Re: [petsc-users] getting EPS to rebuild the BV context

; Thanks for reporting this. > Jose > El 02/04/2015, a las 00:03, Andrew Spott escribió: >> >Are you using master? >> This problem was run into on 3.5.3, but I’m working on trying to get the >> code to work on master. A cursory glance at the code for master seems to >

Re: [petsc-users] getting EPS to rebuild the BV context

l 01/04/2015, a las 22:32, Andrew Spott escribió: >> When resizing an EPS (adjusting the nev, ncv and/or mpd values) after a >> deflation space has been entered, SLEPC complains that you can’t “resize a >> BV with constraints”. >> >> Is there a way of forcing th

[petsc-users] getting EPS to rebuild the BV context

When resizing an EPS (adjusting the nev, ncv and/or mpd values) after a deflation space has been entered, SLEPC complains that you can’t “resize a BV with constraints”. Is there a way of forcing this issue by killing the BV and remaking it?   (re-adding the constraints). -Andrew

Re: [petsc-users] TimeStepper norm problems. EMIL Please read this

near solver is misbehaving when using cn. If you >> use option -snes_mf the problem disappears. >> >> Please do not use -ts_theta_adapt until it is fixed. >> >> In conclusion I don't think that looking at theta.c will be productive. >>

Re: [petsc-users] TimeStepper norm problems. EMIL Please read this

se option -snes_mf the problem disappears. > Please do not use -ts_theta_adapt until it is fixed. > In conclusion I don't think that looking at theta.c will be productive. > We are currently looking at what happens at the lower levels. > Thanks, > Emil > On 3/30/15 4:25 PM, Andre

Re: [petsc-users] HermitianTranspose version of MatCreateTranspose.

? -Andrew On Wed, Mar 18, 2015 at 3:10 PM, Barry Smith wrote: >> On Mar 18, 2015, at 3:41 PM, Andrew Spott wrote: >> >> So, I’ve got a MatCreateHermitianTranspose function that has close to the >> same functionality as the MatCreatTranspose version. So I’m getting

Re: [petsc-users] TimeStepper norm problems. EMIL Please read this

Emil:  If I want to fix this myself, do you have any idea where I should start looking?  I assume in the th->endpoint section of TSStep_Theta in http://www.mcs.anl.gov/petsc/petsc-current/src/ts/impls/implicit/theta/theta.c.html? Thanks, -Andrew On Tue, Mar 24, 2015 at 10:52 AM, Lisandro

Re: [petsc-users] In place access to eigenvectors of EPS

las 21:24, Andrew Spott escribió: >> Is there a way to get in place access to the eigenvectors in the BV >> contained by EPS using the public API? >> >> -Andrew >> > You can do EPSGetBV() and then BVGetColumn() for each of the first nconv > columns. But this

[petsc-users] In place access to eigenvectors of EPS

Is there a way to get in place access to the eigenvectors in the BV contained by EPS using the public API? -Andrew

Re: [petsc-users] TimeStepper norm problems. EMIL Please read this

Thanks! Let me know if I can do anything to help. -Andrew — Andrew On Sun, Mar 22, 2015 at 8:21 PM, Emil Constantinescu wrote: > Hi Andrew, > I can reproduce this issue and I agree that there is something wrong. > I'll look into it. > Emil > On 3/22/15 3:29 PM, Andre

Re: [petsc-users] TimeStepper norm problems. EMIL Please read this

> ~/Src/petsc/test-dir (barry/more-tchem-work *=) arch-debug > $ ./ex2 -ts_type beuler > t: 0 step: 0 norm-1: 0 > t: 0.01 step: 1 norm-1: 0 > t: 0.02 step: 2 norm-1: 0 > t: 0.03 step: 3 norm-1: 0 > ~/Src/petsc/test-dir (barry/more-tchem-work *=) arch-debug > $ ./

Re: [petsc-users] TimeStepper norm problems. EMIL Please read this

heta' scheme=0:'(null)' dt=1.000e-02 >>TSAdapt 'basic': step 2 accepted t=0.02 + 1.000e-02 wlte= >> 0 family='theta' scheme=0:'(null)' dt=1.000e-01 >> 3 TS dt 0.1 time 0.03 >> t: 0.03 step: 3 norm-1: 0 >> 3 TS

Re: [petsc-users] TimeStepper norm problems.

