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<p>Thank you for your help. The problem has been overcome following
your advices.</p>
<p>Now, I give some notes for this problem which might be useful for
others.</p>
<p>1. Up to now, we must use the code in the master branch. The
source code can be downloaded using git with:</p>
<p>git clone <a class="moz-txt-link-freetext" href="https://bitbucket.org/petsc/petsc">https://bitbucket.org/petsc/petsc</a> petsc.</p>
<p>2. Just the other day, I download the code using git with: git
clone -b maint <a class="moz-txt-link-freetext" href="https://bitbucket.org/petsc/petsc">https://bitbucket.org/petsc/petsc</a> petsc. <br>
</p>
<p> But, this copy of code still has such a problem. I am not
sure whether it is available now.<br>
</p>
<p>3. The code downloaded from website of PETSc(Version of 3.7.3) is
not available for this problem, although it is in the branch
master.<br>
</p>
<tt></tt><br>
Thanks for all helps again. Best wishes to you.<br>
<br>
leejearl<br>
<p><br>
</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 2016年08月16日 19:34, Matthew Knepley
wrote:<br>
</div>
<blockquote
cite="mid:CAMYG4G=VkWh_7wNe7q8pNmnEU6PgaJiQjQcH3Eb7vaUL-fdWSQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Mon, Aug 15, 2016 at 9:28 PM,
leejearl <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:leejearl@126.com" target="_blank">leejearl@126.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<p>Thank you for all your helps. I have tried and
reinstalled PETSc lots of times. The error are still
existed.</p>
<p>I can not find out the reasons. Now, I give the some
messages in this letter.</p>
<p>1> The source code is downloaded from the website
of PETSc, and the version is 3.7.2.<br>
</p>
</div>
</blockquote>
<div>You will need to run in the 'master' branch, not the
release since we have fixed some bugs. It is best to</div>
<div>use master for very new features like this. The
instructions are here: <a moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/developers/index.html">http://www.mcs.anl.gov/petsc/developers/index.html</a></div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt <br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<p>2> Configure: <br>
</p>
<p>>export PETSC_DIR=./</p>
<p>>export PETSC_ARCH=arch<br>
</p>
<p>>./configure --prefix=$HOME/Install/petsc
--with-mpi-dir=/home/leejearl/<wbr>Install/mpich_3.1.4/gnu
--download-exodusii=../<wbr>externalpackages/exodus-5.24.<wbr>tar.bz2
--download-netcdf=../<wbr>externalpackages/netcdf-4.3.2.<wbr>tar.gz
--download-hdf5=../<wbr>externalpackages/hdf5-1.8.12.<wbr>tar.gz
--download-metis=../<wbr>externalpackages/git.metis.<wbr>tar.gz
--download-parmetis=yes<br>
</p>
<p>3> The process of installation has no error.</p>
<p>4> After the installation, I added the following
statement into the file ~/.bashrc:</p>
<p>export PETSC_ARCH=""</p>
<p>export PETSC_DIR=$HOME/Install/pets/ <br>
</p>
<p>I wish to get some helps as follows:</p>
<p>1> Is there any problems in my installation? <br>
</p>
<p>2> Can any one help me a simple code in which the
value of overlap used in DMPlexDistribute function is
greater than 1.</p>
<p>3> I attach the code, makefile, grid and the error
messages again, I hope some one can help me to figure
out the problems.</p>
<p> 3.1> code: cavity.c</p>
<p> 3.2> makefile: makefile</p>
<p> 3.3> grid: cavity.exo</p>
<p> 3.4> error messages: error.dat</p>
<p> It is very strange that there is no error message
when I run it using "mpirun -n 3 ./cavity", but when I
run it using "mpirun -n 2 ./cavity", the errors
happed.</p>
<p>The error messages are shown in the file error.dat.<br>
</p>
<p><br>
</p>
<p>Any helps are appreciated.</p>
<p><br>
</p>
<br>
<div>On 2016年08月13日 09:04, leejearl wrote:<br>
</div>
<blockquote type="cite">
<p>Thank you for your reply. The source code I have
used is from the website of PETSc, not from the git
repository.</p>
<p>I will have a test with the code from git
repository.<br>
</p>
<p><br>
</p>
<p>leejearl<br>
</p>
<br>
<div>On 2016年08月13日 08:49, Oxberry, Geoffrey Malcolm
wrote:<br>
</div>
<blockquote type="cite"> <br>
<div>
<blockquote type="cite">
<div>On Aug 12, 2016, at 5:41 PM, leejearl <<a
moz-do-not-send="true"
href="mailto:leejearl@126.com"
target="_blank">leejearl@126.com</a>>
wrote:</div>
<br>
<div>
<div bgcolor="#FFFFFF" text="#000000">
<p>Hi, Matt:<br>
</p>
<br>
<div><br>
</div>
> Can you verify that you are running the
master branch?<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>cd ${PETSC_DIR}</div>
<div>git branch</div>
<div><br>
</div>
<div>The last command should return something like
a list of branch names, and the branch name with
an asterisk to the left of it will be the branch
you are currently on.</div>
<div><br>
</div>
<div>Geoff</div>
<div>
<div><br>
</div>
</div>
<blockquote type="cite">
<div>
<div bgcolor="#FFFFFF" text="#000000">I am not
sure, how can I verify this?<br>
And I configure PETSc with this command <br>
"./configure --prefix=$HOME/Install/petsc-<wbr>openmpi
--with-mpi=/home/leejearl/<wbr>Install/openmpi/gnu/1.8.4
--download-exodusii=yes --download-netcdf
--with-hdf5-dir=/home/<wbr>leejearl/Install/hdf5-1.8.14
--download-metis=yes".<br>
Is there some problem? Can you show me your
command for configuring PETSc?<br>
<br>
<br>
Thanks<br>
<br>
leejearl<br>
<br>
<br>
<br>
<br>
<br>
<div>On 2016年08月13日 01:10, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Thu, Aug
11, 2016 at 8:00 PM, leejearl <span
dir="ltr"> <<a
moz-do-not-send="true"
href="mailto:leejearl@126.com"
