Merge branch 'master' into barry/all-petscoptionssetvalue-beforepetscinitialize

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

Complete update to new PetscOptions interface

remove fatol and frtol concept from Tao; they are redundant and confusing compared to other tolerances

Merge branch 'master' into knepley/fix-examples-plex

* master: (112 commits)
correct expression for implict ODE/DAE in table 11 of users manual
remove warning about deprecated MPI call in exampl

Merge branch 'master' into knepley/fix-examples-plex

* master: (112 commits)
correct expression for implict ODE/DAE in table 11 of users manual
remove warning about deprecated MPI call in examples
rm variables declared in middle of subroutine
tolerance for equality in PETSc test should depend on machine epsilon
tolerance for acccuracy in test example should depend on machine epsilon
increase convergence tolerance to get same result in single precision as double for convergence history
update no change output for gasm test which had not been properly updated
remove C++ // comment
example mistakenly used MPI_COMM_WORLD as if it was rank in print statement thus producing output only with MPI Uni
grep out name of DM object since on some systems the address printed has extra zeros thus producing a false difference in output
increase tolerance for test example
build: revert el6-4 build to cg - as el6 compilers give link errors
fix error type
insure similar convergence history for single, double, quad
fix ex104.c based on Barry's suggestion
increase example convergence tolerance to get matching convergence history in single and double precision
increase convergence tolerance so that test example has similar convergence history in single and double precisions
changed from cg to gmres for eigenestimator since in single precision cg produced a possible indefinite matrix report
change test example tolerance to depend on machine epsilon so as to give correct results in various precisions
loosen convergence tolerance to have similar convergence history with single, double, quad precisions
...

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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

because gnorm0 can be PETSC_INFINITY one can get false gnorm/gnorm0 <= gttol even when gttol is 0.0 and gnorm is not zero
and thus get a false positive convergence

ftp://ftp.mcs.anl.gov/pub/petsc/ni

because gnorm0 can be PETSC_INFINITY one can get false gnorm/gnorm0 <= gttol even when gttol is 0.0 and gnorm is not zero
and thus get a false positive convergence

ftp://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2015/10/23/examples_master_arch-linux-gcc-pgf90_grind.log