E_READ, &view ); > BTW: You do not need to call Mat/VecAssembly on Mats and Vecs after they have > been loaded. > Barry >> On Mar 20, 2015, at 6:39 PM, Andrew Spott wrote: >> >> Sorry it took so long, I wanted to create a “reduced” case (without all my >

Re: [petsc-users] TimeStepper norm problems.

PM, Barry Smith wrote: > Andrew, > Send your entire code. It will be easier and faster than talking past each > other. > Barry >> On Mar 20, 2015, at 5:00 PM, Andrew Spott wrote: >> >> I’m sorry, I’m not trying to be difficult, but I’m not following. >>

Re: [petsc-users] TimeStepper norm problems.

bian function was only meant to create A, since dG/du = A(t) (for this special case). -Andrew On Fri, Mar 20, 2015 at 3:26 PM, Matthew Knepley wrote: > On Fri, Mar 20, 2015 at 3:09 PM, Andrew Spott wrote: >> So, it doesn’t seem that zeroing the given vector in the function passed

Re: [petsc-users] TimeStepper norm problems.

calculation function where a Vec or Mat does not get reset to 0, but it does in your by hand code.    Matt On Mar 20, 2015 2:52 PM, "Andrew Spott" wrote: I have a fairly simple problem that I’m trying to timestep: u’ = A(t) u I’m using the crank-nicholson method, which I under

[petsc-users] TimeStepper norm problems.

I have a fairly simple problem that I’m trying to timestep: u’ = A(t) u I’m using the crank-nicholson method, which I understand (for this problem) to be: u(t + h) = u(t) + h/2[A(t+h)*u(t+h) + A(t)*u(t)] or [1 - h/2 * A(t+1)] u(t+1) = [1 + h/2 * A(t)] u(t) When I attempt to timestep using

Re: [petsc-users] HermitianTranspose version of MatCreateTranspose.

lways see exactly what they are doing. I personally wish I had started with Approach 2 (but I did not), but there could be some flaw with it I am not seeing. Barry > On Feb 23, 2015, at 6:50 PM, Andrew Spott wrote: > > I’m definitely willing to submit it as a pull reques

Re: [petsc-users] HermitianTranspose version of MatCreateTranspose.

I’m definitely willing to submit it as a pull request. Also, while I’m at it, I’m going to write a “duplicate” function for transpose and hermitian_transpose.  Just because this seems 1) easy ( MatHermitianTranspose can return a new copy, as well as MatTranspose), and 2) necessary to use these

[petsc-users] HermitianTranspose version of MatCreateTranspose.

It looks like this function doesn’t exist, but it should be pretty easy to write. A few questions: - Does a new MatType need to be created? or will MATTRANSPOSEMAT work? - Is there any way to write this from outside of the PETSc library proper?   Initial examination makes it seem like it isn’t

Re: [petsc-users] Hang while attempting to run EPSSolve()

Thanks.  I’ll start work on rolling back to another version of MPI On Fri, Feb 13, 2015 at 4:15 PM, Barry Smith wrote: >> On Feb 13, 2015, at 5:07 PM, Andrew Spott wrote: >> >> Is there a known workaround for this? > No. This should be reported as a show stopper to th

Re: [petsc-users] Hang while attempting to run EPSSolve()

Is there a known workaround for this? It also occurs in 1.8.0 (so far I’ve checked 1.8.{0,1,2,3}).  Unfortunately, going back farther requires actually building openMPI, which requires something special (IB drivers, I believe). -Andrew

Re: [petsc-users] Hang while attempting to run EPSSolve()

