[petsc-users] coupling with Matlab and parallel solution
Benjamin Sanderse
B.Sanderse at cwi.nl
Fri Sep 10 16:07:02 CDT 2010
Hi Barry,
That was a useful hint. I found out that once I made an error in calling Petsc subsequent (correct) calls to Petsc often fail as well. Restarting the shell then fixes matters.
After opening a new shell and using the same command things worked.
Ben
Op 10 sep 2010, om 14:53 heeft Barry Smith het volgende geschreven:
>
> I don't know if these means much. Suggest the following, since you cannot see the message returned by the system call. Try doing the mpiexec and redirecting the stdout and stderr into a file in /tmp and then look in that file to see that the error message is.
>
> Barry
>
> On Sep 10, 2010, at 2:57 PM, Benjamin Sanderse wrote:
>
>> I tried the following in Matlab:
>>
>>>> system('printenv PETSC_DIR')
>> /net/shareware/src/petsc-3.1-p4/
>> ans =
>> 0
>>>> system('which petscmpiexec')
>> /net/shareware/src/petsc-3.1-p4/bin//petscmpiexec
>> ans =
>> 0
>>>> system('printenv PETSC_ARCH')
>> linux-gnu-c-debug
>> ans =
>> 0
>>
>> So I guess that this should be ok when running system().
>>
>>
>>
>>
>> Op 10 sep 2010, om 12:05 heeft Barry Smith het volgende geschreven:
>>
>>>
>>> On Sep 10, 2010, at 11:27 AM, Benjamin Sanderse wrote:
>>>
>>>> Hi guys,
>>>>
>>>> Still some other questions popping up:
>>>>
>>>> - Until now I have been using the 'two-shell' approach suggested by Barry for debugging purposes. This approach works fine, but in a later stage I would like to include the petsc execution command back in Matlab. I tried the following in Matlab:
>>>> system('petscmpiexec -n 2 ./petsc_poisson_par -viewer_socket_port 5600 &);
>>>>
>>>> unix('petscmpiexec -n 2 ./petsc_poisson_par -viewer_socket_port 5600 &);
>>>>
>>>> In both cases this doesn't work, while issuing the command in a separate shell works fine. Any ideas?
>>>
>>> Is petscmpiexec in your path when run inside system() and is PETSC_DIR and PETSC_ARCH set in there?
>>>
>>> Barry
>>>
>>>>
>>>> - I am using CG to solve a symmetric positive definite matrix. As preconditioner I normally use ICC (incomplete choleski), but apparently this is not implemented in parallel in Petsc. Suggestions on what to take as preconditioner?
>>>>
>>>> Thanks,
>>>>
>>>> Ben
>>>>
>>>> Op 9 sep 2010, om 14:36 heeft Satish Balay het volgende geschreven:
>>>>
>>>>> I just attempted this on a linux64 box [ubuntu 10.04 with matlab
>>>>> version 7.10.0.499 (R2010a) 64-bit (glnxa64)] with petsc-3.1 - and
>>>>> the loops ran fine.
>>>>>
>>>>> -bash:
>>>>> for i in {1..50}; do mpiexec -n 2 ./petsc_poisson_par_barry2 -viewer_socket_port 20001; echo $i; done
>>>>>
>>>>> matlab:
>>>>> for i=1:500,;i; test_petsc_par_barry; end
>>>>>
>>>>> Perhaps you can try a high port number - and the same loops - and see if you get
>>>>> stuck on this machine.
>>>>>
>>>>> Satish
>>>>>
>>>>> On Thu, 9 Sep 2010, Barry Smith wrote:
>>>>>
>>>>>>
>>>>>> On Sep 9, 2010, at 2:51 PM, Benjamin Sanderse wrote:
>>>>>>
>>>>>>> I have installed Petsc on a remote 64-bits Linux (Fedora). Might there be an issue with the 64-bits?
>>>>>>
>>>>>> Shouldn't mater.
>>>>>>
>>>>>>>
>>>>>>> My own computer is a Macbook Pro, but I am not running Petsc on it, because in the past I have had severe problems with getting mex-files to work under 64-bits Matlab.
>>>>>>
>>>>>> Yes, that is painful, Matlab never respected the Mac
>>>>>>
>>>>>>> I could try to install it, though.
>>>>>>> Another option is that I try it on another remote Linux machine, also 64-bits, running Red Hat.
>>>>>>
>>>>>> You could try this to see if the same problem exists.
>>>>>>
>>>>>>>
>>>>>>> What do you suggest?
