much better than in ancient history; you simply do not preallocate to
get this behavior).
Barry
On Jul 11, 2024, at 4:51 PM, Michael Povolotskyi
wrote:
Thanks a lot.
Is this a new feature? It seems to me that 10 years ago the default
behavior was different.
Michael.
On 7/11/2024 4:
,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);
On Jul 11, 2024, at 4:02 PM, Michael Povolotskyi
wrote:
Thank you,
let me clarify my question.
Imagine that I have a sparse matrix, and the number of non zero
entries that I specified is too small.
I know that I can insert values in it but it will be slow.
I
-info and grep for malloc.
Barry
On Jul 11, 2024, at 1:55 PM, Michael Povolotskyi
wrote:
This Message Is From an External Sender
This message came from outside your organization.
Hello,
is there an option in PETSC that allows to check at run time if a sparse
matrix has been preallocated
Hello, is there an option in PETSC that allows to check at run time if a sparse matrix has been preallocated correctly? I remember there was something like that is the older versions, but cannot find it now. The goal is to get rid of any possible
ZjQcmQRYFpfptBannerStart
Thank you Barry and Jed,
I think I'll go with MatDiagonalScale.
Michael.
On 06/20/2018 02:06 PM, Jed Brown wrote:
Michael Povolotskyi writes:
Dear Petsc team,
what would be the most efficient way to compute the following:
V += A*B*C,
where V is a dense square matrix,
B is a s
Dear Petsc team,
what would be the most efficient way to compute the following:
V += A*B*C,
where V is a dense square matrix,
B is a square diagonal matrix, A and C are dense rectangular matrices?
I would like to benefit from the fact that B is diagonal.
thank you,
Michael.
Dear Petsc developers,
I'm reading a matrix from a file like this:
PetscViewer viewer;
PetscErrorCode ierr;
MatCreate(comm,&matrix);
MatSetType(matrix,MATDENSE);
ierr = PetscViewerBinaryOpen(comm,file_name,FILE_MODE_READ,&viewer);
ierr = MatLoad(matrix,viewer);
Sometimes the file that is ne
onvince myself that what you propose would
be simpler, in terms of lines of code,
number of objects, number of concepts, etc. Right now, that is not
clear to me either.
Baring that, maybe you can argue that new capabilities, such as
the type flexibility described by Michael, are
Hello Filippo,
we had to write a wrapper around Petsc to use both double and double
complex functions in the same code.
We achieved it by creating two shared object libraries and hiding Petsc
symbols.
Once we had to achieve it for a statically linked executable, this was
really painful, we had
Hello everybody,
which function has to be used in petsc 3.7 instead of PetscLogBegin()?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
Hall for Discover and Learning Research, Room 441
207 South Martin Jischke Drive
West
/manualpages/SNES/SNESLINESEARCHBT.html#SNESLINESEARCHBT
Is there any way to set them in the code rather then from the command line?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
Hall for Discover and Learning Research, Room 441
Dear Petsc developers,
in the old days there was a function SNESLineSearchSetParams
How to set a maximum value for the nonlinear step now?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
Hall for Discover and Learning Research
On 10/29/2015 04:50 PM, Barry Smith wrote:
On Oct 29, 2015, at 3:43 PM, Michael Povolotskyi wrote:
Dear PETSc developers,
I need to set many elements into a sparse Hermitian matrix.
I'd like to do this effectively.
Your documentation says that one should use MatSetValues and set as
with MatSetValues
3. Apply complex conjugation and compute a part of the column that
corresponds to upper part of the matrix
4. Set this part of the column to the matrix with MatSetValues
5. move to the next row
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Networ
ecial update code
inside the Newton method.
Do you know what the non-physical solutions are?
Matt
Barry
> On Oct 8, 2015, at 1:05 PM, Michael Povolotskyi
mailto:mpovo...@purdue.edu>> wrote:
>
> Thank you.
> The situation is as follows:
&
guess
2. Do full Newton step
3. If converged, exit
else if the solution improved go to step 2
otherwise "update_solution_in_my_way" ang go to step 2
Is it possible to do this in PETSc?
Michael.