Thanks! On Fri, Feb 13, 2015 at 3:45 PM, Barry Smith wrote: > I think it was introduced in 1.8.1 so I think 1.8.0 should be ok, but if it > hangs then go back to 1.7.4 >> On Feb 13, 2015, at 4:43 PM, Andrew Spott wrote: >> >> What version of OpenMPI was this introd

Re: [petsc-users] Hang while attempting to run EPSSolve()

What version of OpenMPI was this introduced in?  I appear to be finding it in   OpenMPI 1.8.3 and 1.8.1 as well.  Should I go back to 1.8.0 or 1.7.4? Thanks, -Andrew On Fri, Feb 13, 2015 at 2:23 PM, Andrew Spott wrote: > Thanks!  You just saved me hours of debugging. > I’ll loo

Re: [petsc-users] Hang while attempting to run EPSSolve()

you link against an earlier OpenMPI implementation on the > machine? Or do they have MPICH installed you could use? > Barry >> On Feb 13, 2015, at 3:17 PM, Andrew Spott wrote: >> >> Local tests on OS X can’t reproduce, but production tests on our local >> superc

[petsc-users] Hang while attempting to run EPSSolve()

Local tests on OS X can’t reproduce, but production tests on our local supercomputer always hang while waiting for a lock. The back trace: #0  0x2ba2980df054 in __lll_lock_wait () from /lib64/libpthread.so.0 #1  0x2ba2980da388 in _L_lock_854 () from /lib64/libpthread.so.0 #2  0x2ba

Re: [petsc-users] SLEPc: left eigenvectors?

Thanks.  I figured as much and just wanted to confirm it. -Andrew On Tue, Feb 10, 2015 at 3:14 PM, Jose E. Roman wrote: > El 10/02/2015, a las 22:46, Andrew Spott escribió: >> A quick google search shows some work at calculating the left and right >> eigenvalues simultaneous

[petsc-users] SLEPc: left eigenvectors?

A quick google search shows some work at calculating the left and right eigenvalues simultaneously back in 2005, however not much sooner has popped up.  Is this possible yet?  Where can I find more information? Thanks -Andrew

[petsc-users] SLEPc choosing inner product

If I have some inner matrix upon which I want the eigensolver context to check orthogonality and norm, how do I set that? Is it:     BV bv;     EPSGetBV( e, &bv );     BVSetMatrix( bv, InnerProductMatrix, PETSC_FALSE ); This doesn’t appear to be changing the norm that is being used.  Is the

Re: [petsc-users] slepc and overall phase of computed eigenvectors

Thanks. As an aside, another way that seems to work is to set the initial vector to a random REAL vector.  It seems to also fix this problem.  Though I don’t know how robust it is. -Andrew On Wed, Feb 4, 2015 at 11:49 AM, Jose E. Roman wrote: > El 04/02/2015, a las 19:32, Andrew Sp

[petsc-users] slepc and overall phase of computed eigenvectors

When I compute the eigenvectors of a real symmetric matrix, I’m getting eigenvectors that are rotated by approximately pi/4 in the complex plane.  So what could be purely real eigenvectors have some overall phase factor. Why is that?  And is there a way to prevent this overall phase factor? -

Re: [petsc-users] reference, copy or constant view?

ULT);             EPSSetInitialSpace(eps,1,&eigenvector);             EPSSolve(eps); Won’t actually change *A?  What about VecDot? Thanks again, -Andrew On Wed, Dec 10, 2014 at 10:30 AM, Jed Brown wrote: > Andrew Spott writes: >> In the slepc and petsc docs, is there a way to tell if a function

[petsc-users] reference, copy or constant view?

In the slepc and petsc docs, is there a way to tell if a function is going to copy, modify, or just “look” at a petsc object that is a parameter? Specifically there are two examples that I’m curious about (I’m trying to chase down a bug): EPSSetOperators(EPS, Mat, Mat) I know the first argu

Re: [petsc-users] Changing block size.

Awesome, thanks.  I ran into that bug and thought I was doing something wrong. -Andrew — Andrew On Wed, Dec 3, 2014 at 5:40 PM, Barry Smith wrote: >> On Dec 3, 2014, at 5:13 PM, Andrew Spott wrote: >> >> What is the easiest way to change the block size of a matrix? >

[petsc-users] Changing block size.

