[petsc-users] GAMG issue
John Mousel
john.mousel at gmail.com
Tue Mar 20 13:45:30 CDT 2012
Mark,
I run ML with the following options.
-ksp_type bcgsl -pc_type ml -pc_ml_maxNlevels 5 -mg_coarse_ksp_type
richardson -mg_coarse_pc_type sor -mg_coarse_pc_sor_its 8 -ksp_monitor
-ksp_view
Note the lack of scaling. For some reason scaling seems to mess with ML.
As you can see below, ML converges very nicely.
With regards to HYPRE, this one took a bit of work to get convergence. The
options that work are:
-ksp_type bcgsl -pc_type hypre -pc_hypre_type boomeramg
-ksp_monitor_true_residual -pc_hypre_boomeramg_relax_type_coarse
symmetric-SOR/Jacobi -pc_hypre_boomeramg_grid_sweeps_coarse 4
-pc_hypre_boomeramg_coarsen_type PMIS
The problem is that neither of ML or HYPRE seem to scale at all.
ML output:
0 KSP preconditioned resid norm 1.538968715109e+06 true resid norm
2.621342052504e+03 ||r(i)||/||b|| 1.000000000000e+00
2 KSP preconditioned resid norm 1.263129058693e+05 true resid norm
1.096298699671e+04 ||r(i)||/||b|| 4.182203915830e+00
4 KSP preconditioned resid norm 2.277379585186e+04 true resid norm
2.999721659930e+03 ||r(i)||/||b|| 1.144345758717e+00
6 KSP preconditioned resid norm 4.766504457975e+03 true resid norm
6.733421603796e+02 ||r(i)||/||b|| 2.568692474667e-01
8 KSP preconditioned resid norm 2.139020425406e+03 true resid norm
1.360842101250e+02 ||r(i)||/||b|| 5.191394613876e-02
10 KSP preconditioned resid norm 6.621380459944e+02 true resid norm
1.522758800025e+02 ||r(i)||/||b|| 5.809080881188e-02
12 KSP preconditioned resid norm 2.973409610262e+01 true resid norm
1.161046206089e+01 ||r(i)||/||b|| 4.429205280479e-03
14 KSP preconditioned resid norm 2.532665482573e+00 true resid norm
2.557425874623e+00 ||r(i)||/||b|| 9.756170020543e-04
16 KSP preconditioned resid norm 2.375585214826e+00 true resid norm
2.441783841415e+00 ||r(i)||/||b|| 9.315014189327e-04
18 KSP preconditioned resid norm 1.436338060675e-02 true resid norm
1.305304828818e-02 ||r(i)||/||b|| 4.979528816437e-06
20 KSP preconditioned resid norm 4.088293864561e-03 true resid norm
9.841243465634e-04 ||r(i)||/||b|| 3.754276728683e-07
22 KSP preconditioned resid norm 6.140822977383e-04 true resid norm
1.682184150207e-04 ||r(i)||/||b|| 6.417263052718e-08
24 KSP preconditioned resid norm 2.685415483430e-05 true resid norm
1.065041542336e-05 ||r(i)||/||b|| 4.062962867890e-09
26 KSP preconditioned resid norm 1.620776166579e-06 true resid norm
9.563268703474e-07 ||r(i)||/||b|| 3.648233809982e-10
28 KSP preconditioned resid norm 2.823291105652e-07 true resid norm
7.705418741178e-08 ||r(i)||/||b|| 2.939493811507e-11
KSP Object:(pres_) 4 MPI processes
type: bcgsl
BCGSL: Ell = 2
BCGSL: Delta = 0
maximum iterations=5000
tolerances: relative=1e-12, absolute=1e-50, divergence=10000
left preconditioning
has attached null space
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object:(pres_) 4 MPI processes
type: ml
MG: type is MULTIPLICATIVE, levels=5 cycles=v
Cycles per PCApply=1
Using Galerkin computed coarse grid matrices
Coarse grid solver -- level -------------------------------
KSP Object: (pres_mg_coarse_) 4 MPI processes
type: richardson
Richardson: damping factor=1
maximum iterations=1, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using PRECONDITIONED norm type for convergence test
PC Object: (pres_mg_coarse_) 4 MPI processes
type: sor
SOR: type = local_symmetric, iterations = 8, local iterations = 1,
omega = 1
linear system matrix = precond matrix:
Matrix Object: 4 MPI processes
type: mpiaij
rows=4, cols=4
total: nonzeros=16, allocated nonzeros=16
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Down solver (pre-smoother) on level 1 -------------------------------