On 10/08/2015 01:58 PM, Barry Smith wrote:
On Oct 8, 2015, at 12:26 PM, Michael Povolots
s not improve the
residual. As far as I can see I have to define my own SNELLineSearch
object. Is there any example that shows how to do it?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
Hall for Discover and Learning Research,
Will a call to MatZeroEntries
and MatAssemblyBegin/End(mat,MAT_FINAL_ASSEMBLY) do same as
MatSetValues() with zero values?
Michael.
On 06/29/2015 02:38 PM, Barry Smith wrote:
On Jun 29, 2015, at 1:28 PM, Michael Povolotskyi wrote:
Thank you.
Is there a way to disable the squeeze?
Not
Thank you.
Is there a way to disable the squeeze?
Michael.
On 06/29/2015 01:58 PM, Barry Smith wrote:
On Jun 29, 2015, at 10:49 AM, Michael Povolotskyi wrote:
Dear developers,
I have the following question:
Imagine that I have two matrices A and B
Both are created using MatCreateSeqAIJ
e same first 5 arguments.
In addition, for both matrices I call
MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
After this I set some entries to both A and B matrices and assemble them.
Question: can I use MatAXPY with SAME_NONZERO_PATTERN argument?
Thank you,
Michael.
--
Michael Pov
This would be great.
Thank you,
Michael.
On 06/29/2015 11:13 AM, Matthew Knepley wrote:
On Mon, Jun 29, 2015 at 10:12 AM, Michael Povolotskyi
mailto:mpovo...@purdue.edu>> wrote:
Thank you, I can try with a newer release.
Have you re-implemented the function there?
The prob
Thank you, I can try with a newer release.
Have you re-implemented the function there?
The problem is we have not move to the new API completely.
Is there any workaround with Petsc 3.4?
On 06/29/2015 11:08 AM, Matthew Knepley wrote:
On Mon, Jun 29, 2015 at 9:59 AM, Michael Povolotskyi
Dear PETSc developers and users,
what does this error message mean?
[0]PETSC ERROR: - Error Message
[0]PETSC ERROR: Argument out of range!
[0]PETSC ERROR: nnz cannot be greater than row length: local row 0 value
108 rowlength 72!
[0]PETS
Hi, I have a related question.
I need to sort eigenvectors after the eigenvalue problem is solved.
For PETSC/SLEPC 3.4 I do the following
EPSSetEigenvalueComparison(eps, &my_sort_function, NULL);
eps->which = EPS_WHICH_USER;
ierr = EPSSortEigenvalues(eps,eps->nconv,eps->eigr,eps->eigi, eps->perm)
Hello,
will the eigenvectors that correspond to degenerate eigenvalues of a
Hermitian matrix be orthogonal?
I'm using Krylov Schur method.
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke Drive
P
On 6/23/2014 11:33 AM, Wen Jiang wrote:
Hi,
Could anyone tell me whether the current version of petsc supports
pardiso? If so, are there any tricks to configure and use it? Thanks.
Regards,
Wen
We have built the interface and sent it to PETSc team.
It works nicely for us.
Dear Petsc develope
le to configure SLEPC to use FEAST algorithm from MKL?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke Drive
Purdue University, DLR, room 441-10
West Lafayette, Indiana 47907
phone: +1-765-494-9396
fax: +1-765-496-6026
On 11/22/2013 06:36 PM, Jed Brown wrote:
Michael, your time zone is mistakenly set to UTC, though the time is
actually set to CST, so your mails appear out of order.
Michael Povolotskyi writes:
I'm actually interested in implementing it.
Could you, please, tell what has to be do
On 11/22/2013 06:07 PM, Jed Brown wrote:
Michael Povolotskyi writes:
Dear developers of Petsc and users,
I have the following numerical problem.
I need to solve the system Ax = B, where A is a square matrix, x and B
are rectangular matrix
The system is solved by doing LU decomposition.
You
a complex
conjugate of A.
My question: is it possible to reuse the LU decomposition of A for doing
this?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke Drive
Purdue University, DLR, room 441-10
West
On 11/4/2013 10:49 PM, Jed Brown wrote:
Michael Povolotskyi writes:
In my case each right hand side column is an almost empty vector with a
couple of non zero entries.
Is there any way to use the fact that the right hand side is very sparse
and make the calculations faster?
Optimizing for
Dear Petsc developers,
I'm using the MatMatSolve function to solve a linear system with a
right hand side containing many columns.
In my case each right hand side column is an almost empty vector with a
couple of non zero entries.
