I want to learn petsc by solving a small time-dependent problem:
The problem is from chemical kinetics, and consists of the following three
rate equations:
dy1/dt = -.04*y1 + 1.e4*y2*y3
dy2/dt = .04*y1 - 1.e4*y2*y3 - 3.e7*(y2)^2
dy3/dt = 3.e7*(y2)^2
on the interval from t =
I got my program to run. But the results doesn't make any sence.
At t = 0 y =1.00e+00 0.00e+00 0.00e+00,
At t = 0.01 y =9.996000e-01 4.00e-04 0.00e+00,
At t = 0.02 y =9.992002e-01 -4.720016e-02 4.80e-02,
At t = 0.03 y =7.722397e-01
I got the correct results! Thanks!
Could you please tell me whether I can use TS to solve ODE without
providing Jacobian matrix?
On Jun 22, 2010, at 7:19 PM, Jed Brown wrote:
On Tue, 22 Jun 2010 19:09:32 -0400, XUAN YU xxy113 at psu.edu wrote:
I got my program to run. But the results
On Jun 23, 2010, at 12:14 PM, Jed Brown wrote:
On Wed, 23 Jun 2010 10:22:19 -0400, Xuan YU xxy113 at psu.edu wrote:
I got the correct results! Thanks!
If you are feeling like experimenting, you could try -ts_type gl which
is a very new adaptive order adaptive step method for stiff
On Jun 23, 2010, at 1:17 PM, Jed Brown wrote:
On Wed, 23 Jun 2010 12:45:37 -0400, Xuan YU xxy113 at psu.edu wrote:
I changed dt=0.4 and the Monitor function, so GL doesn't work.
Choosing a smaller dt (only an initial value in this case) fixes that
problem, but I still see some difficulties
On Jun 28, 2010, at 2:24 PM, Xuan YU wrote:
Hi,
I run my code by ./xxx -pc_type icc
But it says:
WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
Option left: name:-pc_type value: icc
Could you please tell me what happened?
Xuan YU
xxy113
On Jun 23, 2010, at 10:44 AM, Jed Brown wrote:
On Wed, 23 Jun 2010 10:22:19 -0400, Xuan YU xxy113 at psu.edu wrote:
I got the correct results! Thanks!
Could you please tell me whether I can use TS to solve ODE without
providing Jacobian matrix?
Sure, use -snes_mf to solve it without
On Jul 2, 2010, at 2:21 PM, Jed Brown wrote:
On Fri, 2 Jul 2010 14:08:14 -0400, Xuan YU xxy113 at psu.edu wrote:
If I don't provide Jacobian, it will be: type: euler
total number
of nonlinear solver
iterations=0
assembling the matrix.
Are you calling MatZeroRows() or MatZeroEntries() or something else -
before assembling the matrix?
Satish
On Wed, 7 Jul 2010, Xuan YU wrote:
I made a change: ierr =
MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,5,PETSC_NULL,J);CHKERRQ(ierr);
Time of the code did not change much
On Jul 7, 2010, at 2:06 PM, Satish Balay wrote:
On Wed, 7 Jul 2010, Xuan YU wrote:
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,
10,PETSC_NULL,J);CHKERRQ(ierr);
ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr
correctly and
the manual
section which explains the assembly process.
Matt
On Wed, Jul 7, 2010 at 8:13 PM, Xuan YU xxy113 at psu.edu wrote:
On Jul 7, 2010, at 2:06 PM, Satish Balay wrote:
On Wed, 7 Jul 2010, Xuan YU wrote:
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,
10,PETSC_NULL,J
2010, Xuan YU wrote:
Sorry, this is the complete one:
[0]PETSC ERROR: - Error Message
[0]PETSC ERROR: Object is in wrong state!
[0]PETSC ERROR: Not for unassembled matrix!
[0]PETSC ERROR
down. Am I right?
Thanks!
Xuan YU
xxy113 at psu.edu
Hi,
In SNES, Petsc can compute Jacobian by:
ierr =
SNESSetJacobian
(snes,J,J,SNESDefaultComputeJacobian,PETSC_NULL);CHKERRQ(ierr);
How about TS? I don't want to provide Jacobian function by myself, but
I didn't find something like TSDefaultComputeJacobian.
Many thanks!
Xuan YU
xxy113
Begin forwarded message:
From: Jed Brown jed at 59A2.org
Date: July 21, 2010 8:04:17 PM EDT
To: Xuan YU xxy113 at psu.edu, PETSc users list petsc-users at mcs.anl.gov
Subject: Re: [petsc-users] TSDefaultComputeJacobian
On Wed, 21 Jul 2010 19:52:23 -0400, Xuan YU xxy113 at psu.edu wrote
the residual
function, which
is what the error is complaining about.
-
Could you please give me some suggestions about how to setup residual function?
Is there some example?
Matt
On Thu, Jul 22, 2010 at 11:43 AM, Xuan YU # wrote:
Begin forwarded
used during MatSetValues calls =37
not using I-node routines
Xuan YU
xxy113 at psu.edu
collect2: ld returned 1 exit status
and run with -log_summary to get a summary of where it is spending
the time.
This will give you a better idea of why it is taking so long.
