On Thu, Feb 23, 2012 at 1:33 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>
I sent the code as an attached tarball. I sent it with case I run,
so is 2 MB big. It is now in the cue for moderator's approval. <br></div></blockquote><div><br></div><div>No, you HAVE to send it to <a href="mailto:petsc-maint@mcs.anl.gov">petsc-maint@mcs.anl.gov</a>, as I said last time, for exactly this reason.</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>
<br>
<br>
Kind regards,<br>
<br>
<br>
Bojan<br>
<br>
<br>
On 2/23/2012 8:04 PM, Matthew Knepley wrote:
<blockquote type="cite">On Thu, Feb 23, 2012 at 12:51 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 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:part1.02040900.03040302@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:part2.02060807.05000506@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:part3.09070605.05030208@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:part4.04060304.01030403@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>