Merge remote-tracking branch 'origin/hzhang/vec_node/master-rebased-v2'

Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also rem

Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also removes the CUSP-based preconditioners for now.
SACUSP will be re-added later, after the new release is out.

show more ...

GPUs: Allow ViennaCL and VECCUDA to be used concurrently.

This also gets rid of the weird veccuda.py.

CUSP: Removed VECCUSP and AIJCUSP as well as preconditioners.

SA-AMG from CUSP will be re-added in a follow-up commit,
made to work with AIJCUSPARSE and VECCUDA.

VecScatter: reorganization

implement several vecnode routines
rm mpi3 from _p_VecScatter struct -- nolonger useful
rm using native shared memory from src/ksp/ksp/examples/tests/ex56.c

VecScatter: reorganization

implement several vecnode routines
rm mpi3 from _p_VecScatter struct -- nolonger useful
rm using native shared memory from src/ksp/ksp/examples/tests/ex56.c
fix memory bug in VecScatterCreateLocal_PtoS_MPI3()
bugfix for VecScatterCopy() -- copy scattertype
add flg is_duplicate to _p_VecScatter; use it to prevent using StoP in VecScatterEndMPI3Node()
rename VecScatterCreateGeneral_ -> VecScatterCreate_
rename VecScatterCreate_vectype_mpitype() -> VecScatterCreateLocal_vectype_mpitype()
check for duplicate indices when mpi3node scatter is created; update tests
undo the commit bb8026e126c43792cc81c094ed5610e9a92280e3: add an example for testing MatMult() with node vectors
add MPI_Barrier(mscomm) in VecScatterEndMPI3Node for safe, but would lose correctness due to wright to same variable (see run2_5 and run3_5). Until finding an efficient way to deal with variable racing, we may give up this work :-(
add test output files
bugfix for VecScatterEndMPI3Node; update ex2.c
Merge branch 'hzhang/vec_node/master-rebased' of bitbucket.org:petsc/petsc into hzhang/vec_node/master-rebased
add an example for testing MatMult() with node vectors
bugfix for VecScatterEndMPI3Node()
rm checking vec_type in VecScatterCreate_mpi3node()
add winarray to Vec_node struct to avoid calls to MPI_Win_shared_query() in scatterEnd()
optionize a loop for xv -> yv
small bugfix and optimization
implement several Vec routines for node type
using object state counter for vector to rm 2 MPI_Barrier()
small optimization and cleanup
small build fix
add few vector routines for node type
add VecScatterCreate_vectype_private() for cleanup
replace MPI_Barrier(comm) by MPI_Barrier(mscomm)
add tests for StoP scatter
bugfix: src/vec/vscat/examples/ex1 and ex2 are working well now
update ex1 and ex2
reverse scatter PtoS works for bs=1
cleanup; fixed memory bug for bs>1
PtoP and PtoS(forward) scatter work for bs>1
mpi3node works for PtoP
forward scatter, I can read on-core xvalues in VecScatterEndMPI3Node
check vectypes for VecScatterCreate_MPI3Node()
add VecScatterCreate_MPI2Node() -- not done yet
rename VecScatterCreate_StoS() -> xxx_Seq(); add VecScatterCreate_type(); reorganize
cleanup and organization -- all seems working well
cleanup; update VecScatterSetFromOptions()
add VecScatterSetFromOptions()
rm VecScatterCreate_MPI1(); cleanup
cleanup VecScatterCreateGeneral_StoP()
add VecScatterCreateGeneral_StoP()
cleanup VecScatterCreateGeneral_PtoS()
VecScatterCreateGeneral_PtoS() works
bugfix after rebase -- passed local tests for both mpi1 and mpi3

add VecScatterCreate_StoS()
add GetInputISType_private()
update src/vec/vscat/examples/ex1.c and its output
new VecScatterCreate() as an interface function
add src/vec/vscat/interface/dlregisvecscat.c
mv vecscatter routines from src/vec/vec/ to src/vec/vscat/
add src/vec/vscat/interface/vscreate.c
reorganize files: create src/vec/vscat
small fix for mmaij.c
add VecScatterType
rename VecScatterType -> VecScatterFormat
add new VecType VECNODE for creating vector over on-node shared memory

show more ...

Merge branch 'barry/add-fortran-custom-interfaces'

a few more Fortran interfaces

Commit-type: feature

removed VecScatterCreateLocal() since it was incomplete and never used

Commit-type: style-fix

Merge branch 'tmunson/tao-pounders-fix-code'

manual merge because our work flow for petsc/git SUCKSSSSS

Commit-type: i.e. bug-fix, portability-fix, testing-fix,style-fix, feature, documentation, example
Funded-by:
Project:
Time: hours
Repo

manual merge because our work flow for petsc/git SUCKSSSSS

Commit-type: i.e. bug-fix, portability-fix, testing-fix,style-fix, feature, documentation, example
Funded-by:
Project:
Time: hours
Reported-by:
Thanks-to:
Development Tools: Vim, Emacs, Eclipse

show more ...

