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On 11/5/2012 3:30 PM, Matthew Knepley wrote:
<blockquote
cite="mid:CAMYG4GmW=A9UKr0qQT7t8UTsns_ORr_UB97wUZsJtx87fibOTQ@mail.gmail.com"
type="cite">On Fri, May 11, 2012 at 9:24 AM, TAY wee-beng <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi,<br>
<br>
I have been using the GUI environment to do debugging so I
am a bit reluctant to learn Valgrind as its outputs seems a
bit daunting. But I guess John is right. I've been spending
these few days learning bit by bit.<br>
<br>
I realised that the error occurs in computerhs, at:<br>
</div>
</blockquote>
<div><br>
</div>
<div>I bet this is a beautiful Fortranism. Do you include the
F90 header file with the interface definition?</div>
<div>If not, Fortran just craps out like this. I can't stress
enough how much time would be saved by</div>
<div>switching languages to something with at least a modicum of
error checking.</div>
</div>
</blockquote>
<br>
I initially used:<br>
<br>
#include "finclude/petsc.h90"<br>
<br>
Compilation and linking was fine in Linux and vs2008.<br>
<br>
Now I changed it to what ex22.F was using :<br>
<br>
#include <finclude/petscsys.h><br>
#include <finclude/petscvec.h><br>
#include <finclude/petscmat.h><br>
#include <finclude/petscpc.h><br>
#include <finclude/petscksp.h><br>
#include <finclude/petscdmda.h><br>
<br>
Compiling was ok but linking failed in Linux and VS2008: <br>
<br>
undefined reference to `dmdavecgetarrayf90_'<br>
<br>
I tried changing #include <finclude/petscdmda.h> to #include
<finclude/petscdmda.h90> and everything was ok in VS2008
again, giving the right answers.<br>
<br>
However, in Linux, I got the following error:<br>
<br>
[wtay@hpc12:tutorials]$ /opt/openmpi-1.5.3/bin/mpif90 -c -fPIC -g
-I/home/wtay/Lib/petsc-3.2-dev_shared_debug/include
-I/home/wtay/Lib/petsc-3.2-dev_shared_debug/include
-I/opt/openmpi-1.5.3/include -o ex29f.o ex29f.F90<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(25):
error #5082: Syntax error, found '::' when expecting one of: ( % : .
= =><br>
DMDABoundaryType :: pt<br>
-------------------------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(26):
error #5082: Syntax error, found '::' when expecting one of: ( % : .
= =><br>
DMDAStencilType :: st<br>
-------------------------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(25):
error #6590: This statement is not permitted as a statement within a
derived-type-def<br>
DMDABoundaryType :: pt<br>
--------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(26):
error #6590: This statement is not permitted as a statement within a
derived-type-def<br>
DMDAStencilType :: st<br>
--------^<br>
ex29f.F90(68): error #6404: This name does not have a type, and must
have an explicit type. [DMDA_BOUNDARY_NONE]<br>
call
DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,i3,i3,PETSC_DECIDE,PETSC_DECIDE,i1,i1,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,da,ierr)<br>
-----------------------------------^<br>
ex29f.F90(68): error #6404: This name does not have a type, and must
have an explicit type. [DMDA_STENCIL_STAR]<br>
call
DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,i3,i3,PETSC_DECIDE,PETSC_DECIDE,i1,i1,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,da,ierr)<br>
-------------------------------------------------------------------------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(25):
error #5082: Syntax error, found '::' when expecting one of: ( % : .
= =><br>
DMDABoundaryType :: pt<br>
-------------------------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(26):
error #5082: Syntax error, found '::' when expecting one of: ( % : .
= =><br>
DMDAStencilType :: st<br>
-------------------------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(25):
error #6590: This statement is not permitted as a statement within a
derived-type-def<br>
DMDABoundaryType :: pt<br>
--------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(26):
error #6590: This statement is not permitted as a statement within a
derived-type-def<br>
DMDAStencilType :: st<br>
--------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(25):
error #5082: Syntax error, found '::' when expecting one of: ( % : .
= =><br>
DMDABoundaryType :: pt<br>
-------------------------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(26):
error #5082: Syntax error, found '::' when expecting one of: ( % : .
