Merge

Hg-commit: 674bc8187eb8d0423d5e5713bd4ba8a46a2b8020

Now requirepackage is only used for proper packages, functions use requiresfunction, and the rest use requiresdefine

Hg-commit: dd65fd3461c02753386917514e6ebe12d345a30e

when writing vector to binary file always write the block size to the info file even when size one so that outdated values in the options database don't get used.

Hg-commit: 78016a9f6dd83870e0896c4e

when writing vector to binary file always write the block size to the info file even when size one so that outdated values in the options database don't get used.

Hg-commit: 78016a9f6dd83870e0896c4e504cdee0c23dea53

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Fixed bug where local Vec size of 0 caused HDF5 error when creating memspace with zero in one of the dimensions. Create a null memspace and then use H5Sselect_none() to reset the filespace to none af

Fixed bug where local Vec size of 0 caused HDF5 error when creating memspace with zero in one of the dimensions. Create a null memspace and then use H5Sselect_none() to reset the filespace to none after selecting hyperslab.

Hg-commit: 8d262f2637166759c312d0ba93fedcc6216337da

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added .cu to .rm rule to makefiles
updated manual merge to use cusp

Hg-commit: 84dcc031450529677736345609eb641ad34aeb9f

commit after manual merge

Hg-commit: 7297db73518173332630bb41c7f3242a65f459f4

finished converting cuda to cusp in source code

Hg-commit: 7d2435fd6968de7d5739915853d92ec73d2998c0

Fixed bad merge

Hg-commit: 2254290672032c34a7e4042700d4e34c4723245a

changed more file names from cuda to cusp

Hg-commit: c5000cb46896546bd89b0a3eaeeef63664d38ffc

changed CUDA copysome to use new cudagetarray methods (maybe this will help?)

Hg-commit: 7abed4906277a23f6f89cb5a3e0638e8618c383d

changed names of directories that had cuda to cusp
changed names of some files that had cuda to cusp

Hg-commit: 7e265e74bd58a9e4b021e6c83e3146332a07fbdb

changed names of all GPU related functions, macros and variables that involve CUSP to use the string CUSP instead of the misleading CUDA

Hg-commit: 3264fa4049fd83eceb12c85feb980ef207360220

fix bad merge

Hg-commit: a9232016f92cf0c34830127bf9ef48494495d1c9

merge from 31

Hg-commit: 362d882ffa7f19081a40ee99fdb89b9b6325a049

Small change to HDF5 output (now Vec always has blocksize dim)

Hg-commit: befa73e0225288e1ffca8093c2fc0850ff30cb6d

Fixed some naming errors with Barry's back port from petsc-dev

Hg-commit: d8953a43088b3b55020d1d5921aea73416b89d7b

initializing to 0 in VecCUDAGetArray for check to get rid of compiler warnings

Hg-commit: e6cf908276e7b96f7355aa47b0c495683e122536

update output files for dm/examples/tutorials/output/ex3.c

Hg-commit: 91c0981b7dd2ad2f536751f7e0d2f7c37ccd0bb7

added MatFindZeroDiagonals()
added docs about weakness of DMView(), DMDALoad() for DMDA and binary viewer

Hg-commit: 2c69111a371375ded3a523f97ab010afdba2995d

backported HDF viewer for Vec_Seq

Hg-commit: 0c4f7d614bb01a1a07e799cc887cf080b65d6c90

rm useless varible

Hg-commit: a0fa5ba23a828184657af1686374cc32d141015e

do not attempt to free all undestroyed PETSc objects in PetscFinalize() instead just optional print them
if the Petsc_InnerComm_keyval is attached to PETSC_COMM_SELF or PETSC_COMM_WORLD then free inn

do not attempt to free all undestroyed PETSc objects in PetscFinalize() instead just optional print them
if the Petsc_InnerComm_keyval is attached to PETSC_COMM_SELF or PETSC_COMM_WORLD then free inner communicator and delete attribute from outter communicator
Subject: Re: [petsc-maint #60571] DMDestroy crashes if I don't carefully destroy every vector that was created with it
From: Barry Smith <bsmith@mcs.anl.gov>
Date: January 7, 2011 5:51:17 PM CST
To: petsc-maint <petsc-maint@mcs.anl.gov>, Jason Sarich <sarich@mcs.anl.gov>
Reply-To: petsc-maint <petsc-maint@mcs.anl.gov>

Jason,

Thanks for reporting this with a reproduceble example.

This is big trouble and I don't have a good solution yet. The problem comes because I keep a list of ALL outstanding objects and just loop over them deleting them. The problem is if one object has a reference to another object (the ISLocalToGlobalMapping is referenced by the Vec) but the referenced object is destroyed, then when the referencer is destroyed it tries to destroy the previously destroyed object (hence the crash).

The reason I want to destroy all objects before existing PetscFinalize() is to make PETSc reentrant (so you can call PetscInitialize() more than once, which is normal to do in a scripting language like Python or MATLAB). If I don't destroy all objects then the extra MPI communicators and attributes in the MPI communicators are not destroyed and next time you enter PETSc and use one of those attributes it points to something that is not valid and gives trouble. Destroying all objects insures proper cleanup, otherwise we'd need some other way in PetscFinalize() to cleanup which appears like extra infrastructure I don't want to have. In a scripting environment (unlike a real language :-) it is unrealistic to expect users to cleanup all objects themselves.


Barry

On Jan 7, 2011, at 4:37 PM, Jason Sarich wrote:

Using petsc-dev changeset: 18100:5f2967045bc2 (1/07/2011 15:34)

PETSc is throwing some errors when I don't destroy my dm-created vectors
before destroying the DM. I can reproduce this with
snes/examples/tutorials/ex5.c by removing the VecDestroy(x):

sarich@franklin:~/software/petsc-dev/src/snes/examples/tutorials> ./ex5
Number of Newton iterations = 4
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Invalid argument!
[0]PETSC ERROR: Wrong type of object: Parameter # 1!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development HG revision:
c082370134d6559807fdad65fb712d89017dee8f HG Date: Mon Jan 03 22:01:17 2011
-0600
[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: ./ex5 on a linux-gnu named franklin by sarich Fri Jan 7
16:35:50 2011
[0]PETSC ERROR: Libraries linked from
/home/sarich/software/petsc-dev/linux-gnu-cxx-debug/lib
[0]PETSC ERROR: Configure run at Tue Jan 4 09:55:51 2011
[0]PETSC ERROR: Configure options --download-mpich=1 --with-shared=1
--download-sowing=1 --with-dynamic=1 PETSC_ARCH=linux-gnu-cxx-debug

Hg-commit: cdec62f65ff5d1a817cd2a47c5f6f27c0b729322

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win32 fixes

Hg-commit: 230d0338dff89fcff00cccf115250758903e9357

fixed some unitialized variables warnings with MPI-uni

Hg-commit: 925a462303ee56a402b0355f3680130c52d4c99c

Add VECNEST and MATNEST man pages

Hg-commit: bed0ed4aa7c044e74c299856847fba970f8828e2