Is there any way to use the fact that the right hand side is v
On 11/4/2013 3:37 PM, Jed Brown wrote:
Michael Povolotskyi writes:
Dear Petsc developers,
in my work I need to measure the multi threading performance of LAPACK
function dgetrf
Since all matrices are of PETSc type I'd like to call Petsc functions
for the LU decomposition.
My code reads
r = KSPSetUp(ksp);
ierr = PCFactorGetMatrix(pc, &F);
Is this a correct way to call dgetrf ?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke Drive
Purdue University, DLR, room 441-10
West Lafayette, I
(libmpi_mt.so)
We had to specify the exact library to solve the issue.
Question: is there any better way to insure that petsc picks the thread
safe mpi library during configuration?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational
On 8/23/2013 7:37 PM, Jed Brown wrote:
Barry Smith writes:
We call free() at that point. But not that in Unix this does not
mean the memory is returned to the operating system so you will not
see the process memory go down. If you then allocate new objects
they will reuse this
Dear Petsc developers,
I have a question about the MatDestroy function.
Does it free the memory immediately?
Or do you keep the memory for further usage?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke
Thank you!
This very helpful information.
Michael.
On 07/17/2013 03:31 PM, Barry Smith wrote:
On Jul 17, 2013, at 2:26 PM, Michael Povolotskyi wrote:
Hello,
at some point the configuration script prints a warning that valgrind is not
found in the system.
Is petsc going to link some
Hello,
at some point the configuration script prints a warning that valgrind is
not found in the system.
Is petsc going to link some valgrind related libraries if valgrind is
installed?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational
has
blas/scalapack split.
So you would have to specify both libs with the --with-scalapack-lib option.
Satish
On Tue, 16 Jul 2013, Michael Povolotskyi wrote:
Dear Petsc developers and users,
I'm trying to configure petsc with scalapack from mkl library.
From the configure.log (see attached
On 07/10/2013 02:13 PM, Barry Smith wrote:
On Jul 10, 2013, at 1:09 PM, Michael Povolotskyi wrote:
Hello everybody,
does anybody know if it makes sense to build petsc with --with-fortran-kernels?
No. It is just their so people who think Fortran code compiles to faster
code than C can
Hello everybody,
does anybody know if it makes sense to build petsc with
--with-fortran-kernels?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke Drive
Purdue University, DLR, room 441-10
West Lafayette
CXXCPPFLAGS [for the c++ compiler]
Satish
On Wed, 10 Jul 2013, Michael Povolotskyi wrote:
Hi Satish,
it looks like I have this file but not in "standard" location:
locate bits/c++config.h
/usr/include/x86_64-linux-gnu/c++/4.7/bits/c++config.h
/usr/share/gccxml-0.9/GCC/4.4/bits/c++config.h
piler]
Satish
On Wed, 10 Jul 2013, Michael Povolotskyi wrote:
Hi Satish,
it looks like I have this file but not in "standard" location:
locate bits/c++config.h
/usr/include/x86_64-linux-gnu/c++/4.7/bits/c++config.h
/usr/share/gccxml-0.9/GCC/4.4/bits/c++config.h
/usr/share/gccxml-0.9
g it?]
Satish
On Wed, 10 Jul 2013, Michael Povolotskyi wrote:
Thank you Matt.
Unfortunately 'make all-legacy' gives the same error:
=
libfast in: /home/mpovolot/Code_intel/libs/petsc/build-real/src
libfast in: /home/mpovolot/Code_intel/libs/petsc/
(code 4)
compilation aborted for
/home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/logging/plog.c
(code 4)
I attach here the log files.
Any advise is highly appreciated.
Michael.
On 7/9/2013 4:34 PM, Matthew Knepley wrote:
On Tue, Jul 9, 2013 at 3:32 PM, Mich
On 07/09/2013 04:37 PM, Satish Balay wrote:
On Tue, 9 Jul 2013, Michael Povolotskyi wrote:
Dear Petsc users and developers,
I'm trying to build petsc with Intel compiler.
What is strange to me that it has something to do with Gfortran, while I want
to build everything with Intel.
Looks
On 07/09/2013 04:37 PM, Satish Balay wrote:
On Tue, 9 Jul 2013, Michael Povolotskyi wrote:
Dear Petsc users and developers,
I'm trying to build petsc with Intel compiler.
