Ian,
You need to use brew to uninstall the MPI in /usr/local before you use the
other install of MPI. There is no easy systematic way to force
the compiler and linker to find the "other" mpi.h first.
Barry
Having multiple MPI's installed on the system is often problematic.
>
Hmm, the intent of all three first arguments should be in since they are
passed in from the routine above. Does it work if you replace
> Vec, INTENT(out) :: rr_system
with
> Vec, INTENT(in) :: rr_system
?
Barry
> On Oct 19, 2018, at 3:51 AM, Klaij, Christiaan wrote:
>
> I've re
> On Oct 19, 2018, at 7:56 AM, Zhang, Junchao wrote:
>
>
> On Fri, Oct 19, 2018 at 4:02 AM Jan Grießer
> wrote:
> With more than 1 MPI process you mean i should use spectrum slicing in divide
> the full problem in smaller subproblems?
> The --with-64-bit-indices is not a possibility for me
arch & Development
> MARIN | T +31 317 49 33 44 | mailto:c.kl...@marin.nl | http://www.marin.nl
>
> MARIN news:
> http://www.marin.nl/web/News/News-items/Seminar-Scheepsbrandstof-en-de-mondiale-zwavelnorm-2020.htm
>
>
> From: Smith,
> On Oct 19, 2018, at 2:08 PM, Moritz Cygorek wrote:
>
> Hi,
>
> I'm using SLEPc to diagonalize a huge sparse matrix and I've encountered
> random segmentation faults.
https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
>
> I'm actually using a the slepc example 4 without m
> On Oct 20, 2018, at 4:14 PM, Isaac, Tobin G wrote:
>
> I think adler32 is in zlib: p4est typically finds it in configure. Can you
> send along config.log from externalpackages/git.p4est?
Is there a way to pass the zlib information to ./configure? We should add
that to p4est.py Reason:
pment
> MARIN | T +31 317 49 33 44 | mailto:c.kl...@marin.nl | http://www.marin.nl
>
> MARIN news:
> http://www.marin.nl/web/News/News-items/Seminar-Scheepsbrandstof-en-de-mondiale-zwavelnorm-2020.htm
>
>
> From: Smith, Barry F.
&g
You are calling the routine incorrectly. Take a look at usage in
src/dm/examples/tutorials/ex11f90.F90
Barry
> On Oct 26, 2018, at 5:16 AM, SONG Pengyang wrote:
>
> Hi all,
> I am trying to change a KSP tutorial code ex34.c to ex34f.F90. I found that
> after I changed DMDAVecGetArray t
g, China
> TEL: (+86) 15762264643
>
> -邮件原件-
> 发件人: Smith, Barry F.
> 发送时间: 2018年10月27日 9:02
> 收件人: SONG Pengyang
> 抄送: petsc-users@mcs.anl.gov
> 主题: Re: [petsc-users] Problems with fortran subroutine DMDAVecGetArrayF90
>
>
> You are calling the routi
> On Oct 27, 2018, at 9:45 AM, Balay, Satish wrote:
>
> On Fri, 26 Oct 2018, avatar wrote:
>
>> Thank Satish. I would like to call Matlab function in Pestc. For example,
>> calculating the condition number of a petsc matrix.
>
> Hm - sounds like you need --with-matlab-engine. I'm not sure
Matt,
How difficult would it be to impose such boundary conditions with
DMPlex? Presumably you just connect the mesh up "properly" and it is
straightforward?
Barry
> On Oct 27, 2018, at 10:23 AM, Matthew Knepley wrote:
>
> On Sat, Oct 27, 2018 at 2:02 AM Fengwen Wang wrote:
> On Oct 28, 2018, at 12:16 PM, Manav Bhatia wrote:
>
> Hi,
>
>I am attempting to solve a Mindlin plate bending problem with AMG solver
> in petsc. This test case is with a mesh of 300x300 elements and 543,606 dofs.
>
>The discretization includes 6 variables (u, v, w, tx, ty, tz),
Exactly how much does it increase with number of levels? Send a chart number
of levels and number of iterations. With say -mg_levels_ksp_maxit 4
Thanks
Barry
> On Oct 29, 2018, at 12:59 PM, Manav Bhatia wrote:
>
> Thanks for the clarification.
