? " configure:6076: mpif90 -v >&5 mpifort for MPICH version 3.3 Reading specs from /home/lin/.linuxbrew/Cellar/gcc/5.5.0_7/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.5.0/specs " MOOSE environment package should carry everything you need: compiler,

Re: [petsc-users] --download-fblaslapack libraries cannot be used

A PR here https://gitlab.com/petsc/petsc/-/merge_requests/2612 On Wed, Mar 18, 2020 at 3:35 PM Fande Kong wrote: > Thanks, Satish, > > I keep investigating into this issue. Now, I have more insights. The > fundamental reason is that: Conda-compilers (installed by: conda install -c &

Re: [petsc-users] --download-fblaslapack libraries cannot be used

t arg in lflags: lflags.append(arg) self.logPrint('Found library directory: '+arg, 4, 'compilers') PETSc should treat these libs as system-level libs??? Have a branch here: Fande-Kong/skip_sysroot_libs_maint Any suggestion are appreciated, Thanks, Fande, On Tue, Mar 17,

Re: [petsc-users] --download-fblaslapack libraries cannot be used

Without touching the configuration file, the option: --download-hypre-configure-arguments='LIBS="-lmpifort -lgfortran"', also works. Thanks, Satish, Fande, On Sat, Mar 14, 2020 at 4:37 PM Fande Kong wrote: > OK. I finally got PETSc complied. > > "-lgfortran"

Re: [petsc-users] --download-fblaslapack libraries cannot be used

ay via petsc-users wrote: > > > > > Its the same location as before. For some reason configure is not > saving the relevant logs. > > > > > > I don't understand saveLog() restoreLog() stuff. Matt, can you check > on this? > > > > > > Satish &

Re: [petsc-users] --download-fblaslapack libraries cannot be used

r libraries check worked fine > without -lgfortran. > > > > But now - flbaslapack check is failing without it. > > > > To work arround - you can use option LIBS=-lgfortran > > > > Satish > > > > On Thu, 12 Mar 2020, Fande Kong wrote: > > >

Re: [petsc-users] Condition Number and GMRES iteration

On Fri, Feb 7, 2020 at 11:43 AM Victor Eijkhout wrote: > > > On , 2020Feb7, at 12:31, Mark Adams wrote: > > BTW, one of my earliest talks, in grad school before I had any real > results, was called "condition number does not matter” > > > After you learn that the condition number gives an

Re: [petsc-users] Condition Number and GMRES iteration

020 at 7:37 PM Fande Kong wrote: > >> Hi All, >> >> MOOSE team, Alex and I are working on some variable scaling techniques to >> improve the condition number of the matrix of linear systems. The goal of >> variable scaling is to make the diagonal of matrix as

[petsc-users] Condition Number and GMRES iteration

How to count eigenvalue clusters? For example, how many eigenvalue clusters we have in the attach image respectively? If you need more details, please let us know. Alex and I are happy to provide any details you are interested in. Thanks, Fande Kong,

Re: [petsc-users] Fwd: Running moose/scripts/update_and_rebuild_petsc.sh on HPC

t; > > > > > > The issue is: > > > > > > > > > > >>> > > > > > [Errno 13] Permission denied: '/pbs/SLB' > > > > > <<< > > > > > > > > > > Try removing this from PATH - a

[petsc-users] Fwd: Moose install troubleshooting help

Satish, Do you have any suggestions for this? Chris, It may be helpful if you could share the petsc configuration log file with us? Fande, -- Forwarded message - From: Chris Thompson Date: Tue, Dec 31, 2019 at 9:53 AM Subject: Moose install troubleshooting help To:

Re: [petsc-users] Running moose/scripts/update_and_rebuild_petsc.sh on HPC

Did you try "--with-batch=1"? A suggestion was proposed by Satish earlier (CCing here). Fande, On Wed, Dec 18, 2019 at 12:36 PM Tomas Mondragon < tom.alex.mondra...@gmail.com> wrote: > Yes, but now that I have tried this a couple of different ways with > different --with-mpiexec options, I am

Re: [petsc-users] Running moose/scripts/update_and_rebuild_petsc.sh on HPC

Are you able to run your MPI code using " mpiexec_mpt -n 1 ./yourbinary"? You need to use --with-mpiexec to specify what exactly command lines you can run, e.g., --with-mpiexec="mpirun -n 1". I am also CCing the email to PETSc guys who may know the answer to these questions. Thanks, Fande, On

Re: [petsc-users] Edge-cut information for CHACO

On Thu, Dec 5, 2019 at 12:34 PM Mark Adams wrote: > > > On Thu, Dec 5, 2019 at 11:20 AM Eda Oktay wrote: > >> Hello all, >> >> I am trying to find edge cut information of ParMETIS and CHACO. When I >> use ParMETIS, >> MatPartitioningViewImbalance(part,partitioning) >> works and it gives also

