Actually, I have some related issues:
In a previous thread, I saw that to output as hdf5/mxf you basically need
the following two runtime options:
-dm_view hdf5:sol.h5 -snes_view_solution hdf5:sol.h5::append
1) For the code that I had shown earlier in this thread (test.c), it works
serially if I used the SNES solver instead of the TaoSolver. However, when
I run it on multiple processors I get the following error:
HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 0:
#000: H5F.c line 2061 in H5Fclose(): decrementing file ID failed
major: Object atom
minor: Unable to close file
#001: H5I.c line 1479 in H5I_dec_app_ref(): can't decrement ID ref count
major: Object atom
minor: Unable to decrement reference count
#002: H5F.c line 1838 in H5F_close(): can't close file
major: File accessibilty
minor: Unable to close file
#003: H5F.c line 2000 in H5F_try_close(): problems closing file
major: File accessibilty
minor: Unable to close file
#004: H5F.c line 1145 in H5F_dest(): low level truncate failed
major: File accessibilty
minor: Write failed
#005: H5FD.c line 1897 in H5FD_truncate(): driver truncate request failed
major: Virtual File Layer
minor: Can't update object
#006: H5FDmpio.c line 1989 in H5FD_mpio_truncate(): MPI_File_set_size
failed
major: Internal error (too specific to document in detail)
minor: Some MPI function failed
#007: H5FDmpio.c line 1989 in H5FD_mpio_truncate(): Invalid argument,
error stack:
MPI_FILE_SET_SIZE(74): Inconsistent arguments to collective routine
major: Internal error (too specific to document in detail)
minor: MPI Error String
HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 1:
#000: H5F.c line 2061 in H5Fclose(): decrementing file ID failed
major: Object atom
minor: Unable to close file
#001: H5I.c line 1479 in H5I_dec_app_ref(): can't decrement ID ref count
major: Object atom
minor: Unable to decrement reference count
#002: H5F.c line 1838 in H5F_close(): can't close file
major: File accessibilty
minor: Unable to close file
#003: H5F.c line 2000 in H5F_try_close(): problems closing file
major: File accessibilty
minor: Unable to close file
#004: H5F.c line 1145 in H5F_dest(): low level truncate failed
major: File accessibilty
minor: Write failed
#005: H5FD.c line 1897 in H5FD_truncate(): driver truncate request failed
major: Virtual File Layer
minor: Can't update object
#006: H5FDmpio.c line 1989 in H5FD_mpio_truncate(): MPI_File_set_size
failed
major: Internal error (too specific to document in detail)
minor: Some MPI function failed
#007: H5FDmpio.c line 1989 in H5FD_mpio_truncate(): Invalid argument,
error stack:
MPI_FILE_SET_SIZE(74): Inconsistent arguments to collective routine
major: Internal error (too specific to document in detail)
minor: MPI Error String
I compared my code with what was in SNES ex12 and I don't seem to
understand why I am getting this error.
2) Is there a way to output as HDF5/xmf via the Tao Solver? I tried using
-ksp_view_solution hdf5:sol.h5::append but it gave me no solution. The
multiple processor issue also applies to this
Any help appreciated. Thanks
On Tue, Oct 14, 2014 at 11:58 PM, Justin Chang <jychan...@gmail.com> wrote:
> Hi Jason,
>
> Both of those algorithms resolved my problem. Thanks!
>
> Justin
>
> On Tue, Oct 14, 2014 at 10:12 PM, Jason Sarich <jason.sar...@gmail.com>
> wrote:
>
>> Hi Justin,
>>
>> If the only constraints you have are bounds on the variables, then you
>> are much better off using the TAO algorithms tron or blmvm. IPM builds its
>> own KKT matrix for a ksp solve that is undoubtably much less efficient than
>> what will be used in tron (blmvm avoids ksp solves all together).
>>
>> That begin said, it looks like there's a bug in IPM and I'll try to track
>> it down, thanks for the report.
>>
>> Jason
>>
>>
>> On Tue, Oct 14, 2014 at 9:34 PM, Justin Chang <jychan...@gmail.com>
>> wrote:
>>
>>> Attached is the source code and the makefile used to compile/run the
>>> code.
>>>
>>> The source code is basically a dumbed down version of SNES ex12 plus
>>> necessary TAO routines.
>>>
>>> Thanks
>>>
>>> On Tue, Oct 14, 2014 at 8:39 PM, Matthew Knepley <knep...@gmail.com>
>>> wrote:
>>>
>>>> On Tue, Oct 14, 2014 at 8:04 PM, Justin Chang <jychan...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> So I am writing a non-negative diffusion equation using DMPlex's FEM
>>>>> and Tao's SetVariableBounds functions. My code works really perfectly when
>>>>> I run it with one processor. However, once I use 2 or more processors, I
>>>>> get this error:
>>>>>
>>>>
>>>> It looks like the problem is in the TAO definition, but you can check
>>>> by just solving your problem with, for instance, BJacobi-LU in parallel.
>>>>
>>>>
>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>> --------------------------------------------------------------
>>>>> [0]PETSC ERROR: Nonconforming object sizes
>>>>> [0]PETSC ERROR: Vector wrong size 89 for scatter 88 (scatter reverse
>>>>> and vector to != ctx from size)
>>>>> [1]PETSC ERROR: --------------------- Error Message
>>>>> --------------------------------------------------------------
>>>>> [1]PETSC ERROR: Nonconforming object sizes
>>>>> [1]PETSC ERROR: Vector wrong size 87 for scatter 88 (scatter reverse
>>>>> and vector to != ctx from size)
>>>>> [1]PETSC ERROR: See
>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>>>> shooting.
