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Hi,<br>
<br>
I have modified the C version of the ex29 example in ksp to Fortran.
I have attached it. Feel free to include it in the distribution of
PETSc.<br>
<br>
The DMDAVecGetArrayF90 and DMDAVecRestoreArrayF90 are not working in
linux with ifort, so VecSetValues was used. Worked in VS2008 though.<br>
<br>
Btw, I need to solve the Poisson equation multiple times using
different RHS vector. <br>
<br>
Which subroutines do I need to call only once?<br>
<br>
Can I also add :<br>
<br>
call MatSetOption(jac,MAT_STRUCTURALLY_SYMMETRIC,PETSC_TRUE,ierr)<br>
<br>
call MatSetOption(jac,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE,ierr)<br>
<br>
call MatSetOption(jac,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE,ierr)<br>
<br>
call KSPSetOperators(ksp,A_mat,A_mat,SAME_NONZERO_PATTERN,ierr)<br>
<pre class="moz-signature" cols="72">Yours sincerely,
TAY wee-beng</pre>
<br>
On 11/5/2012 4:04 PM, John Mousel wrote:
<blockquote
cite="mid:CA+zegpm5Ca=6rKMBEjQ3vJZM0hCvMyor1BF2Re27Hb_vHwCRRg@mail.gmail.com"
type="cite">Include both header files. <br>
<br>
#include <finclude/petscdmda.h><br>
#include <finclude/petscdmda.h90><br>
<br>
The h90 header only includes the interface definitions for
Fortran.<br>
<br>
John<br>
<br>
<div class="gmail_quote">On Fri, May 11, 2012 at 8:51 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>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div class="im"> <br>
<br>
On 11/5/2012 3:30 PM, Matthew Knepley wrote:
<blockquote 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>
</div>
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?
<div>
<div class="h5"><br>
<br>
<br>
<blockquote 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
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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
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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><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><font color="#888888">
<span><font
color="#888888"> </font></span></font></span></blockquote>
<span><font color="#888888"> <span><font
color="#888888"> </font></span></font></span></div>
<span><font color="#888888"> <span><font
color="#888888"> </font></span></font></span></blockquote>
<span><font color="#888888"> <span><font
color="#888888"> </font></span></font></span></div>
<span><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><font color="#888888"> </font></span></blockquote>
<span><font color="#888888"> </font></span></div>
<span><font color="#888888"> </font></span></blockquote>
<span><font color="#888888"> </font></span></div>
<span><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>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</blockquote>
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