Re: [petsc-users] Nodes coordinates in distributed dmplex

Hi, when looping over the nodal coordinates, is there a way to get the corresponding DOF in the index set for the DM Field(s) that is used in the residual vector? I would like to update the jacobian/residual entries obtained from DMCreateFieldIS that correspond to particular nodal coordinates that

Re: [petsc-users] DMPlexSetRefinementFunction

/8ca66eb7de95b82f7969984bab6aacada6626b1d/ctetgen.c?at=master&fileviewer=file-view-default#ctetgen.c-22245 [image: Screen Shot 2019-04-13 at 4.50.06 AM.png] On Tue, Jan 8, 2019 at 11:29 AM David Fuentes wrote: > sounds great! i've been working out of this guy - > https://github.com/fuent

Re: [petsc-users] PetscFEIntegrateBdResidual_Basic

:33 AM, David Fuentes wrote: > Thanks! will give that a try! > df > > On Mon, Nov 20, 2017 at 11:23 AM, Matthew Knepley > wrote: > >> On Mon, Nov 20, 2017 at 12:20 PM, David Fuentes >> wrote: >> >>> Thanks for the quick reply. Indeed it does work like

Re: [petsc-users] PetscFEIntegrateBdResidual_Basic

Thanks! will give that a try! df On Mon, Nov 20, 2017 at 11:23 AM, Matthew Knepley wrote: > On Mon, Nov 20, 2017 at 12:20 PM, David Fuentes > wrote: > >> Thanks for the quick reply. Indeed it does work like this. I have added a >> location dependence on the boundary to

Re: [petsc-users] PetscFEIntegrateBdResidual_Basic

stants[**3**] ; * *}* *} * On Mon, Nov 20, 2017 at 11:02 AM, Matthew Knepley wrote: > On Mon, Nov 20, 2017 at 11:46 AM, David Fuentes > wrote: > >> *Is there a way to pass the boundary set id to the function pointers for >> the residual evaluation on t

[petsc-users] PetscFEIntegrateBdResidual_Basic

*Is there a way to pass the boundary set id to the function pointers for the residual evaluation on the boundary ?* *https://bitbucket.org/petsc/petsc/src/d89bd21cf2b5366df29efb6006298d2bc22fb509/src/dm/dt/interface/dtfe.c?at=master&fileviewer=file-view-default#dtfe.c-4245

[petsc-users] ex12 poisson solver

Hi, I'm trying to use petsc 3.8.0 with ex12.c example to setup a poisson solver: http://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex12.c.html I seem to be getting zeros in my jacobian with this example? I attached a debugger and the assembly routines seems ok... but am getti

[petsc-users] PetscFEIntegrateResidual_OpenCL w/ viennacl

Hi, when using the snes/ex12 example https://bitbucket.org/petsc/petsc/src/f5476a2b443e0eedb22d31cb1b2d85b9b918f73f/src/snes/examples/tutorials/ex12.c?at=master with -variable_coefficient field -petscfe_type opencl -mat_petscfe_type opencl and -dm_vec_type viennacl -dm_mat_type seqaijviennacl

Re: [petsc-users] petscfe_type opencl, variable_coefficient field

Thanks. Also, the physics seems to be controlled by the "op" variable? Is there an interface to change the physics from the user code ? https://bitbucket.org/petsc/petsc/src/fb3a4ffdea0449562fb0f58dad4b44552b6d3589/src/dm/dt/interface/dtfe.c?at=master#cl-5028 switch (op) { case LAPLACIAN:if

[petsc-users] petscfe_type opencl, variable_coefficient field

Hi, Building off of snes/ex12, I'm trying to use -variable_coefficient field with -petscfe_type opencl -mat_petscfe_type opencl constant coefficients "-variable_coefficient none" works fine, but I am getting NaN in my residual vector for spatially varying coefficients. I tried changing N_t m

[petsc-users] CPU utilization during GPU solver

re 6 Tesla M2070 on this box, but i'm only running on one of them. On Sat, Nov 17, 2012 at 2:42 PM, Matthew Knepley wrote: > On Sat, Nov 17, 2012 at 3:05 PM, David Fuentes > wrote: > > Thanks Jed. > > I was trying to run it in dbg mode to verify if all significant parts

