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<p>Thanks Matt,</p>
<p>I got it figured out. As with a lot of uninitialised value bugs
it started a long way away (in a scalar value) and propagated
through. What is slightly bizarre is that valgrind didn't pick it
up where I define and first use it, even with --track-origins=yes.<br>
</p>
<p>Thank you for your help.</p>
<p>Phil<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 26/10/2018 15:01, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMYG4GmESp2aEf0687VninbjEhZC+Z0WX0FOi=1QRYr6sYnACA@mail.gmail.com">
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<div class="gmail_quote">
<div dir="ltr">On Fri, Oct 26, 2018 at 9:54 AM Phil Tooley
<<a href="mailto:phil.tooley@sheffield.ac.uk"
moz-do-not-send="true">phil.tooley@sheffield.ac.uk</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi All,<br>
<br>
Running valgrind over my code reveals a huge number (it
stops collecting<br>
after 1e6) of uninitialised value errors occuring the
KSPSolve routine. <br>
These don't occur with the ksp example scripts but I can't
figure out<br>
what I am doing wrong in my code. My code works as
expected. The same<br>
errors occur with both version 3.9.4 and 3.10.0.<br>
<br>
I am developing in c++ and using smart pointers to allow
autodestruction<br>
of Petsc objects, but I don't think this should have any
side effects. <br>
</blockquote>
<div><br>
</div>
<div>From casual inspection, it sure seems like the matrix you
are passing KSP has unitialized</div>
<div>values.</div>
<div><br>
</div>
<div><Editorial comment>I used smart pointers for years,
and work on packages that had smart</div>
<div>pointers. In almost every case, we ended up ripping out
the smart pointers and going with</div>
<div>explicit destruction, the amount of work they save never
outweighed the problems with</div>
<div>detecting errors</Editorial comment></div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</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">
I do the ksp setup as:<br>
<br>
KSP_unique m_ksp = create_unique_ksp();<br>
<br>
perr = KSPCreate(m_comm, m_ksp.get());CHKERRABORT(m_comm,
perr);<br>
<br>
perr = KSPSetOperators(*m_ksp, *normmat,
*normmat);CHKERRABORT(m_comm,<br>
perr);<br>
perr = KSPSetUp(*m_ksp);CHKERRABORT(m_comm, perr);<br>
<br>
perr = KSPSetFromOptions(*m_ksp);CHKERRABORT(m_comm, perr);<br>
perr = KSPSetUp(*m_ksp);CHKERRABORT(m_comm, perr);<br>
<br>
perr = KSPSolve(*m_ksp, *m_rhs,
*m_delta);CHKERRABORT(m_comm, perr);<br>
<br>
Where normmat is a smart pointer to a previously created Mat
object and<br>
m_rhs and m_delta are smart pointers to Vec objects which
are<br>
initialised using MatCreateVecs on normmat.<br>
<br>
I am using MPICH to provide a (hopefully) valgrind clean MPI
implementation.<br>
<br>
Any insights are appreciated.<br>
<br>
Many Thanks<br>
<br>
Phil Tooley<br>
<br>
Typical errors are as follows:<br>
<br>
==7368== Conditional jump or move depends on uninitialised
value(s)<br>
==7368== at 0x58894EE: PetscAbsScalar(double)
(petscmath.h:389)<br>
==7368== by 0x5891702: MatLUFactorNumeric_SeqAIJ
(aijfact.c:553)<br>
==7368== by 0x5406B83: MatLUFactorNumeric (matrix.c:3031)<br>
==7368== by 0x609F317: PCSetUp_ILU(_p_PC*) (ilu.c:176)<br>
==7368== by 0x6192D4F: PCSetUp (precon.c:923)<br>
==7368== by 0x62EAE56: KSPSetUp (itfunc.c:381)<br>
==7368== by 0x60190BB:
PCSetUpOnBlocks_BJacobi_Singleblock(_p_PC*)<br>
(bjacobi.c:621)<br>
==7368== by 0x619352C: PCSetUpOnBlocks (precon.c:954)<br>
==7368== by 0x62E8F0A: KSPSetUpOnBlocks (itfunc.c:213)<br>
==7368== by 0x62ECCB1: KSPSolve (itfunc.c:613)<br>
==7368== by 0x10FCDD: Elastic::innerstep(double) (in<br>
/home/telemin/repos/pfire_petsc/bin/pfire)<br>
==7368== by 0x110600: Elastic::innerloop(int) (in<br>
/home/telemin/repos/pfire_petsc/bin/pfire)<br>
==7368==<br>
==7368== Conditional jump or move depends on uninitialised
value(s)<br>
==7368== at 0x58894EE: PetscAbsScalar(double)
(petscmath.h:389)<br>
==7368== by 0x588A75F: MatPivotCheck_none(_p_Mat*,
_p_Mat*,<br>
MatFactorInfo const*, FactorShiftCtx*, int) (matimpl.h:704)<br>