= =><br>
DMDAStencilType :: st<br>
-------------------------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(25):
error #6590: This statement is not permitted as a statement within a
derived-type-def<br>
DMDABoundaryType :: pt<br>
--------^<br>
/home/wtay/Lib/petsc-3.2-dev_shared_debug/include/finclude/ftn-custom/petscdmda.h90(26):
error #6590: This statement is not permitted as a statement within a
derived-type-def<br>
DMDAStencilType :: st<br>
<br>
Is there some errors in petscdmda.h90?<br>
<br>
<br>
<blockquote
cite="mid:CAMYG4GmW=A9UKr0qQT7t8UTsns_ORr_UB97wUZsJtx87fibOTQ@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> <b>call
DMDAVecRestoreArrayF90(da,b,array,ierr)</b><br>
<br>
==27464== Invalid write of size 8<br>
==27464== at 0x402835: computerhs_ (ex29f.F90:119)<br>
==27464== Address 0xfffffffffffffef0 is not stack'd,
malloc'd or (recently) free'd<br>
==27464== <br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
Violation, probably memory access out of range<br>
[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger<br>
[0]PETSC ERROR: or see <a moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind"
target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>[0]PETSC
ERROR: or try <a moz-do-not-send="true"
href="http://valgrind.org" target="_blank">http://valgrind.org</a>
on GNU/linux and Apple Mac OS X to find memory corruption
errors<br>
[0]PETSC ERROR: likely location of problem given in stack
below<br>
[0]PETSC ERROR: --------------------- Stack Frames
------------------------------------<br>
[0]PETSC ERROR: Note: The EXACT line numbers in the stack
are not available,<br>
[0]PETSC ERROR: INSTEAD the line number of the start
of the function<br>
[0]PETSC ERROR: is given.<br>
[0]PETSC ERROR: [0] DM user function line 0 unknownunknown<br>
[0]PETSC ERROR: [0] DMComputeFunction line 2085
/home/wtay/Codes/petsc-dev/src/dm/interface/dm.c<br>
[0]PETSC ERROR: [0] KSPSetUp line 182
/home/wtay/Codes/petsc-dev/src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[0]PETSC ERROR: Signal received!<br>
<br>
I have checked that "array" 's values are correct. This
statement executed without problems in VS2008. If I replace
the above with something like:<br>
<br>
<b>call VecSet(b,Hy,ierr)</b><br>
<br>
Everything is fine in Linux.<br>
<br>
Is there something wrong with <b>DMDAVecRestoreArrayF90</b>?<br>
<br>
My code in the area is:<br>
<br>
call
DMDAGetCorners(da,xs,ys,PETSC_NULL_INTEGER,xm,ym,PETSC_NULL_INTEGER,ierr)<br>
<br>
call DMDAVecGetArrayF90(da,b,array,ierr)<br>
<br>
do j = ys,ys+ym-1<br>
<br>
do i = xs,xs+xm-1<br>
<br>
array(i,j) =
exp(-(i*Hx)*(i*Hx)/nu)*exp(-(j*Hy)*(j*Hy)/nu)*Hx*Hy<br>
<br>
end do<br>
<br>
end do<br>
<br>
call DMDAVecRestoreArrayF90(da,b,array,ierr)<br>
<br>
call VecAssemblyBegin(b,ierr)<br>
<br>
call VecAssemblyEnd(b,ierr)<br>
<br>
<br>
<pre cols="72">Yours sincerely,
TAY wee-beng</pre>
<br>
On 8/5/2012 9:41 PM, John Mousel wrote:
<blockquote type="cite">TAY wee-bing,<br>
<br>
If you want to be a programmer that writes interesting and
reliable code, you need to be willing to use the tools of
the trade. I can't think of a bigger time-saver than
Valgrind. I would suggest that you learn to use it and use
it a lot. I bet it will lead you to the root of your
problem pretty quickly.<br>
<br>
John<br>
<br>
<div class="gmail_quote">On Tue, May 8, 2012 at 2:17 PM,
TAY wee-beng <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi,<br>
<br>
I compiled and run my code under visual studio 2008
