[petsc-users] GAMG issue

Wed Mar 14 16:40:54 CDT 2012

John, I've committed these changes, give a try.

Mark

On Mar 14, 2012, at 3:46 PM, Satish Balay wrote:

> This is the usual merge [with uncommited changes] issue.
> 
> You could use 'hg shelf' extension to shelve your local changes and
> then do a merge [as Sean would suggest] - or do the merge in a
> separate/clean clone [I normally do this..]
> 
> i.e
> cd ~/Codes
> hg clone petsc-dev petsc-dev-merge
> cd petsc-dev-merge
> hg pull ssh://petsc@petsc.cs.iit.edu//hg/petsc/petsc-dev   #just to be sure, look for latest chagnes before merge..
> hg merge
> hg commit
> hg push ssh://petsc@petsc.cs.iit.edu//hg/petsc/petsc-dev
> 
> [now update your petsc-dev to latest]
> cd ~/Codes/petsc-dev
> hg pull
> hg update
> 
> Satish
> 
> On Wed, 14 Mar 2012, Mark F. Adams wrote:
> 
>> Great, that seems to work.
>> 
>> I did a 'hg commit tools.c'
>> 
>> and I want to push this file only.  I guess its the only thing in the change set so 'hg push' should be fine.  But I see this:
>> 
>> ~/Codes/petsc-dev/src/ksp/pc/impls/gamg>hg update
>> abort: crosses branches (merge branches or use --clean to discard changes)
>> ~/Codes/petsc-dev/src/ksp/pc/impls/gamg>hg merge
>> abort: outstanding uncommitted changes (use 'hg status' to list changes)
>> ~/Codes/petsc-dev/src/ksp/pc/impls/gamg>hg status
>> M include/petscmat.h
>> M include/private/matimpl.h
>> M src/ksp/pc/impls/gamg/agg.c
>> M src/ksp/pc/impls/gamg/gamg.c
>> M src/ksp/pc/impls/gamg/gamg.h
>> M src/ksp/pc/impls/gamg/geo.c
>> M src/mat/coarsen/coarsen.c
>> M src/mat/coarsen/impls/hem/hem.c
>> M src/mat/coarsen/impls/mis/mis.c
>> 
>> Am I ready to do a push?
>> 
>> Thanks,
>> Mark
>> 
>> On Mar 14, 2012, at 2:44 PM, Satish Balay wrote:
>> 
>>> If commit is the last hg operation that you've done - then 'hg rollback' would undo this commit.
>>> 
>>> Satish
>>> 
>>> On Wed, 14 Mar 2012, Mark F. Adams wrote:
>>> 
>>>> Damn, I'm not preallocating the graph perfectly for unsymmetric matrices and PETSc now dies on this.
>>>> 
>>>> I have a fix but I committed it with other changes that I do not want to commit.  The changes are all in one file so I should be able to just commit this file.
>>>> 
>>>> Anyone know how to delete a commit?
>>>> 
>>>> I've tried:
>>>> 
>>>> ~/Codes/petsc-dev/src/ksp/pc/impls/gamg>hg strip 22487:26ffb9eef17f
>>>> hg: unknown command 'strip'
>>>> 'strip' is provided by the following extension:
>>>> 
>>>>   mq  manage a stack of patches
>>>> 
>>>> use "hg help extensions" for information on enabling extensions
>>>> 
>>>> But have not figured out how to load extensions.
>>>> 
>>>> Mark
>>>> 
>>>> On Mar 14, 2012, at 12:54 PM, John Mousel wrote:
>>>> 
>>>>> Mark,
>>>>> 
>>>>> I have a non-symmetric matrix. I am running with the following options.
>>>>> 
>>>>> -pc_type gamg -pc_gamg_sym_graph -ksp_monitor_true_residual
>>>>> 
>>>>> and with the inclusion of -pc_gamg_sym_graph, I get a new malloc error:
>>>>> 
>>>>> 
>>>>> 0]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>> [0]PETSC ERROR: Argument out of range!
>>>>> [0]PETSC ERROR: New nonzero at (5150,9319) caused a malloc!
>>>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>>>> [0]PETSC ERROR: Petsc Development HG revision: 587b25035091aaa309c87c90ac64c13408ecf34e  HG Date: Wed Mar 14 09:22:54 2012 -0500
