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[0] ISLocalToGlobalMappingBlock() line 271 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp() line 465 in /home/devel/petsc/dev/src/dm/interface/dm.c
[ 0]64 bytes ISLocalToGlobalMappingCreate() line 227 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA() line 15 in /home/devel/petsc/dev/src/dm/impls/da/dareg.c
[0] DMSetUp() line 465 in /home/devel/petsc/dev/src/dm/interface/dm.c
[ 0]528 bytes ISLocalToGlobalMappingCreate() line 227 in
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[0] ISLocalToGlobalMappingBlock() line 271 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA() line 15 in /home/devel/petsc/dev/src/dm/impls/da/dareg.c
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[ 0]4000000 bytes ISLocalToGlobalMappingBlock() line 277 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA() line 15 in /home/devel/petsc/dev/src/dm/impls/da/dareg.c
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA_3D() line 205 in
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[ 0]64 bytes ISLocalToGlobalMappingCreate() line 227 in
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[0] DMSetUp_DA_3D() line 205 in
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[ 0]528 bytes ISLocalToGlobalMappingCreate() line 227 in
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[0] ISLocalToGlobalMappingCreateIS() line 128 in
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[0] DMSetUp_DA_3D() line 205 in
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[ 0]12000000 bytes VecScatterCreate() line 1171 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA_3D() line 205 in
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[ 0]48 bytes VecScatterCreate() line 1170 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA() line 15 in /home/devel/petsc/dev/src/dm/impls/da/dareg.c
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[ 0]576 bytes VecScatterCreate() line 938 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA() line 15 in /home/devel/petsc/dev/src/dm/impls/da/dareg.c
[0] DMSetUp() line 465 in /home/devel/petsc/dev/src/dm/interface/dm.c
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[0] DMSetUp_DA() line 15 in /home/devel/petsc/dev/src/dm/impls/da/dareg.c
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[ 0]12000000 bytes VecScatterCreate() line 1171 in
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[0] DMSetUp_DA_3D() line 205 in
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[ 0]12000000 bytes VecScatterCreate() line 1171 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA_3D() line 205 in
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[ 0]48 bytes VecScatterCreate() line 1170 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] DMSetUp_DA_3D() line 205 in
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[0] VecCreate() line 32 in
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[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]128 bytes PetscThreadCommReductionCreate() line 436 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcommred.c
[0] PetscThreadCommReductionCreate() line 436 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcommred.c
[0] PetscThreadCommWorldInitialize() line 1227 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]1280 bytes PetscThreadCommReductionCreate() line 435 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcommred.c
[0] PetscThreadCommReductionCreate() line 435 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcommred.c
[0] PetscThreadCommWorldInitialize() line 1227 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]32 bytes PetscThreadCommReductionCreate() line 432 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcommred.c
[0] PetscThreadCommReductionCreate() line 432 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcommred.c
[0] PetscThreadCommWorldInitialize() line 1227 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]64 bytes PetscThreadCommWorldInitialize() line 1241 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscThreadCommWorldInitialize() line 1241 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]2432 bytes PetscThreadCommWorldInitialize() line 1240 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscThreadCommWorldInitialize() line 1240 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]16 bytes PetscThreadCommWorldInitialize() line 1232 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscThreadCommWorldInitialize() line 1232 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]16 bytes PetscThreadCommSetAffinities() line 423 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscThreadCommSetAffinities() line 423 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscThreadCommWorldInitialize() line 1227 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]48 bytes PetscThreadCommCreate() line 150 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscThreadCommCreate() line 150 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscThreadCommWorldInitialize() line 1227 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]320 bytes PetscThreadCommCreate() line 146 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscThreadCommCreate() line 146 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscThreadCommWorldInitialize() line 1227 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscGetThreadCommWorld() line 80 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommGetThreadComm() line 114 in
/home/devel/petsc/dev/src/sys/threadcomm/interface/threadcomm.c
[0] PetscCommDuplicate() line 139 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]16 bytes PetscCommDuplicate() line 151 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscCommDuplicate() line 151 in
/home/devel/petsc/dev/src/sys/objects/tagm.c
[0] PetscHeaderCreate_Private() line 31 in
/home/devel/petsc/dev/src/sys/objects/inherit.c
[0] DMCreate() line 58 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]240 bytes DMCreate() line 67 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMCreate() line 67 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]64 bytes DMCreate() line 67 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMCreate() line 67 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
[ 0]4048 bytes DMCreate() line 67 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMCreate() line 67 in /home/devel/petsc/dev/src/dm/interface/dm.c
[0] DMDACreate() line 390 in
/home/devel/petsc/dev/src/dm/impls/da/dacreate.c
[0] DMDACreateND() line 711 in petsc4py-3.3.1/src/include/custom.h
On 9 May 2013 00:58, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> Lisandro,
>
> Thanks. But we can we get this in master since all changes are made from
> there and show enough lines of the stack to see the line number of the DMDA
> code that calls the eventual culprit so we don't need to hunt for them
> manually?
>
> Barry
>
> On May 8, 2013, at 3:51 PM, Lisandro Dalcin <dalcinl at gmail.com> wrote:
>
>> On 8 May 2013 16:30, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>
>>> On May 8, 2013, at 7:54 AM, Peter Brune <prbrune at gmail.com> wrote:
>>>
>>>> DMGetCoordinateDM is, however, collective. Looking deeper, it is created
>>>> only when used, but setting uniform coordinates is using it. We might
>>>> want to be more upfront about this. It's probably not their problem.
>>>
>>> You guys are speculating too much. Create a DMDA characteristic for
>>> their code with reasonably large array dimensions and then -malloc_dump it
>>> (or something similar) to find out where the memory actually is. Then given
>>> this table of sizes propose changes, not before.