with intel fortran. Everything works ok.<br>
<br>
However, when I tried to run the code in linux, I
got the error as below. The error happens when
KSPSetUp(ksp,ierr) is called.<br>
<br>
However, I am not able to print VecView or MatView
to view if there's any errors. Is there any
recommendation for debugging? I hope I do not need
to valgrind if possible.<br>
<br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: Caught signal number 11 SEGV:
Segmentation Violation, probably memory access out
of range<br>
[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger<br>
[0]PETSC ERROR: or see <a moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind"
target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>[0]PETSC
ERROR: or try <a moz-do-not-send="true"
href="http://valgrind.org" target="_blank">http://valgrind.org</a>
on GNU/linux and Apple Mac OS X to find memory
corruption errors<br>
[0]PETSC ERROR: likely location of problem given in
stack below<br>
[0]PETSC ERROR: --------------------- Stack Frames
------------------------------------<br>
[0]PETSC ERROR: Note: The EXACT line numbers in the
stack are not available,<br>
[0]PETSC ERROR: INSTEAD the line number of the
start of the function<br>
[0]PETSC ERROR: is given.<br>
[0]PETSC ERROR: [0] DM user function line 0
unknownunknown<br>
[0]PETSC ERROR: [0] DMComputeFunction line 2085
/home/wtay/Codes/petsc-dev/src/dm/interface/dm.c<br>
[0]PETSC ERROR: [0] KSPSetUp line 182
/home/wtay/Codes/petsc-dev/src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[0]PETSC ERROR: Signal received!<br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Development HG revision:
7ecdd63ec420b1659b960e65d96e822c5ac1a968 HG Date:
Mon May 07 21:42:26 2012 -0500<br>
[0]PETSC ERROR: See docs/changes/index.html for
recent updates.<br>
[0]PETSC ERROR: See docs/faq.html for hints about
trouble shooting.<br>
[0]PETSC ERROR: See docs/index.html for manual
pages.<br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: ./ex29f on a petsc-3.2 named hpc12
by wtay Tue May 8 20:45:42 2012<br>
[0]PETSC ERROR: Libraries linked from
/home/wtay/Lib/petsc-3.2-dev_shared_debug/lib<br>
[0]PETSC ERROR: Configure run at Tue May 8 10:47:59
2012<br>
[0]PETSC ERROR: Configure options
--with-mpi-dir=/opt/openmpi-1.5.3/
--with-blas-lapack-dir=/opt/intelcpro-11.1.059/mkl/lib/em64t/
--with-debugging=1 --download-hypre=1
--prefix=/home/wtay/Lib/petsc-3.2-dev_shared_debug
--known-mpi-shared=1 --with-shared-libraries<br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: User provided function() line 0 in
unknown directory unknown file<br>
--------------------------------------------------------------------------<br>
MPI_ABORT was invoked on rank 0 in communicator
MPI_COMM_WORLD <br>
with errorcode 59.<br>
<br>
NOTE: invoking MPI_ABORT causes Open MPI to kill all
MPI processes.<br>
You may or may not see output from other processes,
depending on<br>
exactly when Open MPI kills them.<br>
<br>
<pre cols="72">Yours sincerely,
TAY wee-beng</pre>
<br>
On 5/5/2012 1:43 AM, Matthew Knepley wrote:
<blockquote type="cite">
<div class="gmail_extra">On Fri, May 4, 2012 at
5:42 PM, TAY wee-beng <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:zonexo@gmail.com"
target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi,<br>
<br>
I wonder if you people are interested to
include my ex29 fortran version in the
petsc examples, which can help people who
are using fortran.<br>
</div>
</blockquote>
<div><br>
</div>
<div>Yes, we will definitely include it.