==7368== by 0x588AD6E: MatPivotCheck(_p_Mat*, _p_Mat*,
MatFactorInfo<br>
const*, FactorShiftCtx*, int) (matimpl.h:727)<br>
==7368== by 0x589177D: MatLUFactorNumeric_SeqAIJ
(aijfact.c:558)<br>
==7368== by 0x5406B83: MatLUFactorNumeric (matrix.c:3031)<br>
==7368== by 0x609F317: PCSetUp_ILU(_p_PC*) (ilu.c:176)<br>
==7368== by 0x6192D4F: PCSetUp (precon.c:923)<br>
==7368== by 0x62EAE56: KSPSetUp (itfunc.c:381)<br>
==7368== by 0x60190BB:
PCSetUpOnBlocks_BJacobi_Singleblock(_p_PC*)<br>
(bjacobi.c:621)<br>
==7368== by 0x619352C: PCSetUpOnBlocks (precon.c:954)<br>
==7368== by 0x62E8F0A: KSPSetUpOnBlocks (itfunc.c:213)<br>
==7368== by 0x62ECCB1: KSPSolve (itfunc.c:613)<br>
==7368==<br>
==7368== Conditional jump or move depends on uninitialised
value(s)<br>
==7368== at 0x588A76D: MatPivotCheck_none(_p_Mat*,
_p_Mat*,<br>
MatFactorInfo const*, FactorShiftCtx*, int) (matimpl.h:704)<br>
==7368== by 0x588AD6E: MatPivotCheck(_p_Mat*, _p_Mat*,
MatFactorInfo<br>
const*, FactorShiftCtx*, int) (matimpl.h:727)<br>
==7368== by 0x589177D: MatLUFactorNumeric_SeqAIJ
(aijfact.c:558)<br>
==7368== by 0x5406B83: MatLUFactorNumeric (matrix.c:3031)<br>
==7368== by 0x609F317: PCSetUp_ILU(_p_PC*) (ilu.c:176)<br>
==7368== by 0x6192D4F: PCSetUp (precon.c:923)<br>
==7368== by 0x62EAE56: KSPSetUp (itfunc.c:381)<br>
==7368== by 0x60190BB:
PCSetUpOnBlocks_BJacobi_Singleblock(_p_PC*)<br>
(bjacobi.c:621)<br>
==7368== by 0x619352C: PCSetUpOnBlocks (precon.c:954)<br>
==7368== by 0x62E8F0A: KSPSetUpOnBlocks (itfunc.c:213)<br>
==7368== by 0x62ECCB1: KSPSolve (itfunc.c:613)<br>
==7368== by 0x10FCDD: Elastic::innerstep(double) (in<br>
/home/telemin/repos/pfire_petsc/bin/pfire)<br>
==7368==<br>
==7368== Conditional jump or move depends on uninitialised
value(s)<br>
==7368== at 0x58894EE: PetscAbsScalar(double)
(petscmath.h:389)<br>
==7368== by 0x5889528: PetscIsNanScalar(double)
(petscmath.h:674)<br>
==7368== by 0x588A784: MatPivotCheck_none(_p_Mat*,
_p_Mat*,<br>
MatFactorInfo const*, FactorShiftCtx*, int) (matimpl.h:704)<br>
==7368== by 0x588AD6E: MatPivotCheck(_p_Mat*, _p_Mat*,
MatFactorInfo<br>
const*, FactorShiftCtx*, int) (matimpl.h:727)<br>
==7368== by 0x589177D: MatLUFactorNumeric_SeqAIJ
(aijfact.c:558)<br>
==7368== by 0x5406B83: MatLUFactorNumeric (matrix.c:3031)<br>
==7368== by 0x609F317: PCSetUp_ILU(_p_PC*) (ilu.c:176)<br>
==7368== by 0x6192D4F: PCSetUp (precon.c:923)<br>
==7368== by 0x62EAE56: KSPSetUp (itfunc.c:381)<br>
==7368== by 0x60190BB:
PCSetUpOnBlocks_BJacobi_Singleblock(_p_PC*)<br>
(bjacobi.c:621)<br>
==7368== by 0x619352C: PCSetUpOnBlocks (precon.c:954)<br>
==7368== by 0x62E8F0A: KSPSetUpOnBlocks (itfunc.c:213)<br>
==7368==<br>
==7368== Conditional jump or move depends on uninitialised
value(s)<br>
==7368== at 0x4FDACE3: std::isnan(double) (cmath:627)<br>
==7368== by 0x4FDAC8D: PetscIsNanReal (mathinf.c:92)<br>
==7368== by 0x588952D: PetscIsNanScalar(double)
(petscmath.h:674)<br>
==7368== by 0x588A784: MatPivotCheck_none(_p_Mat*,
_p_Mat*,<br>
MatFactorInfo const*, FactorShiftCtx*, int) (matimpl.h:704)<br>
==7368== by 0x588AD6E: MatPivotCheck(_p_Mat*, _p_Mat*,
MatFactorInfo<br>
const*, FactorShiftCtx*, int) (matimpl.h:727)<br>
==7368== by 0x589177D: MatLUFactorNumeric_SeqAIJ
(aijfact.c:558)<br>
==7368== by 0x5406B83: MatLUFactorNumeric (matrix.c:3031)<br>
==7368== by 0x609F317: PCSetUp_ILU(_p_PC*) (ilu.c:176)<br>
==7368== by 0x6192D4F: PCSetUp (precon.c:923)<br>
==7368== by 0x62EAE56: KSPSetUp (itfunc.c:381)<br>
==7368== by 0x60190BB:
PCSetUpOnBlocks_BJacobi_Singleblock(_p_PC*)<br>
(bjacobi.c:621)<br>
==7368== by 0x619352C: PCSetUpOnBlocks (precon.c:954)<br>
<br>
-- <br>
Phil Tooley<br>
Research Software Engineering<br>
University of Sheffield<br>
<br>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>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><br>
</div>
<div><a href="http://www.cse.buffalo.edu/~knepley/"
target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Phil Tooley
Research Software Engineering
University of Sheffield</pre>
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