fix errors from nightlybuilds

Fix clang warning with complex scalars

Plex: Added Exodus Genesis file type

Merge remote-tracking branch 'origin/balay/with-fortran-bindings'

nightlybulds fix variation in output..

configure: add option --with-fortran-bindings

Now one can use --with-fc=gfortran --with-fortran-bindings=0 to detect fortran compiler properly
[for externalpacakge use - for eg: scalapack] but avoid

configure: add option --with-fortran-bindings

Now one can use --with-fc=gfortran --with-fortran-bindings=0 to detect fortran compiler properly
[for externalpacakge use - for eg: scalapack] but avoid building PETSc fortran bindings in library and modules.

Also disable sowing when with-fortran-bindings is disabled

Fix makefiles (corresponding to fortran bindings) to consistantly use PETSC_HAVE_FORTRAN

Also remove unused PETSC_USE_FORTRAN_DATATYPES flag
Reported-by: Patrick Farrell <patrick.farrell@maths.ox.ac.uk>

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Merge branch 'knepley/fix-plex-coord-dim'

* knepley/fix-plex-coord-dim:
Plex: Fix coordinate dimension in creation functions Reported-by: Jonathan Lambrechts <jonathan.lambrechts@uclouvain.be>

Plex: Fix coordinate dimension in creation functions
Reported-by: Jonathan Lambrechts <jonathan.lambrechts@uclouvain.be>

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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PetscFE: No longer need to set tensor property

PetscViewerGLVis: remove any dependency from the DM class in VecView_GLVis

Merge remote-tracking branch 'origin/barry/feature-fortran-petscerror'

fortran: add SETERRA() and CHKERRA() macros as ifort flags 'return' in 'program main' as error

/sandbox/petsc/petsc.clone-2/src/sys/examples/tutorials/ex4f90.F90(42): error #6353: A RETURN statement

fortran: add SETERRA() and CHKERRA() macros as ifort flags 'return' in 'program main' as error

/sandbox/petsc/petsc.clone-2/src/sys/examples/tutorials/ex4f90.F90(42): error #6353: A RETURN statement is invalid in the main program.
call MPI_Comm_size(PETSC_COMM_WORLD,size,ierr);if (ierr .ne. 0) then ; call PetscError(PETSC_COMM_SELF,ierr,PETSC_ERROR_REPEAT,PETSC_NULL_CHARACTER); return; endif

And attempt to shorten the macros by using PetscErrorF() subroutine

And fix all examples to use SETERRA/CHKERRA in main program (instead of SETERRQ/CHKERRQ)

Note: CHKERRA are different from CHKERRABORT on the C interface - as it does not take 'comm' option

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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 remote-tracking branch 'origin/stefano_zampini/feature-gmsh-periodic'

windows fixes

Merge remote-tracking branch 'origin/knepley/fix-ex-types'

Merge remote-tracking branch 'origin/knepley/fix-plex-parallel-load'

Merge remote-tracking branch 'origin/knepley/fix-dm-blocksize'

Merge remote-tracking branch 'origin/knepley/feature-dm-bc-components'

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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disable example with absoft (due to fixed/free form limit)

c89 fixes

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 subc

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

show more ...