<div dir="ltr">On Fri, May 24, 2013 at 4:46 PM, Michele Rosso <span dir="ltr"><<a href="mailto:mrosso@uci.edu" target="_blank">mrosso@uci.edu</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<font face="Ubuntu">In both cases I used -ksp_view and -option_left.<br>
<br>
For case 1 (</font> <font face="Ubuntu"><font face="Ubuntu">-pc_type
gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1 </font><font face="Ubuntu">-mg_coarse_sub_pc_factor_shift_nonzero ) I posted
the only output I had.<br>
<br>
For case 2 (</font></font> <font face="Ubuntu"><font face="Ubuntu"><font face="Ubuntu">-pc_type gamg
-pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1 -mg_coarse_pc_type
svd) the output was too long to fit into an e-mail.<br>
Please find it attached.<br></font></font></font></div></blockquote><div><br></div><div style>It looks like you are running in parallel (never do this until everything works in serial), which probably means you are using</div>
<div style>PCREDUNDANT for the coarse PC, so you need what Jed suggested:</div><div style><br></div><div style> -mg_coarse_sub_pc_type svd</div><div style><br></div><div style> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"><font face="Ubuntu"><font face="Ubuntu"><font face="Ubuntu">
Michele<br>
</font><br>
</font></font>
<div>On 05/24/2013 02:37 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">On Fri, May 24, 2013 at 4:35 PM, Michele Rosso <span dir="ltr"><<a href="mailto:mrosso@uci.edu" target="_blank">mrosso@uci.edu</a>></span>
wrote:<br>
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> <font face="Ubuntu">I tried <br>
</font><br>
<font face="Ubuntu"><font face="Ubuntu">-pc_type gamg
-pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1 </font><font face="Ubuntu">-mg_coarse_sub_pc_factor_shift_nonzero<br>
<br>
but I still get <br>
<br>
[0]PETSC ERROR: Detected zero pivot in LU
factorization:<br>
see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot</a>!<br>
[0]PETSC ERROR: Zero pivot row 280 value 6.58999e-17
tolerance 2.22045e-14!<br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch
3, Wed Aug 29 11:26:24 CDT 2012<br>
[0]PETSC ERROR: See docs/changes/index.html for
recent updates.<br>
[0]PETSC ERROR: See docs/faq.html for hints about
trouble shooting.<br>
[0]PETSC ERROR: See docs/index.html for manual
pages.<br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: ./hit on a named nid21818 by
Unknown Fri May 24 16:08:33 2013<br>
[0]PETSC ERROR: Libraries linked from<br>
[0]PETSC ERROR: Configure run at<br>
[0]PETSC ERROR: Configure options<br>
[0]PETSC ERROR:
------------------------------------------------------------------------<br>
[0]PETSC ERROR: MatPivotCheck_none() line 583 in
src/mat/impls/aij/seq//ptmp/skelly/petsc/3.3.03/cray_interlagos_build/real/src/include/petsc-private/matimpl.h<br>
[0]PETSC ERROR: MatPivotCheck() line 602 in
src/mat/impls/aij/seq//ptmp/skelly/petsc/3.3.03/cray_interlagos_build/real/src/include/petsc-private/matimpl.h<br>
[0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 585
in src/mat/impls/aij/seq/aijfact.c<br>
[0]PETSC ERROR: MatLUFactorNumeric() line 2803 in
src/mat/interface/matrix.c<br>
[0]PETSC ERROR: PCSetUp_LU() line 160 in
src/ksp/pc/impls/factor/lu/lu.c<br>
[0]PETSC ERROR: PCSetUp() line 832 in
src/ksp/pc/interface/precon.c<br>
[0]PETSC ERROR: KSPSetUp() line 278 in
src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR:
PCSetUpOnBlocks_BJacobi_Singleblock() line 715 in
src/ksp/pc/impls/bjacobi/bjacobi.c<br>
[0]PETSC ERROR: PCSetUpOnBlocks() line 865 in
src/ksp/pc/interface/precon.c<br>
[0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in
src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR: KSPSolve() line 403 in
src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR: PCMGMCycle_Private() line 20 in
src/ksp/pc/impls/mg/mg.c<br>
[0]PETSC ERROR: PCMGMCycle_Private() line 49 in
