Re: [petsc-users] Not displaying petsc options with -help

at 7:13 PM To: "Abhyankar, Shrirang G" Cc: PETSc Users , "Mancinelli, Asher J" Subject: Re: [petsc-users] Not displaying petsc options with -help Check twice before you click! This email originated from outside PNNL. Change the value of PetscHelpPrintf() to do nothing be

[petsc-users] Not displaying petsc options with -help

I have an application where I set a bunch of application-specific options in PetscOptionsBegin/End and it uses the default PetscOptions database. When running the application with “-help” option all the application and PETSc options get displayed. Is there a way to suppress displaying PETSc

Re: [petsc-users] DMCreateSectionSF

Sorry, my bad. I had a stale branch. Thanks, Shri From: Matthew Knepley Date: Monday, April 6, 2020 at 12:59 PM To: "Abhyankar, Shrirang G" Cc: PETSc Users Subject: Re: [petsc-users] DMCreateSectionSF On Mon, Apr 6, 2020 at 12:13 PM Abhyankar, Shrirang G via petsc-users mailto:p

[petsc-users] DMCreateSectionSF

I am getting an error for DMCreateSectionSF() with latest petsc-master. I see a DMCreateDefaultSF in petscdm.h. Has DMCreateSectionSF been renamed to DMCreateDefaultSF? Thanks, Shri

Re: [petsc-users] Using PETSc with GPU supported SuperLU_Dist

I was using CUDA v10.2. Switching to 9.2 gives a clean make test. Thanks, Shri From: petsc-users on behalf of "Abhyankar, Shrirang G via petsc-users" Reply-To: "Abhyankar, Shrirang G" Date: Sunday, February 23, 2020 at 3:10 PM To: petsc-users , Junchao Zhang Subje

[petsc-users] Using PETSc with GPU supported SuperLU_Dist

Hi, I want to install PETSc with GPU supported SuperLU_Dist. What are the configure options I should be using? Thanks, Shri

Re: [petsc-users] Flagging the solver to restart

if the criteria are met, it'll move forward, if not, it'll engaged the routine TSRollBack(), which based on my understanding is the proper way yo flag the solver to recalculate n+1. Are you trying to do some kind of zero crossing event or root-finding here? If so, using

Re: [petsc-users] DMNetwork - how to interprete the arguments of DMNetworkSetSizes ?

From: petsc-users on behalf of "von Ramm, Alexander via petsc-users" Reply-To: "von Ramm, Alexander" Date: Thursday, November 7, 2019 at 11:12 AM To: "petsc-users@mcs.anl.gov" Subject: [petsc-users] DMNetwork - how to interprete the arguments of DMNetworkSetSizes ? Hello together, I'm

Re: [petsc-users] Problem with TS and SNES VI

uations (IFunction). I will try to implment your suggestions with SNESLineSearchSetPreCheck. This would mean I dont have to use SNESVISetVariableBounds at all, right? Von: Smith, Barry F. mailto:bsm...@mcs.anl.gov>> Gesendet: Dienstag, 6. August

Re: [petsc-users] Problem with TS and SNES VI

For problems with constraints on the states, I would recommend trying the event functionality, TSEvent, that allows detection and location of discrete events, such as one that you have in your problem. https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/TS/TSSetEventHandler.html. An

Re: [petsc-users] LU Performance

I believe standalone UMFPACK uses appropriate minimum degree (amd) ordering by default provided by package AMD. Use the option -pc_factor_mat_ordering_type amd to use the amd ordering. You can also try quotient minimum degree (qmd) ordering available in PETSc (-pc_factor_mat_ordering_type qmd)

Re: [petsc-users] DMNetwork in petsc4py

Justin, As far as I know, there are no petsc4py wrappers written yet for DMNetwork and I don’t think anyone is working on it currently. If you are planning to do it then go ahead and let us know what you need. Shri From: petsc-users on behalf of Justin Chang via petsc-users Reply-To:

Re: [petsc-users] Extremely slow DMNetwork Jacobian assembly

th, Barry F." wrote: > On May 8, 2019, at 9:53 PM, Abhyankar, Shrirang G via petsc-users wrote: > > > > From: Matthew Knepley > Date: Wednesday, May 8, 2019 at 9:29 PM > To: "Abhyankar, Shrirang G" > Cc: "Zh

