Hi Barry,
Thanks for your help! However, there are still some issues left. In other to
test things, I simplified the program even more and now I am just sending a
vector back and forth: matlab->petsc->matlab:
fd = PETSC_VIEWER_SOCKET_WORLD;
// load rhs vector
ierr = VecLoad(fd,VECMPI,&b);CHKERRQ(ierr);
// send to matlab
ierr = VecView(b,fd);CHKERRQ(ierr);
ierr = VecDestroy(b);CHKERRQ(ierr);
- Your approach with two windows works *sometimes*. I removed the 'launch'
statement and I executed my program 10 times, the first 2 times worked, and in
all other cases I got this:
petscmpiexec -n 2 ./petsc_poisson_par_barry2 -info
[1] PetscInitialize(): PETSc successfully started: number of processors = 2
[1] PetscInitialize(): Running on machine: borr.mas.cwi.nl
[0] PetscInitialize(): PETSc successfully started: number of processors = 2
[0] PetscInitialize(): Running on machine: borr.mas.cwi.nl
[0] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784 max
tags = 2147483647
[1] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784 max
tags = 2147483647
[1] PetscCommDuplicate(): returning tag 2147483647
[0] PetscCommDuplicate(): returning tag 2147483647
[0] PetscViewerSocketSetConnection(): Connecting to socket process on port 5005
machine borr.mas.cwi.nl
[0] PetscOpenSocket(): Connection refused in attaching socket, trying again[0]
PetscOpenSocket(): Connection refused in attaching socket, trying again[0]
PetscOpenSocket(): Connection refused in attaching socket, trying again
[0] PetscOpenSocket(): Connection refused in attaching socket, trying again^C
-bash-4.0$ [0]0:Return code = 0, signaled with Interrupt
[0]1:Return code = 0, signaled with Interrupt
Every time I start the program I use close(socket) and clear all in Matlab, so
the socket from the previous run should not be present anymore. It seems that
the port gets corrupted after a couple of times? Matlab does not respond and I
have to kill it and restart it manually.
- If I include the launch statement, or just type
system('mpiexec -n 2 ./petsc_poisson_par_barry2 &')
the program never works.
Hope you can figure out what is going wrong.
Ben
Op 3 sep 2010, om 13:25 heeft Barry Smith het volgende geschreven:
>
> Ben
>
> Ok, I figured out the problem. It is not fundamental and mostly comes from
> not having a create way to debug this.
>
> The test vector you create is sequential then you try to view it back to
> Matlab with the parallel fd viewer. If you change to
> ierr = VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,1,&test);CHKERRQ(ierr);
> then the code runs.
>
> I've found (just now) that when I use launch all the output from the .c
> program gets lost which makes it impossible to figure out what has gone
> wrong. You can debug by running the two parts of the computation in two
> different windows. So comment out the launch from the matlab script and then
> in Matlab run the script (it will hang waiting for the socket to work) and in
> a separate terminal window run the .c program; for example petscmpiexec -n 2
> ./ex1 -info Now you see exactly what is happening in the PETSc program. You
> can even use -start_in_debugger on the PETSc side to run the debugger on
> crashes.
>
> I'll add this to the docs for launch
>
> Barry
>
>
> On Sep 2, 2010, at 3:28 PM, Benjamin Sanderse wrote:
>
>> Hi Barry,
>>
>> I attached my matlab file, c file and makefile. First I generate the
>> executable with 'make petsc_poisson_par_barry' and then I run
>> test_petsc_par_barry.m.
>> If you change MATMPIAIJ to MATAIJ and VECMPI to VECSEQ the code works fine.
>>
>> Thanks a lot,
>>
>> Benjamin
>>
>> <makefile><test_petsc_par_barry.m><petsc_poisson_par_barry.c>
>>
>> Op 2 sep 2010, om 13:45 heeft Barry Smith het volgende geschreven:
>>
>>>
>>>
>>> Matlab is never aware the vector is parallel. Please send me the code and
>>> I'll figure out what is going on.
>>>
>>> Barry
>>>
>>> On Sep 2, 2010, at 2:07 PM, Benjamin Sanderse wrote:
>>>
>>>> That sounds great, but there is one issue I am encountering. I switched
>>>> vector types to VECMPI and matrix type to MATMPIAIJ, but when running
>>>> Matlab I get the following error:
>>>>
>>>> Found unrecogonized header 0 in file. If your file contains complex numbers
>>>> then call PetscBinaryRead() with "complex" as the second argument
>>>> Error in ==> PetscBinaryRead at 27
>>>> if nargin < 2
>>>>
>>>> ??? Output argument "varargout" (and maybe others) not assigned during
>>>> call to
>>>> "/ufs/sanderse/Software/petsc-3.1-p4/bin/matlab/PetscBinaryRead.m>PetscBinaryRead".
>>>>
>>>> Error in ==> test_petsc_par at 57
>>>> x4 = PetscBinaryReady(PS);
>>>>
>>>> Could it be that Matlab does not understand the "parallel" vector which is
>>>> returned by Petsc? Currently I have this done with VecView as follows:
>>>>
>>>> fd = PETSC_VIEWER_SOCKET_WORLD;
>>>> ...
>>>> KSPSolve(ksp,b,x);
>>>> ...
>>>> VecView(fd,x);
>>>>
>>>> Thanks for the help!
>>>>
>>>> Ben
>>>>
>>>> Op 2 sep 2010, om 10:09 heeft Barry Smith het volgende geschreven:
>>>>
>>>>>
>>>>> On Sep 2, 2010, at 10:51 AM, Benjamin Sanderse wrote:
>>>>>
>>>>>> Hello all,
>>>>>>
>>>>>> I figured out the coupling with Matlab and I can send back and forth
>>>>>> matrices and vectors between Petsc and Matlab. Actually, I send only
>>>>>> once a matrix from Matlab to Petsc and then repeatedly send new right
>>>>>> hand sides from Matlab->Petsc and the solution vector from
>>>>>> Petsc->Matlab. That works great.
>>>>>> I know want to see if the matrix that is send from (serial) Matlab to
>>>>>> Petsc can be stored as a parallel matrix in Petsc so that subsequent
>>>>>> computations with different right hand sides can be performed in
>>>>>> parallel by Petsc. Does this simply work by using MatLoad and setting
>>>>>> Mattype MPIAIJ? Or is something more fancy required?
>>>>>
>>>>> In theory this can be done using the same code as sequential only with
>>>>> parallel vectors VECMPI and matrices. MATMPIAIJ
>>>>>
>>>>> Barry
>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Ben
>>>>>
>>>>
>>>
>>
>
