Hello team,
I'm encountering a problem with my code's behavior on multiple processors. When
I run it on my personal computer it works just fine, but when I use it on our
computing cluster it produces an error (in one of the root-finding functions,
an assert statement is not satisfied) and
estion on KSPSetReusePreconditioner
> On Apr 18, 2019, at 10:44 AM, Yuyun Yang via petsc-users
> wrote:
>
> Hello team,
>
> I have a question on when I should be setting KSPSetReusePreconditioner to
> PETSC_TRUE or PETSC_FALSE. It made a pretty big difference in the solutions I
> get w
: petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] Question on KSPSetReusePreconditioner
On Thu, Apr 18, 2019 at 11:44 AM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
Hello team,
I have a question on when I should be setting KSPSetReusePreconditioner to
PETS
Hello team,
I have a question on when I should be setting KSPSetReusePreconditioner to
PETSC_TRUE or PETSC_FALSE. It made a pretty big difference in the solutions I
get when I ran my code testing both settings, so is recalculating the
preconditioner better since it will make the convergence
;, int)
> (fault.cpp:953)
>
> The first argument of this function is a Petsc array (obtained from
> VecGetArray, and after calling this function, VecRestoreArray was called on
> that same object). I can’t think of a way why valgrind thinks there is an
> uninitialized value. Is this by an
sages?
Thanks for your help on this.
Best regards,
Yuyun
From: petsc-users
mailto:petsc-users-boun...@mcs.anl.gov>> On
Behalf Of Yuyun Yang via petsc-users
Sent: Tuesday, April 16, 2019 7:30 AM
To: Smith, Barry F. mailto:bsm...@mcs.anl.gov>>
Cc: petsc-users@mcs.anl.gov<mailto:p
nd you can keep them under control from
the beginning (when the code is small and growing) rather than wait until the
code is large and there are many unfreed objects to chase down.
Good luck
Barry
> On Apr 16, 2019, at 1:14 AM, Yuyun Yang via petsc-users
> wrote:
>
> H
Hello team,
I'm trying to use the options -malloc_dump and -malloc_debug to examine memory
leaks. The messages however, are quite generic, and don't really tell me where
the problems occur, for example:
[ 0]1520 bytes VecCreate() line 35 in
I won't end up using Cholesky, so it's
>>> not really a big issue.
>>>
>>> Thanks again for the timely help!
>>> Yuyun
>>>
>>> Get Outlook for iOS
>>> From: Smith, Barry F.
>>> Sent: Thursday, April 11, 2019 6:44:54 PM
>
t end up using Cholesky, so it's
> > not really a big issue.
> >
> > Thanks again for the timely help!
> > Yuyun
> >
> > Get Outlook for iOS
> > From: Smith, Barry F.
> > Sent: Thursday, April 11, 2019 6:44:54 PM
> > To: Yuyun Yang
>
ubject: Re: [petsc-users] Question about KSP, and makefile linking MPICH
>
>
>
> > On Apr 11, 2019, at 5:44 PM, Yuyun Yang via petsc-users
> > wrote:
> >
> > Hello team,
> >
> > I’d like to check if it’s ok to use the same ksp object and change its
> &g
ursday, April 11, 2019 6:44:54 PM
To: Yuyun Yang
Cc: petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] Question about KSP, and makefile linking MPICH
> On Apr 11, 2019, at 5:44 PM, Yuyun Yang via petsc-users
> wrote:
>
> Hello team,
>
> I’d like to check if it’s ok to
Hello team,
I'd like to check if it's ok to use the same ksp object and change its operator
(the matrix A) later on in the code to solve a different problem?
Also, I know I've asked this before about linking to MPICH when I call mpirun,
instead of using my computer's default MPI, but I want to
hew Knepley mailto:knep...@gmail.com>>
Sent: Thursday, April 4, 2019 7:30:20 PM
To: Yuyun Yang
Cc: Smith, Barry F.; petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>
Subject: Re: [petsc-users] ASCIIRead error for multiple processors
On Thu, Apr 4, 2019 at 9:19 PM Yuyun Yang via pet
iple processors
On Thu, Apr 4, 2019 at 9:19 PM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
We are probably not going to use hundreds of processors, but i think it would
be good to just have processor 0 read the input and broadcast that to all the
other processors. Wo
ursday, April 4, 2019 7:30:20 PM
To: Yuyun Yang
Cc: Smith, Barry F.; petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] ASCIIRead error for multiple processors
On Thu, Apr 4, 2019 at 9:19 PM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
We are probably not going to
fine but having hundreds or thousands of processes open the same ASCII file and
reading from it will likely not be scalable.
> On Apr 4, 2019, at 3:15 PM, Yuyun Yang via petsc-users
> wrote:
>
> Hello team,
>
> I’m trying to use PetscViewerASCIIRead() to read in a single inter
Hello team,
I'm trying to use PetscViewerASCIIRead() to read in a single interger/scalar
value from an input file. It works for one processor. However, when running on
multiple processors, I'm getting the below error:
[1]PETSC ERROR: Invalid argument
[1]PETSC ERROR: Insufficient data, read
Sounds good, thanks for the advice!
-Original Message-
From: Jed Brown
Sent: Tuesday, March 19, 2019 1:23 PM
To: Yuyun Yang ; zakaryah ;
petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab
Yuyun Yang via petsc-users writes:
> I
h5info and h5read
routines, then I visualize with my own routines. Is there something specific
you need from Matlab?
On Tue, Mar 19, 2019 at 1:18 PM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
Got it, thanks!
From: Matthew Knepley mailto:knep...@gmail.com>
Got it, thanks!
