Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

merge PetscSF implementation

Hg-commit: 98dccc99445b69cb7a66312149eb16fec359e294

removed trailing spaces from all files

Hg-commit: 1cfa55059afe46c5145e0e830cd797b97216abfb

commit after merge

Hg-commit: d0f613618ca66a5aeb1aac97d210d2cc29755d3d

reemove OBJSC and OBJSF from invididual makefiles and auto-define in conf/variables

Hg-commit: 2f01c17f3c19dc4b89aaf306cfd60a12312c270d

tried to add -ts_monitor_sp_eig but doesn't work with FD Jacobian
The logic in TS is too convoluted, we need to string out some cases and simplify
TSComputeIJacobian() doesn't work in monitor with FD

tried to add -ts_monitor_sp_eig but doesn't work with FD Jacobian
The logic in TS is too convoluted, we need to string out some cases and simplify
TSComputeIJacobian() doesn't work in monitor with FD Jacobian yet clearly does work
in the solver, why is that?

Hg-commit: 4be5ac85d54a2ba1c410266ef33e69e1f036536c

show more ...

backout all chmod stuff in bf971ba58125
[but keep diffs to src/mat/impls/aij/mpi/mpimatmatmult.c ]

Hg-commit: 4a812fc1f35496ce2717c7da9ef12ffabbd13258

removed a spurious call to MatSetBlockSize.

Hg-commit: bf971ba58125bd8cf7ceb2a9d0f5cdf27c27cc6a

commit after merge

Hg-commit: 072d3613caf2b1953e19eb41aaee719c87da3dc8

Remove TSDefaultComputeJacobian{,Color}() and MatFDColoringApplyTS(); update all the examples that were still using the old style

Hg-commit: 6677905c965471eda292ff1997e1a953222a27c5

Merge

Hg-commit: 0fb617426806c222fb6fb5e47365b6c3688c614c

commit after merge

Hg-commit: d540875a63b3c979c82b6a7fa7f062571e906d10

Mass revert file modes that were made executable in f6e61ee9c329

Hg-commit: 116d90d0b66125cee0db3e7351047057e756baf5

Merge

Hg-commit: ee8d91ae0580d1d4fa92be38a18d40c838b9a257

changed MatMatMult to MatTranposeMatMult.

Hg-commit: f6e61ee9c329774cd5343eea1ee6b7432be17c3f

Merge

Hg-commit: 7e01025b11c859ecad5b4d890251c24e935a27b5

commit after merge

Hg-commit: 4afddb78e4d16b99952e891a10244a92ea0015ab

Merge

Hg-commit: 9c9e2b0243eedf0151e3676f8f4ccde9f7b93898

merge TrMalloc/MEMALIGN updates

Hg-commit: e66e6e0b392d0e3456a0c4fdee411b9bff8fd74a

removed PETSC_ARCH/conf/base and
added support for not setting PETSC_ARCH and PETSC_DIR with --prefix option

Hg-commit: e478f4df238e5763b64567336d7cf94ca5d89d58

commit aFTERmerge

Hg-commit: 45a698803bd457bdc2ba32be5035e710250a5320

Merge

Hg-commit: 89a88a4570a641b3af1b53853d576da3947e5ca7

changed bmake/common everywhere to conf
fixed a little more for new install system

Hg-commit: 1aa781ff09e652ebafd6f016d84e88c15ea650f1

bk-changeset-1.3097
barrysmith@barry-smiths-computer.local|ChangeSet|20050414014649|30260
ChangeSet
1.3097 05/04/13 20:46:49 barrysmith@barry-smiths-computer.local +0 -0
Merge bk://petsc@petsc.bk

bk-changeset-1.3097
barrysmith@barry-smiths-computer.local|ChangeSet|20050414014649|30260
ChangeSet
1.3097 05/04/13 20:46:49 barrysmith@barry-smiths-computer.local +0 -0
Merge bk://petsc@petsc.bkbits.net/petsc-dev
into barry-smiths-computer.local:/Users/barrysmith/petsc-dev


Hg-commit: ada2cb4da43553824caf1f43b881398751db1824

show more ...

bk-changeset-1.3094.1.1
barrysmith@barry-smiths-computer.local|ChangeSet|20050414014634|22332
ChangeSet
1.3094.1.1 05/04/13 20:46:34 barrysmith@barry-smiths-computer.local +26 -0
changed petscdll