KSP Object: (pres_mg_levels_1_) 4 MPI processes
type: richardson
Richardson: damping factor=1
maximum iterations=1
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: (pres_mg_levels_1_) 4 MPI processes
type: sor
SOR: type = local_symmetric, iterations = 1, local iterations = 1,
omega = 1
linear system matrix = precond matrix:
Matrix Object: 4 MPI processes
type: mpiaij
rows=25, cols=25
total: nonzeros=303, allocated nonzeros=303
total number of mallocs used during MatSetValues calls =0
using I-node (on process 0) routines: found 4 nodes, limit used
is 5
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 2 -------------------------------
KSP Object: (pres_mg_levels_2_) 4 MPI processes
type: richardson
Richardson: damping factor=1
maximum iterations=1
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: (pres_mg_levels_2_) 4 MPI processes
type: sor
SOR: type = local_symmetric, iterations = 1, local iterations = 1,
omega = 1
linear system matrix = precond matrix:
Matrix Object: 4 MPI processes
type: mpiaij
rows=423, cols=423
total: nonzeros=7437, allocated nonzeros=7437
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 3 -------------------------------
KSP Object: (pres_mg_levels_3_) 4 MPI processes
type: richardson
Richardson: damping factor=1
maximum iterations=1
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: (pres_mg_levels_3_) 4 MPI processes
type: sor
SOR: type = local_symmetric, iterations = 1, local iterations = 1,
omega = 1
linear system matrix = precond matrix:
Matrix Object: 4 MPI processes
type: mpiaij
rows=6617, cols=6617
total: nonzeros=88653, allocated nonzeros=88653
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 4 -------------------------------
KSP Object: (pres_mg_levels_4_) 4 MPI processes
type: richardson
Richardson: damping factor=1
maximum iterations=1
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
has attached null space
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: (pres_mg_levels_4_) 4 MPI processes
type: sor
SOR: type = local_symmetric, iterations = 1, local iterations = 1,
omega = 1
linear system matrix = precond matrix:
Matrix Object: 4 MPI processes
type: mpiaij
rows=46330, cols=46330
total: nonzeros=322437, allocated nonzeros=615417
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
linear system matrix = precond matrix:
Matrix Object: 4 MPI processes
type: mpiaij
rows=46330, cols=46330
total: nonzeros=322437, allocated nonzeros=615417
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
John
On Tue, Mar 20, 2012 at 1:33 PM, Mark F. Adams <mark.adams at columbia.edu>wrote:
> John,
>
> I am getting poor results (diverging) from ML also:
>
> 0 KSP preconditioned resid norm 3.699832960909e+22 true resid norm
> 1.310674055116e+03 ||r(i)||/||b|| 1.000000000000e+00
> 2 KSP preconditioned resid norm 5.706378365783e+11 true resid norm
> 1.563902233018e+03 ||r(i)||/||b|| 1.193204539995e+00
> 4 KSP preconditioned resid norm 5.570291685152e+11 true resid norm
> 1.564235542744e+03 ||r(i)||/||b|| 1.193458844050e+00
> 6 KSP preconditioned resid norm 5.202150407298e+10 true resid norm
> 1.749929789082e+03 ||r(i)||/||b|| 1.335137277077e+00
> Linear solve converged due to CONVERGED_RTOL iterations 6
>
> With GAMG I get:
>
> 0 KSP preconditioned resid norm 7.731260075891e+06 true resid norm
> 1.310674055116e+03 ||r(i)||/||b|| 1.000000000000e+00
> 2 KSP preconditioned resid norm 2.856415184685e+05 true resid norm
> 1.310410242531e+03 ||r(i)||/||b|| 9.997987199150e-01
> 4 KSP preconditioned resid norm 1.528467019258e+05 true resid norm
> 1.284856538976e+03 ||r(i)||/||b|| 9.803021078816e-01