src/ksp/pc/impls/mg/mg.c<br>
[0]PETSC ERROR: PCMGMCycle_Private() line 49 in
src/ksp/pc/impls/mg/mg.c<br>
[0]PETSC ERROR: PCMGMCycle_Private() line 49 in
src/ksp/pc/impls/mg/mg.c<br>
[0]PETSC ERROR: PCApply_MG() line 326 in
src/ksp/pc/impls/mg/mg.c<br>
[0]PETSC ERROR: PCApply() line 384 in
src/ksp/pc/interface/precon.c<br>
[0]PETSC ERROR: KSPSolve_CG() line 139 in
src/ksp/ksp/impls/cg/cg.c<br>
[0]PETSC ERROR: KSPSolve() line 446 in
src/ksp/ksp/interface/itfunc.c<br>
<br>
<br>
If instead I use <br>
<br>
</font>-pc_type gamg -pc_mg_cycle_type v
-pc_gamg_agg_nsmooths 1 -mg_coarse_pc_type svd <br>
<br>
as Matthew suggested, I am told that there is an
invalid argument.<br>
</font></div>
</blockquote>
<div><br>
</div>
<div>1) When you send these in, we need to see
-ksp_view, so we know what is begin used</div>
<div>
<br>
</div>
<div>2) This is not enough information above. I use
this all the time, or I would not have suggested it</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"><font face="Ubuntu">
Michele<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
</font><font face="Ubuntu"><br>
<br>
</font>
<div>On 05/24/2013 01:04 PM, Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">On Fri, May 24, 2013 at 2:55 PM, Jed
Brown <span dir="ltr"><<a href="mailto:jedbrown@mcs.anl.gov" target="_blank">jedbrown@mcs.anl.gov</a>></span>
wrote:<br>
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Michele Rosso <<a href="mailto:mrosso@uci.edu" target="_blank">mrosso@uci.edu</a>>
writes:<br>
<br>
> Hi Jed,<br>
><br>
> I followed your suggestion by using:<br>
><br>
> -pc_type gamg -pc_mg_cycle_type v
-pc_gamg_agg_nsmooths 1<br>
><br>
> This works perfectly if I have a
non-singular matrix. When instead I use<br>
> periodic conditions for my system ( I
set the nullspace removal<br>
> correctly ),<br>
> I receive an error saying a zero pivot
is detected in the LU<br>
> factorization. So, after some research,
I found in the mailinglist a fix :<br>
><br>
> -pc_type gamg -pc_mg_cycle_type v
-pc_gamg_agg_nsmooths 1<br>
> -mg_coarse_pc_factor_shift_nonzero<br>
<br>
</div>
It'll need to be
-mg_coarse_sub_pc_factor_shift_nonzero<br>
<br>
With petsc-3.4 (which you should upgrade to),
use<br>
-mg_coarse_sub_pc_factor_shift_type NONZERO<br>
<br>
The reason you need this "sub" prefix is that
the code always restricts<br>
using block Jacobi (usually localized so that
all the entries are in one<br>
block), before applying the direct coarse
solver.</blockquote>
<div><br>
</div>
<div>I think this is less elegant than</div>
<div><br>
</div>
<div> -mg_coarse_pc_type svd</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div> > Still I am receiving the
following error<br>
><br>
><br>
> [0]PETSC ERROR: ---------------------
Error Message<br>
> ------------------------------------<br>
> [0]PETSC ERROR: Detected zero pivot
in LU factorization:<br>
> see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot</a>!<br>
> [0]PETSC ERROR: Zero pivot row 280
value 6.5908e-17 tolerance 2.22045e-14!<br>
> [0]PETSC ERROR:<br>
>
------------------------------------------------------------------------<br>
> [0]PETSC ERROR: Petsc Release Version
3.3.0, Patch 3, Wed Aug 29<br>
> 11:26:24 CDT 2012<br>
> [0]PETSC ERROR: See
docs/changes/index.html for recent
updates.<br>
> [0]PETSC ERROR: See docs/faq.html for
hints about trouble shooting.<br>
> [0]PETSC ERROR: See docs/index.html
for manual pages.<br>
> [0]PETSC ERROR:<br>
>
------------------------------------------------------------------------<br>
> [0]PETSC ERROR: ./hit on a named
nid09458 by Unknown Fri May 24<br>
> 14:40:48 2013<br>
> [0]PETSC ERROR: Libraries linked from<br>
> [0]PETSC ERROR: Configure run at<br>
> [0]PETSC ERROR: Configure options<br>
> [0]PETSC ERROR:<br>
>
------------------------------------------------------------------------<br>
> [0]PETSC ERROR: MatPivotCheck_none()
line 583 in<br>