[petsc-users] CPU utilization during GPU solver

it 72 point blinking red, sorry.) > On Nov 17, 2012 1:41 PM, "David Fuentes" wrote: > >> thanks Matt, >> >> My log summary is below. >> >> >> *

[petsc-users] CPU utilization during GPU solver

-lm -lm -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lpthread -lrt -lgcc_s -ldl - On Sat, Nov 17, 2012 at 11:02 AM, Matthew Knepley wrote: > On Sat, Nov 17, 2012 at 10:50 AM, David Fuentes > wrote: > > Hi, > > > > I&#x

[petsc-users] CPU utilization during GPU solver

Hi, I'm using petsc 3.3p4 I'm trying to run a nonlinear SNES solver on GPU with gmres and jacobi PC using VECSEQCUSP and MATSEQAIJCUSP datatypes for the rhs and jacobian matrix respectively. When running top I still see significant CPU utilization (800-900 %CPU) during the solve ? possibly from so

[petsc-users] ex52_integrateElement.cu

.121284 0.0692962 0.118305 0.126986 -0.106051 On Wed, Apr 25, 2012 at 1:27 PM, Matthew Knepley wrote: > On Wed, Apr 25, 2012 at 2:06 PM, Matthew Knepley wrote: > >> On Wed, Apr 25, 2012 at 1:50 PM, David Fuentes wrote: >> >>> I'm pretty sure I pulled the latest on

[petsc-users] ex52_integrateElement.cu

identifier = 'float2' On Mon, Apr 2, 2012 at 9:37 PM, Matthew Knepley wrote: > On Wed, Mar 28, 2012 at 6:42 PM, Matthew Knepley wrote: > >> On Wed, Mar 28, 2012 at 6:25 PM, David Fuentes wrote: >> >>> Yes. This would work. >>> I had trouble compil

[petsc-users] ex52_integrateElement.cu

vecType f1_laplacian(float thermalconductivity, float u[], vecType gradU[], int comp) { + return thermalconductivity*gradU[comp]; } Thanks, David On Mon, Apr 2, 2012 at 9:37 PM, Matthew Knepley wrote: > On Wed, Mar 28, 2012 at 6:42 PM, Matthew Knepley wrote: > >> On Wed, M

[petsc-users] ex52_integrateElement.cu

thank you Matt, David On Mon, Apr 2, 2012 at 9:37 PM, Matthew Knepley wrote: > On Wed, Mar 28, 2012 at 6:42 PM, Matthew Knepley wrote: > >> On Wed, Mar 28, 2012 at 6:25 PM, David Fuentes wrote: >> >>> Yes. This would work. >>> I had trouble compiling in si

[petsc-users] ex52_integrateElement.cu

Yes. This would work. I had trouble compiling in single precision using the some of the external package options I was using for double. On Wed, Mar 28, 2012 at 4:57 PM, Matthew Knepley wrote: > On Wed, Mar 28, 2012 at 4:12 PM, David Fuentes wrote: > >> works! >> >

[petsc-users] ex52_integrateElement.cu

atch -gpu GPU layout grid(1,2,1) block(3,1,1) with 1 batches N_t: 3, N_cb: 1 Residual: Vector Object: 1 MPI processes type: seq -0.25 -0.5 0.25 -0.5 -1 0.5 0.25 0.5 0.75 SCRGP2$ ./ex52 -dim 2 -compute_function -show_residual -batch Residual: Vector Object: 1 MPI processes type: seq -0.25 -0.5

[petsc-users] ex52_integrateElement.cu

sure. will do. On Wed, Mar 28, 2012 at 1:23 PM, Matthew Knepley wrote: > On Wed, Mar 28, 2012 at 1:14 PM, David Fuentes wrote: > >> thanks! its running, but I seem to be getting different answer for >> cpu/gpu ? >> i had some floating point problems on this Tes

