[Getdp] Out of memory error message

Fri Aug 20 15:49:55 CEST 2010

Lars,

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.

Output follows:
Info    : Running 'getdp Lines -pre EleSta_v -cal -pos Map'
Info    : Started on Fri Aug 20 09:29:56 2010
Info    : Loading problem definition 'Lines.pro'
Info    : Loading problem definition 'parameters.pro'
Info    : Loading problem definition 'Jacobian_Lib.pro'
Info    : Loading problem definition 'Integration_Lib.pro'
Info    : Loading problem definition 'EleSta_v.pro'
Info    : Selected Resolution 'EleSta_v'
Info    : Loaded Geometric data 'Lines.msh'
Info    : System 'Sys_Ele' : Real
P r e - P r o c e s s i n g . . .
Info    : Treatment Formulation 'Electrostatics_v'
(0 %)
Info    :   Generate ExtendedGroup '_CO_Entity_13' (NodesOf)
(10 %)
(20 %)
(30 %)
(40 %)
(50 %)
(50 %)
(60 %)
(70 %)
(80 %)
(90 %)
(100 %)
Done!
Info    : (CPU = 21.8594s)
E n d   P r e - P r o c e s s i n g
P r o c e s s i n g . . .
Info    : Generate[Sys_Ele]
(0 %)
(10 %)
(20 %)
(30 %)
(40 %)
(50 %)
(50 %)
(60 %)
(70 %)
(80 %)
(90 %)
(100 %)
Done!
Info    : (CPU = 51.4063s)
Info    : Solve[Sys_Ele]
Info    : N: 390857

[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Out of memory. This could be due to allocating
[0]PETSC ERROR: too large an object or bleeding by not properly
[0]PETSC ERROR: destroying unneeded objects.
[0]PETSC ERROR: Memory allocated 0 Memory used by process 0
[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
[0]PETSC ERROR: Memory requested 943957912!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 7, Mon Jul  6 11:33:34
CDT 2009
[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: Lines on a umfpack-c named GALILEO by jvillar Fri Aug 20
09:29:56 2010
[0]PETSC ERROR: Libraries linked from
/home/Administrator/src/petsc-3.0.0-p7/umfpack-cxx-opt/lib
[0]PETSC ERROR: Configure run at Wed Mar 24 13:55:40 2010
[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
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
[0]PETSC ERROR: PetscFreeSpaceGet() line 14 in src/mat/utils/freespace.c
[0]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ() line 1322 in
src/mat/impls/aij/seq/aijfact.c
[0]PETSC ERROR: MatILUFactorSymbolic() line 5308 in
src/mat/interface/matrix.c
[0]PETSC ERROR: PCSetUp_ILU() line 293 in src/ksp/pc/impls/factor/ilu/ilu.c
[0]PETSC ERROR: PCSetUp() line 794 in src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSetUp() line 237 in src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: KSPSolve() line 353 in src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: User provided function() line 976 in
unknowndirectory/LinAlg_PETSC.cpp

This application has requested the Runtime to terminate it in an unusual
way.
Please contact the application's support team for more information.

John

On Fri, Aug 20, 2010 at 1:57 AM, Lars Rindorf <lrf at teknologisk.dk> wrote:

> Hi John
>
> Could you send the complete output and/or a simple file that reproduces
> your problem?
>
> KR Lars
>
> -----Oprindelig meddelelse-----
> Fra: getdp-bounces at ace20.montefiore.ulg.ac.be [mailto:
> getdp-bounces at ace20.montefiore.ulg.ac.be] På vegne af John_V
> Sendt: 19. august 2010 19:37
> Til: David Colignon
> Cc: getdp at geuz.org
> Emne: Re: [Getdp] Out of memory error message
>
> Thank you Dave. I expected a possible barrier at 2 GB and was
> surprised that the error message indicated only about half that. I have
> also estimated memory usage by just watching the memory used for that
> process in the Task Manager. This method's estimate is consistent with
> the error message--it also indicates a bit over 1 GB usage when the
> program fails. This is what made me wonder if the limit were something
> else (maybe something more easily correctable). --John
>
> On 8/19/2010 3:00 AM, David Colignon wrote:
> > Hi John,
> >
> > if you use the precompiled windows binary, I think it is compiled in
> > 32 bits mode , and then you hit the 2 GB barrier.
> >
> > Regards,
> >
> > Dave
> >
>
> _______________________________________________
> getdp mailing list
> getdp at geuz.org
> http://www.geuz.org/mailman/listinfo/getdp
>
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