On Thu, Apr 19, 2012 at 10:18 AM, Zhenglun (Alan) Wei <span dir="ltr"><<a href="mailto:zhenglun.wei@gmail.com">zhenglun.wei@gmail.com</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">
<div>
<div>
<div>"</div>
<div> TESTVAR ***a, ***b, ***c;</div>
<div> TESTVAR **aa, **bb, **cc; </div>
<div> TESTVAR *arraya, *arrayb, *arrayc;</div>
</div>
<div><br>
</div>
<div> arraya = (TESTVAR*) calloc(SIZE*SIZE*SIZE,
sizeof(TESTVAR));</div>
<div> arrayb = (TESTVAR*) calloc(SIZE*SIZE*SIZE,
sizeof(TESTVAR));</div>
<div> arrayc = (TESTVAR*) calloc(SIZE*SIZE*SIZE,
sizeof(TESTVAR));</div>
<div><br>
</div>
<div> aa =(TESTVAR**) calloc(SIZE*SIZE, sizeof(TESTVAR*));</div>
<div> bb =(TESTVAR**) calloc(SIZE*SIZE, sizeof(TESTVAR*));</div>
<div> cc =(TESTVAR**) calloc(SIZE*SIZE, sizeof(TESTVAR*));</div>
<div> </div>
<div> for(i = 0; i < SIZE*SIZE; i++) {</div>
<div> aa[i] = &arraya[i*SIZE];</div>
<div> bb[i] = &arrayb[i*SIZE];</div>
<div> cc[i] = &arrayc[i*SIZE]; </div>
<div> }</div>
<div><br>
</div>
<div> a =(TESTVAR***) calloc(SIZE*SIZE, sizeof(TESTVAR**));</div>
<div> b =(TESTVAR***) calloc(SIZE*SIZE, sizeof(TESTVAR**));</div>
<div> c =(TESTVAR***) calloc(SIZE*SIZE, sizeof(TESTVAR**));</div>
<div> </div>
<div> for(i = 0; i < SIZE; i++) {</div>
<div> a[i] = &aa[i*SIZE];</div>
<div> b[i] = &bb[i*SIZE];</div>
<div> c[i] = &cc[i*SIZE];</div>
<div> }</div>
<div>"</div>
<div> It works. However, I wonder if there is any other good
ideas for 3D problem other than this kinda of 'two-layer'
approach.</div>
</div>
<div><br>
</div>
<div><b><u>What is the reason for not using DMDA?</u><br>
</b>In 2D, I established a 2D array for data communication between
nodes by using MPI derived data type. It allows me to easily
communicate both contiguous (i.e. MPI_TYPE_CONTIGUOUS) and
non-contiguous (i.e. MPI_TYPE_VECTOR) data. That is why I use this
similar approach in 3D, though an additional data type, i.e.
MPI_TYPE_INDEXED, need to be used. Does DMDA have those type of
function or derived data type?</div></div></blockquote><div><br></div><div>It definitely does communication between the local pieces. Do you want something else?</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">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>"2, I have a little question on PETSc about 3D processor
ordering. Does PETSc have any function giving me the
nodes/rank number of neighboring nodes/ranks? Are those
'Application Ordering' functions applicable for my case?"</div>
</div>
</blockquote>
<div><br>
</div>
<div><u><b>What do you mean by neighboring? If it is jsut stencil
neighbors, then use a local vector.</b></u></div>
<div>When I send and receive data with MPI_Send and MPI_RECV, I need
provide the 'destination' (in MPI_Send refer to'<a href="http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Send.html" target="_blank">http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Send.html</a>')
and 'source' (in MPI_RECV refer to'<a href="http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Recv.html" target="_blank">http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Recv.html</a>').