[petsc-users] ex52_integrateElement.cu

CRGP2$ ./ex52 -dim 2 -compute_function -show_residual -batch Residual: Vector Object: 1 MPI processes type: seq -0.25 -0.5 0.25 -0.5 -1 0.5 0.25 0.5 0.75 On Wed, Mar 28, 2012 at 11:55 AM, Matthew Knepley wrote: > On Wed, Mar 28, 2012 at 11:45 AM, David Fuentes wrote: > >> The example

[petsc-users] ex52_integrateElement.cu

WORLD, 35) - process 0 On Tue, Mar 27, 2012 at 8:37 PM, Matthew Knepley wrote: > On Tue, Mar 27, 2012 at 2:10 PM, Blaise Bourdin wrote: > >> >> On Mar 27, 2012, at 1:23 PM, Matthew Knepley wrote: >> >> On Tue, Mar 27, 2012 at 12:58 PM, David Fuentes > gmail.c

[petsc-users] ex52_integrateElement.cu

apps/PETSC/petsc-dev/config/PETSc/FEM.py", line 440, in getComputationTypes vecType.type = self.Cxx.typeMap['float'+str(dim)] KeyError: 'float3' On Tue, Mar 27, 2012 at 2:10 PM, Blaise Bourdin wrote: > > On Mar 27, 2012, at 1:23 PM, Matthew Knepley wr

[petsc-users] ex52_integrateElement.cu

Hi, I had a question about the status of example 52. http://petsc.cs.iit.edu/petsc/petsc-dev/file/a8e2f2c19319/src/snes/examples/tutorials/ex52.c http://petsc.cs.iit.edu/petsc/petsc-dev/file/a8e2f2c19319/src/snes/examples/tutorials/ex52_integrateElement.cu Can this example be used with a DM obj

[petsc-users] petsc and goto blas

configure/install mpich to communicate over it accordingly ? either way, thanks! df On Mon, Aug 29, 2011 at 7:40 PM, Barry Smith wrote: > > On Aug 29, 2011, at 5:49 PM, David Fuentes wrote: > >> Is there any reason why petsc compiled to link with goto blas shared >> libraries

[petsc-users] petsc and goto blas

Is there any reason why petsc compiled to link with goto blas shared libraries would not run multi-threaded by default ? I've set (OMP/GOTO)_NUM_THREADS=8 but when I call dgemm from PETSc I can't seem to get it to run on multiple cores (<= 100% cpu usage from top). I checked and the test routines

Convex optimization with linear constraint?

Liu, Unless I'm missing something, I don't think you will directly find what you are looking for. You will prob have to solve A * vec_x = vec_b directly in your FormObjective function then use an adjoint method or something to compute your gradient directly in your FormGradient routine.

MatMatMult_MPIDense_MPIDense() works currently?

py the data into new matrix. > Thanks. > > Regards, > > Yujie > > > On Sun, Apr 5, 2009 at 1:48 PM, David Fuentes wrote: > Hi Yujie, > > > as a work around have you tried converting your dense > matrices to aij format and using Mat

MatMatMult_MPIDense_MPIDense() works currently?

also, MatMatMult_MPIAIJ_MPIDense() and MatMatMult_MPIDense_MPIAIJ() seem to work if you don't want/need to convert both matrices. df On Sun, 5 Apr 2009, David Fuentes wrote: > Hi Yujie, > > > as a work around have you tried converting your dense > matrices to

MatMatMult_MPIDense_MPIDense() works currently?

Hi Yujie, as a work around have you tried converting your dense matrices to aij format and using MatMatMult_MPIAIJ_MPIAIJ()?? df On Fri, 3 Apr 2009, Yujie wrote: > > Dear Barry: > > I am trying to debug the codes you have written with ex123.c. After > commenting the error output >

PetscMalloc petsc-3.0.0-p4

; 2) are you completely sure BOTH things happens, I mean... that malloc > returns null AND the error code is zero? > > > On Mon, Mar 23, 2009 at 7:49 PM, David Fuentes wrote: >> In 3.0.0-p4 >> >> PetscMalloc doesn't seem to return an error code if the requested memo