What is the easiest way to change the block size of a matrix? I have a matrix that was saved with a block size of 1, and I would like to increase it upon load to a larger block size.  Is there a simple way of doing this? Thanks -Andrew Spott

[petsc-users] Determining the correct Preallocation

I want to preallocate a MPIAIJ matrix correctly, using MatMPIAIJSetPreallocation(A, PETSC_NULL, dnnz, PETSC_NULL, onnz); The problem is that I don't know how many local rows, or where the local columns are until I run said function, but I need to know the number of local rows and local columns

[petsc-users] Finding the inner product of a vector with respect to a matrix.

Is there an official way to find v^T A v? Or is it usually just done in two steps? Thanks! -Andrew

[petsc-users] How do you write/read to the .info file

What purpose does the info file have? On May 22, 2012 9:31 PM, "Shri" wrote: > You can also use the option -viewer_binary_skip_info to have PETSc not > create the .info file. > > -- > > On Tue, May 22, 2012 at 8:45 PM, Andrew Spott gmail.

[petsc-users] How do you write/read to the .info file

When writing out a Mat in binary form, the .info file is created, but it usually empty, how do you read/write to it? Thanks -Andrew

[petsc-users] nonzero structure setting and remembering

How do I read the nonzero structure (from an assembled matrix?) -Andrew On May 18, 2012, at 2:31 PM, Jed Brown wrote: > On Fri, May 18, 2012 at 3:26 PM, Andrew Spott > wrote: > I have a couple of questions about how to deal with the nonzero structure. > > 0) Is the "no

[petsc-users] nonzero structure setting and remembering

I have a couple of questions about how to deal with the nonzero structure. 0) Is the "nonzero structure" the same as "number of non zeros per row"? Or are they different? 1) How much of a speedup do you get for copying/creating/loading matrices when you set the number of non zeros per row bef

[petsc-users] explicit symmetric matrices

Is there a way to explicitly say that a sparse matrix is symmetric or hermitian and only save/load half of it? -Andrew

[petsc-users] Petsc Bag example redundancy

Isn't this redundant? 104: PetscBagRegisterReal(bag, &user->alpha, 1.0, "alpha", "Linear coefficient"); 105: PetscBagRegisterReal(bag, &user->lambda, 6.0, "lambda", "Nonlinear coefficient"); 106: PetscBagSetFromOptions(bag); 107: PetscOptionsGetReal(PETSC_NULL,"-alpha",&user->alpha,PETSC

[petsc-users] How much memory does TS use (in terms of # of matrices)

Yea, I think I was. Replacing it fixed the problem Thanks all, sorry for the trouble. -Andrew On May 16, 2012, at 8:33 AM, Jed Brown wrote: > On Wed, May 16, 2012 at 8:22 AM, Aron Ahmadia > wrote: > You do realize that MatDuplicate is making a copy, right? > > Maybe you were intending to us

[petsc-users] How much memory does TS use (in terms of # of matrices)

in(*A, MAT_FINAL_ASSEMBLY); err = MatAssemblyEnd(*A, MAT_FINAL_ASSEMBLY); *flag = DIFFERENT_NONZERO_PATTERN; // absorb! return err; } I'm honestly stumped now? -Andrew On May 16, 2012, at 7:17 AM, Jed Brown wrote: > On Wed, May 16, 2012 at 7:08 AM, Andrew Spott > wro

[petsc-users] How much memory does TS use (in terms of # of matrices)

I'm honestly not sure why I did that, however what I thought would be the obvious fix ( 'Mat h = *A' ) isn't, I'm still getting the error. Is there a reason I can't do that? -Andrew On May 16, 2012, at 7:17 AM, Jed Brown wrote: > On Wed, May 16, 2012 at 7:08

[petsc-users] How much memory does TS use (in terms of # of matrices)

s for the help, -Andrew On May 16, 2012, at 2:51 AM, Aron Ahmadia wrote: > Umnn, I hope this isn't too obvious, but you're duplicating your matrix at > every time step without freeing it and expecting that to not be a problem? > > A > > On Wed, May 16, 2012 a

