Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incor

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incorrect formatting in SNES linesearch routines
ISSetBlockSize_General: removed blockwise contiguity check.
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
config prefix: avoid ad-hoc path substitutions
config/install: no need to rename paths for installBinDir
rules: fix path in (evidently unimportant) uncrustify target
config pkgconfig: use ${prefix} in PETSc.pc and do not modify in install
fix gcov obj path
Improved polymorphism of interfaces for MatSetValuesBlocked()
-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
...

show more ...

Merge remote-tracking branch 'origin/knepley/fix-plex-submesh-projection'

Merge remote-tracking branch 'origin/jed/config-prefix-install'

rules: fix path in (evidently unimportant) uncrustify target

fix gcov obj path

Merge branch 'master' into knepley/fix-plex-submesh-projection

* master: (425 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex

Merge branch 'master' into knepley/fix-plex-submesh-projection

* master: (425 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

show more ...

Merge branch 'knepley/feature-error-logging' of bitbucket.org:arcowie/alpetsc into arcowie-rem/feature-error-logging

# By Albert Cowie
# Via Albert Cowie
* 'knepley/feature-error-logging' of bitbuck

Merge branch 'knepley/feature-error-logging' of bitbucket.org:arcowie/alpetsc into arcowie-rem/feature-error-logging

# By Albert Cowie
# Via Albert Cowie
* 'knepley/feature-error-logging' of bitbucket.org:arcowie/alpetsc:
Changes to be committed: modified: petsc_tas_analysis.py Just tweeks
Changes to be committed: modified: petsc_tas_analysis.py Small tweeks to fonts needed but now supports plotting data from multiple files.
Changes to be committed: modified: petsc_tas_analysis.py Added plotting multiple files onto each graph
Changes to be committed: modified: petsc_tas_analysis.py Added method to parse data from multiple files specified on the command line
Changes to be committed: new file: petsc_tas_style.mplstyle Style sheet for the graphs
Changes to be committed: modified: petsc_tas_analysis.py
Changes to be committed: modified: petsc_tas_analysis.py Cleaned up code and changed comments for sphynx
modified: petsc_tas_analysis.py There a number of changes I have added to help debug, mostly print statements
Changes to be committed: modified: petsc_tas_analysis.py legend now includes the name of the file passed as a command line argument
Changes to be committed: modified: petsc_tas_analysis.py Implemented command line arguments Currently supports 1 file
modified: petsc_tas_analysis.py added date time stamp to file name
Changes to be committed: modified: petsc_tas_analysis.py Added save the graphs as png's
Changes to be committed: modified: lib/petsc/bin/petsc_tas_analysis.py The least squares for the mesh conversion does not appear to be straight line. I will debug.

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

show more ...

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod
Remove use of common block from MPIUNI code
use was in wrong location
Fortran line extends past 72 char
Moved the rest of the PETSc common block variables over to petscsys module
tests: fix breakage due to cd93b0e13c6da70ee1e038f55989cf888bc1d1c5
Need to use petscsys to get PETSC_COMM_SELF defined in example
Mat ex23 and ex40: fix errors reported from nightly tests
Put declaration on too lines because otherwise it generates an error for truncated line
Move PETSC_COMM_WORLD and PETSC_COMM_SELF from common blocks to petscsys module
tests: fix requires - and create out files for seqaijmkl tests
KSP ex72: nested dissection is likely to be different between machines
cmake: downgrade to version 3.9 - as newer versions require cxx11 compiler [which is not universal]. However stick with version 3.11 on opensolaris
Mat ex23: fix memory leaks
Bib: Some new refs
KSP examples: add missing casts to double in printf
updated GAMG KSP tests
PetscRound() should be PetscRoundReal() in __fp16
...

Conflicts:
include/petsclog.h
src/sys/logging/plog.c
src/sys/logging/utils/eventlog.c

show more ...

Changes to be committed:
modified: petsc_tas_analysis.py
Just tweeks

Changes to be committed:
modified: petsc_tas_analysis.py
Small tweeks to fonts needed but now supports plotting
data from multiple files.

modified: petsc_tas_style.mplstyle
Currently need

Changes to be committed:
modified: petsc_tas_analysis.py
Small tweeks to fonts needed but now supports plotting
data from multiple files.

modified: petsc_tas_style.mplstyle
Currently needs to be in ~/.config/matplotlib/stylelib

show more ...

Changes to be committed:
modified: petsc_tas_analysis.py
Added plotting multiple files onto each graph

Changes to be committed:
modified: petsc_tas_analysis.py
Added method to parse data from multiple files specified on the
command line

Changes to be committed:
new file: petsc_tas_style.mplstyle
Style sheet for the graphs

Changes to be committed:
modified: petsc_tas_analysis.py

Merge branch 'maint'

builds: run 'git prune' in build clones to avoid messages of type:

warning: There are too many unreachable loose objects; run 'git prune' to remove them.

Merge branch 'maint'

builds: add an arm test box [si] - and move builds arround for this to work [i.e remove steamroller]

Changes to be committed:
modified: petsc_tas_analysis.py
Cleaned up code and changed comments for sphynx

Build: Should run dsymutil on examples

Merge branch 'maint'

nightlytests: prune old branches in nightlybuild clones

Event logging synchronization

- Remove PetscLogEventBarrierBegin/PetscLogEventBarrierEnd
- Option -log_sync enables barrier synchronization for all events
- A few non-collective events are disabled

Event logging synchronization

- Remove PetscLogEventBarrierBegin/PetscLogEventBarrierEnd
- Option -log_sync enables barrier synchronization for all events
- A few non-collective events are disabled (eg. {Vec|Mat}SetValues)

show more ...

DMPlex: Rename a couple events for the sake of consistency

modified: petsc_tas_analysis.py
There a number of changes I have added to help debug, mostly
print statements