> 6 KSP preconditioned resid norm 1.451091957899e+05 true resid norm
> 1.564309254168e+03 ||r(i)||/||b|| 1.193515083375e+00
>
> <snip>
>
> 122 KSP preconditioned resid norm 2.486245341783e+01 true resid norm
> 1.404397185367e+00 ||r(i)||/||b|| 1.071507580306e-03
> 124 KSP preconditioned resid norm 1.482316853621e+01 true resid norm
> 4.488661881759e-01 ||r(i)||/||b|| 3.424697287811e-04
> 126 KSP preconditioned resid norm 1.481941150253e+01 true resid norm
> 4.484480100832e-01 ||r(i)||/||b|| 3.421506730318e-04
> 128 KSP preconditioned resid norm 8.191887347033e+00 true resid norm
> 6.678630367218e-01 ||r(i)||/||b|| 5.095569215816e-04
>
> And HYPRE:
>
> 0 KSP preconditioned resid norm 3.774510769907e+04 true resid norm
> 1.310674055116e+03 ||r(i)||/||b|| 1.000000000000e+00
> 2 KSP preconditioned resid norm 1.843165835831e+04 true resid norm
> 8.502433792869e+02 ||r(i)||/||b|| 6.487069580482e-01
> 4 KSP preconditioned resid norm 1.573176624705e+04 true resid norm
> 1.167264367302e+03 ||r(i)||/||b|| 8.905832558033e-01
> 6 KSP preconditioned resid norm 1.657958380765e+04 true resid norm
> 8.684701624902e+02 ||r(i)||/||b|| 6.626133775216e-01
> 8 KSP preconditioned resid norm 2.190304455083e+04 true resid norm
> 6.969893263600e+02 ||r(i)||/||b|| 5.317792960344e-01
> 10 KSP preconditioned resid norm 2.485714630000e+04 true resid norm
> 6.642641436830e+02 ||r(i)||/||b|| 5.068110878446e-01
>
> <snip>
>
> 62 KSP preconditioned resid norm 6.432516040957e+00 true resid norm
> 2.124960171419e-01 ||r(i)||/||b|| 1.621272781837e-04
> 64 KSP preconditioned resid norm 5.731033176541e+00 true resid norm
> 1.338816774003e-01 ||r(i)||/||b|| 1.021471943216e-04
> 66 KSP preconditioned resid norm 1.600285935522e-01 true resid norm
> 3.352408932031e-03 ||r(i)||/||b|| 2.557774695353e-06
>
> ML and GAMG should act similarly, but ML seems to have a problem (see the
> preconditioned norm difference and its diverging). ML has a parameter:
>
> -pc_ml_Threshold [.0]
>
> I setting this to 0.05 (GAMG default) helps a bit but it still diverges.
>
> So it would be nice to figure out the difference between ML and GAMG, but
> that is secondary for you as the both suck.
>
> HYPRE is a very different algorithm. It looks like the smoothing in GAMG
> (and ML) may be the problem. If I turn smoothing off
> (-pc_gamg_agg_nsmooths 0) and I get for GAMG:
>
> 0 KSP preconditioned resid norm 2.186148437534e+05 true resid norm
> 1.310674055116e+03 ||r(i)||/||b|| 1.000000000000e+00
> 2 KSP preconditioned resid norm 2.916843959765e+04 true resid norm
> 3.221533667508e+03 ||r(i)||/||b|| 2.457921292432e+00
> 4 KSP preconditioned resid norm 2.396374655925e+04 true resid norm
> 1.834299897412e+03 ||r(i)||/||b|| 1.399508817812e+00
> 6 KSP preconditioned resid norm 2.509576275453e+04 true resid norm
> 1.035475461174e+03 ||r(i)||/||b|| 7.900327752214e-01
>
> <snip>
>
> 64 KSP preconditioned resid norm 1.973859758284e+01 true resid norm
> 7.322674977169e+00 ||r(i)||/||b|| 5.586953482895e-03
> 66 KSP preconditioned resid norm 3.371598890438e+01 true resid norm
> 7.152754930495e+00 ||r(i)||/||b|| 5.457310231004e-03
> 68 KSP preconditioned resid norm 4.687839294418e+00 true resid norm
> 4.605726307025e-01 ||r(i)||/||b|| 3.514013487219e-04
> 70 KSP preconditioned resid norm 1.487545519493e+00 true resid norm
> 1.558723789416e-01 ||r(i)||/||b|| 1.189253562571e-04
> 72 KSP preconditioned resid norm 5.317329808718e-01 true resid norm
> 5.027178038177e-02 ||r(i)||/||b|| 3.835566911967e-05
> 74 KSP preconditioned resid norm 3.405339702462e-01 true resid norm
> 1.897059263835e-02 ||r(i)||/||b|| 1.447392092969e-05
>
> This is almost as good as HYPRE.