>
> I also observed that the number
You can possibly use the PETSc object AO (see AOCreate()) to manage the
reordering. The non-contiguous order you start with is the application ordering
and the new contiguous ordering is the petsc ordering. Note you will likely
need to reorder the cell vertex or edge numbers as well.
Bar
"No, I have an unstructured mesh that increases in resolution away from the
center of the cuboid. See Figure: 5 in the ArXiv paper
https://arxiv.org/pdf/1907.02604.pdf for a slice through the midplane of the
cuboid. Given this type of mesh, will dmplex do a cuboidal domain
decomposition?"
I agree this is confusing. https://gitlab.com/petsc/petsc/merge_requests/2331
the flag PETSC_HAVE_MPI will no longer be set when MPI is not used (only MPIUNI
is used).
Barry
The code API still has MPI* in it with MPI but they are stubs that just
handle the sequential code and do not r
> I am basically trying to solve a finite element problem, which is why in 3D I
> have 7 non-zero diagonals that are quite farm apart from one another. In 2D I
> only have 5 non-zero diagonals that are less far apart. So is it normal that
> the set up time is around 400 times greater in the 3D
> On Nov 28, 2019, at 7:07 PM, baikadi pranay wrote:
>
> Hello PETSc users,
>
> I have a sparse matrix built and I want to output the matrix for viewing in
> matlab. However i'm having difficulty outputting the matrix. I am writing my
> program in Fortran90 and I've included the following
I would first run with -ksp_monitor_true_residual -ksp_converged_reason to
make sure that those "very fast" cases are actually converging in those runs
also use -ksp_view to see what the GMAG parameters are. Also use the -info
option to have it print details on the solution process.
Ba
How many colors is it requiring? And how long is the MatGetColoring()
taking? Are you running in parallel? The MatGetColoring() MATCOLORINGSL uses a
sequential coloring algorithm so if your matrix is large and parallel the
coloring will take a long time. The parallel colorings are MATCOLO
378
> Number of rows 756
> 0 1188
> 1 1188
> 2 1188
> 3 1188
> 4 1188
> 5 1188
> ...
>
> Is this normal?
> When using MCFD, is there any difference using mpiaij and mpibaij?
>
> Best,
> Li
>
>
euse it forever.
You can also try -snes_mf -snes_lag_jacobian -2 which should compute the
Jacobian once, use that original one to build the preconditioner once and reuse
the same preconditioner but use the matrix free to define the operator.
Barry
>
> Regards,
> Li
>
sorry about this. The numerical values between C and Fortran got out of sync.
I've attached a patch file you can apply with
patch -p1 < format.patch
or you can use the branch https://gitlab.com/petsc/petsc/merge_requests/2346
Barry
> On Dec 3, 2019, at 1:10 AM, Marius Buerkle wrot
will the following time steps reuse the Jacobian built
> at the first time step?
>
> Best,
> Li
>
>
>
> On Tue, Dec 3, 2019 at 12:10 AM Smith, Barry F. wrote:
>
>
> > On Dec 2, 2019, at 2:30 PM, Li Luo wrote:
> >
> > -snes_mf fails to converge
It still
> outputs "Elemental matrix (explicit ordering)" to StdOut which is kinda
> annoying, is there anyway to turn this off?
>
>
> Von: "Smith, Barry F."
> An: "Marius Buerkle"
> Cc: "petsc-users@mcs.anl.gov"
> Betreff: Re:
Hmm, MPICH and OpenMPI have also passed this info in there compilers; perhaps
this is a newer version clang that no longer tolerates these options
I think we need to strip out those options as a guess
> On Dec 4, 2019, at 2:18 PM, Balay, Satish wrote:
>
> Yes - this is a link time opti
Are you using cell-centered or vertex centered discretization ( makes a
slight difference)?
Our model is to use DM_BOUNDARY_MIRROR DMBoundaryType. This means that
u_first_real_grid_point - u_its_ghost_point = 0 (since DMGlobalToLocal will
automatically put into the physical ghost locat
Hmm, for DMDA and DMStag is should not have a limit (certain ranges of
values are better optimized than others but more optimizations may be done).
For DMPLEX in theory again it should be what ever you like (again larger
values may require more optimization in our code to get really grea
set it to the value it would get if it wasn't an edge, then the
> derivative isn't preserved anymore.
>
> This is where I get stuck.