Re: [petsc-users] Select a preconditioner for SLEPc eigenvalue solver Jacobi-Davidson

ing a little bit the way in which ST is initialized, and > maybe we modify this as well. It is not decided yet. > > Jose > > > > El 5 nov 2019, a las 0:28, Fande Kong escribió: > > > > Thanks Jose, > > > > I think I understand now. Another question: what is t

Re: [petsc-users] Problem about Residual evaluation

On Mon, Apr 1, 2019 at 10:24 AM Matthew Knepley via petsc-users < petsc-users@mcs.anl.gov> wrote: > On Mon, Apr 1, 2019 at 10:22 AM Yingjie Wu via petsc-users < > petsc-users@mcs.anl.gov> wrote: > >> Dear PETSc developers: >> Hi, >> >> I've been using -snes_mf_operator and I've customized a

[petsc-users] How to use khash in PETSc?

Hi All, Since PetscTable will be replaced by khash in the future somehow, it is better to use khash for new implementations. I was wondering where I can find some examples that use khash? Do we have any petsc wrappers of khash? Thanks, Fande,

Re: [petsc-users] MPI Iterative solver crash on HPC

Hi Hong, According to this PR https://bitbucket.org/petsc/petsc/pull-requests/1061/a_selinger-feature-faster-scalable/diff Should we set the scalable algorithm as default? Thanks, Fande Kong, On Fri, Jan 11, 2019 at 10:34 AM Zhang, Hong via petsc-users < petsc-users@mcs.anl.gov> wrote:

Re: [petsc-users] Any reason for API change: DMGetWorkArray()

OK..., Thanks for the words. Fande, On Thu, Jan 10, 2019 at 3:36 PM Matthew Knepley wrote: > On Thu, Jan 10, 2019 at 5:31 PM Fande Kong wrote: > >> Thanks, Matt, >> >> And then what is the reason to remove PetscDataType? I am out of >> curiosity. >

[petsc-users] Any reason for API change: DMGetWorkArray()

Hi All, The second parameter is changed from PetscDataType to MPI_Datatype starting from PETSc-3.9.x Thanks, Fande Kong,

Re: [petsc-users] GAMG scaling

Sorry, hit the wrong button. On Fri, Dec 21, 2018 at 7:56 PM Fande Kong wrote: > > > On Fri, Dec 21, 2018 at 9:44 AM Mark Adams wrote: > >> Also, you mentioned that you are using 10 levels. This is very strange >> with GAMG. You can run with -info and grep

Re: [petsc-users] GAMG scaling

ed. I understand you may still >> want to reuse these data structures by default but for my simulation, the >> preconditioner is fixed and there is no reason to keep the "c->ptap". >> > >> It would be great, if we could have this optional functionality. >

Re: [petsc-users] GAMG scaling

lt but for my simulation, the preconditioner is fixed and there is no reason to keep the "c->ptap". It would be great, if we could have this optional functionality. Fande Kong, On Thu, Dec 20, 2018 at 9:45 PM Zhang, Hong wrote: > We use nonscalable implementation as default, and swit

Re: [petsc-users] Increasing norm with finer mesh

Use -ksp_view to confirm the options are actually set. Fande Sent from my iPhone > On Oct 16, 2018, at 7:40 PM, Ellen M. Price > wrote: > > Maybe a stupid suggestion, but sometimes I forget to call the > *SetFromOptions function on my object, and then get confused when > changing the

Re: [petsc-users] UCX ERROR KNEM inline copy failed

The error messages may have nothing to do with PETSc and MOOSE. It might be from a package for MPI communication https://github.com/openucx/ucx. I have no experiences on such things. It may be helpful to contact your HPC administer. Thanks, Fande, On Tue, Oct 2, 2018 at 9:24 AM Matthew

Re: [petsc-users] MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable

leaves) then A^2 is dense. > If you have particular stencils for A and P, then we could tell you the > fill ratio. > > Fande Kong writes: > > > Hi All, > > > > I was wondering how much memory is required to get PtAP done? Do you have > > any simple for

[petsc-users] MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable

Hi All, I was wondering how much memory is required to get PtAP done? Do you have any simple formula to this? So that I can have an estimate. Fande, [132]PETSC ERROR: - Error Message -- [132]PETSC ERROR: Out of

Re: [petsc-users] Implementation of Power Iteration method in PETSc

ut finite > element.Or am I still using a loop of KSP in PETSc?I'm a newcomer to petsc, > please give me some advice > > > Thanks, > > Yingjie > > > Fande Kong 于2018年9月27日周四 上午12:25写道： > >> I have implemented this algorithm in SLEPC. Take a look at this exa

