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<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>
<p>2> Configure: <br>
</p>
<p>>export PETSC_DIR=./</p>
<p>>export PETSC_ARCH=arch<br>
</p>
<p>>./configure --prefix=$HOME/Install/petsc
--with-mpi-dir=/home/leejearl/Install/mpich_3.1.4/gnu
--download-exodusii=../externalpackages/exodus-5.24.tar.bz2
--download-netcdf=../externalpackages/netcdf-4.3.2.tar.gz
--download-hdf5=../externalpackages/hdf5-1.8.12.tar.gz
--download-metis=../externalpackages/git.metis.tar.gz
--download-parmetis=yes<br>
</p>
<p>3> The process of installation has no error.</p>
<p>4> After the installation, I added the following statement
into the file ~/.bashrc:</p>
<p>export PETSC_ARCH=""</p>
<p>export PETSC_DIR=$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 class="moz-cite-prefix">On 2016年08月13日 09:04, leejearl wrote:<br>
</div>
<blockquote cite="mid:d278fbe2-e0ad-a325-1cbb-bf778f1eadcc@126.com"
type="cite">
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<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 class="moz-cite-prefix">On 2016年08月13日 08:49, Oxberry,
Geoffrey Malcolm wrote:<br>
</div>
<blockquote
cite="mid:F6F1177B-F91D-4089-A112-86B0FC1834D7@llnl.gov"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=utf-8">
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Aug 12, 2016, at 5:41 PM, leejearl <<a
moz-do-not-send="true" href="mailto:leejearl@126.com"
class="">leejearl@126.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class="">
<p class="">Hi, Matt:<br class="">
</p>
<br class="">
<div class=""><br class="">
</div>
> Can you verify that you are running the master
branch?<br class="">
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>cd ${PETSC_DIR}</div>
<div>git branch</div>
<div><br class="">
</div>
<div>The last command should return something like a list of
branch names, and the branch name with an asterisk to the
left of it will be the branch you are currently on.</div>
<div><br class="">
</div>
<div>Geoff</div>
<div>
<div><br class="">
</div>
</div>
<blockquote type="cite" class="">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class="">I am not
sure, how can I verify this?<br class="">
And I configure PETSc with this command <br class="">
"./configure --prefix=$HOME/Install/petsc-openmpi
--with-mpi=/home/leejearl/Install/openmpi/gnu/1.8.4
--download-exodusii=yes --download-netcdf
--with-hdf5-dir=/home/leejearl/Install/hdf5-1.8.14
--download-metis=yes".<br class="">
Is there some problem? Can you show me your command for
configuring PETSc?<br class="">
<br class="">
<br class="">
Thanks<br class="">
<br class="">
leejearl<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<div class="moz-cite-prefix">On 2016年08月13日 01:10,
Matthew Knepley wrote:<br class="">
</div>
<blockquote
cite="mid:CAMYG4GmtHnQiAmWcZ9Pdb2ZMg9M2Pj+14kqnjd5iM4KmzyuRhw@mail.gmail.com"
type="cite" class="">
<div dir="ltr" class="">
<div class="gmail_extra">
<div class="gmail_quote">On Thu, Aug 11, 2016 at
8:00 PM, leejearl <span dir="ltr" class="">
<<a moz-do-not-send="true"
href="mailto:leejearl@126.com"
target="_blank" class="">leejearl@126.com</a>></span>
wrote:<br class="">
<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" class="">
<p class="">Thank you for your reply. I have
attached the code, grid and the error
message.</p>
<p class="">cavity.c is the code file,
cavity.exo is the grid, and error.dat is
the error message.</p>
<p class="">The command is "mpirun -n 2
./cavity</p>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Can you verify that you are
running the master branch? I just ran this and
got</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">DM Object: 2 MPI processes</div>
<div class=""> type: plex</div>
<div class="">DM_0x84000004_0 in 2 dimensions:</div>
<div class=""> 0-cells: 5253 5252</div>
<div class=""> 1-cells: 10352 10350</div>
<div class=""> 2-cells: 5298 (198) 5297 (198)</div>
<div class="">Labels:</div>
<div class=""> ghost: 2 strata of sizes (199,
400)</div>
<div class=""> vtk: 1 strata of sizes (4901)</div>
<div class=""> Cell Sets: 1 strata of sizes
(5100)</div>
<div class=""> Face Sets: 3 strata of sizes
(53, 99, 50)</div>
<div class=""> depth: 3 strata of sizes
(5253, 10352, 5298)</div>
</div>
<div class=""><br class="">
</div>
<div class=""> Thanks,</div>
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class=""> </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" class="">
<div class="">On 2016年08月11日 23:29, Matthew
Knepley wrote:<br class="">
</div>
<blockquote type="cite" class="">
<div dir="ltr" class="">
<div class="gmail_extra">
<div class="gmail_quote">On Thu, Aug
11, 2016 at 3:14 AM, leejearl <span
dir="ltr" class=""> <<a
moz-do-not-send="true"
href="mailto:leejearl@126.com"
target="_blank" class="">leejearl@126.com</a>></span>
wrote:<br class="">
<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" class="">
<p class="">Hi, <br class="">
Thank you for your reply.
