<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta name=Generator content="Microsoft Word 12 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"Formateret HTML Tegn";
margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.FormateretHTMLTegn
{mso-style-name:"Formateret HTML Tegn";
mso-style-priority:99;
mso-style-link:"Formateret HTML ";
font-family:"Courier New";}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:3.0cm 2.0cm 3.0cm 2.0cm;}
div.WordSection1
{page:WordSection1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=DA link=blue vlink=purple>
<div class=WordSection1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi John<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<pre><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>What goes wrong is that petsc tries to preallocate to much memory. Before your sparse matrix is constructet petsc ‘pre’allocates memory to speed up the assembly of the matrix. You can reduce the preallocated memory by the command line option:</span><span
lang=EN-US><o:p></o:p></span></pre>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>-petsc_prealloc
300<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>I
would try with 50. Assembly will probably be slow. Then I would increase it.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>KR
Lars<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Fra:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> John_V
[mailto:jvillar.john@gmail.com] <br>
<b>Sendt:</b> 20. august 2010 15:50<br>
<b>Til:</b> Lars Rindorf<br>
<b>Cc:</b> getdp@geuz.org<br>
<b>Emne:</b> Re: [Getdp] Out of memory error message<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Lars,<br>
<br>
The mesh file is large (148 MB), as you might expect since it produces an
out-of-memory error. I'm not sure I should post something that large to the
list, but you could regenerate it by 3-D mesh (using gmsh) of the attached
Lines.geo file. That's how I did it. The remaining inputs are also attached.<br>
<br>
Output follows:<o:p></o:p></p>
<div style='margin-left:30.0pt'>
<p class=MsoNormal style='margin-bottom:12.0pt'>Info :
Running 'getdp Lines -pre EleSta_v -cal -pos Map'<br>
Info : Started on Fri Aug 20 09:29:56 2010<br>
Info : Loading problem definition 'Lines.pro'<br>
Info : Loading problem definition '<a
href="http://parameters.pro">parameters.pro</a>'<br>
Info : Loading problem definition 'Jacobian_Lib.pro'<br>
Info : Loading problem definition 'Integration_Lib.pro'<br>
Info : Loading problem definition 'EleSta_v.pro'<br>
Info : Selected Resolution 'EleSta_v'<br>
Info : Loaded Geometric data 'Lines.msh'<br>
Info : System 'Sys_Ele' : Real<br>
P r e - P r o c e s s i n g . . .<br>
Info : Treatment Formulation 'Electrostatics_v'<br>
(0
%)
<br>
Info : Generate ExtendedGroup '_CO_Entity_13'
(NodesOf)<br>
(10
%)
<br>
(20
%)
<br>
(30
%)
<br>
(40
%)
<br>
(50
%)
<br>
(50
%)
<br>
(60
%)
<br>
(70
%)
<br>
(80
%)
<br>
(90
%)
<br>
(100
%)
<br>
Done!
<br>
Info : (CPU = 21.8594s)<br>
E n d P r e - P r o c e s s i n g<br>
P r o c e s s i n g . . .<br>
Info : Generate[Sys_Ele]<br>
(0
%)
<br>
(10
%)
<br>
(20
%)
<br>
(30
%)
<br>
(40
%)
<br>
(50
%)
<br>
(50 %)
<br>
(60
%)
<br>
(70
%)
<br>
(80
%)
<br>
(90
%)
<br>
(100
%)
<br>
Done!