>
src/mat/impls/aij/seq//ptmp/skelly/petsc/3.3.03/cray_interlagos_build/real/src/include/petsc-private/matimpl.h<br>
> [0]PETSC ERROR: MatPivotCheck() line
602 in<br>
>
src/mat/impls/aij/seq//ptmp/skelly/petsc/3.3.03/cray_interlagos_build/real/src/include/petsc-private/matimpl.h<br>
> [0]PETSC ERROR:
MatLUFactorNumeric_SeqAIJ() line 585 in<br>
> src/mat/impls/aij/seq/aijfact.c<br>
> [0]PETSC ERROR: MatLUFactorNumeric()
line 2803 in src/mat/interface/matrix.c<br>
> [0]PETSC ERROR: PCSetUp_LU() line 160
in src/ksp/pc/impls/factor/lu/lu.c<br>
> [0]PETSC ERROR: PCSetUp() line 832 in
src/ksp/pc/interface/precon.c<br>
> [0]PETSC ERROR: KSPSetUp() line 278
in src/ksp/ksp/interface/itfunc.c<br>
> [0]PETSC ERROR:
PCSetUpOnBlocks_BJacobi_Singleblock() line
715 in<br>
> src/ksp/pc/impls/bjacobi/bjacobi.c<br>
> [0]PETSC ERROR: PCSetUpOnBlocks()
line 865 in src/ksp/pc/interface/precon.c<br>
> [0]PETSC ERROR: KSPSetUpOnBlocks()
line 154 in<br>
> src/ksp/ksp/interface/itfunc.c<br>
> [0]PETSC ERROR: KSPSolve() line 403
in src/ksp/ksp/interface/itfunc.c<br>
> [0]PETSC ERROR: PCMGMCycle_Private()
line 20 in src/ksp/pc/impls/mg/mg.c<br>
> [0]PETSC ERROR: PCMGMCycle_Private()
line 49 in src/ksp/pc/impls/mg/mg.c<br>
> [0]PETSC ERROR: PCMGMCycle_Private()
line 49 in src/ksp/pc/impls/mg/mg.c<br>
> [0]PETSC ERROR: PCMGMCycle_Private()
line 49 in src/ksp/pc/impls/mg/mg.c<br>
> [0]PETSC ERROR: PCApply_MG() line 326
in src/ksp/pc/impls/mg/mg.c<br>
> [0]PETSC ERROR: PCApply() line 384 in
src/ksp/pc/interface/precon.c<br>
> [0]PETSC ERROR: KSPSolve_CG() line
139 in src/ksp/ksp/impls/cg/cg.c<br>
> [0]PETSC ERROR: KSPSolve() line 446
in src/ksp/ksp/interface/itfunc.c<br>
><br>
> What could the reason be?<br>
> Thank you,<br>
><br>
> Michele<br>
><br>
><br>
><br>
> On 05/17/2013 07:35 PM, Michele Rosso
wrote:<br>
>> Thank you very much. I will try
and let you know.<br>
>><br>
>> Michele<br>
>><br>
>> On 05/17/2013 07:01 PM, Jed Brown
wrote:<br>
>>> Michele Rosso<<a href="mailto:mrosso@uci.edu" target="_blank">mrosso@uci.edu</a>>
writes:<br>
>>><br>
>>>> I noticed that the
problem appears even if I use CG with the
default<br>
>>>> preconditioner:
commenting KSPSetDM() solves the problem.<br>
>>> Okay, this issue can't show
up if you use SNES, but it's a consequence<br>
>>> of making geometric multigrid
work with a pure KSP interface. You can<br>
>>> either use
KSPSetComputeOperators() to put your
assembly in a function<br>
>>> (which will also be called on
coarse levels if you use -pc_type mg<br>
>>> without Galerkin coarse
operators) or you can can provide the
Jacobian<br>
>>> using KSPSetOperators() as
usual, but also call KSPSetDMActive() so
that<br>
>>> the DM is not used for
computing/updating the Jacobian.<br>
>>><br>
>>> The logic is cleaner in
petsc-3.4 and I think it just does the
right<br>
>>> thing in your case.<br>
>>><br>
>>>> So basically without a
proper grid (it seems no grid with an even<br>
>>>> numbers of nodes
qualifies) and with my own system matrix,
I cannot use<br>
>>>> any type of multigrid<br>
>>>> pre-conditioner?<br>
>>> You can use all the AMG
methods without setting a DM.<br>
>>><br>
>><br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all"><span class="HOEnZb"><font color="#888888">
<span><font color="#888888">
<div><br>
</div>
-- <br>
What most experimenters take for granted
before they begin their experiments is
infinitely more interesting than any results
to which their experiments lead.<br>
-- Norbert Wiener </font></span></font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
<br>
<br clear="all">
<div><br>
</div>
-- <br>
What most experimenters take for granted before they begin
their experiments is infinitely more interesting than any
results to which their experiments lead.<br>
-- Norbert Wiener
</font></span></div>
</div>
</blockquote>
<br>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div>