>
> Ellen
>
>
> On 12/5/19 10:16 AM, Smith, Barry F. wrote:
>>
>> Are you using cell-centered or vertex
Can you actually build and run C++ programs with the MPI?
Executing: mpicxx -o /tmp/petsc-Llvze6/config.setCompilers/conftest.exe
-fopenmp -fPIC /tmp/petsc-Llvze6/config.setCompilers/conftest.o
Possible ERROR while running linker: exit code 1
stderr:
/usr/lib/gcc/x86_64-pc-cygwin/7.4.0/
an build and run C programs
> with MPI.
>
> I have -with-log=0 because there is an overhead if many small objects
> are created, which is my case.
>
> As for the fortran, I will remove --with-fortran=0
>
> On 12/5/2019 11:53 PM, Smith, Barry F. wrote:
>> Can you
There is something missing in the cmake process that is causing needed
libraries not to be linked.
Please email your program and your CMake stuff (files you use) so we can
reproduce the problem and find a fix.
Barry
> On Dec 8, 2019, at 10:06 PM, Yingjie Wu wrote:
>
> Hi,
> Thank
PETSC_ARCH to find the
configuration file AND use the compilers from the configuration file. It works
for me, please let me know if you have trouble.
Barry
> On Dec 8, 2019, at 10:38 PM, Yingjie Wu wrote:
>
> Thank you very much for your help.
> My programs are as follow
>
uerkle wrote:
>
> Hi,
>
> Is it actually possible to submit a pull (merge) request ? I followed the
> petsc wiki but this didn't work.
>
> Best
> Marius
>
>
> Gesendet: Donnerstag, 05. Dezember 2019 um 07:45 Uhr
> Von: "Marius Buerkle"
Can you please send use the exact code and data file that causes the crash?
And any options.
There are bugs in Metis/Parmetis that we need to track down and eliminate
since it is so central to PETSc's work flow.
Barry
> On Dec 18, 2019, at 4:21 AM, Eda Oktay wrote:
>
> Hi all,
>
Thank you for the full and detailed report. The memory leak could be
anywhere but my guess is it is in the interface between PETSc and Hyper.
The first thing to check is if PETSc memory keeps increasing. The simplest
way to do this is run your code 3 independent times with -malloc_debug
There are no leaks but it appears what is happening is that rather than
recycle the memory PETSc is returning to the system the system is generating
new space as needed. Since the old PETSc pages are never used again this should
be harmless.
Barry
> On Dec 24, 2019, at 9:47 AM, Marius
h one (or which revision), I wil check it.
>
>
> Gesendet: Mittwoch, 25. Dezember 2019 um 00:53 Uhr
> Von: "Smith, Barry F."
> An: "Marius Buerkle"
> Cc: "Mark Adams" , "petsc-usersmcs.anl.gov"
>
> Betreff: Re: [petsc-users]
Do you reset the initial tilmestep? Otherwise the second solve thinks it is
at the end. Also you may need to reset the iteration number
Something like
ierr = TSSetTime(appctx->ts, 0);CHKERRQ(ierr);
ierr = TSSetStepNumber(appctx->ts, 0);CHKERRQ(ierr);
ierr = TSSetTimeStep(appctx->ts,
> On Jan 7, 2020, at 8:59 AM, Mark Adams wrote:
>
> I’m not sure what the compilers, and C++ are doing here
>
> On Tue, Jan 7, 2020 at 9:17 AM Кудров Илья wrote:
> However, after configuring
>
> cout<<1. + 1.*PETSC_i<
> outputs (1, 0) instead of (1, 1).
Where after configure? PETSC_
Yeah, this is an annoying feature of DMDA and PCMG in PETSc. Some coarse grid
ranges and particular parallel layouts won't work with geometric multigrid. You
are using 314 on the coarse and 628 on the fine grid. Try changing the them by
1 and start with one process.
Barry
> On Jan 8
> On Oct 25, 2017, at 11:59 AM, Karin&NiKo wrote:
>
> Barry, Matt,
> Thank you very much for that clarification. My question is mainly motivated
> by the will to transfer test matrices from an industrial software to a more
> light and agile PETSc code, in order to run numerical experiments. Si
Since the matrix changes size you will need to create a new matrix, fill it
up, solve with it, destroy it for each time-step. No big deal.