Re: [petsc-users] Extremely slow DMNetwork Jacobian assembly

From: Matthew Knepley Date: Wednesday, May 8, 2019 at 9:29 PM To: "Abhyankar, Shrirang G" Cc: "Zhang, Hong" , Justin Chang , petsc-users Subject: Re: [petsc-users] Extremely slow DMNetwork Jacobian assembly On Wed, May 8, 2019 at 10:17 PM Abhyankar, Shrirang G via petsc

Re: [petsc-users] Extremely slow DMNetwork Jacobian assembly

From: petsc-users on behalf of "Zhang, Hong via petsc-users" Reply-To: "Zhang, Hong" Date: Wednesday, May 8, 2019 at 8:01 PM To: Justin Chang Cc: petsc-users Subject: Re: [petsc-users] Extremely slow DMNetwork Jacobian assembly Justin: Great, the issue is resolved. Why

Re: [petsc-users] Extremely slow DMNetwork Jacobian assembly

From: petsc-users on behalf of Matthew Knepley via petsc-users Reply-To: Matthew Knepley Date: Wednesday, May 8, 2019 at 7:46 AM To: Justin Chang Cc: petsc-users Subject: Re: [petsc-users] Extremely slow DMNetwork Jacobian assembly On Wed, May 8, 2019 at 4:45 AM Justin Chang via

Re: [petsc-users] Preconditioning systems of equations with complex numbers

Hi Justin, Typically, the power grid distribution systems have a radial structure (unless it is an urban area) that leads to a, more or less, staircase type matrix. So a MatLoad() or VecLoad() would presumably just just splits the stairs, akin to a 1-D PDE. However, as you pointed out, it

Re: [petsc-users] [TimeStepping] Eventhandler

h, Barry F. >>>Sent: Monday, February 4, 2019 9:53 PM >>>To: Abhyankar, Shrirang G >>>Cc: Huck, Moritz ; PETSc users list >>us...@mcs.anl.gov> >>>Subject: Re: [petsc-users] [TimeStepping] Eventhandler >>> >>> >>> Ahh, tha

Re: [petsc-users] Using same DMPlex for solving two different problems

On Apr 7, 2017, at 6:25 AM, Matthew Knepley <knep...@gmail.com<mailto:knep...@gmail.com>> wrote: On Thu, Apr 6, 2017 at 1:04 PM, Abhyankar, Shrirang G. <abhy...@anl.gov<mailto:abhy...@anl.gov>> wrote: I am solving a time-dependent problem using DMNetwork (uses DMPl

[petsc-users] Using same DMPlex for solving two different problems

I am solving a time-dependent problem using DMNetwork (uses DMPlex internally) to manage the network. To find the initial conditions, I need to solve a nonlinear problem on the same network but with different number of dofs on the nodes and edges. Question: Can I reuse the same DMNetwork (DMPlex)

Re: [petsc-users] Vec is locked read only

Use VecGetArrayRead instead of VecGetArray http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecGetArray Read.html Shri -Original Message- From: Rongliang Chen Date: Saturday, April 2, 2016 at 3:51 AM To: PETSc users list ,

Re: [petsc-users] petsc KLU

] petsc KLU Hi, You can find below the message from Shri. Best regards, Romain -Original Message- From: Abhyankar, Shrirang G. [mailto:abhy...@anl.gov] Sent: maandag 17 augustus 2015 18:21 To: Romain Thomas; Zhang, Hong Cc: petsc-users@mcs.anl.gov Subject: Re: [petsc-users] petsc KLU Romain

Re: [petsc-users] petsc KLU

Romain, I added the KLU interface to PETSc last year hearing the hype about KLU¹s performance from several power system folks. I must say that I¹m terribly disappointed! I did some performance testing of KLU on power grid problems (power flow application) last year and I got a similar

Re: [petsc-users] TSSolve problems

, Shrirang G. [mailto:abhy...@anl.gov] Sent: Tuesday, June 30, 2015 7:00 AM To: Li, Xinya Cc: petsc-users@mcs.anl.gov Subject: Re: [petsc-users] TSSolve problems Note also that the use of DMDA is incorrect in your example. DMDA is for managing structured grids, while your example application (power

Re: [petsc-users] How to disable KSP message

This seems to be a result of some print statement in GridPACK, not PETSc. Shri From: Jin, Shuangshuang shuangshuang@pnnl.govmailto:shuangshuang@pnnl.gov Date: Tuesday, July 14, 2015 at 10:55 AM To: petsc-users@mcs.anl.govmailto:petsc-users@mcs.anl.gov