>>>>>>
>>>>>> Are you sure it is hanging on the sockets not hanging on running MPI jobs one after each other?
>>>>>>
>>>>>> Barry
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Op 9 sep 2010, om 13:10 heeft Barry Smith het volgende geschreven:
>>>>>>>
>>>>>>>>
>>>>>>>> What OS are you using.
>>>>>>>>
>>>>>>>> On my Apple Mac I made a shell script loop calling petsc_poisson_par_barry2 multiple times and a similar loop in Matlab and start then both off (with parallel PETSc runs). It runs flawlessly, opening the socket sending and receiving, dozens of times in a row with several processes. I think that maybe you are using Linux?
>>>>>>>>
>>>>>>>>
>>>>>>>> Barry
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sep 8, 2010, at 2:32 PM, Benjamin Sanderse wrote:
>>>>>>>>
>>>>>>>>> That's also what I thought. I checked once again, and I found out that when I use
>>>>>>>>>
>>>>>>>>> petscmpiexec -n 1
>>>>>>>>>
>>>>>>>>> the program works, but if I increase the number of processors to 2 it only works once in a while.
>>>>>>>>>
>>>>>>>>> I attached my test code. It is extremely simple and does nothing else than passing a vector to petsc and returning it to matlab.
>>>>>>>>>
>>>>>>>>> I run it as follows:
>>>>>>>>>
>>>>>>>>> shell #1
>>>>>>>>> -bash-4.0$ make petsc_poisson_par_barry2
>>>>>>>>>
>>>>>>>>> shell #2
>>>>>>>>> -bash-4.0$ matlab -nojvm -nodisplay
>>>>>>>>>>> test_petsc_par_barry;
>>>>>>>>>
>>>>>>>>> shell #1
>>>>>>>>> -bash-4.0$ petscmpiexec -n 2 ./petsc_poisson_par_barry2 -viewer_socket_port 5006 -info
>>>>>>>>>
>>>>>>>>> On lucky days, this works, on unlucky days, petsc will stop here:
>>>>>>>>>
>>>>>>>>> [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 5006 machine borr.mas.cwi.nl
>>>>>>>>> [0] PetscCommDuplicate(): returning tag 2147483646
>>>>>>>>> [1] PetscCommDuplicate(): returning tag 2147483646
>>>>>>>>> [1] PetscCommDuplicate(): returning tag 2147483641
>>>>>>>>> [0] PetscCommDuplicate(): returning tag 2147483641
>>>>>>>>> [0] VecAssemblyBegin_MPI(): Stash has 0 entries, uses 0 mallocs.
>>>>>>>>> [0] VecAssemblyBegin_MPI(): Block-Stash has 0 entries, uses 0 mallocs.
>>>>>>>>> ^C
>>>>>>>>>
>>>>>>>>> <makefile>
>>>>>>>>> <test_petsc_par_barry.m>
>>>>>>>>> <petsc_poisson_par_barry2.c>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Op 8 sep 2010, om 12:00 heeft Barry Smith het volgende geschreven:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Sep 8, 2010, at 10:13 AM, Benjamin Sanderse wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Barry,
>>>>>>>>>>>
>>>>>>>>>>> I am indeed closing the socket in Matlab between the two sets, using close(PS), where PS=PetscOpenSocket.
>>>>>>>>>>> I have tried different port numbers, but without guarantee of success. Sometimes it works, sometimes it doesn't. Often times the first time calling the PetscOpenSocket(portnumber) works, but even that is not guaranteed. I think there should be another solution.
>>>>>>>>>>> By the way, all these problems do not appear when using serial vectors instead of parallel.
>>>>>>>>>>
>>>>>>>>>> That is strange. Only the first process ever opens the socket so in theory the fact that the PETSc code is parallel should not matter at all. Please send me your test code that causes trouble again and I'll see if I can reproduce the problem.
>>>>>>>>>>
>>>>>>>>>> Barry
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Ben
>>>>>>>>>>>
>>>>>>>>>>> Op 7 sep 2010, om 17:27 heeft Barry Smith het volgende geschreven:
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Are you closing the socket on Matlab between to the two sets? Just checking.
>>>>>>>>>>>>
>>>>>>>>>>>> You can try running with a different port number each time to see if it is related to trying to reuse the port. Run with PetscOpenSocket(5006) and the PETSc program with -viewer_socket_port 5006
>>>>>>>>>>>> then run both with 5007 then with 5008 etc does this work smoothly?