In a 2D problem with Cartesian grid, 4 processes divide the whole
domain to 4 sub-domain. <br>
---------------------------- <br>
2 | 3 |<br>
----------------------------<br>
0 | 1 |<br>
---------------------------<br>
Then, for node 1, the neighboring nodes are '0' and '3', which
'0' is the left node and '3' is the top node. I wonder if PETSc
has any function that I can call to obtain those neighboring nodes
so that I do not need to construct my function. <br></div></div></blockquote><div><br></div><div>Yes, it looks like you should just use a DMDA. See the manual section.</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"><div>
I'm sorry for confusing you. <br>
<br>
thanks in advance,<br>
Alan <br>
</div>
<br>
On 4/19/2012 4:52 AM, Matthew Knepley wrote:
<blockquote type="cite">On Wed, Apr 18, 2012 at 3:52 PM, Alan Wei <span dir="ltr"><<a href="mailto:zhenglun.wei@gmail.com" target="_blank">zhenglun.wei@gmail.com</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">
Dear all,
<div> I hope you're having a nice day. I have a further
question on this issue in 3D.</div>
<div>1, Following the idea of Dr. Brown and Dr. Knepley, I
finished a 2D test, which works very fine. Here, I did it in
3D by</div>
<div>
<div>
<div>"</div>
<div> TESTVAR ***a, ***b, ***c;</div>
<div> TESTVAR **aa, **bb, **cc; </div>
<div> TESTVAR *arraya, *arrayb, *arrayc;</div>
</div>
<div><br>
</div>
<div> arraya = (TESTVAR*) calloc(SIZE*SIZE*SIZE,
sizeof(TESTVAR));</div>
<div> arrayb = (TESTVAR*) calloc(SIZE*SIZE*SIZE,
sizeof(TESTVAR));</div>
<div> arrayc = (TESTVAR*) calloc(SIZE*SIZE*SIZE,
sizeof(TESTVAR));</div>
<div><br>
</div>
<div> aa =(TESTVAR**) calloc(SIZE*SIZE,
sizeof(TESTVAR*));</div>
<div> bb =(TESTVAR**) calloc(SIZE*SIZE,
sizeof(TESTVAR*));</div>
<div> cc =(TESTVAR**) calloc(SIZE*SIZE,
sizeof(TESTVAR*));</div>
<div> </div>
<div> for(i = 0; i < SIZE*SIZE; i++) {</div>
<div> aa[i] = &arraya[i*SIZE];</div>
<div> bb[i] = &arrayb[i*SIZE];</div>
<div> cc[i] = &arrayc[i*SIZE]; </div>
<div> }</div>
<div><br>
</div>
<div> a =(TESTVAR***) calloc(SIZE*SIZE,
sizeof(TESTVAR**));</div>
<div> b =(TESTVAR***) calloc(SIZE*SIZE,
sizeof(TESTVAR**));</div>
<div> c =(TESTVAR***) calloc(SIZE*SIZE,
sizeof(TESTVAR**));</div>
<div> </div>
<div> for(i = 0; i < SIZE; i++) {</div>
<div> a[i] = &aa[i*SIZE];</div>
<div> b[i] = &bb[i*SIZE];</div>
<div> c[i] = &cc[i*SIZE];</div>
<div> }</div>
<div>"</div>
<div> It works. However, I wonder if there is any other
good ideas for 3D problem other than this kinda of
'two-layer' approach.</div>
</div>
</blockquote>
<div><br>
</div>
<div>What is the reason for not using DMDA?</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>2, I have a little question on PETSc about 3D processor
ordering. Does PETSc have any function giving me the
nodes/rank number of neighboring nodes/ranks? Are those
'Application Ordering' functions applicable for my case?</div>
</div>
</blockquote>
<div><br>
</div>
<div>What do you mean by neighboring? If it is jsut stencil
neighbors, then use a local vector.</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>
<div>thanks,</div>
<div>Alan</div>
<br>
<div class="gmail_quote">On Fri, Apr 13, 2012 at 5:41 PM,
Jed Brown <span dir="ltr"><<a href="mailto:jedbrown@mcs.anl.gov" target="_blank">jedbrown@mcs.anl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div class="gmail_quote">On Fri, Apr 13, 2012 at
17:38, Zhenglun (Alan) Wei <span dir="ltr"><<a href="mailto:zhenglun.wei@gmail.com" target="_blank">zhenglun.wei@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I have a final question on it. Is it taken a
lot of memory for doing this? As I understand,
pointers won't occupy many memories and it works
like an alias. It will not, to my limit knowledge,
take much extra memory by doing this. </blockquote>
</div>
<br>
</div>
<div>A pointer takes about as much space as a floating
point value, so that array of pointers costs about 1*N
compared to the N*N matrix.</div>
</blockquote>
</div>
<br>
</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>
<br>
</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>