Re: [petsc-users] Implementation of Power Iteration method in PETSc

I have implemented this algorithm in SLEPC. Take a look at this example http://slepc.upv.es/documentation/current/src/eps/examples/tutorials/ex34.c.html The motivation of the algorithm is also for neutron calculations (a moose-based application). Fande, On Wed, Sep 26, 2018 at 10:02 AM Yingjie

Re: [petsc-users] Error 404 for mhypre.c.html

ay/petsc (maint=) > $ git ls-files |grep mhypre.c > src/mat/impls/hypre/mhypre.c > > So URL should be: > > > http://www.mcs.anl.gov/petsc/petsc-current/src/mat/impls/hypre/mhypre.c.html#MatHYPRESetPreallocation > > Satish > > On Thu, 13 Sep 2018, Fande Kong wrote: &

[petsc-users] Error 404 for mhypre.c.html

http://www.mcs.anl.gov/petsc/petsc-current/src/mat/impls/aij/hypre/mhypre.c.html#MatHYPRESetPreallocation Fande

Re: [petsc-users] FIELDSPLIT fields

On Wed, Sep 5, 2018 at 9:54 AM Smith, Barry F. wrote: > > 2 should belong to one of the subdomains, either one is fine. > >Barry > > > > On Sep 5, 2018, at 10:46 AM, Rossi, Simone wrote: > > > > I’m trying to setup GASM, but I’m probably misunderstanding something. > > > > If I have this

Re: [petsc-users] Problem with SNES convergence

Hi Barry, I haven't had time to look into TS so far. But it is definitely interesting. One simple question would like this: If I have a simple loop for time steppers, and each step SNES is called. How hard to convert my code to use TS? Any suggestion? Where should I start from? Fande, On

Re: [petsc-users] Whether Petsc will deleted zero entries during the solve

This may help in this situation. http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatResetPreallocation.html Fande, On Thu, Jun 14, 2018 at 1:08 PM, Smith, Barry F. wrote: > >I am guessing your matrix has an "envelope" of nonzero values but the > first time you fill the

[petsc-users] Fwd: Installing PETSC manually.

Hi Satish, A MOOSE user has troubles to build Metis that is "downloaded" from a local directory. Do you have any idea? Vi, Could you share "configure.log" with PETSc team? Thanks, Fande, -- Forwarded message -- From: Vi Ha Date: Wed, Jun 6, 2018 at 11:00 AM Subject: Re:

Re: [petsc-users] SuperLU_dist bug with parallel symbolic factorisation

Hi Eric, I am curious if the parallel symbolic factoriation is faster than the sequential version? Do you have timing? Fande, On Tue, May 22, 2018 at 12:18 PM, Eric Chamberland < eric.chamberl...@giref.ulaval.ca> wrote: > > > On 22/05/18 02:03 PM, Smith, Barry F. wrote: > >> >> Hmm, why

Re: [petsc-users] Could not determine how to create a shared library!

--with-blaslapack-lib=-mkl -L' + os.environ['MKLROOT'] + '/lib/intel64 works. Fande, On Thu, May 3, 2018 at 10:09 AM, Satish Balay wrote: > Ok you are not 'building blaslapack' - but using mkl [as per > configure.log]. > > I'll have to check the issue. It might be something

Re: [petsc-users] Could not execute "['git', 'rev-parse', '--git-dir']"

The default git gives me: *Could not execute "['git', 'rev-parse', '--git-dir']"* when I am configuring PETSc. The manually loaded *gits* work just fine. Fande, On Wed, Apr 4, 2018 at 5:04 PM, Garvey, Cormac T wrote: > I though it was fixed, yes I will look into it

Re: [petsc-users] A bad commit affects MOOSE

On Tue, Apr 3, 2018 at 9:12 AM, Stefano Zampini wrote: > > On Apr 3, 2018, at 4:58 PM, Satish Balay wrote: > > On Tue, 3 Apr 2018, Kong, Fande wrote: > > On Tue, Apr 3, 2018 at 1:17 AM, Smith, Barry F. > wrote: > > > Each

Re: [petsc-users] slepc-master does not configure correctly

re > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> *Checking environment...Traceback (most recent call last): File > >>> "./configure", line 10, in > >>> execfile(os.path.join(os.path.dirname(__file__), 'config', > >>> 'configure.py')) File "./config/configure.py", line 206, in > >>> log.write('PETSc install directory: '+petsc.destdir)AttributeError: > PETSc > >>> instance has no attribute 'destdir'* > >>> > >>> > >>> > >>> SLEPc may be needed to synchronized for new changes in PETSc. > >>> > >>> Thanks, > >>> > >>> Fande Kong > >> > > > >

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