bk-changeset-1.3094.1.1
barrysmith@barry-smiths-computer.local|ChangeSet|20050414014634|22332
ChangeSet
1.3094.1.1 05/04/13 20:46:34 barrysmith@barry-smiths-computer.local +26 -0
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/vec/interface/makefile
1.8 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +1 -1
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/vec/interface/dlregisvec.c
1.27 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +2 -3
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/ts/interface/makefile
1.6 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +1 -1
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/ts/interface/dlregists.c
1.21 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +2 -3
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/sys/src/viewer/interface/dlregispetsc.c
1.23 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +2 -3
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/sys/src/utils/str.c
1.32 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +30 -0
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/sys/src/utils/makefile
1.11 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +1 -1
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/sys/src/dll/dl.c
1.34 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +28 -76
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/sys/examples/tutorials/makefile
1.10 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +1 -2
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/snes/interface/makefile
1.7 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +2 -2
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/snes/interface/dlregissnes.c
1.23 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +2 -3
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/mat/interface/makefile
1.6 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +1 -1
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/mat/interface/dlregismat.c
1.31 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +2 -3
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/ksp/ksp/interface/dlregisksp.c
1.25 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +2 -3
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/dm/ao/interface/dlregisdm.c
1.26 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +1 -2
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

bmake/common/rules.shared.darwin7
1.13 05/04/13 20:46:31 barrysmith@barry-smiths-computer.local +5 -6
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/mat/impls/aij/seq/essl/essl.c
1.39 05/04/13 20:46:30 barrysmith@barry-smiths-computer.local +19 -17
formating

src/ksp/ksp/interface/makefile
1.6 05/04/13 20:46:30 barrysmith@barry-smiths-computer.local +2 -2
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

src/dm/ao/interface/makefile
1.8 05/04/13 20:46:30 barrysmith@barry-smiths-computer.local +1 -1
changed petscdllibraryopen() to load symbol based on filename
so that symbol is different in each dynamic library and hence
can build dynamic libraries on mac

python/PETSc/utilities/dynamicLibraries.py
1.9 05/04/13 20:46:30 barrysmith@barry-smiths-computer.local +2 -3
shared libraries allowed on Mac

include/petsc.h
1.128 05/04/13 20:46:30 barrysmith@barry-smiths-computer.local +1 -0
added search for substring starting from end

BitKeeper/deleted/.del-ex4.c~dbd43215a9eb8a1b
1.9 05/04/13 19:17:33 barrysmith@barry-smiths-computer.local +0 -0
Delete: src/sys/examples/tutorials/ex4.c

src/dm/da/src/da2.c
1.65 05/04/13 19:00:52 barrysmith@barry-smiths-computer.local +31 -50
always set x,xs,y,ys from lx, ly and removed unneeded code

src/dm/da/src/da3.c
1.36 05/04/13 18:56:40 barrysmith@barry-smiths-computer.local +18 -38
eliminate code that manually sets x,xs,y,ys,z,zs when PETSc sets lx,ly, lz

BitKeeper/deleted/.del-dlregis.h~65e71245d21434f
1.11 05/04/13 17:25:29 barrysmith@barry-smiths-computer.local +1 -1
Delete: src/sys/src/utils/dlregis.h

src/dm/ao/interface/dlregisdm.c
1.25 05/04/13 17:24:55 barrysmith@barry-smiths-computer.local +1 -1
*** empty log message ***

bmake/common/rules.shared.darwin7
1.12 05/04/13 14:56:41 barrysmith@barrysmith-57.mcs.anl.gov +1 -1
save tries

bmake/common/rules.shared.darwin7
1.11 05/04/13 13:36:18 barrysmith@barrysmith-57.mcs.anl.gov +12 -12
try adding other stuff

src/ts/interface/dlregists.c
1.20 05/04/13 13:19:50 barrysmith@barrysmith-57.mcs.anl.gov +0 -0
Rename: src/ts/interface/dlregis.c -> src/ts/interface/dlregists.c

BitKeeper/deleted/.del-dlregis.c~e51dcaca1281f61b
1.5 05/04/13 13:19:33 barrysmith@barrysmith-57.mcs.anl.gov +0 -0
Delete: src/sys/src/viewer/interface/dlregis.c

src/snes/interface/dlregissnes.c
1.22 05/04/13 13:18:51 barrysmith@barrysmith-57.mcs.anl.gov +0 -0
Rename: src/snes/interface/dlregis.c -> src/snes/interface/dlregissnes.c

src/mat/interface/dlregismat.c
1.30 05/04/13 13:18:23 barrysmith@barrysmith-57.mcs.anl.gov +0 -0
Rename: src/mat/interface/dlregis.c -> src/mat/interface/dlregismat.c

src/ksp/ksp/interface/dlregisksp.c
1.24 05/04/13 13:17:46 barrysmith@barrysmith-57.mcs.anl.gov +0 -0
Rename: src/ksp/ksp/interface/dlregis.c -> src/ksp/ksp/interface/dlregisksp.c

src/dm/ao/interface/dlregisdm.c
1.24 05/04/13 13:17:16 barrysmith@barrysmith-57.mcs.anl.gov +0 -0
Rename: src/dm/ao/interface/dlregis.c -> src/dm/ao/interface/dlregisdm.c

src/vec/interface/dlregisvec.c
1.26 05/04/13 13:16:24 barrysmith@barrysmith-57.mcs.anl.gov +0 -0
Rename: src/vec/interface/dlregis.c -> src/vec/interface/dlregisvec.c


Hg-commit: adbb991a27b625ba59426a49bb8f5fb43da1236e

show more ...