Merge branch 'master' into knepley/feature-snes-patch

Support domain errors in SNESComputeJacobian

Merge branch 'Fande-Kong/feature-retrieve-sol-and-step-norms-snes' [PR #1321]

* Fande-Kong/feature-retrieve-sol-and-step-norms-snes:
Add two APIs: SNESGetUpdateNorm and SNESGetSolutionNorm
Retrieve

Merge branch 'Fande-Kong/feature-retrieve-sol-and-step-norms-snes' [PR #1321]

* Fande-Kong/feature-retrieve-sol-and-step-norms-snes:
Add two APIs: SNESGetUpdateNorm and SNESGetSolutionNorm
Retrieve update and solution norms

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Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and dom

Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and domain size for test _2."
DMStag tutorial ex4: fix stencil errors
Hierarchical partitioner: added an alt output file
Add support for DMGetMatrix() with periodic boundary conditions in one dimension for DMDA.
Fixed incorrect 'ntext' argument in PetscOptionsEList call in SNES ex12.c
ISCreateSubIS: Initialize variables owner and lidx to avoid compiler warnings
metis: provide -download-metis-use-doubleprecision option
KSP ex56: Updated test output and domain size for test _2.
Hierarchical partitioner: add a bit documentation
ISCreateSubIS: Added checkers for parameters
Added a test for hierarchical partitioning vertex weights
Plex+Doc: Document options for DMPlexCreateBoxMesh()
Hierarchical partitioner supports vertex weights
Create an API ISCreateSubIS that extracts
Add an alt output file
Plex: Can now give bounds to DMPlexCreateBoxMesh() from options - Use -dm_plex_box_lower and dm_plex_box_upper
PCMG: These methods should be optional
PCMG: Make PCMGGet/SetLevels() proper member functions - Also need to compose them in GAMG
...

Conflicts:
src/dm/impls/plex/plexsection.c

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Add two APIs: SNESGetUpdateNorm and SNESGetSolutionNorm

Retrieve update and solution norms

We may/might want to print update and solution norms in a user-provided convergence checker if the SNES co

Add two APIs: SNESGetUpdateNorm and SNESGetSolutionNorm

Retrieve update and solution norms

We may/might want to print update and solution norms in a user-provided convergence checker if the SNES converged due to a small update length.

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Merge branch 'barry/fix-todo'

Fix several of the TODO: items from the testig of examples

Still a variety of problems to resolve including memory corruption

Commit-type: testing-fix

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patc

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patchlevel to 3.10.3
petsc4py: updat to latest maint snapshot with SNESTEST updates
Fix link for CUDA example in PETSc from GPUs.html page Minor fixes to installation instructions
Mat: Fixed types in Pardiso interface
Converted example comment to latex
This example crashes (for unknown reasons, probably related to the handling of extended derived types passed as arguments) with the PGI Fortran compiler
Remove outdated requires: from top of several examples
remove outdated test requires: command from top of source file
Fix the documentation for -ksp_gmres_cgs_refinement_type
Commit f20c2d659b168217cb455989f28afe052d71a64c broke lex.py so the users manual was no longer being built. There reverted the changes to lex.py
Plex: Add PetscPartitioner to fort list Suggested-by: Jiaoyan Li <Jiaoyan.Li@inl.gov>
Doc: Fix spelling Suggested-by: Manuel Colera Rico <m.colera@upm.es>
Mat ex88: check in double or quad precision only
Fix error with PetscComplex when PETSc is compiled with C and used in C++
configure: fix typo endwith -> endswith
Sys ex23: Migrated to ts_max_time in yaml file as well.
AO ex5: Fixed missing CHKERRQ();
Mat test ex88: add tests for MatMultAdd and MatMultTranposeAdd
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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Merge branch 'jed/snes-ksp-its/maint' into maint [PR #1267]

* jed/snes-ksp-its/maint:
SNES: move logging of KSP iterations into SNESCheckKSPSolve

Merge branch 'jed/snes-ksp-its/maint' [PR #1267]

* jed/snes-ksp-its/maint:
SNES: move logging of KSP iterations into SNESCheckKSPSolve

SNES: move logging of KSP iterations into SNESCheckKSPSolve

This fixes inconsistencies noticed by snes/examples/tutorials/ex5.c
which checks that the number of linear iterations reported by the KSP

SNES: move logging of KSP iterations into SNESCheckKSPSolve

This fixes inconsistencies noticed by snes/examples/tutorials/ex5.c
which checks that the number of linear iterations reported by the KSP
matches that reported by SNES. Prior to this change, lack of
convergence would cause an early return without including the KSP
iterations.