> On Oct 25, 2017, at 1:52 PM, Cetinbas, Cankur Firat wrote:
>
> Hi,
>
> We have a code in python to solve for 3D water transport in a nano scale
Run with something like -snes_divergence_tolerance 1e20
Barry
> On Oct 28, 2017, at 9:31 AM, David Knezevic
> wrote:
>
> Hi all,
>
> I updated to the head of the maint branch (b5b0337). Previously (with version
> 3.7), I had a SNES test case that converged like this:
>
> NL s
> On Oct 29, 2017, at 5:20 PM, Guido Giuntoli wrote:
>
> I have a ghost vector "b" and I want to work with my local representation
> adding values in my local part and my ghost padding region. Is this possible
> or I have to use VecSetValues ?
What do you really want to do?
put values in
> On Oct 29, 2017, at 11:50 AM, Mark Lohry wrote:
>
> Thanks again Barry, I've got the preconditioners hooked up with
> -snes_mf_operator and at least AMG looks to be working great on a high order
> unstructured DG problem.
>
> Couple questions on the SNESSetLagJacobian + SNESSetLagPreconditi
If you using DMDA then you can't just "remove" some grid points from the
vector.
What you need to do is for your function evaluation at these interior grid
points do f[j][i] = u[j][i] - ub in the FormFunction (ub is the Dirichlet
value) and put a 1 one the diagonal of that row of the Jac
Please clarify.
1) You can successfully update to 3.8 and compile and run the code?
2) You do not have a way to support both 3.7 and 3.8 except by putting a large
number of #ifdef in the code?
Yes, 3.8 is a dramatic shift in API (to one we feel is much better), it is
not simple to write
the info on the lag logic, I'll play with the TS pre/post calls
> for the time-accurate problems and only use LagJacobian.
>
> On Mon, Oct 30, 2017 at 11:29 AM, Smith, Barry F. wrote:
>
> > On Oct 29, 2017, at 11:50 AM, Mark Lohry wrote:
> >
> > Thanks again Bar
called
binaryoutput and we can run the coloring codes local to performance debug.
Barry
>
> On Mon, Oct 30, 2017 at 1:55 PM, Smith, Barry F. wrote:
>
> > On Oct 30, 2017, at 12:39 PM, Mark Lohry wrote:
> >
> >
> > >
> > > 3) Are there any h
debug.
>
>
> Will send this evening.
Thanks but send for the AIJ case, not BAIJ
>
>
> On Mon, Oct 30, 2017 at 3:02 PM, Smith, Barry F. wrote:
>
> > On Oct 30, 2017, at 1:58 PM, Mark Lohry wrote:
> >
> > Hmm, metis doesn't really have anything to
You also need to make sure that most matrix entries are generated on the
process that they will belong on.
Barry
> On Oct 30, 2017, at 8:01 PM, Matthew Knepley wrote:
>
> On Mon, Oct 30, 2017 at 8:06 PM, Cetinbas, Cankur Firat
> wrote:
> Hello,
>
>
>
> I am a beginner both in PETSc
> On Oct 30, 2017, at 9:32 PM, zakaryah . wrote:
>
> You were right, of course. I fixed the problem with the function evaluation
> and the code seems to be working now, at least on small test problems.
>
> Is there a way to setup preallocation of the Jacobian matrix, with the entire
> first
> On Oct 31, 2017, at 10:26 AM, zakaryah . wrote:
>
> OK Barry, I'll have a look - thanks. Should I use DMShellSetCreateMatrix to
> set the routine I write for matrix allocation?
What do you do now and how do you create/set the matrix? Are you creating one
big old matrix that has all rows
> On Oct 31, 2017, at 11:59 AM, zakaryah . wrote:
>
> First I set up the composite DM, which contains one redundant field coupled
> to everything else, and a DMDA, which of course only has local couplings
> given by the stencil. I then create the matrix with DMCreateMatrix, with the
> compo
Looks like you need to first call DMCompositeSetCoupling()
> On Oct 31, 2017, at 11:59 AM, zakaryah . wrote:
>
> First I set up the composite DM, which contains one redundant field coupled
> to everything else, and a DMDA, which of course only has local couplings
> given by the stencil. I
Manav,
Thanks for reporting the problem
Fande,
Thanks for the pointer.
Satish determined the correct long term fix and it is in the branch
barry/fix-lto_library-option-maint and will be put in the maint branch and
master branch if it passes the testing tonight.