>>>
>>
>> $ python test2-dalcinl.py -malloc_dump | grep "\[ 0\]" | cut -f 2 -d
>> "]" | sort -r -n
>> 12000000 bytes VecScatterCreate() line 1095 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 12000000 bytes VecScatterCreate() line 1095 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 12000000 bytes VecScatterCreate() line 1095 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 12000000 bytes VecScatterCreate() line 1095 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 12000000 bytes ISLocalToGlobalMappingCreate() line 211 in
>> /home/devel/petsc/3.3/src/vec/is/utils/isltog.c
>> 12000000 bytes DMSetUp_DA_3D() line 1290 in
>> /home/devel/petsc/3.3/src/dm/impls/da/da3.c
>> 4000000 bytes ISLocalToGlobalMappingBlock() line 254 in
>> /home/devel/petsc/3.3/src/vec/is/utils/isltog.c
>> 3856 bytes DMCreate() line 41 in /home/devel/petsc/3.3/src/dm/interface/dm.c
>> 816 bytes DMCreate_DA() line 235 in
>> /home/devel/petsc/3.3/src/dm/impls/da/dacreate.c
>> 624 bytes PetscSFCreate() line 73 in /home/devel/petsc/3.3/src/sys/sf/sf.c
>> 624 bytes PetscSFCreate() line 73 in /home/devel/petsc/3.3/src/sys/sf/sf.c
>> 560 bytes VecScatterCreate() line 863 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 560 bytes VecScatterCreate() line 863 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 496 bytes ISLocalToGlobalMappingCreate() line 203 in
>> /home/devel/petsc/3.3/src/vec/is/utils/isltog.c
>> 496 bytes ISLocalToGlobalMappingCreate() line 203 in
>> /home/devel/petsc/3.3/src/vec/is/utils/isltog.c
>> 256 bytes DMCreate() line 41 in /home/devel/petsc/3.3/src/dm/interface/dm.c
>> 112 bytes DMSetUp_DA_3D() line 694 in
>> /home/devel/petsc/3.3/src/dm/impls/da/da3.c
>> 64 bytes VecScatterCreate() line 863 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 64 bytes VecScatterCreate() line 863 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 64 bytes PetscSFCreate() line 73 in /home/devel/petsc/3.3/src/sys/sf/sf.c
>> 64 bytes PetscSFCreate() line 73 in /home/devel/petsc/3.3/src/sys/sf/sf.c
>> 64 bytes ISLocalToGlobalMappingCreate() line 203 in
>> /home/devel/petsc/3.3/src/vec/is/utils/isltog.c
>> 64 bytes ISLocalToGlobalMappingCreate() line 203 in
>> /home/devel/petsc/3.3/src/vec/is/utils/isltog.c
>> 64 bytes DMCreate() line 41 in /home/devel/petsc/3.3/src/dm/interface/dm.c
>> 48 bytes VecScatterCreate() line 1094 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 48 bytes VecScatterCreate() line 1094 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 48 bytes VecScatterCreate() line 1094 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 48 bytes VecScatterCreate() line 1094 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 32 bytes DMSetUp_DA_3D() line 216 in
>> /home/devel/petsc/3.3/src/dm/impls/da/da3.c
>> 16 bytes VecScatterCreate() line 863 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 16 bytes VecScatterCreate() line 863 in
>> /home/devel/petsc/3.3/src/vec/vec/utils/vscat.c
>> 16 bytes PetscStrallocpy() line 186 in
>> /home/devel/petsc/3.3/src/sys/utils/str.c
>> 16 bytes PetscStrallocpy() line 186 in
>> /home/devel/petsc/3.3/src/sys/utils/str.c
>> 16 bytes PetscSFCreate() line 73 in /home/devel/petsc/3.3/src/sys/sf/sf.c
>> 16 bytes PetscSFCreate() line 73 in /home/devel/petsc/3.3/src/sys/sf/sf.c
>> 16 bytes PetscCommDuplicate() line 156 in
>> /home/devel/petsc/3.3/src/sys/objects/tagm.c
>> 16 bytes PetscCommDuplicate() line 156 in
>> /home/devel/petsc/3.3/src/sys/objects/tagm.c
>> 16 bytes ISLocalToGlobalMappingCreate() line 203 in
>> /home/devel/petsc/3.3/src/vec/is/utils/isltog.c
>> 16 bytes ISLocalToGlobalMappingCreate() line 203 in
>> /home/devel/petsc/3.3/src/vec/is/utils/isltog.c
>> 16 bytes DMSetUp_DA_3D() line 329 in
>> /home/devel/petsc/3.3/src/dm/impls/da/da3.c
>> 16 bytes DMSetUp_DA_3D() line 316 in
>> /home/devel/petsc/3.3/src/dm/impls/da/da3.c
>> 16 bytes DMSetUp_DA_3D() line 304 in
>> /home/devel/petsc/3.3/src/dm/impls/da/da3.c
>>
>>
>>
>> --
>> Lisandro Dalcin
>> ---------------
>> CIMEC (INTEC/CONICET-UNL)
>> Predio CONICET-Santa Fe
>> Colectora RN 168 Km 472, Paraje El Pozo
>> 3000 Santa Fe, Argentina
>> Tel: +54-342-4511594 (ext 1011)
>> Tel/Fax: +54-342-4511169
>
--
Lisandro Dalcin
---------------
CIMEC (INTEC/CONICET-UNL)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
3000 Santa Fe, Argentina
Tel: +54-342-4511594 (ext 1011)
Tel/Fax: +54-342-4511169