Merge branch 'barry/tao-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'jed/tests-cxx-linker' into barry/more-to-new-test-harness

Merge branch 'master' into knepley/feature-ts-plasma-example

* master: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13: Update test output

Merge branch 'master' into knepley/feature-ts-plasma-example

* master: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13: Update test output
PetscFE: Complex fixes for PetscFEIntegrate()
SNE ex13: Got adjoint solution and almost have a good error estimate
Section: Fix init in PetscSectionCreateSupersection()
DM: Remove debugging view
SNES ex13: Updated output after fix
Section: If global section allocates bc indices, must copy them
Section: Cleaned up PetscSectionCreateGlobalSection() - Used local variable and added input checks
Bib: Added pages
Section: Fix leaks in DMCreateSuperDM()
SNES ex13: Adding adjoint capability
DM: Use new PetscGlobalMinMaxInt()
DM: Added DMCreateSuperDM()
Plex: Refactor computation of integrals over the domain - Added DMPlexComputeCellwiseIntegral()
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
Adaptor: Use new PetscGlobalMinMaxInt()
Section: Added PetscSectionCreateSupersection() - This merges several sections together
Vec+Doc: Fix docs for VecISAXPY()
Vec: Added VecISCopy() - Use ScatterMode to determine direction of copying
...

show more ...

Merge branch 'knepley/feature-plex-adjoint-prelim'

* knepley/feature-plex-adjoint-prelim: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13:

Merge branch 'knepley/feature-plex-adjoint-prelim'

* knepley/feature-plex-adjoint-prelim: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13: Update test output
PetscFE: Complex fixes for PetscFEIntegrate()
SNE ex13: Got adjoint solution and almost have a good error estimate
Section: Fix init in PetscSectionCreateSupersection()
DM: Remove debugging view
SNES ex13: Updated output after fix
Section: If global section allocates bc indices, must copy them
Section: Cleaned up PetscSectionCreateGlobalSection() - Used local variable and added input checks
Bib: Added pages
Section: Fix leaks in DMCreateSuperDM()
SNES ex13: Adding adjoint capability
DM: Use new PetscGlobalMinMaxInt()
DM: Added DMCreateSuperDM()
Plex: Refactor computation of integrals over the domain - Added DMPlexComputeCellwiseIntegral()
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
Adaptor: Use new PetscGlobalMinMaxInt()
Section: Added PetscSectionCreateSupersection() - This merges several sections together
Vec+Doc: Fix docs for VecISAXPY()
Vec: Added VecISCopy() - Use ScatterMode to determine direction of copying
...

show more ...

Fixes to get VecScatter MPI3 code to work properly without MPI 3 support

Commit-type: bug-fix, portability-fix, testing-fix

rm vscat_mpi1.c

rm duplicate routines

rename VecScatterCreateMPI1 -> VecScatterCreate_MPI1

additional rename

add vscat_mpi1.c

bugfix for fortran build

Merge branch 'knepley/feature-plex-adjoint-prelim' into knepley/feature-plex-exodus-update

* knepley/feature-plex-adjoint-prelim:
SNE ex13: Got adjoint solution and almost have a good error estima

Merge branch 'knepley/feature-plex-adjoint-prelim' into knepley/feature-plex-exodus-update

* knepley/feature-plex-adjoint-prelim:
SNE ex13: Got adjoint solution and almost have a good error estimate
Section: Fix init in PetscSectionCreateSupersection()
DM: Remove debugging view
SNES ex13: Updated output after fix
Section: If global section allocates bc indices, must copy them
Section: Cleaned up PetscSectionCreateGlobalSection() - Used local variable and added input checks
Bib: Added pages
Section: Fix leaks in DMCreateSuperDM()
SNES ex13: Adding adjoint capability
DM: Use new PetscGlobalMinMaxInt()
DM: Added DMCreateSuperDM()
Plex: Refactor computation of integrals over the domain - Added DMPlexComputeCellwiseIntegral()
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
Adaptor: Use new PetscGlobalMinMaxInt()
Section: Added PetscSectionCreateSupersection() - This merges several sections together
Vec+Doc: Fix docs for VecISAXPY()
Vec: Added VecISCopy() - Use ScatterMode to determine direction of copying
Sys: Added PetscGlobalMinMaxReal/Int()
Plex: Make preallocation debugging work in serial

show more ...

Vec: Added VecISCopy()
- Use ScatterMode to determine direction of copying

Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
...

Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

show more ...