>
> An other thing to keep in mind is the cost of each iteration, not just
> then number of iterations, You can
> use -pc_hypre_boomeramg_print_statistics to get some data on this from
> HYPRE:
>
> Average Convergence Factor = 0.537664
>
> Complexity: grid = 1.780207
> operator = 2.624910
> cycle = 5.249670
>
> And GAMG prints this with verbose set:
>
> [0]PCSetUp_GAMG 6 levels, grid compexity [sic] = 1.1316
>
> I believe that the hypre "Complexity: grid" is the same as my "grid
> complexity". So hypre actually looks more expensive at this point.
>
> I've worked on optimizing parameters for hypre with the hypre people and
> here are a set of arguments that I've used:
>
> -pc_hypre_boomeramg_no_CF -pc_hypre_boomeramg_agg_nl 1
> -pc_hypre_boomeramg_coarsen_type HMIS -pc_hypre_boomeramg_interp_type ext+i
> -pc_hypre_boomeramg_P_max 4 -pc_hypre_boomeramg_agg_num_paths 2
>
> With these parmeters I get:
>
> Complexity: grid = 1.244140
> operator = 1.396722
> cycle = 2.793442
>
> and:
>
> 0 KSP preconditioned resid norm 4.698624821403e+04 true resid norm
> 1.310674055116e+03 ||r(i)||/||b|| 1.000000000000e+00
> 2 KSP preconditioned resid norm 2.207967626172e+04 true resid norm
> 3.466160021150e+03 ||r(i)||/||b|| 2.644562931280e+00
> 4 KSP preconditioned resid norm 2.278468320876e+04 true resid norm
> 1.246784122467e+03 ||r(i)||/||b|| 9.512541410282e-01
>
> <snip>
>
> 56 KSP preconditioned resid norm 1.108460232262e+00 true resid norm
> 8.276869475681e-02 ||r(i)||/||b|| 6.314971631105e-05
> 58 KSP preconditioned resid norm 3.617217454336e-01 true resid norm
> 3.764556404754e-02 ||r(i)||/||b|| 2.872229285428e-05
> 60 KSP preconditioned resid norm 1.666532560770e-01 true resid norm
> 5.149302513338e-03 ||r(i)||/||b|| 3.928743758404e-06
> Linear solve converged due to CONVERGED_RTOL iterations 60
>
> So this actually converged faster with lower complexity.
>
> Anyway these result seem different from what you are getting, so I've
> appended my options. This uses ex10 in the KSP tutorials to read in your
> binary file.
>
> Mark
>
> #PETSc Option Table entries:
> -f ./binaryoutput
> -ksp_converged_reason
> -ksp_diagonal_scale
> -ksp_diagonal_scale_fix
> -ksp_monitor_true_residual
> -ksp_type bcgsl
> -mg_coarse_ksp_type richardson
> -mg_coarse_pc_sor_its 8
> -mg_coarse_pc_type sor
> -mg_levels_ksp_type richardson
> -mg_levels_pc_type sor
> -options_left
> -pc_gamg_agg_nsmooths 0
> -pc_gamg_coarse_eq_limit 10
> -pc_gamg_sym_graph
> -pc_gamg_verbose 2
> -pc_hypre_boomeramg_P_max 4
> -pc_hypre_boomeramg_agg_nl 1
> -pc_hypre_boomeramg_agg_num_paths 2
> -pc_hypre_boomeramg_coarsen_type HMIS
> -pc_hypre_boomeramg_interp_type ext+i
> -pc_hypre_boomeramg_no_CF
> -pc_ml_Threshold .01
> -pc_type gamg
> -vecload_block_size 1
> #End of PETSc Option Table entries
> There are 7 unused database options. They are:
> Option left: name:-pc_hypre_boomeramg_P_max value: 4
> Option left: name:-pc_hypre_boomeramg_agg_nl value: 1
> Option left: name:-pc_hypre_boomeramg_agg_num_paths value: 2
> Option left: name:-pc_hypre_boomeramg_coarsen_type value: HMIS
> Option left: name:-pc_hypre_boomeramg_interp_type value: ext+i
> Option left: name:-pc_hypre_boomeramg_no_CF no value
> Option left: name:-pc_ml_Threshold value: .01
>
>
> On Mar 20, 2012, at 10:19 AM, John Mousel wrote:
>
> Mark,
>
> Sorry for the late reply. I've been on travel and hadn't had a chance to