1,84c11,64
< iter = 10, Function value 2416.67, Residual: 178.849
< iter = 11, Function value 2416.67, Residual: 3.77357
< iter = 12, Function value 2415.51, Residual: 10.0153
< iter = 13, Function value 2411.15, Residual: 391.763
< iter = 14, Function value 2411.15, Residual: 311.476
< iter = 15, Function value 2411.15, Residual: 24.0925
< iter = 16, Function value 2410.86, Residual: 141.568
< iter = 17, Function value 2410.86, Residual: 9.82914
< iter = 18, Function value 2409.03, Residual: 19.0147
< iter = 19, Function value 2405.37, Residual: 187.39
< iter = 20, Function value 2405.37, Residual: 36.1224
< iter = 21, Function value 2403.96, Residual: 461.641
< iter = 22, Function value 2403.96, Residual: 88.53
< iter = 23, Function value 2401.43, Residual: 125.36
< iter = 24, Function value 2400.63, Residual: 71.9882
< iter = 25, Function value 2396.47, Residual: 153.581
< iter = 26, Function value 2388.32, Residual: 693.398
< iter = 27, Function value 2384.75, Residual: 149.291
< iter = 28, Function value 2384.75, Residual: 156.177
< iter = 29, Function value 2384.74, Residual: 21.6924
< iter = 30, Function value 2384.74, Residual: 3.76519
< iter = 31, Function value 2384.5, Residual: 0.0942887
< iter = 32, Function value 2384.48, Residual: 0.762227
< iter = 33, Function value 2384.48, Residual: 0.287334
< iter = 34, Function value 2384.48, Residual: 0.221261
< iter = 35, Function value 2384.48, Residual: 0.0183731
< iter = 36, Function value 2384.48, Residual: 0.0155648
< iter = 37, Function value 2384.48, Residual: 0.0473363
< iter = 38, Function value 2384.48, Residual: 0.00108368
< iter = 39, Function value 2384.48, Residual: 0.00487713
< iter = 40, Function value 2384.48, Residual: 0.000172856
< iter = 41, Function value 2384.48, Residual: 5.48164e-06
< 4575.7085175608709 4.4942328371557893E+307
< 4575.7085175608709 1815.2985516599065
< 4575.7085175608709 4838.2083666605959
< 4575.7085175608709 1404.4509372826872
< 3627.3927583129494 11279.715346421122
< 2584.9214240354881 16120.497699152949
< 2584.9214240354881 1143.9964691546586
< 2524.6912329226511 257.61363944306333
< 2500.2432503157597 1072.2480219597619
< 2418.1438534115305 16.920666223362254
< 2416.6681259821662 178.84868221303151
< 2416.6681259821662 3.7735723004899953
< 2415.5103186576657 10.015315131908833
< 2411.1478828901513 391.76278493043350
< 2411.1478828901513 311.47645419742167
< 2411.1478828901513 24.092477935507905
< 2410.8560348505721 141.56770482743312
< 2410.8560348505721 9.8291448260766465
< 2409.0324456803005 19.014689846065945
< 2405.3739964265242 187.39038474373950
< 2405.3739964265242 36.122443687575149
< 2403.9568709863192 461.64120477249253
< 2403.9568709863192 88.529967780196770
< 2401.4334252131084 125.35992515000555
< 2400.6257885667246 71.988183117061809
< 2396.4652276331276 153.58121719436181
< 2388.3184558101684 693.39843432256225
< 2384.7468187163477 149.29114901422918
< 2384.7463243759134 156.17731464402209
< 2384.7444039122361 21.692395955680837
< 2384.7444039122361 3.7651902219828197
< 2384.5019577079884 9.4288701695413590E-002
< 2384.4811654195523 0.76222743780397162
< 2384.4775172870586 0.28733366291505030
< 2384.4774835782791 0.22126089137917193
< 2384.4774835782791 1.8373137553614825E-002
< 2384.4770104266977 1.5564772320028585E-002
< 2384.4770104266977 4.7336288381090962E-002
< 2384.4770104266977 1.0836785323014985E-003
< 2384.4769959665418 4.8771273138846754E-003
< 2384.4769959665418 1.7285550186436704E-004
< 2384.4769950856239 5.4816440789146458E-006
---
> iter = 10, Function value 2416.67, Residual: 178.848
> iter = 11, Function value 2416.67, Residual: 3.77354
> iter = 12, Function value 2415.51, Residual: 10.0152
> iter = 13, Function value 2411.15, Residual: 391.762
> iter = 14, Function value 2411.15, Residual: 311.485
> iter = 15, Function value 2411.15, Residual: 24.0923
> iter = 16, Function value 2410.86, Residual: 141.566
> iter = 17, Function value 2410.86, Residual: 9.82925
> iter = 18, Function value 2409.03, Residual: 19.0148
> iter = 19, Function value 2405.37, Residual: 187.386
> iter = 20, Function value 2405.37, Residual: 36.1251
> iter = 21, Function value 2403.96, Residual: 461.668
> iter = 22, Function value 2403.96, Residual: 88.5331
> iter = 23, Function value 2401.43, Residual: 125.336
> iter = 24, Function value 2400.63, Residual: 71.9888
> iter = 25, Function value 2396.47, Residual: 153.517
> iter = 26, Function value 2388.32, Residual: 693.48
> iter = 27, Function value 2384.75, Residual: 149.213
> iter = 28, Function value 2384.75, Residual: 155.989
> iter = 29, Function value 2384.74, Residual: 21.693
> iter = 30, Function value 2384.74, Residual: 3.76568
> iter = 31, Function value 2384.5, Residual: 0.0944167
> 4575.709237872599 4.4942328371557893E+307
> 4575.709237872599 1815.299097035091
> 4575.709237872599 4838.211023807340
> 4575.709237872599 1404.451476651041
> 3627.393451094771 11279.72339237862
> 2584.921547425445 16120.47402759046
> 2584.921547425445 1143.996822397298
> 2524.691880989573 257.6142334482682
> 2500.243663647243 1072.250646127577
> 2418.143843854654 16.92068765006729
> 2416.668115647490 178.8482347419252
> 2416.668115647490 3.773542861935354
> 2415.510308753632 10.01522134695003
> 2411.147874535623 391.7622989687072
> 2411.147874535623 311.4852217790456
> 2411.147874535623 24.09225353032197
> 2410.856001083221 141.5657075065890
> 2410.856001083221 9.829250038838696
> 2409.032437701279 19.01475432423581
> 2405.373981543032 187.3859379562852
> 2405.373981543032 36.12514004734248
> 2403.956903740529 461.6682968186628
> 2403.956903740529 88.53313263679679
> 2401.433405170609 125.3358752678410
> 2400.625643950743 71.98880933148733
> 2396.465077162101 153.5169470075242
> 2388.318463061776 693.4800677788330
> 2384.746784861173 149.2130864980433
> 2384.746318005369 155.9885985568999
> 2384.744454905304 21.69300201158603
> 2384.744454905304 3.765677006955844
> 2384.501947107490 9.4416733419311727E-002
88c68
< final delta: 0.0015625
---
> final delta: 0.025
91c71
< total subproblem iterations: 91
---
> total subproblem iterations: 65
94,98c74,78
< Residual in Function/Gradient:=5.48164e-06
< Objective value=2384.48
< total number of iterations=41, (max: 100)
< total number of function evaluations=44, max: 4000
< Solution converged: ||g(X)||/|f(X)| <= grtol
---
> Residual in Function/Gradient:=0.0944167
> Objective value=2384.5
> total number of iterations=31, (max: 100)
> total number of function evaluations=34, max: 4000
> Solution converged: ||g(X)||/||g(X0)|| <= gttol
/sandbox/petsc/petsc.clone-2/src/tao/leastsquares/examples/tutorials
Possible problem with chwirut1f_1 stdout, diffs above