>>>>> [1]PETSC ERROR: Petsc Development GIT revision: v3.5.2-526-gfaecc80
>>>>> GIT Date: 2014-10-04 20:10:35 -0500
>>>>> [1]PETSC ERROR: [0]PETSC ERROR: See
>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>>>> shooting.
>>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.5.2-526-gfaecc80
>>>>> GIT Date: 2014-10-04 20:10:35 -0500
>>>>> [0]PETSC ERROR: ./bin/diff2D on a arch-linux2-c-debug named pacotaco
>>>>> by justin Tue Oct 14 19:48:50 2014
>>>>> [0]PETSC ERROR: ./bin/diff2D on a arch-linux2-c-debug named pacotaco
>>>>> by justin Tue Oct 14 19:48:50 2014
>>>>> [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>>>>> --with-fc=gfortran --download-fblaslapack --download-mpich
>>>>> --with-debugging=1 --download-metis --download-parmetis
>>>>> --download-triangle
>>>>> --with-cmake=cmake --download-ctetgen --download-superlu
>>>>> --download-scalapack --download-mumps --download-hdf5 --with-valgrind=1
>>>>> -with-cmake=cmake
>>>>> [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>>>>> --with-fc=gfortran --download-fblaslapack --download-mpich
>>>>> --with-debugging=1 --download-metis --download-parmetis
>>>>> --download-triangle
>>>>> --with-cmake=cmake --download-ctetgen --download-superlu
>>>>> --download-scalapack --download-mumps --download-hdf5 --with-valgrind=1
>>>>> -with-cmake=cmake
>>>>> [0]PETSC ERROR: #1 VecScatterBegin() line 1713 in
>>>>> /home/justin/petsc-master/src/vec/vec/utils/vscat.c
>>>>> #1 VecScatterBegin() line 1713 in
>>>>> /home/justin/petsc-master/src/vec/vec/utils/vscat.c
>>>>> [1]PETSC ERROR: [0]PETSC ERROR: #2 MatMultTranspose_MPIAIJ() line 1010
>>>>> in /home/justin/petsc-master/src/mat/impls/aij/mpi/mpiaij.c
>>>>> [0]PETSC ERROR: #2 MatMultTranspose_MPIAIJ() line 1010 in
>>>>> /home/justin/petsc-master/src/mat/impls/aij/mpi/mpiaij.c
>>>>> [1]PETSC ERROR: #3 MatMultTranspose() line 2242 in
>>>>> /home/justin/petsc-master/src/mat/interface/matrix.c
>>>>> #3 MatMultTranspose() line 2242 in
>>>>> /home/justin/petsc-master/src/mat/interface/matrix.c
>>>>> [0]PETSC ERROR: #4 IPMComputeKKT() line 616 in
>>>>> /home/justin/petsc-master/src/tao/constrained/impls/ipm/ipm.c
>>>>> [1]PETSC ERROR: #4 IPMComputeKKT() line 616 in
>>>>> /home/justin/petsc-master/src/tao/constrained/impls/ipm/ipm.c
>>>>> [1]PETSC ERROR: [0]PETSC ERROR: #5 TaoSolve_IPM() line 50 in
>>>>> /home/justin/petsc-master/src/tao/constrained/impls/ipm/ipm.c
>>>>> [0]PETSC ERROR: #5 TaoSolve_IPM() line 50 in
>>>>> /home/justin/petsc-master/src/tao/constrained/impls/ipm/ipm.c
>>>>> [1]PETSC ERROR: #6 TaoSolve() line 190 in
>>>>> /home/justin/petsc-master/src/tao/interface/taosolver.c
>>>>> #6 TaoSolve() line 190 in
>>>>> /home/justin/petsc-master/src/tao/interface/taosolver.c
>>>>> [0]PETSC ERROR: #7 main() line 341 in
>>>>> /home/justin/Dropbox/Research_Topics/Petsc_Nonneg_diffusion/src/diff2D.c
>>>>> [1]PETSC ERROR: #7 main() line 341 in
>>>>> /home/justin/Dropbox/Research_Topics/Petsc_Nonneg_diffusion/src/diff2D.c
>>>>> [1]PETSC ERROR: [0]PETSC ERROR: ----------------End of Error Message
>>>>> -------send entire error message to petsc-ma...@mcs.anl.gov----------
>>>>> ----------------End of Error Message -------send entire error message
>>>>> to petsc-ma...@mcs.anl.gov----------
>>>>> application called MPI_Abort(MPI_COMM_WORLD, 60) - process 0
>>>>> application called MPI_Abort(MPI_COMM_WORLD, 60) - process 1
>>>>> [cli_1]: aborting job:
>>>>> application called MPI_Abort(MPI_COMM_WORLD, 60) - process 1
>>>>> [cli_0]: aborting job:
>>>>> application called MPI_Abort(MPI_COMM_WORLD, 60) - process 0
>>>>>
>>>>>
>>>>> I have no idea how or why I am getting this error. What does this
>>>>> mean?
>>>>>
>>>>
>>>> It looks like one dof is given to proc 0 which should live on proc
>>>> 1. We have to look at the divisions
>>>> made in the KKT solver. Can you send a small example?
>>>>
>>>> Matt
>>>>
>>>>
>>>>> My code is essentially built off of SNES ex12.c. The Jacobian
>>>>> matrix, residual vector, and solution vector were created using DMPlex and
>>>>> the built-in FEM functions within. The Hessian matrix and gradient vector
>>>>> were created by simple matmult() functions of the jacobian and residual.
>>>>> The lower bounds vector was created by duplicating the solution vector
>>>>> (initial guess set to zero). My FormFunctionGradient() is basically the
>>>>> same thing as in the maros.c example. can give more information if needed.
>>>>>
>>>>> Thanks,
>>>>> Justin
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>
>>>
>>
>