From: Matthew Knepley
Sent: Tuesday, March 19, 2019 10:10 AM
To: Yuyun Yang
Cc: petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab
On Tue, Mar 19, 2019 at 11:58 AM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov
Hello team,
Currently we're using the PETSc binary file format to save Vecs and Mats and
visualize them in Matlab. It looks like HDF5 works more efficiently with large
data sets (faster I/O), and we're wondering if PETSc Vecs/Mats saved in HDF5
viewer can be visualized in Matlab as well?
nl.gov
Subject: Re: [petsc-users] Using PETSc with GPU
Yuyun Yang via petsc-users writes:
> Currently we are forming the sparse matrices explicitly, but I think the goal
> is to move towards matrix-free methods and use a stencil, which I suppose is
> good to use GPUs for and more efficien
Friday, March 15, 2019 2:54:02 PM
To: Yuyun Yang
Cc: petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] Using PETSc with GPU
On Fri, Mar 15, 2019 at 5:30 PM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
Hello team,
Our group is thinking of using GPUs for the linear solves
Hello team,
Our group is thinking of using GPUs for the linear solves in our code, which is
written in PETSc. I was reading the 2013 book chapter on implementation of
PETSc using GPUs but wonder if there is any more updated reference that I check
out? I also saw one example cuda code online
Hello team,
May I know for what types of computations is DMDA better to use compared to
regular Vec/Mat? It is more complicated in terms of usage, thus so far I've
only used Vec/Mat. Would DMDA improve the performance of solving large linear
systems (say for variable grid spacing as a result
I see, thank you!
Yuyun
From: Matthew Knepley
Sent: Friday, March 8, 2019 4:51 PM
To: Yuyun Yang
Cc: petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] Append vector to existing file
On Fri, Mar 8, 2019 at 5:53 PM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
Hell
Hello team,
This is a very simple question, but I just want to be sure I understand how the
viewer works. I have a file with some vectors already written into it. Now I'm
calling PetscViewerASCIIOpen, setting the format and then the file mode into
append:
PetscViewer viewer;
ierr =
;
- ierr = d.setFields(); CHKERRQ(ierr);
- ierr = d.setScatters(); CHKERRQ(ierr);
-
+ierr = d.setFields(); CHKERRQ(ierr);
+ierr = d.setScatters(); CHKERRQ(ierr); }
PetscFinalize();
return ierr;
}
Yuyun Yang via petsc-users writes:
> Yes, please see the attached files for a mini
l.gov<mailto:petsc-users@mcs.anl.gov>
Subject: Re: [petsc-users] AddressSanitizer: attempting free on address which
was not malloc()-ed
On Sun, Mar 3, 2019 at 1:03 PM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
I tried compiling without the sanitizer and running
()-ed
On Sun, Mar 3, 2019 at 1:03 PM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
I tried compiling without the sanitizer and running on valgrind. Got a bunch of
errors “Uninitialised value was created by a stack allocation at 0x41B280:
ComputeVel_qd::computeVel(
Yang mailto:yyan...@stanford.edu>>
Cc: Matthew Knepley mailto:knep...@gmail.com>>;
petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>
Subject: Re: [petsc-users] AddressSanitizer: attempting free on address which
was not malloc()-ed
On Wed, Feb 27, 2019 at 10:41 AM Yuyun Yan
Knepley mailto:knep...@gmail.com>>;
petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>
Subject: Re: [petsc-users] AddressSanitizer: attempting free on address which
was not malloc()-ed
On Wed, Feb 27, 2019 at 10:41 AM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>&
t malloc()-ed
On Wed, Feb 27, 2019 at 10:41 AM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
I called VecDestroy() in the destructor for this object – is that not the right
way to do it?
In Domain::testScatters(), you have many VecDuplicate(,), You need to
VecDestroy(
:50 AM
To: Yuyun Yang
Cc: Matthew Knepley ; petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] AddressSanitizer: attempting free on address which
was not malloc()-ed
On Wed, Feb 27, 2019 at 10:41 AM Yuyun Yang via petsc-users
mailto:petsc-users@mcs.anl.gov>> wrote:
I called VecD
: attempting free on address which
was not malloc()-ed
You call VecDuplicate() a bunch, but VecDestroy() only once in the bottom
function. This is wrong.
Also, CHECK ALL RETURN CODES. This is the fastest way to find errors.
Matt
On Wed, Feb 27, 2019 at 2:06 AM Yuyun Yang via petsc-users
Hello team,
I ran into the address sanitizer error that I hope you could help me with. I
don't really know what's wrong with the way the code frees memory. The relevant
code file is attached. The line number following domain.cpp specifically
referenced to the vector _q, which seems a little
Hello team,
I'd like to ask whether PETSc has a function to compute the Kronecker product
of a sparse matrix with an identity matrix? A Google search didn't lead me to a
manual page (like most of the other PETSc functions), so I'm wondering if this
has been implemented yet.
Thanks very much!
unction.
>
> Thanks a lot!
> Yuyun
>
> -Original Message-
> From: Smith, Barry F.
> Sent: Monday, February 18, 2019 6:41 PM
> To: Yuyun Yang
> Cc: petsc-users@mcs.anl.gov
> Subject: Re: [petsc-users] PetscBinaryRead fails
>
>
> Send program and data file if you
-
From: Smith, Barry F.
Sent: Monday, February 18, 2019 6:41 PM
To: Yuyun Yang
Cc: petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] PetscBinaryRead fails
Send program and data file if you cannot get it to work.
> On Feb 18, 2019, at 8:08 PM, Yuyun Yang via petsc-users
> wrote:
>
Hello,
I am writing a very simple function just to read in a single value from an
input file (which also just contains one single scalar value). Using
PetscBinaryRead(fd, , 1, PETSC_SCALAR) gives me the following error.
Could you help me figure out why?
[0]PETSC ERROR: -
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