> pick this back up. I've tried running with the suggested options:
>
> -ksp_type bcgsl -pc_type gamg -pc_gamg_coarse_eq_limit 10
> -pc_gamg_agg_nsmooths 1 -pc_gamg_sym_graph -mg_coarse_ksp_type richardson
> -mg_coarse_pc_type sor -mg_coarse_pc_sor_its 8 -ksp_diagonal_scale
> -ksp_diagonal_scale_fix -ksp_monitor_true_residual -ksp_view
> -pc_gamg_verbose 1
>
> With these options, the convergence starts to hang (see attached
> GAMG_kspview.txt). The hanging happens for both -mg_coarse_ksp_type
> richardson and preonly. It was my understanding from previous emails that
> using preonly made it so that only the preconditioner was run, which in
> this case would be 8 sweeps of SOR. If I get rid of the
> -pc_gamg_agg_nsmooths 1 (see GAMG_kspview_nosmooth.txt), the problem
> converges, but again the convergence is slow. Without this option, both
> Richardson and preonly converge in 172 iterations.
>
> Matt, I've checked and the problem does converge in the true residual
> using GAMG, ML, HYPRE, and ILU preconditioned BiCG. I explicitly ensure
> that a solution exists by projecting the rhs vector out of the nullity of
> the transpose of operator.
>
> John
>
>
> On Fri, Mar 16, 2012 at 2:04 PM, Mark F. Adams <mark.adams at columbia.edu>wrote:
>
>> John, did this get resolved?
>> Mark
>>
>> On Mar 15, 2012, at 4:24 PM, John Mousel wrote:
>>
>> Mark,
>>
>> Running without the options you mentioned before leads to slightly worse
>> performance (175 iterations).
>> I have not been able to get run coarse grid solve to work with LU while
>> running ML. It keeps experiencing a zero pivot, and all the combinations of
>> shifting i've tried haven't lead me anywhere, hence the SOR on the course
>> grid. Also, the ML manual suggests limiting the number of levels to 3 or 4
>> and performing a few sweeps of an iterative method as opposed to a direct
>> solve.
>>
>> John
>>
>> On Thu, Mar 15, 2012 at 12:04 PM, Mark F. Adams <mark.adams at columbia.edu>wrote:
>>
>>> You also want: -pc_gamg_agg_nsmooths 1
>>>
>>> You are running plain aggregation. If it is Poisson then smoothing is
>>> good.
>>>
>>> Is this problem singular? Can you try running ML with these parameters
>>> and see if its performance degrades? The ML implementation uses the PETSC
>>> infrastructure and uses a very similar algorithm to GAMG-SA. We should be
>>> able to get these two to match pretty well.
>>>
>>> Mark
>>>
>>>
>>> On Mar 15, 2012, at 12:21 PM, John Mousel wrote:
>>>
>>> Mark,
>>>
>>> I ran with those options removed (see the run options listed below).
>>> Things actually got slightly worse. Now it's up to 142 iterations. I have
>>> attached the ksp_view output.
>>>
>>> -ksp_type bcgsl -pc_type gamg -pc_gamg_sym_graph -ksp_diagonal_scale
>>> -ksp_diagonal_scale_fix -mg_levels_ksp_type richardson -mg_levels_pc_type
>>> sor -pc_gamg_verbose 1
>>>
>>>
>>> John
>>>
>>>
>>> On Thu, Mar 15, 2012 at 10:55 AM, Mark F. Adams <mark.adams at columbia.edu
>>> > wrote:
>>>
>>>> John, can you run again with: -pc_gamg_verbose 1
>>>>
>>>> And I would not use: -pc_mg_levels 4 -mg_coarse_ksp_type preonly
>>>> -mg_coarse_pc_type sor -mg_coarse_pc_sor_its 8
>>>>
>>>> 1) I think -mg_coarse_ksp_type preonly and -mg_coarse_pc_sor_its 8 do
>>>> not do what you think. I think this is the same as 1 iteration. I think
>>>> you want 'richardson' not 'preonly'.