target="_blank">leejearl@126.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF"
text="#000000">
<p>Thank you for your reply. I
have attached the code, grid
and the error message.</p>
<p>cavity.c is the code file,
cavity.exo is the grid, and
error.dat is the error
message.</p>
<p>The command is "mpirun -n 2
./cavity</p>
</div>
</blockquote>
<div><br>
</div>
<div>Can you verify that you are
running the master branch? I just
ran this and got</div>
<div><br>
</div>
<div>
<div>DM Object: 2 MPI processes</div>
<div> type: plex</div>
<div>DM_0x84000004_0 in 2
dimensions:</div>
<div> 0-cells: 5253 5252</div>
<div> 1-cells: 10352 10350</div>
<div> 2-cells: 5298 (198) 5297
(198)</div>
<div>Labels:</div>
<div> ghost: 2 strata of sizes
(199, 400)</div>
<div> vtk: 1 strata of sizes
(4901)</div>
<div> Cell Sets: 1 strata of
sizes (5100)</div>
<div> Face Sets: 3 strata of
sizes (53, 99, 50)</div>
<div> depth: 3 strata of sizes
(5253, 10352, 5298)</div>
</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF"
text="#000000">
<div>On 2016年08月11日 23:29,
Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On
Thu, Aug 11, 2016 at
3:14 AM, leejearl <span
dir="ltr"> <<a
moz-do-not-send="true"
href="mailto:leejearl@126.com" target="_blank">leejearl@126.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px 0px
0px
0.8ex;border-left:1px
solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF"
text="#000000">
<p>Hi, <br>
Thank you for
your reply. It
help me very much.<br>
But, for
"/petsc-3.7.2/src/ts/examples/<wbr>tutorials/ex11.c",
when I set the
overlap to 2
levels, the
command is <br>
"mpirun -n 3
./ex11 -f
annulus-20.exo
-ufv_mesh_overlap
2 -physics sw", it
suffers a error.<br>
It seems to me
that setting
overlap to 2 is
very common. Are
there issues that
I have not take
into
consideration?<br>
Any help are
appreciated.</p>
</div>
</blockquote>
<div>I will check this
out. I have not tested
an overlap of 2 here
since I generally use
nearest neighbor FV
methods for</div>
<div>unstructured stuff.
I have test examples
that run fine for
overlap > 1. Can
you send the entire
error message?</div>
<div><br>
</div>
<div>If the error is not
in the distribution,
but rather in the
analytics, that is
understandable because
this example is only</div>
<div>intended to be run
using a nearest
neighbor FV method,
and thus might be
confused if we give it
two layers of ghost</div>
<div>cells.</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote
class="gmail_quote"
style="margin:0px 0px
0px
0.8ex;border-left:1px
solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF"
text="#000000">
<p><span><font
color="#888888"><br>
leejearl</font></span></p>
<div>
<div><br>
<div>On
2016年08月11日
14:57, Julian
Andrej wrote:<br>
</div>
<blockquote
type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>take a
look at slide
10 of [1],
there is
visually
explained what
the overlap
between
partitions is.</div>
<div><br>
</div>
<div>[1] <a
moz-do-not-send="true"
href="https://www.archer.ac.uk/training/virtual/files/2015/06-PETSc/slides.pdf"
target="_blank">https://www.archer.ac.uk/t<wbr>raining/virtual/files/2015/06-<wbr>PETSc/slides.pdf</a></div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
Thu, Aug 11,
2016 at 8:48
AM, leejearl <span
dir="ltr">
<<a
moz-do-not-send="true"
href="mailto:leejearl@126.com" target="_blank">leejearl@126.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Hi, all:<br>
I want to
use PETSc to
build my FVM
code. Now, I
have a
question about<br>
the function
DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap) .<br>
<br>
In the
example
"/petsc-3.7.2/src/ts/examples/<wbr>tutorials/ex11.c".
When I set the
overlap<br>
as 0 or 1, it
works well.
But, if I set
the overlap as
2, it suffers
a problem.<br>
I am
confused about
the value of
overlap. Can
it be set as
2? What is the
meaning of<br>
the parameter
overlap?<br>
Any helps
are
appreciated!<span><font
color="#888888"><br>
<br>
leejearl<br>
<br>
<br>
<br>
</font></span></blockquote>
</div>
<br>
</div>
</blockquote>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<span class=""><font
color="#888888"> <span><font
color="#888888">
<div><br>
</div>
-- <br>
<div
data-smartmail="gmail_signature">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</div>
</font></span></font></span></div>
<span class=""><font
color="#888888"> </font></span></div>
<span class=""><font
color="#888888"> </font></span></blockquote>
<span class=""><font
color="#888888"> <br>
</font></span></div>
<span class=""><font
color="#888888"> </font></span></blockquote>
<span class=""><font color="#888888">
</font></span></div>
<span class=""><font color="#888888">
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div
data-smartmail="gmail_signature">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</div>
</font></span></div>
<span class=""><font color="#888888"> </font></span></div>
<span class=""><font color="#888888"> </font></span></blockquote>
<span class=""><font color="#888888"> <br>
</font></span></div>
<span class=""><font color="#888888"> </font></span></div>
<span class=""><font color="#888888"> </font></span></blockquote>
<span class=""><font color="#888888"> </font></span></div>
<span class=""><font color="#888888"> <br>
</font></span></blockquote>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail_signature" data-smartmail="gmail_signature">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</div>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">
</pre>
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