Re: [petsc-users] TSSolve problems

Note also that the use of DMDA is incorrect in your example. DMDA is for managing structured grids, while your example application (power grid dynamics simulation) has an unstructured network. Using DMNetwork or DMPlex would be more appropriate. Shri -Original Message- From: barry smith

Re: [petsc-users] arkimex rejecting all dt in petsc 3.6.0

Can the DAE equation type be supplied via a run-time option? Shri -Original Message- From: barry smith bsm...@mcs.anl.gov Date: Thursday, June 18, 2015 at 11:08 AM To: Italo Tasso it...@tasso.com.br, Constantinescu, Emil M. emcon...@mcs.anl.gov Cc: petsc-users@mcs.anl.gov

Re: [petsc-users] DMNetwork usage example

From: Dharmendar Reddy dharmaredd...@gmail.com Date: Wednesday, April 8, 2015 at 11:04 PM To: hong zhang hzh...@mcs.anl.gov Cc: PETSc users list petsc-users@mcs.anl.gov Subject: Re: [petsc-users] DMNetwork usage example Hello, I have a few question regarding the usage. In

Re: [petsc-users] DMNetworkGetEdgeRange() in parallel

AM, Abhyankar, Shrirang G. abhy...@mcs.anl.govmailto:abhy...@mcs.anl.gov wrote: Miguel, One possible way is to store the global numbering of any edge/vertex in the component attached to it. Once the mesh gets partitioned, the components are also distributed so you can easily retrieve

Re: [petsc-users] DMNetworkGetEdgeRange() in parallel

...@gmail.commailto:salazardetr...@gmail.com, petsc-users@mcs.anl.govmailto:petsc-users@mcs.anl.gov petsc-users@mcs.anl.govmailto:petsc-users@mcs.anl.gov Subject: Re: [petsc-users] DMNetworkGetEdgeRange() in parallel On Wed, Feb 25, 2015 at 9:59 AM, Abhyankar, Shrirang G. abhy...@mcs.anl.govmailto:abhy...@mcs.anl.gov

Re: [petsc-users] DMNetworkGetEdgeRange() in parallel

Miguel, One possible way is to store the global numbering of any edge/vertex in the component attached to it. Once the mesh gets partitioned, the components are also distributed so you can easily retrieve the global number of any edge/vertex by accessing its component. This is what is done

Re: [petsc-users] DMNetworkGetEdgeRange() in parallel

of the vector? I think it would help to know what you want to accomplish. This is how you are proposing to do it.' If you just want to put data on edges, DMNetwork has a facility for that already. Thanks, Matt Miguel On Feb 23, 2015 8:08 AM, Abhyankar, Shrirang G. abhy

Re: [petsc-users] DMNetworkSetSizes called by all processors

Miguel, In this example the DM is created initially only on proc. 0. Once the DM gets partitioned (DMNetworkDistribute()), another DM is created that has the appropriate node,edge,component info on each processor. Shri From: Miguel Angel Salazar de Troya

[petsc-users] DMPlex and MatSetValuesLocal

Matt, Does MatSetValuesLocal work with a matrix that is created with DMPlex? Well, actually I am using DMNetwork. I am getting the following error because ISLocalToGlobalMapping mat-rmap-mapping and mat-cmap-mapping are not set on the matrix. Perhaps I am not setting up something correctly?

Re: [petsc-users] a simple question

http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecPointwiseDivide.html From: paul zhang paulhuaizh...@gmail.commailto:paulhuaizh...@gmail.com Date: Tue, 9 Dec 2014 11:47:09 -0500 To: PETSc users list petsc-users@mcs.anl.govmailto:petsc-users@mcs.anl.gov Subject: [petsc-users] a

Re: [petsc-users] Why does CHOLMOD solution time differs between PETSc and MATLAB?

I think this may have to do with the matrix reodering scheme. I think CHOLMOD, used by MATLAB backslash operator, uses AMD (approximate min. degree) ordering scheme by default. PETSc's default reordering scheme is nested dissection. For PETSc + MATLAB, use the option

Re: [petsc-users] PetscFunctionBegin, -malloc_dump and C++ classes with PETSc objects

The DM keeps track of the local vectors created by DMGetLocalVector(). So, if your routine gets called a million times with exactly one DMGetLocalVector() followed by one call to DMRestoreLocalVector(), then only one vector is created. Shri From: Miguel Angel Salazar de Troya

