Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]' to showup in '-help' Reported-by: Mark Adams <mfadams@lbl.gov>
Plex: Remove dead code
TS tutorials ex11: remove unused functions
TSAdapt: Set TSADAPTNONE as default adapt type
DMPlex: missed viewer change in synchronized output
Revert "Merge branch 'hzhang/ts-ex9busdmnetwork'"
TSAdapt: Update changes/dev.html
TSAdapt: Set default type for TSGLEE
TS tutorials ex11: make work with complex scalars
Bib: Added ref
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
f2cblaslapack: remove duplicate xerbla.o and xerbla_array.o from lapack [they are already in blas]
TSAdapt: Refactor handling of default adapt type
TSAdapt: Update changes/dev.html
TSAdapt: Update manual
TSAdapt: Refactor interface and implementations
...

show more ...

Merged in dalcinl/ts-adapt-default-type (pull request #674)

TSAdapt: Refactor handling of default adapt type

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

TSAdapt: Set TSADAPTNONE as default adapt type

* TSCreate() set TSADAPTNONE as default adapt type
* TSSetType() set TSADAPTNONE before running the constructor
* Add missing error checking in TSXXXSe

TSAdapt: Set TSADAPTNONE as default adapt type

* TSCreate() set TSADAPTNONE as default adapt type
* TSSetType() set TSADAPTNONE before running the constructor
* Add missing error checking in TSXXXSetType()

show more ...

TSAdapt: Refactor handling of default adapt type

* Let TS subtypes state its preference for adaptivity
* Methods without embedded error estimators prefer TSADAPTNONE
* If not set, use TS_EXACTFINALT

TSAdapt: Refactor handling of default adapt type

* Let TS subtypes state its preference for adaptivity
* Methods without embedded error estimators prefer TSADAPTNONE
* If not set, use TS_EXACTFINALTIME_MATCHSTEP when using adaptivity

* Remove command line option -ts_theta_adapt
* Use `-ts_adapt_type basic` to turn on adaptivity in TSTHETA

* Remove command line option -ts_alpha_adapt
* Remove routine TSAlphaUseAdapt() and TSAlpha2UseAdapt()
* Use `-ts_adapt_type basic` to turn on adaptivity in TSALPHA/TSALPHA2

show more ...

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

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so a

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

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so avoid it
TSBDF: Update changes/dev.html
Added Fortran TaoType and TaoLineSearchType definitions
Add Fortran TaoType and TaoLineSearchType definitions
setblocksize for iscol_sub
TSBDF: Use standard TS API and options to control adaptivity
Bib: More refs and a correction
SNESTest: Bug-fix in SNESTest when threshold printing option is turned on.
fix warning and valgrind complains reported by the nightly tests
Section+Doc: Small doc fix
pflotran: switch to using the new upstream git repo
DMPlex: Error if attempt to partition a distributed graph with Chaco
fix complex build error
fix complex build
PetscError() did not properly copy over the specific error message when error type was PETSC_ERROR_INITIAL
TSAdapt: Refactor handling of the always_accept flag
Additional clarification for MatMeshToCellGraph() manual page
optimize MatCreateSubMatrix_MPIAIJ() by merging check of sameXXXDist() into one MPI_AllReduce
...

Conflicts:
config/BuildSystem/config/packages/med.py

show more ...

Add physically reasonably dt_min and max for tchem examples
Plot dt as a function of time using log scale
add simple script for running tchem cases

Commit-type: style-fix, feature, example
Funded-by

Add physically reasonably dt_min and max for tchem examples
Plot dt as a function of time using log scale
add simple script for running tchem cases

Commit-type: style-fix, feature, example
Funded-by: IMEX
Project: chemistry

show more ...

Fix bug where user provided only RHSJacobian and uses -snes_mf_operator

trouble because IJacobian now thinks there are separate IJacobian and
RHS matrices. Make TS aware that Jacobian is managed by

Fix bug where user provided only RHSJacobian and uses -snes_mf_operator

trouble because IJacobian now thinks there are separate IJacobian and
RHS matrices. Make TS aware that Jacobian is managed by SNES so that TS should
not adjust the matrix for the timestep

Commit-type: bug-fix
Funded-by: IMEX
Time: 2 hour
Reported-by: Ed Bueler <elbueler@alaska.edu>

show more ...

Fix flaw with TSSetRHSJacobian() and no TSSetIJacobian() where DM provides the Jacobian matrix

For example src/ts/examples/tutorials/advection-diffusion-reaction/ex5.c
TS would create the Jacobian f

Fix flaw with TSSetRHSJacobian() and no TSSetIJacobian() where DM provides the Jacobian matrix

For example src/ts/examples/tutorials/advection-diffusion-reaction/ex5.c
TS would create the Jacobian from the DM in TSGetRHSMats_Private() and then make
a copy of it resulting in unneeded matrix creation and unneeded MatAXPY computations at
each Jacobian computation. MatAXPY() would take up to 80% of time.