Please send the source, and a representative
output with run options.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Thanks.<br>
<pre cols="72">Yours sincerely,
TAY wee-beng</pre>
<br>
On 4/5/2012 9:28 PM, Matthew Knepley
wrote:
<blockquote type="cite">
<div class="gmail_extra">On Fri, May 4,
2012 at 3:24 PM, TAY wee-beng <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:zonexo@gmail.com"
target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> <br>
On 4/5/2012 9:16 PM, Barry Smith
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> Do
an hg pull and then run make in
src/mat/interface/ftn-custom/<br>
<br>
Then it should link.<br>
<br>
Barry<br>
<br>
There was a E missing from
the all caps name of the
function.<br>
</blockquote>
After hg pull, I did:<br>
<br>
cd src//mat/interface/ftn-custom/<br>
<br>
User@User-PC
/cygdrive/c/temp/petsc-dev/src/mat/interface/ftn-custom<br>
$ make<br>
make[1]: Warning: File
`/cygdrive/c/temp/petsc-dev/petsc-3.2-dev_win32_vs2008/lib/libpetsc.lib(zmatregf.o)'
has modification time 787 s in the
future<br>
make[1]: Nothing to be done for
`libc'.<br>
make[1]: warning: Clock skew
detected. Your build may be
incomplete.<br>
<br>
But it still can't work.<br>
</blockquote>
<div><br>
</div>
<div>Something is messed up with the
clock on this machine.</div>
<div><br>
</div>
<div>HOWEVER, development requires
certain basic skills in order to
debug your work. We</div>
<div>cannot be the ones debugging
your code. Now</div>
<div><br>
</div>
<div> nm $PETSC_ARCH/lib/libpetsc.a
| grep -i MatNullSpaceRemove</div>
<div><br>
</div>
<div> will look for the symbol.</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> <br>
<br>
On May 4, 2012, at 2:11 PM,
Matthew Knepley wrote:<br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> On
Fri, May 4, 2012 at 3:01 PM,
TAY wee-beng<<a
moz-do-not-send="true"
href="mailto:zonexo@gmail.com"
target="_blank">zonexo@gmail.com</a>>
wrote:<br>
<br>
On 4/5/2012 5:17 PM, Matthew
Knepley wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> On
Fri, May 4, 2012 at 11:05
AM, TAY wee-beng<<a
moz-do-not-send="true"
href="mailto:zonexo@gmail.com"
target="_blank">zonexo@gmail.com</a>>
wrote:<br>
<br>
On 4/5/2012 3:05 PM, Matthew
Knepley wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
On Fri, May 4, 2012 at
8:59 AM, TAY wee-beng<<a
moz-do-not-send="true"
href="mailto:zonexo@gmail.com"
target="_blank">zonexo@gmail.com</a>>
wrote:<br>
<br>
Hi,<br>
<br>
Is there anything else I
can try to get it working
right?<br>
<br>
The
MatGetNullSpaceRemove() is
missing.<br>
</blockquote>
Where should I add
MatGetNullSpaceRemove and
what are its syntax? I
googled but there's no
results.<br>
<br>
Fixed in p;etsc-dev:<br>
<br>
<a moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/Mat/MatNullSpaceRemove.html"
target="_blank">http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/Mat/MatNullSpaceRemove.html</a><br>
</blockquote>
I just compiled the updated
petsc-dev but I got the same
error msg when I use:<br>
<br>
call
MatNullSpaceRemove(nullspace,b,PETSC_NULL,ierr)<br>
<br>
error LNK2019: unresolved
external symbol
MATNULLSPACEREMOVE referenced
in function COMPUTERHS<br>
1>c:\obj_tmp\ex29f\Debug\ex29f.exe
: fatal error LNK1120: 1
unresolved externals<br>
<br>
That function is in:<br>
<br>
src/mat/interface/ftn-custom/zmatrixf.c<br>
<br>
Did that compile? Can you see
the symbol in libpetsc.a?<br>
<br>
Matt<br>
<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
Matt<br>
<br>
Thanks.<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
Matt<br>
<br>
Thanks！<br>
<br>
<br>
On 2/5/2012 10:11 PM,
Matthew Knepley wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
On Wed, May 2, 2012 at
1:55 PM, TAY
wee-beng<<a
moz-do-not-send="true"
href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>>
wrote:<br>
Hi,<br>
<br>
I did a MatView and
VecView on both C and
Fortran, right after Mat
and Vec assembly. I have
attached the printout
below. They are exactly
the same, but yet the
result is different in
Neumann condition.
