Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ m

Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
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
output has changed with e6d0a238963c2a97dd04845ea512b529992c7cdb so update the output file
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Merge remote-tracking branch 'origin/scott/test-datafiles-fix'

migrate 'build requires: !mpiuni' to new format

Plex: Added DMPlexCreateRigidBodies()
- Handles disconnected pieces, like sides of a fault

Merge branch 'knepley/feature-dm-bc-components' into knepley/feature-rigid-bodies

* knepley/feature-dm-bc-components:
DM: Fixed problem with setting boundary conditions for selected components - T

Merge branch 'knepley/feature-dm-bc-components' into knepley/feature-rigid-bodies

* knepley/feature-dm-bc-components:
DM: Fixed problem with setting boundary conditions for selected components - The problem was that projection always set every component of a field, even when the BC was only for a certain component. Now you can pass in masking components. - Added masking components to projections over labels - Changed interface to boundary value insertion

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Plex ex19: Updated output for DM prefix
- Allow visualization of partition

Plex: Update MED output, use simple partitioner

Plex: Fix MED URL

Plex: Allow visualization of partition along with mesh using -dm_partition_view

Doc: Small fix

Plex: Added DMPlexCreateRankField()

Change MPIUni to not immediately abort on operations it cannot perform, instead return error code

So people see immediately why it is failing instead of just having a very uninformation message abou

Change MPIUni to not immediately abort on operations it cannot perform, instead return error code

So people see immediately why it is failing instead of just having a very uninformation message about abort.
Mark examples that use PetscSF as requires: !mpiuni since Jed has not fixed bug in PetscSF for MPIUni

Commit-type: portability-fix, feature, example
Funded-by: ECP
Time: 1 hour
Reported-by: nightly tests

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Plex: Make sure submeshes inherit the right coordinate dimension

DM+SNES: Put in array initialization and missing CHKERRQ

Sys+DM+SNES: Small example fixes

Various fixes from nightly builds

Merge branch 'knepley/test-process-arg' into knepley/feature-adapt-interface

* knepley/test-process-arg: (49 commits)
Test: Can now use make test NP=<num procs>
Testing: Fix error reporting
I

Merge branch 'knepley/test-process-arg' into knepley/feature-adapt-interface

* knepley/test-process-arg: (49 commits)
Test: Can now use make test NP=<num procs>
Testing: Fix error reporting
I didn't realize there was a hacky special case for dense B matrix
Fix example to support -snes_mf_operator
cleanup src/ksp/ksp/examples/tutorials/network/makefile
add missing input in the help menu of PetscOptionsView() Reported-by: Richard Katz <richard.katz@earth.ox.ac.uk>
Fix docs for MatMatMult() that C matrix can only be created by user for sequential case.
protect '-' in macros
fix compile error with --download-petsc4py
Plex: Removed useless CHKERRQ
Configure: Replace use of PETSc modules
Plex ex7: Damn, quad precision is named __float128
TSSetFromOptions: Give subtypes a chance to set the default adapt type
TS ex11.c: fix corrupt filename initialization
small fix
Plex ex1: Update output
DT: Fixed Fortran module - Add DT module to DM and Petsc modules - Fix makefile to generate DT F90 module - Fix PetscQuadratureGet/Restore/SetData() F90 defs
Plex ex19: Updated output
Plex ex7: Update output
p4est: Update to new API
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Added initial implementation of GLVis viewer

Plex: Removed useless CHKERRQ

Plex ex19: Updated to new API

DM: Refactored mesh adaptivity into DMAdaptLabel() and DMAdaptMetric()
- These are now DM functions, instead of composed functions
- Refactor Plex refine and coarsen to feed through adaptivity
- Adde

DM: Refactored mesh adaptivity into DMAdaptLabel() and DMAdaptMetric()
- These are now DM functions, instead of composed functions
- Refactor Plex refine and coarsen to feed through adaptivity
- Added helper functions to convert Label to volume constraints and metric constraints
- Got the label name out of the Metric interface

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Merge branch 'knepley/feature-plex-wedge'

* knepley/feature-plex-wedge:
Plex ex1: Update output
Plex ex1: Added a wedge test
Plex: Added DMPlexCreateWedgeCylinderMesh()
Xdmf: Also handle wed

Merge branch 'knepley/feature-plex-wedge'

* knepley/feature-plex-wedge:
Plex ex1: Update output
Plex ex1: Added a wedge test
Plex: Added DMPlexCreateWedgeCylinderMesh()
Xdmf: Also handle wedge elements

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Merge branch 'knepley/fix-test-requirements'

* knepley/fix-test-requirements:
Plex ex7: Damn, quad precision is named __float128

Plex ex7: Damn, quad precision is named __float128

Merge branch 'knepley/feature-ex11-simplex'

* knepley/feature-ex11-simplex: (22 commits)
TS ex11.c: fix corrupt filename initialization
Plex ex19: Updated output
Plex ex7: Update output
p4es

Merge branch 'knepley/feature-ex11-simplex'

* knepley/feature-ex11-simplex: (22 commits)
TS ex11.c: fix corrupt filename initialization
Plex ex19: Updated output
Plex ex7: Update output
p4est: Update to new API
TS ex11: Added pest tests
TS ex18: Update test output
SNES ex69: Update test output
Plex ex14: Update test output
Plex ex2f90: Update test output
Plex ex19: Update test output
Plex: Fix end of line in test output
Plex ex1: Update test output
TS ex11: MUST use FV type leastsquares for adaptivity. Need some sort of warning for this
TS ex11: Cleaning up adaptivity, WIP
Share: Added mesh of TX
TS ex11: Added advection tests for tris and quads
TS ex11: Allow simplex meshes
TS ex11: Small cleanup, now use -orig_dm_view for the mesh before ghost cells
Plex: Better ASCII output of labels
Plex: Triangle generation now respects FaceSets label
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