[petsc-users] How much memory does TS use (in terms of # of matrices)

I'm attempting to run some code with a rather large (>1GB) sparse matrix, and I keep getting kicked out of the que for what I believe is using too much memory. The unfortunate thing is that as the steps go up, the memory usage seems to as well, which would normally indicate a memory leak. But

[petsc-users] Modifying the structure of a matrix.

ibution of values before > the assembly, but does it redistribute during assembly?) > > Thanks, > > -Andrew > > On May 15, 2012, at 6:40 AM, Jed Brown wrote: > > On Mon, May 14, 2012 at 10:39 PM, Andrew Spott gmail.com>wrote: > >> That is what I figure. &g

[petsc-users] Modifying the structure of a matrix.

istribute during assembly?) Thanks, -Andrew On May 15, 2012, at 6:40 AM, Jed Brown wrote: > On Mon, May 14, 2012 at 10:39 PM, Andrew Spott > wrote: > That is what I figure. > > I'm curious though if you need to manually determine the local row > distribution after you do th

[petsc-users] Modifying the structure of a matrix.

the matrix) -Andrew On May 14, 2012, at 10:30 PM, Shri wrote: > > On May 14, 2012, at 11:07 PM, Andrew Spott wrote: > >> I'm attempting to do a convergence study on my basis, see how large my basis >> need to be to make my results accurate, does that help? > >You

[petsc-users] Modifying the structure of a matrix.

at you want to treat as constants and hence eliminating > the rows and columns? > > Shri > > On May 14, 2012, at 10:51 PM, Andrew Spott wrote: > >> Is there a computational cost to using a sparse matrix that is much bigger >> than it should be? >> >>

[petsc-users] Modifying the structure of a matrix.

and, or will PETSC do it for you? Thanks for the quick reply -Andrew On May 14, 2012, at 9:38 PM, Jed Brown wrote: > On Mon, May 14, 2012 at 9:33 PM, Andrew Spott > wrote: > What is the best way to selectively add/remove columns/rows of a Mat? > > Is there a way to do it in

[petsc-users] Modifying the structure of a matrix.

What is the best way to selectively add/remove columns/rows of a Mat? Is there a way to do it in place, or does it require essentially moving the values to a new matrix? Thanks for the help. -Andrew

[petsc-users] Solving a very simple time step problem:

Thanks! -Andrew On May 1, 2012, at 2:12 PM, Matthew Knepley wrote: > On Tue, May 1, 2012 at 2:27 PM, Andrew Spott > wrote: > This is actually what I figured, but I haven't seen the jacobian used in this > context before, and wanted to make sure before I bugged you

[petsc-users] Solving a very simple time step problem:

This is actually what I figured, but I haven't seen the jacobian used in this context before, and wanted to make sure before I bugged you guys with a more complicated problem. I am attempting to do a very basic linear time stepping problem: u_t = H(t) u Where H(t) = H0 + a(t) * H' Where a(t)

[petsc-users] Solving a very simple time step problem:

I want to solve a very simple equation: u_t = F(t) u Where F(t) = H_0 + a(t) H' (H_0 and H' are constant matrices, and a(t) is a time dependent scalar). But I'm not sure how to go about doing this using the TS context. I don't have a Jacobian that I need to be worried about, so should I be doi

[petsc-users] floating point exception… but only when >4 cores are used...

I found my bug. Thanks a lot everyone, I really appreciate the help. -Andrew On Apr 28, 2012, at 7:16 PM, Andrew Spott wrote: > Yes it did? now I have a bunch of GDB windows open and ready, thanks. > > -Andrew > On Apr 28, 2012, at 7:10 PM, Matthew Knepley wrote: > >> On

[petsc-users] floating point exception… but only when >4 cores are used...

