<div dir="ltr">On Wed, May 29, 2013 at 8:29 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">1) How do I solve this?<br></font></div></blockquote><div><br></div><div style>We will fix this, but any fix will necessitate upgrading.</div><div><br></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">
2) So upgrading to version 3.4 would take care of the shift
without the need to specify any option?<br></font></div></blockquote><div><br></div><div style>Yes</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">
Michele<br>
<br>
</font>
<div>On 05/29/2013 05:17 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">On Wed, May 29, 2013 at 7:22 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 attached the complete output.<br>
I used 2 processors for this run. I wanted to use only
one to have a cleaner output but I could not because
of this error:<br>
</font></div>
</blockquote>
<div><br>
</div>
<div>There are 2 problems here:</div>
<div><br>
</div>
<div> 1) GAMG is not accepting options for the
coarse grid solver</div>
<div><br>
</div>
<div> 2) You do not appear to using PETSc 3.4, or
the shift you are trying to set would be there by default</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">
[0]PCSetData_AGG bs=1 MM=32768<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[0]PETSC ERROR: Arguments are incompatible!<br>
[0]PETSC ERROR: MatMatMult requires A, mpiaij, to be
compatible with B, seqaij!<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 nid15343 by Unknown
Wed May 29 18:15:24 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: MatMatMult() line 8614 in
src/mat/interface/matrix.c<br>
[0]PETSC ERROR: PCGAMGOptprol_AGG() line 1358 in
src/ksp/pc/impls/gamg/agg.c<br>
[0]PETSC ERROR: PCSetUp_GAMG() line 673 in
src/ksp/pc/impls/gamg/gamg.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>
hit: gamg.c:568: PCSetUp_GAMG: Assertion
`pc->setupcalled' failed.<br>
<br>
</font>
<div>On 05/29/2013 02:29 PM, Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">On Wed, May 29, 2013 at 5:25 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">Hi,<br>
<br>
I proceeded as Matt suggested. I am
running without nullspace (Dirichlet's
BCs) with the following options:<br>
<br>
-pc_type gamg -pc_mg_cycle_type v
-pc_gamg_agg_nsmooths 1
-mg_coarse_sub_pc_factor_shift_type
NONZERO -ksp_view -options_left<br>
<br>
The results are fine and the run finishes.
The output of -ksp_view does not say
anything about the coarse solver being
shifted.<br>
In fact the option </font><font face="Ubuntu"><font face="Ubuntu">-mg_coarse_sub_pc_factor_shift_type
NONZERO is not used:<br>
</font></font></div>
</blockquote>
<div><br>
</div>
<div>Please show us the COMPLETE output.</div>
<div><br>
</div>
<div> Thanks,</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"><font face="Ubuntu"> #PETSc
Option Table entries:<br>
-ksp_view<br>
-mg_coarse_sub_pc_factor_shift_type
NONZERO<br>
-options_left<br>
-pc_gamg_agg_nsmooths 1<br>
-pc_mg_cycle_type v<br>
-pc_type gamg<br>
#End of PETSc Option Table entries<br>
There is one unused database option. It
is:<br>
Option left:
name:-mg_coarse_sub_pc_factor_shift_type
value: NONZERO<br>
<br>
Michele<br>
<br>
<br>
</font></font>
<div>On 05/24/2013 03:20 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">On Fri, May 24, 2013 at
5:18 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">Using <br>
<br>
-pc_type gamg
-pc_mg_cycle_type v
-pc_gamg_agg_nsmooths 1
-mg_coarse_sub_pc_factor_shift_type
NONZERO -option_left
-ksp_view <br>
</font></div>
</blockquote>
<div><br>
</div>
<div>This is what debugging is
about. We are not running your
problem. How could this be
debugged?</div>
<div><br>
</div>
<div>1) Run the problem w/o a null
space so that it finishes</div>
<div><br>
</div>
<div>2) Look at the output for
-ksp_view</div>
<div><br>
</div>
<div>3) Does the coarse solver say
that it is shifted?</div>
<div><br>
</div>
<div>4) Are there options which were
unused?</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"> still produces
the same error:<br>
<br>
[0]PCSetData_AGG bs=1
MM=131072<br>
[0]PETSC ERROR:
--------------------- Error
Message
------------------------------------<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 6.56964e-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 nid15363 by Unknown Fri
May 24 17:06:50 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:
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>
</font>
<div>On 05/24/2013 02:51 PM, Jed
Brown wrote:<br>
</div>
<blockquote type="cite">
<pre>Michele Rosso <a href="mailto:mrosso@uci.edu" target="_blank"><mrosso@uci.edu></a> writes:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre> With petsc-3.4 (which you should upgrade to), use
-mg_coarse_sub_pc_factor_shift_type NONZERO
</pre>
</blockquote>
</blockquote>
<pre>Actually, use this with petsc-3.3 also (and please upgrade to
petsc-3.4).
The option you were passing was not being used.
</pre>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<span><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><font color="#888888"> </font></span></div>
<span><font color="#888888">
</font></span></blockquote>
<span><font color="#888888">
<br>
</font></span></div>
<span><font color="#888888"> </font></span></blockquote>
<span><font color="#888888"> </font></span></div>
<span><font color="#888888"> <br>
<br clear="all"><span class="HOEnZb"><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>