Re: [petsc-users] sundials results do not agree with beuler/rosw/pseudo

PETSc only supports the ODE solver (CVODE) from Sundials. Shri From: Gautam Bisht gbi...@lbl.govmailto:gbi...@lbl.gov Date: Mon, 3 Nov 2014 22:56:58 -0800 To: petsc-users@mcs.anl.govmailto:petsc-users@mcs.anl.gov Subject: [petsc-users] sundials results do not agree with beuler/rosw/pseudo Hi,

Re: [petsc-users] Cloning a DMNetwork

Miguel, I've added DMClone_Network to shri/clone-dmnetwork and next branch. Not that DMClone() creates a shallow copy of DMNetwork. If you change the values of the components in the cloned DM then those will also be reflected in the original DM (since they share the address space). Shri

Re: [petsc-users] Cloning a DMNetwork

There is no clone method implemented for DMNetwork yet. I'll work on it tomorrow. Thanks, Shri From: Miguel Angel Salazar de Troya salazardetr...@gmail.com Date: Tue, 21 Oct 2014 18:10:42 -0500 To: petsc-users@mcs.anl.gov petsc-users@mcs.anl.gov Subject: [petsc-users] Cloning a DMNetwork

Re: [petsc-users] DMPlex with spring elements

...@gmail.com wrote: I understand. Thanks a lot. Miguel On Fri, Sep 26, 2014 at 10:53 AM, Abhyankar, Shrirang G. abhy...@mcs.anl.gov wrote: What Matt is saying is that there are two interfaces in PETSc for setting the residual evaluation routine: i) SNESSetFunction takes in a function pointer

Re: [petsc-users] DMPlex with spring elements

for your responses. I'm assuming you suggested to use DMNetworkIsGhostVertex() and not modify its value for the case in which I were using the global vectors and not the local vectors, where it is possible, as Matt suggested. Miguel On Tue, Sep 30, 2014 at 11:22 AM, Abhyankar, Shrirang G. abhy

Re: [petsc-users] DMPlex with spring elements

...@gmail.com writes: On Thu, Sep 25, 2014 at 1:46 PM, Abhyankar, Shrirang G. abhy...@mcs.anl.gov wrote: You are right. The Jacobian for the power grid application is indeed non-symmetric. Is that a problem for your application? If you need a symmetric Jacobian, you can use the BC facility

Re: [petsc-users] DMPlex with spring elements

at 1:46 PM, Abhyankar, Shrirang G. abhy...@mcs.anl.gov wrote: You are right. The Jacobian for the power grid application is indeed non-symmetric. Is that a problem for your application? If you need a symmetric Jacobian, you can use the BC facility in PetscSection, which eliminates

Re: [petsc-users] DMPlex with spring elements

for the first degree of freedom in that node and the second degree of freedom would just be offset+1? Yes. Shri Miguel On Wed, Sep 24, 2014 at 9:52 PM, Abhyankar, Shrirang G. abhy...@mcs.anl.gov wrote: If you have equations only at the nodes, with a part of it contributed by the edges (springs

Re: [petsc-users] DMPlex with spring elements

the component data structure, how can I process it later? I mean, at what point does the solver know that those degrees of freedom are actually fixed and how I can tell it that they are fixed? Miguel On Thu, Sep 25, 2014 at 10:27 AM, Abhyankar, Shrirang G. abhy...@mcs.anl.govmailto:abhy

Re: [petsc-users] DMPlex with spring elements

elements I see, and I guess I would have to assign a value of one to the diagonal entry of that degree of freedom in the Jacobian right? Yes. Wouldn't this break the symmetry of the Jacobian (in case it were symmetric)? No. Shri Thanks Miguel On Sep 25, 2014 11:32 AM, Abhyankar, Shrirang G. abhy

Re: [petsc-users] DMPlex with spring elements

: Re: [petsc-users] DMPlex with spring elements Why not? Wouldn't we have a row of zeros except for the diagonal term? The column that corresponds to that degree of from doesn't have to be zero, right? Thanks Miguel On Sep 25, 2014 12:38 PM, Abhyankar, Shrirang G. abhy...@mcs.anl.gov wrote

Re: [petsc-users] DMPlex with spring elements

-users] DMPlex with spring elements Thanks for your response. I'm attaching a pdf with a description of the model. The description of the PetscSection is necessary for the DMNetwork? It looks like DMNetwork does not use a PetscSection. Miguel On Wed, Sep 24, 2014 at 1:43 PM, Abhyankar, Shrirang G