It help me very much.<br
class="">
But, for
"/petsc-3.7.2/src/ts/examples/<wbr
class="">tutorials/ex11.c",
when I set the overlap to 2
levels, the command is <br
class="">
"mpirun -n 3 ./ex11 -f
annulus-20.exo
-ufv_mesh_overlap 2 -physics
sw", it suffers a error.<br
class="">
It seems to me that
setting overlap to 2 is very
common. Are there issues that
I have not take into
consideration?<br class="">
Any help are appreciated.</p>
</div>
</blockquote>
<div class="">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 class="">unstructured stuff. I
have test examples that run fine
for overlap > 1. Can you send
the entire error message?</div>
<div class=""><br class="">
</div>
<div class="">If the error is not in
the distribution, but rather in
the analytics, that is
understandable because this
example is only</div>
<div class="">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 class="">cells.</div>
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class=""> </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" class="">
<p class=""><span class=""><font
class="" color="#888888"><br
class="">
leejearl</font></span></p>
<div class="">
<div class=""><br class="">
<div class="">On 2016年08月11日
14:57, Julian Andrej
wrote:<br class="">
</div>
<blockquote type="cite"
class="">
<div dir="ltr" class="">Hi,
<div class=""><br
class="">
</div>
<div class="">take a
look at slide 10 of
[1], there is visually
explained what the
overlap between
partitions is.</div>
<div class=""><br
class="">
</div>
<div class="">[1] <a
moz-do-not-send="true"
href="https://www.archer.ac.uk/training/virtual/files/2015/06-PETSc/slides.pdf"
target="_blank"
class="">https://www.archer.ac.uk/t<wbr
class="">raining/virtual/files/2015/06-<wbr
class="">PETSc/slides.pdf</a></div>
</div>
<div class="gmail_extra"><br
class="">
<div class="gmail_quote">On
Thu, Aug 11, 2016 at
8:48 AM, leejearl <span
dir="ltr" class="">
<<a
moz-do-not-send="true"
href="mailto:leejearl@126.com" target="_blank" class="">leejearl@126.com</a>></span>
wrote:<br class="">
<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 class="">
I want to use
PETSc to build my
FVM code. Now, I
have a question
about<br class="">
the function
DMPlexDistribute(DM
dm, PetscInt
overlap, PetscSF
*sf, DM *dmOverlap)
.<br class="">
<br class="">
In the example
"/petsc-3.7.2/src/ts/examples/<wbr
class="">tutorials/ex11.c".
When I set the
overlap<br class="">
as 0 or 1, it works
well. But, if I set
the overlap as 2, it
suffers a problem.<br
class="">
I am confused
about the value of
overlap. Can it be
set as 2? What is
the meaning of<br
class="">
the parameter
overlap?<br class="">
Any helps are
appreciated!<span
class=""><font
class=""
color="#888888"><br
class="">
<br class="">
leejearl<br
class="">
<br class="">
<br class="">
<br class="">
</font></span></blockquote>
</div>
<br class="">
</div>
</blockquote>
<br class="">
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
<br class="" clear="all">
<span class=""><font class=""
color="#888888">
<div class=""><br class="">
</div>
-- <br class="">
<div
data-smartmail="gmail_signature"
class="">What most experimenters
take for granted before they
begin their experiments is
infinitely more interesting than
any results to which their
experiments lead.<br class="">
-- Norbert Wiener</div>
</font></span></div>
</div>
</blockquote>
<br class="">
</div>
</blockquote>
</div>
<br class="">
<br class="" clear="all">
<div class=""><br class="">
</div>
-- <br class="">
<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 class="">
-- Norbert Wiener</div>
</div>
</div>
</blockquote>
<br class="">
</div>
</div>
</blockquote>
</div>
<br class="">
</blockquote>
</blockquote>
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