Barry
>
> On Nov 1, 2017, at 10:23 AM, Thibaut Appel wrote:
>
> Dear PETSc/SLEPc users,
>
> I am encountering a problem when I try to isolate my calls to PETSc/SLEPc
> routines in a module. When I have a single file everything works fine, but
> when I have, say:
> - modA.f90 (Independant modules)
>
> On Nov 1, 2017, at 10:32 PM, zakaryah . wrote:
>
> I worked on the assumptions in my previous email and I at least partially
> implemented the function to assign the couplings. For row 0, which is the
> redundant field, I set dnz[0] to end-start, and onz[0] to the size of the
> matrix min
l to the processor, i.e.
> should my iterations go from 0 to nrows-1? What is the general idea behind
> setting the structure from within FormCoupleLocations? I'm currently not
> doing that at all.
>
> Thanks for all the help!
>
> On Thu, Nov 2, 2017 at 12:31 PM, Smith, Barry
> On Nov 3, 2017, at 10:59 AM, zakaryah . wrote:
>
> Hi - I think I managed to get this to work. The second call to
> FormCoupleLocations is actually pretty simple - it just has to set the matrix
> values! One thing that was hard to figure out was why line 168 calls
> MatGetOwnershipRange
You should not need to "tamper" with the solution process to achieve this.
I would just change how my FormFunction and FormJacobian behave to implement
the different boundary conditions. Why would that not work?
Barry
> On Nov 3, 2017, at 4:39 PM, Bikash Kanungo wrote:
>
> Hi Matt,
>
o add this option to the implementation and make a
pull request).
Barry
>
> Thanks,
> Bikash
>
>
>
> On Fri, Nov 3, 2017 at 6:20 PM, Smith, Barry F. wrote:
>
>
> You should not need to "tamper" with the solution process to achieve this.
>
>
> On Nov 3, 2017, at 5:41 PM, Satish Balay wrote:
>
> On Fri, 3 Nov 2017, Ed D'Azevedo wrote:
>
>> Dear PETSc expert,
>>
>> I have a question on the correct way to use Fortran module in petsc.
>>
>> In this url on "UsingFortran"
>>
>>
>> http://www.mcs.anl.gov/petsc/petsc-current/docs/man
> On Nov 9, 2017, at 3:33 PM, zakaryah . wrote:
>
> Hi Stefano - when I referred to the iterations, I was trying to point out
> that my method solves a series of nonlinear systems, with the solution to the
> first problem being used to initialize the state vector for the second
> problem, et
To use the PETSc coloring based Jacobian computer (which uses finite
differences) you absolutely have to be able to provide the nonzero structure of
the Jacobian.
Now once you provide the nonzero structure of the Jacobian the PETSc
MatColoring routines can actually compute the coloring f
> On Nov 7, 2017, at 6:47 AM, Gard Spreemann wrote:
>
> On Tuesday 7 November 2017 07:35:36 CET Mark Adams wrote:
>> PETSc's signal handler is for segvs, etc. I don't know the details but I
>> don't think we care about external signals.
>
> I see. I'll sketch what I'm trying to achieve in case
Henrik,
Please describe in some detail how you are handling phase change. If you
have if () tests of any sort in your FormFunction() or FormJacobian() this can
kill Newton's method. If you are using "variable switching" this WILL kill
Newtons' method. Are you monkeying with phase definiti
e that all of this has something to do with the spectrums of the
> matrices involved in the solve but I don't know enough to improve the results
> I'm obtaining.
>
> On Thu, Nov 9, 2017 at 11:09 PM, Smith, Barry F. wrote:
>
>
> > On Nov 9, 2017, at 3:33 PM,
nonzero entries in the Jacobian
due to the stencil.
> If not I would really appreciate an example illustrating how I should do it.
>
> Thanks in advance!!
>
> Javier
>
>
>
> On Friday, November 10, 2017 05:09 CET, "Smith, Barry F."
> wrote:
>
&g
Tobias,
When you use PETSc in quad precision you need to ./configure with
--download-f2cblaslapack this uses a version of BLAS/LAPACK obtained by running
f2c on the reference version of BLAS/LAPACK (that is, fortran code from netlib)
and then massages the source code for quad precision.
Use MKL versions of block formats?
