[petsc-users] A problem with MPI Derived Data Type and 'calloc'

Zhenglun (Alan) Wei zhenglun.wei at gmail.com
Thu Apr 19 09:49:06 CDT 2012


Dear Dr. Knepley,
      It is very nice to hear that. I will read the manual. Do we have 
any examples showing its functions?

thank you so much,
Alan
On 4/19/2012 9:35 AM, Matthew Knepley wrote:
> On Thu, Apr 19, 2012 at 10:18 AM, Zhenglun (Alan) Wei 
> <zhenglun.wei at gmail.com <mailto:zhenglun.wei at gmail.com>> wrote:
>
>     "
>         TESTVAR ***a, ***b, ***c;
>         TESTVAR **aa, **bb, **cc;
>         TESTVAR *arraya, *arrayb, *arrayc;
>
>         arraya = (TESTVAR*) calloc(SIZE*SIZE*SIZE, sizeof(TESTVAR));
>         arrayb = (TESTVAR*) calloc(SIZE*SIZE*SIZE, sizeof(TESTVAR));
>         arrayc = (TESTVAR*) calloc(SIZE*SIZE*SIZE, sizeof(TESTVAR));
>
>         aa =(TESTVAR**) calloc(SIZE*SIZE, sizeof(TESTVAR*));
>         bb =(TESTVAR**) calloc(SIZE*SIZE, sizeof(TESTVAR*));
>         cc =(TESTVAR**) calloc(SIZE*SIZE, sizeof(TESTVAR*));
>         for(i = 0; i < SIZE*SIZE; i++) {
>           aa[i] = &arraya[i*SIZE];
>           bb[i] = &arrayb[i*SIZE];
>           cc[i] = &arrayc[i*SIZE];
>         }
>
>         a =(TESTVAR***) calloc(SIZE*SIZE, sizeof(TESTVAR**));
>         b =(TESTVAR***) calloc(SIZE*SIZE, sizeof(TESTVAR**));
>         c =(TESTVAR***) calloc(SIZE*SIZE, sizeof(TESTVAR**));
>         for(i = 0; i < SIZE; i++) {
>           a[i] = &aa[i*SIZE];
>           b[i] = &bb[i*SIZE];
>           c[i] = &cc[i*SIZE];
>         }
>     "
>       It works. However, I wonder if there is any other good ideas for
>     3D problem other than this kinda of 'two-layer' approach.
>
>     *_What is the reason for not using DMDA?_
>     *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?
>
>
> It definitely does communication between the local pieces. Do you want 
> something else?
>
>         "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?"
>
>
>     _*What do you mean by neighboring? If it is jsut stencil
>     neighbors, then use a local vector.*_
>     When I send and receive data with MPI_Send and MPI_RECV, I need
>     provide the 'destination' (in MPI_Send refer
>     to'http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Send.html')
>     and 'source' (in MPI_RECV refer
>     to'http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Recv.html').
>     In a 2D problem with Cartesian grid, 4 processes divide the whole
>     domain to 4 sub-domain.
>     ----------------------------
>           2      |      3      |
>     ----------------------------
>           0      |      1      |
>     ---------------------------
>      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.
>
>
> Yes, it looks like you should just use a DMDA. See the manual section.
>
>    Matt
>
>     I'm sorry for confusing you.
>
>     thanks in advance,
>     Alan
>
>     On 4/19/2012 4:52 AM, Matthew Knepley wrote:
>>     On Wed, Apr 18, 2012 at 3:52 PM, Alan Wei <zhenglun.wei at gmail.com
>>     <mailto:zhenglun.wei at gmail.com>> wrote:
>>
>>         Dear all,
>>             I hope you're having a nice day. I have a further
>>         question on this issue in 3D.
>>         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
>>         "
>>             TESTVAR ***a, ***b, ***c;
>>             TESTVAR **aa, **bb, **cc;
>>             TESTVAR *arraya, *arrayb, *arrayc;
>>
>>             arraya = (TESTVAR*) calloc(SIZE*SIZE*SIZE, sizeof(TESTVAR));
>>             arrayb = (TESTVAR*) calloc(SIZE*SIZE*SIZE, sizeof(TESTVAR));
>>             arrayc = (TESTVAR*) calloc(SIZE*SIZE*SIZE, sizeof(TESTVAR));
>>
>>             aa =(TESTVAR**) calloc(SIZE*SIZE, sizeof(TESTVAR*));
>>             bb =(TESTVAR**) calloc(SIZE*SIZE, sizeof(TESTVAR*));
>>             cc =(TESTVAR**) calloc(SIZE*SIZE, sizeof(TESTVAR*));
>>             for(i = 0; i < SIZE*SIZE; i++) {
>>               aa[i] = &arraya[i*SIZE];
>>               bb[i] = &arrayb[i*SIZE];
>>               cc[i] = &arrayc[i*SIZE];
>>             }
>>
>>             a =(TESTVAR***) calloc(SIZE*SIZE, sizeof(TESTVAR**));
>>             b =(TESTVAR***) calloc(SIZE*SIZE, sizeof(TESTVAR**));
>>             c =(TESTVAR***) calloc(SIZE*SIZE, sizeof(TESTVAR**));
>>             for(i = 0; i < SIZE; i++) {
>>               a[i] = &aa[i*SIZE];
>>               b[i] = &bb[i*SIZE];
>>               c[i] = &cc[i*SIZE];
>>             }
>>         "
>>           It works. However, I wonder if there is any other good
>>         ideas for 3D problem other than this kinda of 'two-layer'
>>         approach.
>>
>>
>>     What is the reason for not using DMDA?
>>
>>         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?
>>
>>
>>     What do you mean by neighboring? If it is jsut stencil neighbors,
>>     then use a local vector.
>>
>>        Matt
>>
>>         thanks,
>>         Alan
>>
>>         On Fri, Apr 13, 2012 at 5:41 PM, Jed Brown
>>         <jedbrown at mcs.anl.gov <mailto:jedbrown at mcs.anl.gov>> wrote:
>>
>>             On Fri, Apr 13, 2012 at 17:38, Zhenglun (Alan) Wei
>>             <zhenglun.wei at gmail.com <mailto:zhenglun.wei at gmail.com>>
>>             wrote:
>>
>>                     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. 
>>
>>
>>             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.
>>
>>
>>
>>
>>
>>     -- 
>>     What most experimenters take for granted before they begin their
>>     experiments is infinitely more interesting than any results to
>>     which their experiments lead.
>>     -- Norbert Wiener
>
>
>
>
> -- 
> What most experimenters take for granted before they begin their 
> experiments is infinitely more interesting than any results to which 
> their experiments lead.
> -- Norbert Wiener

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