<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Tue, Nov 15, 2016 at 6:07 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
Hi, Matt:<br>
Thank you for your kind reply. Since it is a low level routine,
is there any method which I can used for creating a <br>
dynamic array?<br>
</div></blockquote><div><br></div><div>I am not sure what you are asking for?</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"><div> Thanks<br>
leejearl<br>
<br>
<div class="m_-5870127340255563735moz-cite-prefix">On 2016年11月15日 16:20, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Tue, Nov 15, 2016 at 1:00 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 Lawrence:<br>
<br>
Thank you for your prompt reply. It works well, but I
encounter another problem.<br>
<br>
The code is as follows:<br>
<br>
PetscScalar *arrayConVar, *arrayDeltaX,
*arrayDeltaY;<br>
<br>
ierr = DMPlexGetAdjacency(dm, c, &adjSize,
&adj); CHKERRQ(ierr);<br>
<br>
/*PetscSynchronizedPrintf(PETS<wbr>C_COMM_WORLD,
"adjSize = %d\n", adjSize);*/<br>
adjSizeInterior = -1;<br>
for(i = 0; i < adjSize; i++)<br>
{<br>
if(adj[i] < cEndInterior)<br>
{<br>
adjSizeInterior++;<br>
/*PetscSynchronizedPrintf(PETS<wbr>C_COMM_WORLD,
"adj[%d]= %d\n", i, adj[i]);*/<br>
}<br>
}<br>
/*<br>
PetscSynchronizedPrintf(PETSC_<wbr>COMM_WORLD,
"adjSizeInterior = %d\n", adjSizeInterior);<br>
PetscSynchronizedFlush(PETSC_C<wbr>OMM_WORLD,PETSC_STDOUT);<br>
*/<br>
<br>
ierr = PetscMalloc3(adjSizeInterior*4<wbr>,
&arrayConVar, adjSizeInterior, &arrayDeltaX,
adjSizeInterior, &arrayDeltaY); CHKERRQ(ierr);<br>
<br>
PetscFree3(arrayConVar, arrayDeltaX, arrayDeltaY);
CHKERRQ(ierr);<br>
ierr = PetscFree(adj); CHKERRQ(ierr);<br>
<br>
The error messages are like as :<br>
<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------<wbr>------------------------------<wbr>--<br>
[0]PETSC ERROR: Petsc has generated inconsistent data<br>
[0]PETSC ERROR: Invalid mesh exceeded adjacency allocation
(0)<br>
</blockquote>
<div><br>
</div>
<div>You are resetting the size to 0 in your loop. It needs
to be set to PETSC_DETERMINE.</div>
<div><br>
</div>
<div>This is a very low level routine with complicated
memory management for efficiency. It is not intended for</div>
<div>most user code. However, here is an example:</div>
<div><br>
</div>
<div> <a href="https://bitbucket.org/petsc/petsc/src/f98bafe09724ec53686c21e51e969e41f10d977b/src/dm/impls/plex/plexdistribute.c?at=master&fileviewer=file-view-default#plexdistribute.c-570" target="_blank">https://bitbucket.org/petsc/<wbr>petsc/src/<wbr>f98bafe09724ec53686c21e51e969e<wbr>41f10d977b/src/dm/impls/plex/<wbr>plexdistribute.c?at=master&<wbr>fileviewer=file-view-default#<wbr>plexdistribute.c-570</a></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">
[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/faq.html</a>
for trouble shooting.<br>
[0]PETSC ERROR: Petsc Development GIT revision:
v3.7.4-1864-ga10654c GIT Date: 2016-11-01 22:25:06 -0500<br>
[0]PETSC ERROR: ./cavity on a arch-linux2-c-debug named
leejearl by leejearl Tue Nov 15 14:48:57 2016<br>
[0]PETSC ERROR: Configure options
--prefix=/home/leejearl/Instal<wbr>l/Petsc
--with-mpi-dir=/home/leejearl/<wbr>Install/openmpi/1.8.5_gnu
--download-exodusii=../externa<wbr>lpackages/exodus-5.24.tar.bz2
--download-netcdf=../externalp<wbr>ackages/netcdf-4.3.2.tar.gz
--download-hdf5=../externalpac<wbr>kages/hdf5-1.8.12.tar.gz
--download-triangle=../externa<wbr>lpackages/Triangle.tar.gz
--download-sowing=../externalp<wbr>ackages/git.sowing.tar.gz<br>
[0]PETSC ERROR: #1 DMPlexGetAdjacency_Cone_Intern<wbr>al()
line 193 in /home/leejearl/Software/petsc/<wbr>petsc/src/dm/impls/plex/plexdi<wbr>stribute.c<br>
[0]PETSC ERROR: #2 DMPlexGetAdjacency_Internal() line 298
in /home/leejearl/Software/petsc/<wbr>petsc/src/dm/impls/plex/plexdi<wbr>stribute.c<br>
[0]PETSC ERROR: #3 DMPlexGetAdjacency() line 372 in
/home/leejearl/Software/petsc/<wbr>petsc/src/dm/impls/plex/plexdi<wbr>stribute.c<br>
[0]PETSC ERROR: #4 CalcConVarGradient() line 126 in
/home/leejearl/Desktop/PETSc/G<wbr>KSCavity_Petsc/cavity.c<br>
<br>
It is very strange that PetscMalloc3 can arouse such an
error. If I comment the statement relative with
PetscMalloc3, it is ok! I can not understand what
happened.<br>
<br>
Can anyone figure me out the problems of my codes?<br>
<br>
I attach the code and the grid, so you can compile in your
workstation.<br>
<br>
Thanks<br>
<br>
leejearl<br>
<br>
<br>
On 2016年11月14日 23:09, Lawrence Mitchell wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
On 14 Nov 2016, at 14:59, leejearl <<a href="mailto:leejearl@126.com" target="_blank">leejearl@126.com</a>>
wrote:<br>
<br>
Hi all:<br>
<br>
I am not sure the using of the function
"DMPlexGetAdjacency".<br>
<br>
My codes are as follows:<br>
<br>
PetscInt adj, *adjSize=NULL;<br>
<br>
ierr = DMPlexGetAdjacency(dm, p, &adj,
&adj);<br>
</blockquote>
<br>
Your calling sequence is wrong:<br>
<br>
PetscInt adjSize;<br>
PetscInt *adj = NULL;<br>
<br>
ierr = DMPlexGetAdjacency(dm, p, &adjSize,
&adj); CHKERRQ(ierr);<br>
<br>
adjSize is now the size of the adj array. You should
remember to free it afterwards:<br>
<br>
/* use adj here *<br>
...<br>
<br>
ierr = PetscFree(adj); CHKERRQ(ierr);<br>
<br>
Lawrence<br>
</blockquote>
<br>
</blockquote>
</div>
<br>
<br clear="all"><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div class="m_-5870127340255563735gmail_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>
</div>
</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>