> On Nov 14, 2017, at 4:40 PM, Richard Tran Mills wrote:
>
> On Tue, Nov 14, 2017 at 12:13 PM, Zhang, Hong wrote:
>
>
>> On Nov 13, 2017, at 10:49 PM, Xiangdong wrote:
>>
>> 1) How about the vectorization of BAIJ format?
>
> BAIJ kernels are optimized
> On Nov 15, 2017, at 6:38 AM, Mark Lohry wrote:
>
> I've found ILU(0) or (1) to be working well for my problem, but the petsc
> implementation is serial only. Running with -pc_type hypre -pc_hypre_type
> pilut with default settings has considerably worse convergence. I've tried
> using -pc_
Meaningless differences
> On Nov 15, 2017, at 2:26 PM, Kong, Fande wrote:
>
> Hi,
>
> There is a heat conduction problem. When superlu_dist is used as a
> preconditioner, we have random results from different runs. Is there a random
> algorithm in superlu_dist? If we use ASM or MUMPS as t
n() is always positive.
>
>
> Fande,
>
>
>
>
> On Wed, Nov 15, 2017 at 1:59 PM, Smith, Barry F. wrote:
>
> Meaningless differences
>
>
> > On Nov 15, 2017, at 2:26 PM, Kong, Fande wrote:
> >
> > Hi,
> >
> > There is a
t 4:24 PM, Kong, Fande wrote:
>
>
>
> On Wed, Nov 15, 2017 at 2:52 PM, Smith, Barry F. wrote:
>
>
> > On Nov 15, 2017, at 3:36 PM, Kong, Fande wrote:
> >
> > Hi Barry,
> >
> > Thanks for your reply. I was wondering why this happens only when we u
>
> On Wed, Nov 15, 2017 at 3:35 PM, Smith, Barry F. wrote:
>
> Since the convergence labeled linear does not converge to 14 digits in one
> iteration I am assuming you are using lagged preconditioning and or lagged
> Jacobian?
>
> We are using Jacobian-free Newton.
> On Nov 15, 2017, at 9:40 PM, Jed Brown wrote:
>
> "Smith, Barry F." writes:
>
>>> On Nov 15, 2017, at 6:38 AM, Mark Lohry wrote:
>>>
>>> I've found ILU(0) or (1) to be working well for my problem, but the petsc
>>
nst ILU generally speaking.
Barry
>
> On Nov 15, 2017 10:50 PM, "Smith, Barry F." wrote:
>
>
> > On Nov 15, 2017, at 9:40 PM, Jed Brown wrote:
> >
> > "Smith, Barry F." writes:
> >
> >>> On Nov 15, 2017, at 6:38 AM, Mark
In some of the Fortran examples we have code like
call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
if (ierr .ne. 0) then
print*,'Unable to initialize PETSc'
stop
endif
Eventually we should update all the examples with this, or something even
better
> On Nov 22, 2017, at 3:48 AM, Julian Andrej wrote:
>
> Hello,
>
> we prepared a small example which computes the gradient via the continuous
> adjoint method of a heating problem with a cost functional.
Julian,
The first thing to note is that the continuous adjoint is not exactly t
> On Nov 22, 2017, at 10:13 AM, Eric Chamberland
> wrote:
>
> Hi,
>
> I have 2 questions:
>
> First, I am looking for a function that is almost like MatMissingDiagonal,
> but that would return me *all* missing diagonal entries.
>
> Does it exists?
I'm afraid not.
>
> If not, is there
MatZeroRowsColumns() as two vector arguments you are missing
> On Nov 23, 2017, at 2:43 PM, Samuel Lanthaler wrote:
>
> Hi there,
> I'm new to PETSc and have been trying to do some basic manipulation of
> matrices in fortran, but don't seem to be able to set a row/column to zero
> using the
First run under valgrind.
https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
If that doesn't help send the exact output from the debugger (cut and paste)
and the exact version of PETSc you are using.
Also out put from -ksp_view_pre
Barry
> On Nov 24, 2017, at 8:03 AM, Dani
> On Nov 24, 2017, at 1:21 PM, Matteo Semplice wrote:
>
> Hi.
>
> The manual for DMCreateMatrix says "Notes: This properly preallocates the
> number of nonzeros in the sparse matrix so you do not need to do it
> yourself", so I got the impression that one does not need to call the
> preallo
smoothers.