PetscMalloc petsc-3.0.0-p4

In 3.0.0-p4 PetscMalloc doesn't seem to return an error code if the requested memory wasn't allocated ? Is this correct ? I'm trying to allocate a dense matrix for which there was not enough memory and PetscMalloc is returning a null pointer but no errorcode to catch. which is causing seg faults

multiple rhs

On Sat, 14 Mar 2009, Hong Zhang wrote: > >> Very Many Thanks for your efforts on this Barry. The PLAPACK >> website looks like it hasn't been updated since 2007. Maybe PLAPACK >> is in need of some maintenance? You said "nonsquare", is plapack working >> for you for square matrices ? > > Yes, it

Performance of MatMatSolve

+00 0.0 3.1e+06 2.3e+03 1.2e+02 81 0 96 6 0 86 0 99 6 6 0 -------- > On Sat, 14 Mar 2009, David Fuentes wrote: > >> Thanks a lot Hong, >> >> The switch definitely seemed to balance the load during the SuperLU >> matmatsolve. >&

Performance of MatMatSolve

symbolic factorization > in the latest release. > > Let us know what you get, > > Hong > > On Fri, 13 Mar 2009, David Fuentes wrote: > >> >> The majority of time in my code is spent in the MatMatSolve. I'm running >> MatMatSolve in parallel usi

multiple rhs

Very Many Thanks for your efforts on this Barry. The PLAPACK website looks like it hasn't been updated since 2007. Maybe PLAPACK is in need of some maintenance? You said "nonsquare", is plapack working for you for square matrices ? thanks again, df >> >> >> >> [0]PETSC ERROR: -

Performance of MatMatSolve

a problem with the matrices that I'm passing in? thank you, David Fuentes

multiple rhs

t; >>> df >>> >>> On Thu, 12 Mar 2009, Matthew Knepley wrote: >>> >>> You can try using a sparse direct solver like MUMPS instead of PETSc LU. >>>> >>>> Matt >>>> >>>> On Thu, Mar 12, 2009 at 9:17 AM, D

multiple rhs

gt;> On Thu, 12 Mar 2009, Matthew Knepley wrote: >>> >>> You can try using a sparse direct solver like MUMPS instead of PETSc LU. >>>> >>>> Matt >>>> >>>> On Thu, Mar 12, 2009 at 9:17 AM, David Fuentes >>>> wrote: &

parallel MatMatMult

MatMatMult(X,Y,...,...,Z) where X is MPIDENSE and Y is MPIAIJ seems to work but when X is MPIAIJ and Y is MPIDENSE doesn't ? says its not supported. there seems to be all permuations in the source MatMatMult_MPIAIJ_MPIDense MatMatMult_MPIDense_MPIAIJ MatMatMult_MPIAIJ_MPIAIJ MatMatMult_MPI

multiple rhs

gt; Matt > > On Thu, Mar 12, 2009 at 9:17 AM, David Fuentes wrote: > >> Thanks Hong, >> >> The complete error message is attached. I think I just had too big >> of a matrix. The matrix i'm trying to factor is 327680 x 327680 >> >

multiple rhs

; > Hong > > On Wed, 11 Mar 2009, David Fuentes wrote: > >> >> Hello, >> >> I have a sparse matrix, A, with which I want to solve multiple right hand >> sides >> with a direct solver. Is this the correct call sequence ? >> >> >>

multiple rhs

form my machine or if I just have bug in the call sequence. thank you, David Fuentes

Petsc Vec

Hello, I would like to write a Vec to a file and read it in at a later point in time. Are there any utilities in Petsc to do this? thank you, David Fuentes

MPI_Send and PetscScalar

Hello, I need to send a single PetscScalar Value from one processor to another. I want to use MPI_Send. Is MPIU_SCALAR the correct MPI_Datatype to MPI_Send a PetscScalar value between processors? thank you, David Fuentes

MPI forum similar to PETSc for MPI problems?

Hello, I had a similiar problem, I used the "sequence" statement in the type definition and it worked for me. type particle sequence real x,y,z integer number end type particle good luck, david On Sat, 20 Jan 2007, Ben Tay wrote: > Hi, > > I've encountered some MPI programming problems.

profiling

I would like to create two communicator subgroups of PETSC_COMM_WORLD. Is it possible to use the petsc profiling utilities to profile the two communicator sub-groups individually? thank you, David Fuentes