What is strange to me that it has something to do with Gfortran, while I want
to build everything with Intel.
Looks
its not sufficient to
catch this issue.
satish
On Tue, 9 Jul 2013, Matthew Knepley wrote:
On Tue, Jul 9, 2013 at 3:11 PM, Michael Povolotskyi wrote:
Dear Petsc users and developers,
I'm trying to build petsc with Intel compiler.
1) First, ask yourself whether you really want to build
Thank you,
this worked.
I have another question:
what does this option mean: --with-fortran-kernels?
Michael.
On 07/09/2013 01:35 PM, Matthew Knepley wrote:
On Tue, Jul 9, 2013 at 12:30 PM, Michael Povolotskyi
mailto:mpovo...@purdue.edu>> wrote:
Dear Petsc developers and users,
***
What is the meaning of that message?
I checked in my file system and the file names contain "_" instead of "-"
ls /opt/intel/mkl//lib/intel64/libmkl_intel_lp64.*
/opt/intel/mkl//lib/intel64/libmkl_intel_lp64.a
/opt/intel/mkl//lib/intel64/libmkl_intel_lp64.so
On 07/08/2013 04:47 PM, Jed Brown wrote:
Michael Povolotskyi writes:
Dear Petsc developers and users,
is there any example that shows how to use the
PetscMemoryGetMaximumUsage function?
It works like this:
PetscMemorySetGetMaximumUsage(); // somewhere early in your program, or run
with
Dear Petsc developers and users,
is there any example that shows how to use the
PetscMemoryGetMaximumUsage function?
thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke Drive
Purdue University, DLR, room 441
On 07/02/2013 01:41 PM, Matthew Knepley wrote:
On Tue, Jul 2, 2013 at 12:19 PM, Michael Povolotskyi
mailto:mpovo...@purdue.edu>> wrote:
On 07/02/2013 12:46 PM, Hong Zhang wrote:
Michael :
Dear Petsc developers,
I'm gradually moving from the version 3.2 to
On 07/02/2013 12:46 PM, Hong Zhang wrote:
Michael :
Dear Petsc developers,
I'm gradually moving from the version 3.2 to the version 3.4.
I had to skip the version 3.3 because of the bug in MatMatMult
that has been reported to you.
What I see is that the MatMatMult works well
x was multiplied by a dense matrix
the result was dense.
In the version 3.4 the result is sparse.
Is my observation correct?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke Drive
Purdue University, DLR, roo
On 06/24/2013 06:07 PM, Jed Brown wrote:
Michael Povolotskyi writes:
Hello everybody,
I have a sparse matrix defined on 1 MPI process.
I want to extract all entries from it (including zeros) and put them
into an array to use as an argument for some lapack functions.
What is the most optimal
thank you,
Michael.
On 06/24/2013 06:06 PM, Matthew Knepley wrote:
On Tue, Jun 25, 2013 at 12:01 AM, Michael Povolotskyi
mailto:mpovo...@purdue.edu>> wrote:
Hello everybody,
I have a sparse matrix defined on 1 MPI process.
I want to extract all entries from it (including
Hello everybody,
I have a sparse matrix defined on 1 MPI process.
I want to extract all entries from it (including zeros) and put them
into an array to use as an argument for some lapack functions.
What is the most optimal way of doing this?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
ctor layouts for vectors compatible with the matrix.
Barry
On Jun 6, 2013, at 4:55 PM, Michael Povolotskyi wrote:
Dear Petsc developers,
petsc gives error with the error code equal to 60 when I'm doing the following:
ierr = MatCreateMPIDense(comm, m, num_cols ,num_rows,num_cols,data,p
Dear Petsc developers,
petsc gives error with the error code equal to 60 when I'm doing the
following:
ierr = MatCreateMPIDense(comm, m, num_cols
,num_rows,num_cols,data,petsc_matrix)
on rank = 0 the gebugger gives:
(gdb) print m
$1 = 240
(gdb) print num_cols
$2 = 18
(gdb) print num_rows
$3
We just started, but I will let the PETSc community know as soon as we
have the results.
Michael.
