<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 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>
<p></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 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 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 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 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 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 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>