>>>>
>>>> 2) Why are you using sor as the coarse solver? If your problem is
>>>> singular then you want to use as many levels as possible to get the coarse
>>>> grid to be tiny. I'm pretty sure HYPRE ignores the coarse solver
>>>> parameters. But ML uses them and it is converging well.
>>>>
>>>> 3) I would not specify the number of levels. GAMG, and I think the
>>>> rest, have internal logic for stopping a the right level. If the coarse
>>>> level is large and you use just 8 iterations of sor then convergence will
>>>> suffer.
>>>>
>>>> Mark
>>>>
>>>> On Mar 15, 2012, at 11:13 AM, John Mousel wrote:
>>>>
>>>> Mark,
>>>>
>>>> The changes pulled through this morning. I've run it with the options
>>>>
>>>> -ksp_type bcgsl -pc_type gamg -pc_gamg_sym_graph -ksp_diagonal_scale
>>>> -ksp_diagonal_scale_fix -pc_mg_levels 4 -mg_levels_ksp_type richardson
>>>> -mg_levels_pc_type sor -mg_coarse_ksp_type preonly -mg_coarse_pc_type sor
>>>> -mg_coarse_pc_sor_its 8
>>>>
>>>> and it converges in the true residual, but it's not converging as fast
>>>> as anticpated. The matrix arises from a non-symmetric discretization of the
>>>> Poisson equation. The solve takes GAMG 114 iterations, whereas ML takes 24
>>>> iterations, BoomerAMG takes 22 iterations, and -ksp_type bcgsl -pc_type
>>>> bjacobi -sub_pc_type ilu -sub_pc_factor_levels 4 takes around 170. I've
>>>> attached the -ksp_view results for ML,GAMG, and HYPRE. I've attempted to
>>>> make all the options the same on all levels for ML and GAMG.
>>>>
>>>> Any thoughts?
>>>>
>>>> John
>>>>
>>>>
>>>> On Wed, Mar 14, 2012 at 6:04 PM, Mark F. Adams <mark.adams at columbia.edu
>>>> > wrote:
>>>>
>>>>> Humm, I see it with hg view (appended).
>>>>>
>>>>> Satish, my main repo looks hosed. I see this:
>>>>>
>>>>> ~/Codes/petsc-dev>hg update
>>>>> abort: crosses branches (merge branches or use --clean to discard
>>>>> changes)
>>>>> ~/Codes/petsc-dev>hg merge
>>>>> abort: branch 'default' has 3 heads - please merge with an explicit rev
>>>>> (run 'hg heads .' to see heads)
>>>>> ~/Codes/petsc-dev>hg heads
>>>>> changeset: 22496:8e2a98268179
>>>>> tag: tip
>>>>> user: Barry Smith <bsmith at mcs.anl.gov>
>>>>> date: Wed Mar 14 16:42:25 2012 -0500
>>>>> files: src/vec/is/interface/f90-custom/zindexf90.c
>>>>> src/vec/vec/interface/f90-custom/zvectorf90.c
>>>>> description:
>>>>> undoing manually changes I put in because Satish had a better fix
>>>>>
>>>>>
>>>>> changeset: 22492:bda4df63072d
>>>>> user: Mark F. Adams <mark.adams at columbia.edu>
>>>>> date: Wed Mar 14 17:39:52 2012 -0400
>>>>> files: src/ksp/pc/impls/gamg/tools.c
>>>>> description:
>>>>> fix for unsymmetric matrices.
>>>>>
>>>>>
>>>>> changeset: 22469:b063baf366e4
>>>>> user: Mark F. Adams <mark.adams at columbia.edu>
>>>>> date: Wed Mar 14 14:22:28 2012 -0400
>>>>> files: src/ksp/pc/impls/gamg/tools.c
>>>>> description:
>>>>> added fix for preallocation for unsymetric matrices.
>>>>>
>>>>> Mark
>>>>>
>>>>> my 'hg view' on my merge repo:
>>>>>
>>>>> Revision: 22492
>>>>> Branch: default
>>>>> Author: Mark F. Adams <mark.adams at columbia.edu> 2012-03-14 17:39:52
>>>>> Committer: Mark F. Adams <mark.adams at columbia.edu> 2012-03-14
>>>>> 17:39:52
>>>>> Tags: tip
>>>>> Parent: 22491:451bbbd291c2 (Small fixes to the BT linesearch)
>>>>>
>>>>> fix for unsymmetric matrices.