On 05/24/2013 01:30 PM, Eric Chamberland wrote:
Hi,
we are interested in beta-testing your interface if you need some
beta-testers!
thanks,
Eric
On 05/20/2013 02:37 PM, Michael Povolotskyi
On 05/20/2013 03:18 PM, Jed Brown wrote:
Michael Povolotskyi writes:
Hello,
does SNESSolve closes the solution vector?
What do you mean "closes"?
I mean VecAssemblyBegin() and VecAssemblyEnd()
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nano
Hello,
does SNESSolve closes the solution vector?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke Drive
Purdue University, DLR, room 441-10
West Lafayette, Indiana 47907
phone: +1-765-494-9396
fax: +1-765
On 05/20/2013 02:31 PM, Jed Brown wrote:
Michael Povolotskyi writes:
Hello everybody,
does PETSc support interface to MKL PARDISO linear solver?
I did not find PARDISO in the documentation of PETSc, but may be
somebody tried this out already?
Licensing is the main reason I have had no
Hello everybody,
does PETSc support interface to MKL PARDISO linear solver?
I did not find PARDISO in the documentation of PETSc, but may be
somebody tried this out already?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
Paul Mullowney
> Adri?n N?meth
> Jack Poulson
> Jose Roman
> Karl Rupp
> Patrick Sanan
> Barry Smith
> Tim Tautges
> Richard Tran Mills
> Stefano Zampini
> Hong Zhang (ANL/IIT)
> Hong Zhang (Virginia Tech)
> Xuan Zhou
>
> Thanks
>
> Barry
>
--
On 04/17/2013 01:37 PM, Matthew Knepley wrote:
> On Wed, Apr 17, 2013 at 1:23 PM, Michael Povolotskyi
> mailto:mpovolot at purdue.edu>> wrote:
>
> Dear Petsc developers,
> does the function MatDenseGetArray allocate additional memory or
> just returns a po
Dear Petsc developers,
does the function MatDenseGetArray allocate additional memory or just
returns a pointer to existing memory ?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechnology
207 S Martin Jischke Drive
Purdue University
Dear Petsc developers,
Does the function MatGetArray allocates additional memory, or it simply
returns a pointer to the existing memory?
I'm talking about an MPI dense matrix.
Thank you.
Michael.
--
Michael Povolotskyi, PhD
Research Assistant Professor
Network for Computational Nanotechn
On 04/03/2013 01:52 PM, Jed Brown wrote:
> On Wed, Apr 3, 2013 at 11:55 AM, Michael Povolotskyi
> mailto:mpovolot at purdue.edu>> wrote:
>
> Dear PETSc developers,
> I have a following question:
>
> I have a dense serial matrix of M x N size
> I have
Dear PETSc developers,
I have a following question:
I have a dense serial matrix of M x N size
I have a N vectors of size M.
I need to copy content of those vectors to the columns of the matrix.
What is the fastest way of doing this?
Thank you,
Michael.
--
Michael Povolotskyi, PhD
Research
On 3/31/2013 11:02 AM, Matthew Knepley wrote:
> On Mon, Apr 1, 2013 at 2:00 AM, Michael Povolotskyi
> mailto:mpovolot at purdue.edu>> wrote:
>
> On 3/31/2013 10:19 AM, Jed Brown wrote:
>>
>> On Sun, Mar 31, 2013 at 9:15 AM, Michael Povolotskyi
>> m
On 3/31/2013 10:19 AM, Jed Brown wrote:
>
> On Sun, Mar 31, 2013 at 9:15 AM, Michael Povolotskyi
> mailto:mpovolot at purdue.edu>> wrote:
>
> In our code we have our own linear system solver, optimized for a
> distributed 3 block diagonal matrix.
> We
On 3/31/2013 10:03 AM, Jed Brown wrote:
> On Sun, Mar 31, 2013 at 8:58 AM, Michael Povolotskyi
> mailto:mpovolot at purdue.edu>> wrote:
>
> Dear PETSc developers,
> I have the following question.
> PETSc has memory reporting system. Does it report the memory
Dear PETSc developers,
I have the following question.
PETSc has memory reporting system. Does it report the memory allocated
inside a library (e.g MUMPS) when I call it from PETSc program?
Thank you,
Michael.
Hello,
I have to perform multiplications of a Hermitian distributed matrix by a
distributed vector.
Questions:
1) will setting the MAT_HERMITIAN option save the memory of the matrix
storage?
2) will it save me time during the multiplication?
Thank you,
Michael.
**
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