>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>>>> [0]PETSC ERROR: ../JohnRepo/VFOLD_exe on a linux-deb named wv.iihr.uiowa.edu by jmousel Wed Mar 14 11:51:35 2012
>>>>> [0]PETSC ERROR: Libraries linked from /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/linux-debug/lib
>>>>> [0]PETSC ERROR: Configure run at Wed Mar 14 09:46:39 2012
>>>>> [0]PETSC ERROR: Configure options --download-blacs=1 --download-hypre=1 --download-metis=1 --download-ml=1 --download-mpich=1 --download-parmetis=1 --download-scalapack=1 --with-blas-lapack-dir=/opt/intel11/mkl/lib/em64t --with-cc=gcc --with-cmake=/usr/local/bin/cmake --with-cxx=g++ --with-fc=ifort PETSC_ARCH=linux-debug
>>>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>>>> [0]PETSC ERROR: MatSetValues_MPIAIJ() line 506 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c
>>>>> [0]PETSC ERROR: MatSetValues() line 1141 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/mat/interface/matrix.c
>>>>> [0]PETSC ERROR: scaleFilterGraph() line 155 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/impls/gamg/tools.c
>>>>> [0]PETSC ERROR: PCGAMGgraph_AGG() line 865 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/impls/gamg/agg.c
>>>>> [0]PETSC ERROR: PCSetUp_GAMG() line 516 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/impls/gamg/gamg.c
>>>>> [0]PETSC ERROR: PCSetUp() line 832 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/interface/precon.c
>>>>> [0]PETSC ERROR: KSPSetUp() line 261 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/ksp/interface/itfunc.c
>>>>> [0]PETSC ERROR: KSPSolve() line 385 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/ksp/interface/itfunc.c
>>>>> 
>>>>> 
>>>>> John
>>>>> 
>>>>> 
>>>>> On Wed, Mar 14, 2012 at 11:27 AM, Mark F. Adams <mark.adams at columbia.edu> wrote:
>>>>> 
>>>>> On Mar 14, 2012, at 11:56 AM, John Mousel wrote:
>>>>> 
>>>>>> Mark,
>>>>>> 
>>>>>> The matrix is asymmetric. Does this require the setting of an option?
>>>>> 
>>>>> Yes:  -pc_gamg_sym_graph
>>>>> 
>>>>> Mark
>>>>> 
>>>>>> I pulled petsc-dev this morning, so I should have (at least close to) the latest code.
>>>>>> 
>>>>>> John
>>>>>> 
>>>>>> On Wed, Mar 14, 2012 at 10:54 AM, Mark F. Adams <mark.adams at columbia.edu> wrote:
>>>>>> 
>>>>>> On Mar 14, 2012, at 11:08 AM, John Mousel wrote:
>>>>>> 
>>>>>>> I'm getting the following error when using GAMG.
>>>>>>> 
>>>>>>> petsc-dev/src/ksp/pc/impls/gamg/agg.c:508: smoothAggs: Assertion `sgid==-1' failed.
>>>>>> 
>>>>>> Is it possible that your matrix is structurally asymmetric?
>>>>>> 
>>>>>> This code is evolving fast and so you will need to move to the dev version if you are not already using it. (I think I fixed a bug that hit this assert).
>>>>>> 
>>>>>>> 
>>>>>>> When I try to alter the type of aggregation at the command line using -pc_gamg_type pa, I'm getting 
>>>>>>> 
>>>>>>> [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>>>> [1]PETSC ERROR: Unknown type. Check for miss-spelling or missing external package needed for type:
>>>>>>> see http://www.mcs.anl.gov/petsc/documentation/installation.html#external!
>>>>>>> [1]PETSC ERROR: Unknown GAMG type pa given!
>>>>>>> 
>>>>>>> Has there been a change in the aggregation options? I just pulled petsc-dev this morning.
>>>>>>> 
>>>>>> 
>>>>>> Yes, this option is gone now.  You can use -pc_gamg_type agg for now.
>>>>>> 
>>>>>> Mark
>>>>>> 
>>>>>>> John
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
> 
> 