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 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 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 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 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 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 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 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 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 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 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 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">
<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>
<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></div>
</blockquote>
</div>
</blockquote></div><br>