> HYPRE BoomerAMG: Measure typelocal
> HYPRE BoomerAMG: Coarsen type Falgout
> HYPRE BoomerAMG: Interpolation type classical
> linear system matrix = precond matrix:
> Mat Object: 24 MPI processes
> type: mpiaij
> rows=1122000, cols=
Storm,
Specifically for TS there is an abstract object called TSTrajectory which is
a way to store histories of simulations (it is used by TSAdjoint but also
useable for other purposes). It has several ways to store histories and more
can be added.
One draw back to saving everything i
> On Nov 27, 2017, at 5:01 AM, Stefano Zampini
> wrote:
>
>
>
>
> - I'm dealing with matrices that change the value of the coeffs in time, but
> maintain the same zero pattern. Is it possible to create a ksp (linear solver
> + preconditioner) object before the time loop and pass it to th
You have headed down the wrong track.
You must ./configure PETSc with the option --with-scalar-type=complex to
work with complex numbers and should declare the variables with PetscScalar
just like in the example.
Barry
> On Dec 4, 2017, at 3:26 PM, Swenson, Jennifer wrote:
>
> De
I'm not sure what your goal is. In general two different IC(0) codes might
produce slightly different factorizations based on implementation details even
if they claim to run the same algorithm so I don't think there is a reason to
try to compare the factors they produce.
In addition PETSc
in
a format callable from R.
Barry
> Not sure if I used the easiest way to get IC so I also seek for help on
> getting a concise version of IC().
>
> -Wendy
>
>
> On Mon, Dec 4, 2017 at 10:07 PM, Smith, Barry F. wrote:
>
> I'm not sure what you
s R not have a ICC(0)? ICC(0) with the natural ordering is actually
> very simple to write. You could easily write it presumably directly in R or
> in C in a format callable from R.
>
>Barry
>
>
>
> > Not sure if I used the easiest way to get IC so I also seek for
They call the function and provide zero rows
> On Dec 6, 2017, at 10:52 AM, Felipe Giacomelli wrote:
>
> Hello,
> According to PETSc documentation, all processes that share the matrix MUST
> call this routine for the parallel case. However, it is possible that, after
> the domain decomposi
> On Dec 12, 2017, at 9:54 AM, Alexander Lindsay
> wrote:
>
> I'm working with a relatively new set of physics (new to me) and the
> Jacobians are bad. While debugging the Jacobians, I've been running with
> different finite difference approximations. I've found in general that
> matrix-
> On Dec 12, 2017, at 12:04 PM, Hao Zhang wrote:
>
> hi,
>
> before I introduce HYPRE with BOOMERAMG to my CFD code, I will have output
> with good convergence rate. with BOOMERAMG, the same code will take longer
> time to run and there's a good chance that no output will be produced
> what
> On Dec 12, 2017, at 11:26 AM, Alexander Lindsay
> wrote:
>
> Ok, I'm going to go back on my original statement...the physics being run
> here is a sub-set of a much larger set of physics; for the current set the
> hand-coded Jacobian actually appears to be quite good.
>
> With hand-coded
> On Dec 12, 2017, at 1:48 PM, Alexander Lindsay
> wrote:
>
> On Tue, Dec 12, 2017 at 10:39 AM, Matthew Knepley wrote:
> On Tue, Dec 12, 2017 at 12:26 PM, Alexander Lindsay
> wrote:
> Ok, I'm going to go back on my original statement...the physics being run
> here is a sub-set of a much la
; 0 Nonlinear |R| = 2.259203e-02
> 0 Linear |R| = 2.259203e-02
> 1 Linear |R| = 1.312921e-06
> 2 Linear |R| = 7.714018e-09
> 1 Nonlinear |R| = 4.780690e-03
> 0 Linear |R| = 4.780690e-03
> 1 Linear |R| = 7.773053e-09
> 2 Nonlinear |R| = 1.22683
Can you send a code that reproduces the crash so I can debug it?
Barry
> On Dec 12, 2017, at 2:44 PM, Jordan Wagner wrote:
>
> Hi,
>
> I am trying to use the function MatMeshToCellGraph. I currently have a matrix
> that holds the cell connectivity of simplex elements. So it is a numCel
Samuel,
I have attached a fixed up version of your example that works correctly.
Your basic problem was that you did not "use" the final module in the main
program so it did know the interfaces for the routines. I have included this
example in PETSc for others to benefit from in the br
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