>>>>>>>>>>>>
>>>>>>>>>>>> Let me know and the will tell me the next step to try,
>>>>>>>>>>>>
>>>>>>>>>>>> Barry
>>>>>>>>>>>>
>>>>>>>>>>>> On Sep 7, 2010, at 10:53 AM, Benjamin Sanderse wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Barry,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am still not too happy with the execution in parallel. I am working under Linux (64 bits) and still using your approach with two command windows (since it gives the best debugging possibility).
>>>>>>>>>>>>> As I said, sometimes things work, but most of the time not. Here is the output of two successive runs
>>>>>>>>>>>>>
>>>>>>>>>>>>> -bash-4.0$ 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] PetscCommDuplicate(): returning tag 2147483646
>>>>>>>>>>>>> [1] PetscCommDuplicate(): returning tag 2147483646
>>>>>>>>>>>>> [1] PetscCommDuplicate(): returning tag 2147483641
>>>>>>>>>>>>> [0] PetscCommDuplicate(): returning tag 2147483641
>>>>>>>>>>>>> [0] VecAssemblyBegin_MPI(): Stash has 0 entries, uses 0 mallocs.
>>>>>>>>>>>>> [0] VecAssemblyBegin_MPI(): Block-Stash has 0 entries, uses 0 mallocs.
>>>>>>>>>>>>> [1] PetscFinalize(): PetscFinalize() called
>>>>>>>>>>>>> [1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm 1140850688
>>>>>>>>>>>>> [1] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
>>>>>>>>>>>>> [1] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374784
>>>>>>>>>>>>> [1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm -2080374784
>>>>>>>>>>>>> [0] PetscFinalize(): PetscFinalize() called
>>>>>>>>>>>>> [0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm 1140850688
>>>>>>>>>>>>> [0] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
>>>>>>>>>>>>> [0] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374784
>>>>>>>>>>>>> [0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm -2080374784
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> -bash-4.0$ netstat | grep 5005
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> -bash-4.0$ 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
>>>>>>>>>>>>> [0] PetscCommDuplicate(): returning tag 2147483647
>>>>>>>>>>>>> [0] PetscViewerSocketSetConnection(): Connecting to socket process on port 5005 machine borr.mas.cwi.nl
>>>>>>>>>>>>> [1] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784 max tags = 2147483647
>>>>>>>>>>>>> [1] PetscCommDuplicate(): returning tag 2147483647
>>>>>>>>>>>>> [1] PetscCommDuplicate(): returning tag 2147483646
>>>>>>>>>>>>> [0] PetscCommDuplicate(): returning tag 2147483646
>>>>>>>>>>>>> [0] PetscCommDuplicate(): returning tag 2147483641
>>>>>>>>>>>>> [1] PetscCommDuplicate(): returning tag 2147483641
>>>>>>>>>>>>> [0] VecAssemblyBegin_MPI(): Stash has 0 entries, uses 0 mallocs.
>>>>>>>>>>>>> [0] VecAssemblyBegin_MPI(): Block-Stash has 0 entries, uses 0 mallocs.
>>>>>>>>>>>>> ^C
>>>>>>>>>>>>> -bash-4.0$ [0]0:Return code = 0, signaled with Interrupt
>>>>>>>>>>>>> [0]1:Return code = 0, signaled with Interrupt
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> In both cases I first started the Matlab program. I am currently starting Matlab without a GUI, but with a GUI I have the same problems.
>>>>>>>>>>>>> As you can see, in the first case everything works fine, and Petsc finalizes and closes. Matlab gives me the correct output. The second case, run just a couple of seconds later, does not reach PetscFinalize and Matlab does not give the correct output. In between the two cases I checked if port 5005 was in use, and it was not.
>>>>>>>>>>>>> Do you have any more suggestions on how to get this to work properly?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Benjamin
>>>>>>>>>>>>>
>>>>>>>>>>>>> Op 3 sep 2010, om 21:11 heeft Barry Smith het volgende geschreven:
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Sep 3, 2010, at 4:32 PM, Benjamin Sanderse wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sometimes when you close a socket connection it doesn't close for a very long time so that if you try to open it again it doesn't work. When it appears the socket can not be used try using netstat | grep 5005 to see if the socket is still active.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> - If I include the launch statement, or just type
>>>>>>>>>>>>>>> system('mpiexec -n 2 ./petsc_poisson_par_barry2 &')
>>>>>>>>>>>>>>> the program never works.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Are you sure mpiexec is in the path of system and it is the right one? The problem is that we are kind of cheating with system because we start a new job in the background and have no idea what the output is. Are you using unix and running Matlab on the command line or in a GUI?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Barry
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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