The management of Jacobians for the various cases of implicit, explicit, IMEX, with and without RHSJacobian
or IJacobian is excessively convoluted and should be refactored to make the code much simplier and
clearer.

Commit-type: bug-fix
Funded-by: IMEX
Project: IMEX
Time: .7 hours
Reported-by: Hong Zhang <hongzhang@anl.gov>

show more ...

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and h

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and handling of rpath argument with gfortran
help menu update for MatCreateSubMatrices() Reported-by: Brad Aagaard <baagaard@usgs.gov>
fix flops for PCApply_PBJacobi_1 and PCApply_PBJacobi_7 Reported-by: Pierre Jolivet <pierre.jolivet@enseeiht.fr>
TSRK: Fix FSAL optimization to not skip update and check or stages.
Travis-CI: Workaround too long TMPDIR in macOS with Open MPI
test: Fix type mismatch in KSP test.
test: Fix warnings from gfortran -Wconversion (OS X, Homebrew build)
MPIUNI: Silence GCC -Wconversion warnings
Fortran: Add error checking for incorrect PETSC_NULL_XXX argument when expecting function
fix test output per changes in 517c9301b2e9239931bfd644803fd6bb859387ea
MUMPS: update to version 5.1.1 with opensolaris compile fixes
TSRK: Mention 5BS in the changelog.
TSRK: Mention the new 5BS scheme in the manual.
fix 'unused variable' warning
Remove unused code
added hbw_realloc
fixed undefined ptr
...

Conflicts:
config/BuildSystem/config/packages/med.py

show more ...

Merge remote-tracking branch 'origin/barry/improve-ts-trajectory-viz'

Fix flaw with TSSetRHSJacobian() and no TSSetIJacobian() where DM provides the Jacobian matrix

For example src/ts/examples/tutorials/advection-diffusion-reaction/ex5.c
TS would create the Jacobian f

Fix flaw with TSSetRHSJacobian() and no TSSetIJacobian() where DM provides the Jacobian matrix

For example src/ts/examples/tutorials/advection-diffusion-reaction/ex5.c
TS would create the Jacobian from the DM in TSGetRHSMats_Private() and then make
a copy of it resulting in unneeded matrix creation and unneeded MatAXPY computations at
each Jacobian computation. MatAXPY() would take up to 80% of time.

The management of Jacobians for the various cases of implicit, explicit, IMEX, with and without RHSJacobian
or IJacobian is excessively convoluted and should be refactored to make the code much simplier and
clearer.

Commit-type: bug-fix
Funded-by: IMEX
Project: IMEX
Time: .7 hours
Reported-by: Hong Zhang <hongzhang@anl.gov>

show more ...

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

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

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

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

show more ...

A variety of improvements/fixes for saving and accessing trajectories.

Fixed bugs in PetscReadBinaryTrajectory.m
Added PetscBinaryIOTrajectory.py to read in trajectories in Python
Fixed bug in all t

A variety of improvements/fixes for saving and accessing trajectories.

Fixed bugs in PetscReadBinaryTrajectory.m
Added PetscBinaryIOTrajectory.py to read in trajectories in Python
Fixed bug in all the trajectory file saving routines that used PETSC_COMM_WORLD instead of the MPI_Comm associated with the TS object.

Funded-by: IMEX
Project: adjoints
Time: 2 hours
Reported-by: Shashikant M. Aithal <aithal@cels.anl.gov>

show more ...

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newe

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
fix build warning as reported by the nightly tests
Update alquimia.py to use Glenn's branch that updates alquimia for pflotran xsdk
fix divide by zero exposed by 8534686b5096cd4c91a8f3895408b386c0628431 - and produced by petsc4py testsuite
...

Conflicts:
src/dm/impls/plex/examples/tests/ex13.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tests/ex2.c
src/snes/examples/tests/output/ex2_3.out
src/snes/examples/tests/output/ex2_4.out
src/snes/examples/tests/output/ex2_5.out

show more ...

Merge branch 'master' into scott/test-harness-forloopfix

Merge remote-tracking branch 'origin/maint'

TSSetPreStep: Update documentation

Only attempt to get TS right hand side Jacobian matrices from SNES if specifically requested

Otherwise if they are not available while the user is only requesting the function pointer it generates a

Only attempt to get TS right hand side Jacobian matrices from SNES if specifically requested

Otherwise if they are not available while the user is only requesting the function pointer it generates an error

Reported-by: Hong Zhang <hongzhang@anl.gov>
Thanks-to: Stefano Zampini <stefano.zampini@gmail.com>

show more ...

Merge branch 'maint'

Merged in stefano_zampini/fix-tsgetijacobian (pull request #622)

TS: setup SNES matrices if needed

Clear explanation of TSSetForcingFunction() in the manual page

Thanks-to: Onan Marin <oanam@mcs.anl.gov>

TS: setup SNES matrices if needed

This fix is to retrieve just the jacobian context

Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

show more ...

Merge branch 'barry/allow-multiple-downloaddirnames'