Commit-type: bug-fix

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Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
fix gcov obj path
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
...

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Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
...

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Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/feature-pc-patch

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing

Merge branch 'master' into knepley/feature-pc-patch

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing CHKERRQ()
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Add a test for ex21
Fix error in ex21
Add missing fortran interface that handles null objects
DMComposite: add missing guards
MatPreallocate: fix overpreallocation of local rows
style fixes
MatView_MPI_DA: do not print twice the class prefix
MatSetOperation: stash the original MatView_XXX in the viewnative function pointer
DMCreateInterpolation_DA gracefully error instead of catching FPE signals
MatIncreaseOverlap: preserve communicator of index sets
MatMPIAIJ: fix indentation and missing CHKERRQ
ISBuildTwoSided: remove tabs and fix style
Fix documentation
PetscViewerDraw: fix unininitialized warning from valgrind
MatConvert_SeqAIJ_SeqBAIJ: remove error for non square matrices and add MAT_REUSE_MATRIX case
Mat: MAT_INPLACE_MATRIX can be used for transposition with rectangular matrices
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexfem.c
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/makefile
src/snes/examples/tutorials/output/ex62_18.out
src/snes/examples/tutorials/output/ex62_19.out
src/snes/examples/tutorials/output/ex62_20.out
src/snes/examples/tutorials/output/ex62_20_parmetis.out
src/snes/examples/tutorials/output/ex62_21.out
src/snes/examples/tutorials/output/ex62_22.out
src/snes/examples/tutorials/output/ex62_23.out
src/snes/examples/tutorials/output/ex62_24.out
src/snes/examples/tutorials/output/ex62_25.out
src/snes/examples/tutorials/output/ex62_26.out
src/snes/examples/tutorials/output/ex62_27.out
src/snes/examples/tutorials/output/ex62_28.out
src/snes/examples/tutorials/output/ex62_29.out
src/snes/examples/tutorials/output/ex62_2d_p3_1.out
src/snes/examples/tutorials/output/ex62_30.out
src/snes/examples/tutorials/output/ex62_31.out
src/snes/examples/tutorials/output/ex62_32.out
src/snes/examples/tutorials/output/ex62_33.out
src/snes/examples/tutorials/output/ex62_34.out
src/snes/examples/tutorials/output/ex62_35.out
src/snes/examples/tutorials/output/ex62_36.out
src/snes/examples/tutorials/output/ex62_pc_simple.out
src/snes/examples/tutorials/output/ex62_pc_simplec.out
src/snes/examples/tutorials/output/ex62_quad_q2p1_full.out
src/snes/examples/tutorials/output/ex62_quad_q2q1_full.out
src/snes/utils/dmplexsnes.c

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Merge branch 'master' into knepley/feature-error-logging

* master: (221 commits)
dashboard: count and list example compile failures like:
fix fix-pr879-jczhang-optimize-vecscatter-multi-copy
a