Re: [petsc-users] DMPlex with spring elements

You may also want to take a look at the DMNetwork framework that can be used for general unstructured networks that don't use PDEs. Its description is given in the manual and an example is in src/snes/examples/tutorials/network/pflow. Shri From: Matthew Knepley knep...@gmail.com Date: Tue, 23

Re: [petsc-users] General query, default preconditioner

PETSc defaults to using an ILU(0) preconditioner in serial and Block-Jacobi + ILU(0) on blocks in parallel. You can see the preconditioner details using the option -ksp_view. Shri -Original Message- From: Ghosh, Swarnava sghosh2...@gatech.edumailto:sghosh2...@gatech.edu Date: Tue, 16

Re: [petsc-users] Error with SNESVISetVariableBounds

This error is also seen in src/snes/examples/tutorials/ex53.c. [Shri@Shrirangs-MacBook-Pro tutorials (master)]$ ./ex53 Vec Object: 1 MPI processes type: seq 1 1 1 1 1 -1 -1 0 -1 -1 [0]PETSC ERROR: - Error Message --

Re: [petsc-users] How to set KSP Solver Options at Runtime?

Shuangshuang, You don't need PCRegister(ourjacobi, PCCreate_Jacobi); KSPGetPC(ksp, pc); PCSetType(pc, ourjacobi); in your code if you want to use PETSc's native Jacobi preconditioner. All you have to do is set it at run-time -pc_type jacobi. In PETSc, XXXSetFromOptions routine checks

Re: [petsc-users] How to set the value in Ax=b.

Zero out the sixth row, set A[5][5]= 1.0 and b[5]=3.14. On Apr 28, 2014, at 7:00 PM, 丁老师 ztdepya...@163.commailto:ztdepya...@163.com wrote: Dear group: I have assembled the coefficients of A and b. My computation alogrithm need to specify a component of x to be a constant value. for

Re: [petsc-users] Extra Variable in DMCircuit

Hi, I got quite far with my project, although I still have not managed (or better have not tried...) to get the parallelization running (Shri: Any news about that?). We've figured out what needs to be done but haven't done it yet :-). Your application needs either a vertex distribution with

Re: [petsc-users] Extra Variable in DMCircuit

in DMCircuit On 03/14/2014 06:24 PM, Abhyankar, Shrirang G. wrote: That sounds great! Although, this solution seems to be very specific to the equations. Does this approach still work when the equations get more complex (e.g. handling multiple variables like PRODUCT(1+t*(a-1)) or SUM(R*q*(1-f

Re: [petsc-users] Extra Variable in DMCircuit

email quoting style is really hard to read. What part is you and what part is supposed to be cited? (Microsoft is at-fault for this breakage, but we need a work-around.) http://lists.mcs.anl.gov/pipermail/petsc-users/2014-March/020931.html Abhyankar, Shrirang G. abhy...@mcs.anl.gov writes

Re: [petsc-users] Modeling a Network with DMPlex?

Hi Florian, I was able to run your example with a small change (used PetscMalloc instead of PetscMalloc1). However, the solution on more than 1 processor is different presumably because of some work TODO for the ghost vertices. Answers to some of your questions in the code: I) You can change

Re: [petsc-users] Modeling a Network with DMPlex?

Florian, Thanks for the example! I'll take a look at it and get back to you. Shri On 2/14/14 11:25 AM, Florian Meier florian.me...@koalo.de wrote: Ok, that was just a stupid typo. I have now build the first attempt of an example. I am sure that can be programmed in a much better way, so I

Re: [petsc-users] Modeling a Network with DMPlex?

that have small distances) or will this be done automatically. There is no need to preprocess the data. Once the circuit layout is set up, it will set up the vertex connectivity and create the graph accordingly. Shri On 02/10/2014 07:33 PM, Abhyankar, Shrirang G. wrote: On 2/10/14 11:45 AM

Re: [petsc-users] Modeling a Network with DMPlex?

. As DMCircuit is a recent development, your questions/comments/suggestions will help us to improve this feature. It would be great if you could contribute your simple example as a tutorial example for DMCircuit. Thanks, Shri Thanks again, Florian On 02/10/2014 08:33 AM, Abhyankar, Shrirang G. wrote: Hi

Re: [petsc-users] Modeling a Network with DMPlex?

Hi Florian, You can use DMPlex directly as Jed suggests or you can use a new DM that has been added recently to PETSc specifically for circuit/network/graph applications. This DM, named DMCircuit, is built on top of DMPlex. It is currently in the next branch of PETSc and there is an example from