show more ...

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

Merge branch 'master' into barry/improve-git-download

tao->reason is an enum, not a PetscInt therefore should use a %d for printing not a %D

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

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

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs in Fortran test example in order to have same result with real and complex builds
changed outdate mpirun and -np to mpiexec and -n
force sqrt to be taken in the precision of PetscReal in fortran examples
continuation line too soon for some compilers
stop configure if user selected C++ clanguage, single precision, complex combination since we do not support it
fixes for Fortran examples to compile cleanly in single precision that do not involve complex numbers
fixes to Fortran examples to compile cleanly in single precision complex
fix previous mistake
must cast 1. to PetscScalar before dividing by a PetscScalar (C++ complex class is terrible)
must cast 0.0 to PetscScalar before comparison with a PetscScalar
changed order of suggested locations of downloadable PETSc to Barry's preference
Increase patchlevel to 3.6.2
remove debug print statement from two commits before
remove debug print statements I accidently left in the last commit
PetscDraw: Fix dummy definition of PetscDrawCollective{Begin|End}()
remove cleanupMumps flag from MatDestroy_Mumps() it should always free the memory it allocated Bug detected while adding features to libMesh
improved viewing of fractional counts in xml nested log viewing fixed bug in output of doubles to xml nested log files
chombo: build only libs - not examples
fix typo. 'gcc-4.8 --with-cxx-dialect=C++11' gives a warning with this line - even though its in a #ifdef thats never enabled.
...

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To refactor the comments to follow petsc style.

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
src/mat/examples/tests/makefile

To refactor the comments to follow petsc style.

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiov.c

show more ...