However, the dirichlet
condition gives the
correct ans. Is there
anything else that could
be wrong even if the Mat
and Vec are the same?<br>
<br>
Did you set the null
space for the matrix
when you have Neumann
conditions?<br>
</blockquote>
Yes, for the matrix, I set
as:<br>
<br>
call
MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,PETSC_NULL_OBJECT,nullspace,ierr)<br>
<br>
call
MatSetNullSpace(jac,nullspace,ierr)<br>
<br>
call
MatNullSpaceDestroy(nullspace,ierr)<br>
<br>
for the Vec,<br>
<br>
call
MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,PETSC_NULL_OBJECT,nullspace,ierr)<br>
<br>
!call
MatNullSpaceRemove(nullspace,b,PETSC_NULL,ierr)<br>
<br>
call
MatNullSpaceDestroy(nullspace,ierr)<br>
<br>
MatNullSpaceRemove was
comment out because
there's error during
linking<br>
<br>
<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
Matt<br>
<br>
Thanks!<br>
<br>
Fortran:<br>
<br>
Matrix Object: 1 MPI
processes<br>
type: seqaij<br>
row 0: (0, 2) (1, -1)
(3, -1)<br>
row 1: (0, -1) (1, 3)
(2, -1) (4, -1)<br>
row 2: (1, -1) (2, 2)
(5, -1)<br>
row 3: (0, -1) (3, 3)
(4, -1) (6, -1)<br>
row 4: (1, -1) (3, -1)
(4, 4) (5, -1) (7,
-1)<br>
row 5: (2, -1) (4, -1)
(5, 3) (8, -1)<br>
row 6: (3, -1) (6, 2)
(7, -1)<br>
row 7: (4, -1) (6, -1)
(7, 3) (8, -1)<br>
row 8: (5, -1) (7, -1)
(8, 2)<br>
Vector
Object:Vec_0000000084000000_0
1 MPI processes<br>
type: mpi<br>
Process [0]<br>
0.25<br>
0.0205213<br>
1.135e-005<br>
0.0205213<br>
0.00168449<br>
9.31663e-007<br>
1.135e-005<br>
9.31663e-007<br>
5.15289e-010<br>
Vector
Object:Vec_0000000084000000_1
1 MPI processes<br>
type: mpi<br>
Process [0]<br>
0.14924<br>
0.0242397<br>
-0.0260347<br>
0.0242397<br>
-0.0256192<br>
-0.0400102<br>
-0.0260347<br>
-0.0400102<br>
-0.0400102<br>
Press any key to
continue . . .<br>
<br>
C:<br>
<br>
Matrix Object: 1 MPI
processes<br>
type: seqaij<br>
row 0: (0, 2) (1, -1)
(3, -1)<br>
row 1: (0, -1) (1, 3)
(2, -1) (4, -1)<br>
row 2: (1, -1) (2, 2)
(5, -1)<br>
row 3: (0, -1) (3, 3)
(4, -1) (6, -1)<br>
row 4: (1, -1) (3, -1)
(4, 4) (5, -1) (7,
-1)<br>
row 5: (2, -1) (4, -1)
(5, 3) (8, -1)<br>
row 6: (3, -1) (6, 2)
(7, -1)<br>
row 7: (4, -1) (6, -1)
(7, 3) (8, -1)<br>
row 8: (5, -1) (7, -1)
(8, 2)<br>
Vector
Object:Vec_0x1d3b000_0 1
MPI processes<br>
type: mpi<br>
Process [0]<br>
0.25<br>
0.0205212<br>
1.135e-05<br>
0.0205212<br>
0.00168449<br>
9.31663e-07<br>
1.135e-05<br>
9.31663e-07<br>
5.15288e-10<br>
Vector
Object:Vec_0x1d3b000_1 1
MPI processes<br>
type: mpi<br>
Process [0]<br>
0.139311<br>
0.0305751<br>
-0.0220633<br>
0.0305751<br>
-0.0135158<br>
-0.042185<br>
-0.0220633<br>
-0.042185<br>
-0.058449<br>
<br>
<br>
<br>
Yours sincerely,<br>
<br>
TAY wee-beng<br>
<br>
<br>
On 1/5/2012 11:54 PM,
Matthew Knepley wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
On Tue, May 1, 2012 at
5:48 PM, TAY
wee-beng<<a
moz-do-not-send="true"
href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>>
wrote:<br>
Hi,<br>
<br>
Do you mean my method
is wrong?<br>
<br>
I am following the
template of ex22f,<br>
<br>
where the variables
are declared as :<br>
<br>
PetscScalar v(5)<br>
<br>
MatStencil
row(4),col(4,5)<br>
<br>
Hence,<br>
<br>
for the neumann BC<br>
<br>
num = 1<br>
<br>
if
(j/=0) then<br>
<br>
v(num) = -rho*HxdHy<br>
<br>
col(MatStencil_i,num)
= i<br>
<br>
col(MatStencil_j,num)
= j-1<br>
<br>
num
= num + 1<br>
<br>
end if<br>
<br>
if
(i/=0) then<br>
<br>
v(num) = -rho*HydHx<br>
<br>
col(MatStencil_i,num)
= i-1<br>
<br>
col(MatStencil_j,num)
= j<br>
<br>
num
= num + 1<br>
<br>
end if<br>
<br>
if
(i/=mx-1) then<br>
<br>
v(num) = -rho*HydHx<br>
<br>
col(MatStencil_i,num)
= i+1<br>
<br>
col(MatStencil_j,num)
= j<br>
<br>
num
= num + 1<br>
<br>
end if<br>
<br>
if
(j/=my-1) then<br>
<br>
v(num) = -rho*HxdHy<br>
<br>
col(MatStencil_i,num)
= i<br>
<br>
col(MatStencil_j,num)
= j+1<br>
<br>
num
= num + 1<br>
<br>
end if<br>
<br>
v(num)
=
((num-1)/2.0)*rho*(HxdHy
+ HydHx)<br>
<br>
print
*, v<br>
<br>
col(MatStencil_i,num)
= i<br>
<br>
col(MatStencil_j,num)
= j<br>
<br>
!num =
num + 1<br>
<br>
call
MatSetValuesStencil(jac,i1,row,num,col,v,INSERT_VALUES,ierr)<br>
<br>
I do not get any more
out of range error.