<br>
Info : (CPU = 51.4063s)<br>
Info : Solve[Sys_Ele]<br>
Info : N: 390857<br>
<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[0]PETSC ERROR: Out of memory. This could be due to allocating<br>
[0]PETSC ERROR: too large an object or bleeding by not properly<br>
[0]PETSC ERROR: destroying unneeded objects.<br>
[0]PETSC ERROR: Memory allocated 0 Memory used by process 0<br>
[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.<br>
[0]PETSC ERROR: Memory requested 943957912!<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 7, Mon Jul 6 11:33:34
CDT 2009<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: Lines on a umfpack-c named GALILEO by jvillar Fri Aug 20
09:29:56 2010<br>
[0]PETSC ERROR: Libraries linked from
/home/Administrator/src/petsc-3.0.0-p7/umfpack-cxx-opt/lib<br>
[0]PETSC ERROR: Configure run at Wed Mar 24 13:55:40 2010<br>
[0]PETSC ERROR: Configure options --with-debugging=0 --with-scalar-type=complex
--with-clanguage=cxx --with-shared=0 --with-mpi=0 --with-x=0 --with-fortran=0
--with-cc="gcc -mno-cygwin" --with-cxx="g++ -mno-cygwin"
COPTFLAGS=-O2 CXXOPTFLAGS=-O2 --with-umfpack=1 --download-umfpack=ifneeded
--useThreads=0 --useThreads=0<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c<br>
[0]PETSC ERROR: PetscFreeSpaceGet() line 14 in src/mat/utils/freespace.c<br>
[0]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ() line 1322 in
src/mat/impls/aij/seq/aijfact.c<br>
[0]PETSC ERROR: MatILUFactorSymbolic() line 5308 in src/mat/interface/matrix.c<br>
[0]PETSC ERROR: PCSetUp_ILU() line 293 in src/ksp/pc/impls/factor/ilu/ilu.c<br>
[0]PETSC ERROR: PCSetUp() line 794 in src/ksp/pc/interface/precon.c<br>
[0]PETSC ERROR: KSPSetUp() line 237 in src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR: KSPSolve() line 353 in src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR: User provided function() line 976 in
unknowndirectory/LinAlg_PETSC.cpp<br>
<br>
This application has requested the Runtime to terminate it in an unusual way.<br>
Please contact the application's support team for more information.<o:p></o:p></p>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'>John<o:p></o:p></p>
<div style='margin-left:30.0pt'>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal>On Fri, Aug 20, 2010 at 1:57 AM, Lars Rindorf <<a
href="mailto:lrf@teknologisk.dk">lrf@teknologisk.dk</a>> wrote:<o:p></o:p></p>
<p class=MsoNormal>Hi John<br>
<br>
Could you send the complete output and/or a simple file that reproduces your
problem?<br>
<br>
KR Lars<br>
<br>
-----Oprindelig meddelelse-----<br>
Fra: <a href="mailto:getdp-bounces@ace20.montefiore.ulg.ac.be">getdp-bounces@ace20.montefiore.ulg.ac.be</a>
[mailto:<a href="mailto:getdp-bounces@ace20.montefiore.ulg.ac.be">getdp-bounces@ace20.montefiore.ulg.ac.be</a>]
På vegne af John_V<br>
Sendt: 19. august 2010 19:37<br>
Til: David Colignon<br>
Cc: <a href="mailto:getdp@geuz.org">getdp@geuz.org</a><br>
Emne: Re: [Getdp] Out of memory error message<o:p></o:p></p>
<div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><br>
Thank you Dave. I expected a possible barrier at 2 GB and was<br>
surprised that the error message indicated only about half that. I have<br>
also estimated memory usage by just watching the memory used for that<br>
process in the Task Manager. This method's estimate is consistent with<br>
the error message--it also indicates a bit over 1 GB usage when the<br>
program fails. This is what made me wonder if the limit were something<br>
else (maybe something more easily correctable). --John<br>
<br>
On 8/19/2010 3:00 AM, David Colignon wrote:<br>
> Hi John,<br>
><br>
> if you use the precompiled windows binary, I think it is compiled in<br>
> 32 bits mode , and then you hit the 2 GB barrier.<br>
><br>
> Regards,<br>
><br>
> Dave<br>
><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal>_______________________________________________<br>
getdp mailing list<br>
<a href="mailto:getdp@geuz.org">getdp@geuz.org</a><br>
<a href="http://www.geuz.org/mailman/listinfo/getdp" target="_blank">http://www.geuz.org/mailman/listinfo/getdp</a><o:p></o:p></p>
</div>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
</body>
</html>