Barry
On Jul 26, 2010, at 2:49 PM, Xuan YU wrote:
Hi,
I am using TS solving a nonlinear problem. I
Desc: not available
URL:
http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20100726/48f5111a/attachment-0005.png
-- next part --
Barry
On Jul 26, 2010, at 2:49 PM, Xuan YU wrote:
Hi,
I am using TS solving a nonlinear problem. I created an approximate
for this case?
Barry
On Jul 26, 2010, at 5:50 PM, Xuan YU wrote:
On Jul 26, 2010, at 3:53 PM, Barry Smith wrote:
./configure an optimized version of PETSc (that is with the ./
configure flag of --with-debugging=0) and run with -log_summary to
get a summary of where it is spending
much faster than sundails, so I tried Petsc.
Without knowing more information about what sundials/cvode is doing
there is no way to know why it is much faster. Could be larger time-
steps, less function evaluations, etc.
Barry
On Jul 27, 2010, at 8:22 AM, Xuan YU wrote:
On Jul
'
collect2: ld returned 1 exit status
Does this mean that I didn't install sundials correctly?
Xuan YU
xxy113 at psu.edu
On Jul 27, 2010, at 5:59 PM, Jed Brown wrote:
On Tue, 27 Jul 2010 17:48:12 -0400, Xuan YU xxy113 at psu.edu wrote:
Hi,
I run config/configure.py --download-sundials=1
make all
make test
and then, when I compile the code, there is no error but
pihm.o: In function `main':
pihm.c:(.text
On Jul 27, 2010, at 6:22 PM, Jed Brown wrote:
On Tue, 27 Jul 2010 18:14:46 -0400, Xuan YU xxy113 at psu.edu wrote:
How are you linking PETSc? I wonder if you're linking a different
build
than you just configured.
my PETSC_DIR = is the same to that of makefile of ex4
What about
Hi
I am running the example: src/ts/examples/tutorials/ex4.c
For this example, why sundials(./ex4 -ts_type sundials) only output
the first time step and the last time step, but beuler can output
every time step?
How can I make sundials output every time step?
Thanks!
Timestep 8: time = 0.000135787, 2-norm error = 0.000278648, max norm
error = 0.000401418
Timestep 9: time = 0.000195002, 2-norm error = 0.000388956, max norm
error = 0.000560541
Can I custom the output time of sundials?
Hong
On Wed, Jul 28, 2010 at 9:17 AM, Xuan YU xxy113 at psu.edu wrote:
Hi
On Jul 27, 2010, at 8:40 PM, Satish Balay wrote:
You list one compile with linux-gnu-c-debug - and the other with
linux-gnu-c-opt.
You are right!
How can I build sundials in linux-gun-c-opt? I want to run it without
debugging option.
Looks like you rebuilt linux-gnu-c-debug with
On Jul 28, 2010, at 3:05 PM, Jed Brown wrote:
On Wed, 28 Jul 2010 14:55:58 -0400, Xuan YU xxy113 at psu.edu wrote:
How can I build sundials in linux-gun-c-opt?
linux-gnu-c-opt/conf/reconfigure-linux-gnu-c-opt.py --download-
sundials make PETSC_ARCH=linux-gnu-c-opt all test
Why
On Jul 28, 2010, at 5:07 PM, Jed Brown wrote:
On Wed, 28 Jul 2010 17:01:34 -0400, Xuan YU xxy113 at psu.edu wrote:
On Jul 28, 2010, at 3:05 PM, Jed Brown wrote:
On Wed, 28 Jul 2010 14:55:58 -0400, Xuan YU xxy113 at psu.edu wrote:
How can I build sundials in linux-gun-c-opt?
linux-gnu-c
--
-- next part --
A non-text attachment was scrubbed...
Name: Picture 5.png
Type: image/png
Size: 23544 bytes
Desc: not available
URL:
http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20100729/b2e2864e/attachment-0011.png
-- next part --
Xuan YU
Hi,
Could you please tell me the interface of CVodeSetMaxStep and
CVodeSetInitStep in Petsc?
I failed to find them in the page
http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-3.0.0/src/ts/impls/implicit/sundials/sundials.c.html
Thanks!
Xuan YU
xxy113 at psu.edu
Hi,
I used several types of pc in TS solver. Only ilu and jacobi
accelerates my codes. But both of the preconditioners changed a lot of
the results comparing with result without pc. Could you please tell me
what should I do?
Xuan YU
xxy113 at psu.edu
Hi
I am using Petsc solve ODE nonlinear problem.
I was told to use direct method: umfpackage because of the jacobian matrix is
1860 by 1860.
But the time consumption is still too big:
TSSetType(ts,TSBEULER)
time ./pihm -log_summary -ksp_type preonly -pc_type lu
On Oct 21, 2010, at 5:56 PM, Matthew Knepley wrote:
On Thu, Oct 21, 2010 at 4:46 PM, Xuan Yu xxy113 at psu.edu wrote:
Hi
I am using Petsc solve ODE nonlinear problem.
I was told to use direct method: umfpackage because of the jacobian matrix is
1860 by 1860.
But the time
34 matches
Mail list logo