>>>>>
>>>>>
>>>>> ------------------------ src/ksp/pc/impls/gamg/tools.c
>>>>> ------------------------
>>>>> @@ -103,7 +103,7 @@
>>>>> PetscErrorCode ierr;
>>>>> PetscInt Istart,Iend,Ii,jj,ncols,nnz0,nnz1, NN, MM, nloc;
>>>>> PetscMPIInt mype, npe;
>>>>> - Mat Gmat = *a_Gmat, tGmat;
>>>>> + Mat Gmat = *a_Gmat, tGmat, matTrans;
>>>>> MPI_Comm wcomm = ((PetscObject)Gmat)->comm;
>>>>> const PetscScalar *vals;
>>>>> const PetscInt *idx;
>>>>> @@ -127,6 +127,10 @@
>>>>> ierr = MatDiagonalScale( Gmat, diag, diag ); CHKERRQ(ierr);
>>>>> ierr = VecDestroy( &diag ); CHKERRQ(ierr);
>>>>>
>>>>> + if( symm ) {
>>>>> + ierr = MatTranspose( Gmat, MAT_INITIAL_MATRIX, &matTrans );
>>>>> CHKERRQ(ierr);
>>>>> + }
>>>>> +
>>>>> /* filter - dup zeros out matrix */
>>>>> ierr = PetscMalloc( nloc*sizeof(PetscInt), &d_nnz ); CHKERRQ(ierr);
>>>>> ierr = PetscMalloc( nloc*sizeof(PetscInt), &o_nnz ); CHKERRQ(ierr);
>>>>> @@ -135,6 +139,12 @@
>>>>> d_nnz[jj] = ncols;
>>>>> o_nnz[jj] = ncols;
>>>>> ierr = MatRestoreRow(Gmat,Ii,&ncols,PETSC_NULL,PETSC_NULL);
>>>>> CHKERRQ(ierr);
>>>>> + if( symm ) {
>>>>> + ierr = MatGetRow(matTrans,Ii,&ncols,PETSC_NULL,PETSC_NULL);
>>>>> CHKERRQ(ierr);
>>>>> + d_nnz[jj] += ncols;
>>>>> + o_nnz[jj] += ncols;
>>>>> + ierr = MatRestoreRow(matTrans,Ii,&ncols,PETSC_NULL,PETSC_NULL);
>>>>> CHKERRQ(ierr);
>>>>> + }
>>>>> if( d_nnz[jj] > nloc ) d_nnz[jj] = nloc;
>>>>> if( o_nnz[jj] > (MM-nloc) ) o_nnz[jj] = MM - nloc;
>>>>> }
>>>>> @@ -142,6 +152,9 @@
>>>>> CHKERRQ(ierr);
>>>>> ierr = PetscFree( d_nnz ); CHKERRQ(ierr);
>>>>> ierr = PetscFree( o_nnz ); CHKERRQ(ierr);
>>>>> + if( symm ) {
>>>>> + ierr = MatDestroy( &matTrans ); CHKERRQ(ierr);
>>>>> + }
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mar 14, 2012, at 5:53 PM, John Mousel wrote:
>>>>>
>>>>> Mark,
>>>>>
>>>>> No change. Can you give me the location that you patched so I can
>>>>> check to make sure it pulled?
>>>>> I don't see it on the petsc-dev change log.
>>>>>
>>>>> John
>>>>>
>>>>> On Wed, Mar 14, 2012 at 4:40 PM, Mark F. Adams <
>>>>> mark.adams at columbia.edu> wrote:
>>>>>
>>>>>> 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
>>>>>> >>>>>>
>>>>>> >>>>>>
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>
>>>>>> >>>>
>>>>>> >>>
>>>>>> >>>
>>>>>> >>
>>>>>> >>
>>>>>> >
>>>>>> >
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>> <GAMG_kspview.txt><ML_kspview.txt><HYPRE_kspview.txt>
>>>>
>>>>
>>>>
>>> <GAMG_kspview.txt>
>>>
>>>
>>>
>>
>>
> <GAMG_kspview.txt><GAMG_kspview_nosmooth.txt>
>
>
>
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