Yes it did? now I have a bunch of GDB windows open and ready, thanks. -Andrew On Apr 28, 2012, at 7:10 PM, Matthew Knepley wrote: > On Sat, Apr 28, 2012 at 8:59 PM, Andrew Spott > wrote: > What makes it easier if autotools makes it hard? > > > This is a joke, but I do thi

[petsc-users] floating point exception… but only when >4 cores are used...

What makes it easier if autotools makes it hard? On Apr 28, 2012 6:43 PM, "Matthew Knepley" wrote: > On Sat, Apr 28, 2012 at 8:36 PM, Andrew Spott gmail.com>wrote: > >> When I attach debugger on error on the local machine, I get a bunch of >> lines like this one

[petsc-users] floating point exception… but only when >4 cores are used...

st don't' get the "MPI_Abort" thing, but everything else is the same. any ideas? -Andrew On Apr 28, 2012, at 6:11 PM, Matthew Knepley wrote: > On Sat, Apr 28, 2012 at 8:07 PM, Andrew Spott > wrote: > are there any tricks to doing this across ssh? > > I

[petsc-users] floating point exception… but only when >4 cores are used...

> On Sat, Apr 28, 2012 at 6:39 PM, Andrew Spott > wrote: > >-start_in-debugger noxterm -debugger_nodes 14 > > All my cores are on the same machine, is this supposed to start a debugger on > processor 14? or computer 14? > > Neither. This spawns a gdb process on the same

[petsc-users] floating point exception… but only when >4 cores are used...

w On Apr 27, 2012, at 7:26 PM, Satish Balay wrote: > On Fri, 27 Apr 2012, Andrew Spott wrote: > >> I'm honestly stumped. >> >> I have some petsc code that essentially just populates a matrix in parallel, >> then puts it in a file. All my code that uses floating

[petsc-users] floating point exception… but only when >4 cores are used...

I'm honestly stumped. I have some petsc code that essentially just populates a matrix in parallel, then puts it in a file. All my code that uses floating point computations is checked for NaN's and infinities and it doesn't seem to show up. However, when I run it on more than 4 cores, I get f

[petsc-users] Turning off PETSC errors

I keep getting a floating point error, unfortunately I can't seem to figure out where it is coming from, because the PETSC error codes keep being kicked out before my own code can tell me anything. (And the error codes aren't telling me where my errors are). Is there anyway to turn off the erro

[petsc-users] Errors in PETSc

How do I get line numbers to show up in the errors that petsc generates? Instead of getting line numbers I get line=0 or just no information. -Andrew

[petsc-users] Most efficient way to transfer a vector to a single processor

I'm interested in moving a vector to a single processor (so I can output it in some custom way), but I can't find a simple way to do that. Is the easiest way to output the parallel vector to a file and then read it in to a single processor vector? Also, an unrelated question: If I have a vecto

[petsc-users] Matrix/Vector Assembly

When is it necessary to assemble a matrix/vector? Do I need to do it after every change in the matrix/vector? Or just after "AddValue(s)" type functions? -Andrew

[petsc-users] TSSetMatrices structure?

Thanks again for the quick reply! Thankfully I don't have a mass matrix, I'm just solving the schrodinger equation. Thanks again. -Andrew On Mar 29, 2012, at 8:07 PM, Barry Smith wrote: > > On Mar 29, 2012, at 8:58 PM, Andrew Spott wrote: > >> This: >> htt

[petsc-users] TSSetMatrices structure?

Jacobian() > http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/TS/index.html and > work with petsc-dev http://www.mcs.anl.gov/petsc/developers/index.html > > > >Barry > > On Mar 29, 2012, at 8:09 PM, Andrew Spott wrote: > >> In the Petsc manual, th

[petsc-users] TSSetMatrices structure?

In the Petsc manual, there is a TSSetMatrices function, however there is no further documentation for it. It is referenced in the manual as: TSSetMatrices(TS ts, Mat A,PetscErrorCode (*frhs)(TS,PetscReal,Mat*,Mat*,MatStructure*,void*), Mat B,PetscErrorCode (*flhs)(TS,PetscReal,Mat*,Mat*,MatStru