On Thu, Feb 23, 2012 at 12:51 PM, Bojan Niceno <span dir="ltr"><<a href="mailto:bojan.niceno@psi.ch">bojan.niceno@psi.ch</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">
Dear Matt, <br>
<br>
<br>
are you sure? It is almost 4000 lines long! Shall I send only the
function which bother me?<br>
<br>
If the entire code is what you need, shall I make a tarball and
attach it?<br></div></blockquote><div><br></div><div>Send something the builds and runs. Don't care how long it is.</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">
Kind regards,<br>
<br>
<br>
Bojan<br>
<br>
On 2/23/2012 7:44 PM, Matthew Knepley wrote:
<blockquote type="cite">On Thu, Feb 23, 2012 at 12:28 PM, Bojan Niceno <span dir="ltr"><<a href="mailto:bojan.niceno@psi.ch" target="_blank">bojan.niceno@psi.ch</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"> On 2/23/2012 7:24 PM,
Matthew Knepley wrote:
<blockquote type="cite">On Thu, Feb 23, 2012 at 12:05 PM,
Bojan Niceno <span dir="ltr"><<a href="mailto:bojan.niceno@psi.ch" target="_blank">bojan.niceno@psi.ch</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"> Dear Matthew,<br>
<br>
<br>
thank you for your response. When I use
VecCreateGhost, I get the following:<br>
</div>
</blockquote>
<div><br>
</div>
<div>It appears that you passed a bad communicator. Did
you not initialize a 'comm' variable?</div>
</div>
</blockquote>
<br>
I pass PETSC_COMM_WORLD to VecCreateGhost. <br>
<br>
I don't know what you mean by 'comm' variable :-( I called
all the routines to initialize PETSc.</div>
</blockquote>
<div><br>
</div>
<div>Send your code to <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a>.</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"> <br>
Cheers,<br>
<br>
<br>
Bojan<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"> [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/petsc-as/documentation/faq.html#valgrind" target="_blank">http://www.mcs.anl.gov/petsc/petsc-as/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] PetscCommDuplicate line 140
src/sys/objects/tagm.c<br>
[0]PETSC ERROR: [0] PetscHeaderCreate_Private line
30 src/sys/objects/inherit.c<br>
[0]PETSC ERROR: [0] VecCreate line 32
src/vec/vec/interface/veccreate.c<br>
[0]PETSC ERROR: [0] VecCreateGhostWithArray line 567
src/vec/vec/impls/mpi/pbvec.c<br>
[0]PETSC ERROR: [0] VecCreateGhost line 647
src/vec/vec/impls/mpi/pbvec.c<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[0]PETSC ERROR: Signal received!<br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Release Version 3.2.0, Patch
6, Wed Jan 11 09:28:45 CST 2012<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: ./PSI-Flow on a arch-linu named
lccfd06 by niceno Thu Feb 23 19:02:45 2012<br>
[0]PETSC ERROR: Libraries linked from
/homecfd/niceno/PETSc-3.2-p6/arch-linux2-c-debug/lib<br>
[0]PETSC ERROR: Configure run at Fri Feb 10 10:24:13
2012<br>
[0]PETSC ERROR: Configure options<br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: User provided function() line 0 in
unknown directory unknown file<br>
<br>
I don't understand what could be causing it. I took
very good care to match the global numbers of ghost
cells when calling VecCreateGhost<br>
<br>
<br>
Kind regards,<br>
<br>
<br>
Bojan<br>
<br>
<br>
On 2/23/2012 5:53 PM, Matthew Knepley wrote:
<blockquote type="cite">On Thu, Feb 23, 2012 at
10:46 AM, Bojan Niceno <span dir="ltr"><<a href="mailto:bojan.niceno@psi.ch" target="_blank">bojan.niceno@psi.ch</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"> Hi all,<br>
<br>
I've never used a mailing list before, so I
hope this message will reach PETSc users and
experts and someone might be willing to help
me. I am also novice in PETSc.<br>
<br>
I have developed an unstructured finite volume
solver on top of PETSc libraries. In
sequential, it works like a charm. For the
parallel version, I do domain decomposition
externally with Metis, and work out local and
global numberings, as well as communication
patterns between processor. (The latter don't
seem to be needed for PETSc, though.) When I
run my program in parallel, it also works, but
I miss values in vectors' ghost points.<br>
<br>
I create vectors with command:
VecCreate(PETSC_COMM_WORLD, &x);<br>
<br>
Is it possible to get the ghost values if a
vector is created like this?<br>
</blockquote>
<div><br>
</div>
<div>I do not understand this question. By
definition, "ghost values" are those not
stored in the global vector.</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> I have tried to use
VecCreateGhost, but for some reason which is
beyond my comprehension, PETSc goes berserk
when it reaches the command:
VecCreateGhost(PETSC_COMM_WORLD, n,
PETSC_DECIDE, nghost, ifrom, &x)<br>
</blockquote>
<div><br>
</div>
<div>I think you can understand that "berserk"
tells me absolutely nothing. Error message?
Stack trace? Did you try to run an</div>
<div>example which uses VecGhost?</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"> Can anyone help me?
Either how to reach ghost values for vector
created by VecCreate, or how to use
VecCreateGhost properly?<br>
<br>
<br>
Kind regards,<br>
<br>
Bojan<br>
</blockquote>
</div>
<br>
<br clear="all">
<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></blockquote>
<span><font color="#888888"> <br>
<br>
<div>-- <br>
<img src="cid:part1.07080600.05050800@psi.ch" border="0"></div>
</font></span></div>
</blockquote>
</div>
<br>
<br clear="all">
<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></blockquote>
<span><font color="#888888"> <br>
<br>
<div>-- <br>
<img src="cid:part2.07040807.04050702@psi.ch" border="0"></div>
</font></span></div>
</blockquote>
</div>
<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></blockquote><span class="HOEnZb"><font color="#888888">
<br>
<br>
<div>-- <br>
<img src="cid:part3.09010509.02040600@psi.ch" border="0"></div>
</font></span></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>