Merge branch 'master' into knepley/feature-error-logging

* master: (221 commits)
dashboard: count and list example compile failures like:
fix fix-pr879-jczhang-optimize-vecscatter-multi-copy
add manual page cross links for SNESLineSearchSetPostCheck() and related routines
fix help manual of MatCreateSubmatrices() Reported-by: Tim Steinhoff <kandanovian@gmail.com>
Add manual pages for PetscRealPart() and PetscImaginaryPart()
fix compile error with missing MPI_C_DOBULE_COMPLEX
fix typo Reported-by: Febrian Setianto <febrian.setianto@gmail.com>
plex tutorial ex5: updated test requirements
DMPlexLoad_HDF5_Xdmf_Internal: fix for complex PetscScalar.
DMPlexLoad_HDF5_Xdmf_Internal: fix for 64-bit PetscInt.
DMPlexBuildFromCellList_Internal: use DMPlexInvertCell_Internal (with PetscInt* arg)
petscviewer.h: removed notice which is no longer relevant
DMPlexCreateFromFile: document option
check only if PETSC_USE_DEBUG
DMPlexBuildFromCellList_Internal optionally inverts cells.
ex5: new test 4 with -compare without repartitioning
ex5: new test 3 using -compare
ex5: HDF5 write+read moved to separate function
ex5: option -format processed in ProcessOptions()
ex5: added missing hdf5 requirement
...

Conflicts:
include/petsclog.h

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Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortr

Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortran Notes:", or "Developer Notes:".
This batch adds those newlines, with 4 spaces of indentation afterwards.
The uniform indentation arguably makes the man pages a little less readable in the source itself,
but overall this hopefully has a large positive impact on the readability of the HTML pages.

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Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \(

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'

This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/

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

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

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page information about convergence testing when using KSPRICHARDSON
SNES ex5: Restore old output since this breaks an example I have
Noted that some Cray XC systems will use 'aprun' instead of 'srun'. Thanks to Herr Doktor Hong Zhang for this suggestion.
Added example configure script for Cray XC40 with KNL processors (e.g., NERSC Cori).
Fix possible sprintf -Wformat-overflow
PetscMalloc2-7: fix -Wint-in-bool-context for GCC 7
SNES ex5: make boundary condition handling consistent for symmetry
SNES ex5: use L2 norm and *_monitor_short for output
SNES ex5: the L^2 norm scales with the l^2 norm over sqrt(N)
SNES ex5: refactor MMS capability to avoid extreme code duplication
Documentation fix: typo in PetscLogStageRegister manual page.
nodes -> vertices
rename DMNetworkGetComponentTypeOffset -> DMNetworkGetComponentKeyOffset
rename DMNetworkGetConnectedNodes() -> DMNetworkGetConnectedVertices()
Jacobians for adjoints for explicit methods and constant Jacobians never got initialized
fix complex build error
fix build failure with fortran interface
fix compile error with cdc753b64c658d532d7813e942002e67025667a6
...

Conflicts:
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/ex69.c

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Merge branch 'master' into knepley/feature-rigid-bodies

* master: (204 commits)
windows fixes
revert this change as a relavent fix is already in origin/knepley/fix-ex-types
regenerate output l

Merge branch 'master' into knepley/feature-rigid-bodies

* master: (204 commits)
windows fixes
revert this change as a relavent fix is already in origin/knepley/fix-ex-types
regenerate output log for snes_tutorials-ex62_fetidp_3d_tet that got corrupted in 188e10d6f1cffa866ec0197053a0e55fa4e7da41
fix opensolaris build error with --with-log=0 Undefined first referenced symbol in file PetscLogEventGetPerfInfo arch-opensolaris-misc/tests/src/dm/impls/plex/examples/tests/ex9.o
fix warnings on windows C:\cygwin64\home\petsc\PETSC~1.CLO\src\tao\examples\TUTORI~1\ex1.c(217): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)'
disable example with absoft (due to fixed/free form limit)
c89 fixes
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
Plex ex19: Remove unneeded code
Plex: Fix projection when we have a dmAux which is a domain boundary - If we are projecting on a lower dimension thing (effectiveHeight > 0), then we need to get the space and dual space on this subcell - The tabulation needs to be in the right dimension for both dm and dmAux
PetscFE: Added height subspaces to PetscFE - Added PetscFEGetHeightSubspace() - Added array in struct
PetscDualSpace: Small cleanup of parameter name
PetscSpace: Added height subspaces for PetscSpace - Added PetscSapceGetHeightSubspace() and member function - Added subspaces array
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 some minor style issues
Extend AMS/ADS to support high-order element.
...

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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

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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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