However,my ans is
still different from
that of ex29 in C.<br>
<br>
This is very simple.
You have an error in
your code. Checking it
is very simple: run
the code and<br>
break in
MatSetValues(). Make
sure ex29 makes calls
with exactly the same
indices as your ex29f.<br>
<br>
Matt<br>
<br>
Yours sincerely,<br>
<br>
TAY wee-beng<br>
<br>
-- <br>
What most
experimenters take for
granted before they
begin their
experiments is
infinitely more
interesting than any
results to which their
experiments lead.<br>
-- Norbert Wiener<br>
</blockquote>
<br>
<br>
-- <br>
What most experimenters
take for granted before
they begin their
experiments is
infinitely more
interesting than any
results to which their
experiments lead.<br>
-- Norbert Wiener<br>
</blockquote>
<br>
<br>
-- <br>
What most experimenters
take for granted before
they begin their
experiments is infinitely
more interesting than any
results to which their
experiments lead.<br>
-- Norbert Wiener<br>
</blockquote>
<br>
<span><font color="#888888">
<br>
-- <br>
What most experimenters
take for granted before
they begin their
experiments is
infinitely more
interesting than any
results to which their
experiments lead.<br>
-- Norbert Wiener<br>
</font></span></blockquote>
<span><font color="#888888"> <br>
<span><font
color="#888888"> <br>
-- <br>
What most
experimenters take for
granted before they
begin their
experiments is
infinitely more
interesting than any
results to which their
experiments lead.<br>
-- Norbert Wiener<br>
</font></span></font></span></blockquote>
<span><font color="#888888"> </font></span></blockquote>
<span><font color="#888888"> </font></span></blockquote>
<span><font color="#888888"> </font></span></div>
<span><font color="#888888"> <br>
<br clear="all">
<span class="HOEnZb"><font
color="#888888"> <span><font
color="#888888">
<div><br>
</div>
-- <br>
What most experimenters
take for granted before
they begin their
experiments is infinitely
more interesting than any
results to which their
experiments lead.<br>
-- Norbert Wiener<br>
</font></span></font></span></font></span></div>
<span class="HOEnZb"><font
color="#888888"> <span><font
color="#888888"> </font></span></font></span></blockquote>
<span class="HOEnZb"><font color="#888888">
<span><font color="#888888"> </font></span></font></span></div>
<span class="HOEnZb"><font color="#888888">
<span><font color="#888888"> </font></span></font></span></blockquote>
<span class="HOEnZb"><font color="#888888"> <span><font
color="#888888"> </font></span></font></span></div>
<span class="HOEnZb"><font color="#888888"> <span><font
color="#888888"> <br>
<br clear="all">
<div><br>
</div>
-- <br>
What most experimenters take for granted
before they begin their experiments is
infinitely more interesting than any
results to which their experiments lead.<br>
-- Norbert Wiener<br>
</font></span></font></span></div>
<span class="HOEnZb"><font color="#888888"> </font></span></blockquote>
<span class="HOEnZb"><font color="#888888"> </font></span></div>
<span class="HOEnZb"><font color="#888888"> </font></span></blockquote>
<span class="HOEnZb"><font color="#888888"> </font></span></div>
<span class="HOEnZb"><font color="#888888"> <br>
</font></span></blockquote>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to
which their experiments lead.<br>
-- Norbert Wiener<br>
</blockquote>
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