make --download-pflotran and friends work correctly with --prefix
This means running the make install after make from within pflotran.py

Funded-by: IDEAS
Project: xSDK
Time: .5 hours including testi

make --download-pflotran and friends work correctly with --prefix
This means running the make install after make from within pflotran.py

Funded-by: IDEAS
Project: xSDK
Time: .5 hours including testing

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Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

Package libraries were not being correctly added to petscvariables variable due
to improper indent

Funded-by: IDEAS
Project: xSDK
Time: 0 hours

Merge branch 'barry/download-pflowtran' into barry/downloads

New category of packages that are NOT linked after PETSc libraries
Since some silly packages require make xxx instead of simply make for building added variable to handle that
Finally got --download-

New category of packages that are NOT linked after PETSc libraries
Since some silly packages require make xxx instead of simply make for building added variable to handle that
Finally got --download-alquimia working on my Mac with and without shared libraries
Lot of time debugging

Funded-by: IDEAS
Project: xSDK
Time: 5 hours

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Added --download-alquimia
Currently requires fork of alquimia with fixes

Updated --download-pflotran to also install libpflotranchem.a

Funded-by: IDEAS
Project: xSDK
Time: 5 hours

Merge branch 'hzhang/update-networkex'

configure: fix breakage on win32 with attribute(aligned) check.

configure: fix configureAlign() to use runtest - not just compile test.

And do not run 'pf' test - if PETSC_HAVE_ATTRIBUTEALIGNED is not set

Merge branch 'master' into tisaac/dmforest

* master: (177 commits)
DT ex3: The test should check the number of digits requested
DT ex3: One test fails in single precision
Plex: Do not automati

Merge branch 'master' into tisaac/dmforest

* master: (177 commits)
DT ex3: The test should check the number of digits requested
DT ex3: One test fails in single precision
Plex: Do not automatically create a default section if no fields are defined
Plex: DMPlexCopyCoordinates() needs to create the coordinate section if it is missing
superlu: no longer requires xerbla slamch dlamch ?
superlu: update to v5.1
skip MatSolve() if matrix factorization fails
replacing SETERRQ with error output info and continue execution
SNES ex12: Added parallel tests - These test parallel, unstructured interpolation/restriction using FAS
Plex+SNES: Now in DMPlexComputeJacobian_Internal(), we also form the Jacobian preconditioner matrix
FE: Now we can form either the Jacobian or the Jacobian preconditioned matrix using a flag
DS: Now have point wise function slots for the Jacobian preconditioned matrix - This will allow us to form the "right" operator for preconditioning, like M in the (2,2) block for Stokes
Plex: When swapping Plexes, also swap point SF
Plex: Fix parallel error in Injector
Mat+Plex: Added MatPreallocator which can be called with MatSetValues() and preallocates another Mat - This could have been another "mode" of Mat, but I thought this was cleaner - Use MatPreallocator to preallocator Plex interpolators
DT ex3: Change tolerance and eliminate tests which need MPFR from regular runs
superlu: fix complex build
superlu: update to using 5.0 tarball with the fix for -Werror=format-security
superlu: update to use tarball with -Werror=format-security fix
DM: Clone the coordinate DM instead of reusing in Clone()
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexcreate.c

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added PETSC_ATTRIBUTEALIGNED() so that structs used with DMNETWORK could be aligned with PetscScalar
problems occured with __float128 due to lack of alignment of PetscScalar arguments within the stru

added PETSC_ATTRIBUTEALIGNED() so that structs used with DMNETWORK could be aligned with PetscScalar
problems occured with __float128 due to lack of alignment of PetscScalar arguments within the structs
in the pf.c example

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Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master

Merge branch 'master' into pr391/zianekhodja/lilia/tsirm/master

Merge branch 'maint'

pkg-config: fix bad listing /foo/bar/libfoobar.a in PETSc.pc. Use -Lfoo/bar -lfoobar

Reported-by: Arne Morten Kvarving <arne.morten.kvarving@sintef.no>

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part o

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all DMs
builder: update regression tests
builder: update some missing package requirements
DM: set coordinate vector name
ts tutorials ex11_sa: make it compile
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
Error message should say use negative threshold value to prevent filtering out zeros
Calls to HYPRE_BoomerAMGSetInterpVectors() did not actually copy the vector data pointer from the PETSc vector to the hypre vector thus resulting in the hypre interp vectors being identically zero and hence not affecting the quality of the AMG hierarchy produced/
DMPlex: Silence overzealous compiler warnings
add row/col orientation to MatConvert_Elemental_Dense
fix formatting error in previous commit [broke nightlybuilds]
fix formating of TSTHETA manual page and add missing command line option
run hwloc with MPIEXEC and binding so it runs on the correct machine
fix: memory leaks [in valgrind test]
...

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Merge branch 'master' into barry-allow-vecset-nan-3.6

Merge branch 'stefano_zampini/feature-pardiso-schur' of https://bitbucket.org/petsc/petsc into stefano_zampini/feature-pardiso-schur

Merge branch 'master' into shri/add-tsevent-to-powergrid-examples

Merge branch 'master' into stefano_zampini/feature-pardiso-schur

Branch got out of sync with master

We always start with petsc/master. Trying to fix a bug (submatrix reuse) reported by
Dmitry.
Merge remote-tracking branch 'petsc/master' into fix-pcgasm-reuse

Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master

Merge branch 'master' into barry/always-mark-floats

Needed to merge in master to resolve conflicts that will appear when this branch is merged with master

cmake: rename PETScConfig.cmake to PETScBuildInternal.cmake to avoid confusion as
<Package>Config.cmake generally refers to the cmake config mode file for <Package>

Reported-by: Arne Morten Kvarving

cmake: rename PETScConfig.cmake to PETScBuildInternal.cmake to avoid confusion as
<Package>Config.cmake generally refers to the cmake config mode file for <Package>

Reported-by: Arne Morten Kvarving <Arne.Morten.Kvarving@sintef.no>

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c