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-c

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
include/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefi

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'master' into pr352/dmay/pctelescope/master

Merge branch 'master' into pr358/buptphyphy/addmatcreatenormalhermitian/master

Merge branch 'master' into tisaac/plex-feature-tree-fv

Merge in Barry's fix to synchonized print out of plex objects into
updated output files.

* master: (31 commits)
fix %nd for plex printf that

Merge branch 'master' into tisaac/plex-feature-tree-fv

Merge in Barry's fix to synchonized print out of plex objects into
updated output files.

* master: (31 commits)
fix %nd for plex printf that should be %nD
PGI compiler requires cast to char* of this array for some reason
Incorrect use of %d for %D in viewing of PetscSection
update output for suitesparse examples with new KSP view data
changed boomeramg advanced smoother output files to use short format so there are less differences with different systems
fix some issues with PetscViewerFlush() and PetscViewerASCIIPushSynchronized() within the plex object viewing
incorrectly used stride value instead of local size in check that ISSTRIDE has same layout as columns of matrix
try using int(w) for Fortran case to integer instead of int(w,integer) since the latter failed on most systems claiming integer was not a constant. Very unclear to me what that second argument is suppose to be
SNES function evaluations were not counted for certain Jacobian computations
nightlybuilds: fix vec/ex7,ex7f link issue by using the correct LIBS option
nightlybuilds: move location of petsc.clone(s) on bb44 from nfs to /sandbox
nightlybuilds: arch-linux-complex-gcov -> arch-linux-cmplx-gcov to be consistant with other config tests
add __float128 data file neeed by test example 10 otherwise test example crashes with --with-precision=__float128 builds
cast fortran integer that may be 64bit with int() to prevent compiler warning about Warning: Possible change of value in conversion from INTEGER(8) to INTEGER(4) at (1)
removed unneeded definition of Sqr in example since PetscSqr should be used, and was in other parts of the same example!
nightlybuilds: run 'git gc' in the build clones
opensolaris: use 'FFLAGS=-ftrap=%none' this way fortran examples on solaris do not crash in lapack during 'div by zero' Also use the updated path to mpich
when I swapped the role of coulping and rest in fieldsplit I missed a place
cannot use PetscMalloc2() on arrays that will be freed as two seperate arrays
C++ cannot handle [PETSC_RESTRICT]
...

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Merge branch 'master' into mark/eigen-rand

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix t

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
PGI compiler cannot handle [restrict] usage therefor disable restrict for PGI compiler Fix ex48.c to use PETSc standard way of marking restrict
PETSC_UNUSED must occur before the typename. With PGI compilers they error if it is after the type name
on solaris in TSAdaptChoose_Basic() negative root for zero could produce -infinity thus causing time step to be decreased even though the error estimate was zero
MatGetSchurComplement: revert test from LUMP back to DIAG and update output
there are no tests for opencl or viennacl so prevent warning message: make[2]: *** No rule to make target `testexamples_OPENCL', needed by `tree'. Stop. make[2]: *** No rule to make target `testexamples_VIENNACL', needed by `tree'. Stop.
incorrect initial conditions function that could produce floating point exception value (and does on windows) due to squareroot of non-negative number
forgot to fix rule for building ex194
move ex193.c to ex194 because someone else created a 193
remove outdate manual page comment
add missing VecRestoreArray()
add missing VecRestoreArray()
missing restore array in example
formating for print statements of test example with __float128 precision
fix example for __float128 precision by using PETSc math macros and casting PetscReal in print statements
remove Tao example custom monitor that produced different results for __float128 precision
all PETSc built in monitors require a valid PetscViewer, NULL is not acceptable
PETSc built in monitors always require viewers to be passed in, no longer support a NULL viewer
use tigher haptol for minres for quad precision because otherwise false positive of indefinite matrix appeared in example
check for PetscMPIInt overflow in ISAllGather()
...

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Merge branch 'sarich/fix-vec-stepbound'

Merge branch 'master' into jed/process-options-handler