Error if user provides --with-sowing=0 but has PETSc git clone and Fortran compiler

Reported-by: Pierre Jolivet <Pierre.Jolivet@enseeiht.fr>

List pflotran library as well as pflotran chem library when downloading

Merge branch 'barry/fortran-update'

Merge branch 'barry/update-trilinos-build'

Remove rpath information passed to Trilinos since cmake manages it for them

All the rpath information caused cmake to fail on Apple systems

Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .5 hour
Thanks

Remove rpath information passed to Trilinos since cmake manages it for them

All the rpath information caused cmake to fail on Apple systems

Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .5 hour
Thanks-to: Roscoe A. Bartlett

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cusp: fix compile warning with non-existant include dir by assuming self.includedir list can have optional paths.
This happens because --download-cups vs --with-cups-dir have different include paths.

cusp: fix compile warning with non-existant include dir by assuming self.includedir list can have optional paths.
This happens because --download-cups vs --with-cups-dir have different include paths.

FC arch-cuda-double/obj/src/ksp/f90-mod/petsckspmod.o
Warning: Nonexistent include directory "/home/balay/soft/cusplibrary-0.4.0/include"

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Merge branch 'knepley/fix-configure-pragmatic'

* knepley/fix-configure-pragmatic:
Configure: Correct flag for optimized Pragmatic build

--download-sowing=0 does not mean do not search for it if needed!

Update so that ssl support will compile and run with SSL 1.1

Tested on Apple with brew install openssl@1.1 and on linux with manual install of 1.1
Please report any problems

Resolves issue #145
Rep

Update so that ssl support will compile and run with SSL 1.1

Tested on Apple with brew install openssl@1.1 and on linux with manual install of 1.1
Please report any problems

Resolves issue #145
Reported-by: Drew Parsons

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Updated and simplified Fortran interface

Reduced from 4 distinct approaches to using PETSc from Fortran to 1
No more .h90 files (Fortran 90 functionality is now always available)
Parameters and func

Updated and simplified Fortran interface

Reduced from 4 distinct approaches to using PETSc from Fortran to 1
No more .h90 files (Fortran 90 functionality is now always available)
Parameters and function prototypes are now provide through Fortran modules, not includes;
only #define are provided in the petscXXXdef.h files
PETSc objects can be declared as either type(tXXX) or XXX. For example type(tVec) or Vec
Moved now private Fortran include files out of public include directory since uses don't use them;
they are only used to generate the Fortran modules
Easier to support and test; we can now easily add more function prototypes
Also had to rework generation of manual pages to consistently use MANSEC and SUBMANSEC
since these variables also handle how the Fortran modules are generated.

Time: 57 hours

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Merge branch 'balay/update-cmake-elemental-v0.87-squashed'

cmake: update to use version 3.7

Use v3.0 on opensolaris as newer versions do not build properly - due to
curses vs ncurses conflict. This results in unresolved symbol error for
wattr_on, wattr_off

cmake: update to use version 3.7

Use v3.0 on opensolaris as newer versions do not build properly - due to
curses vs ncurses conflict. This results in unresolved symbol error for
wattr_on, wattr_off [which should be in /usr/gnu/lib/libncurses.so]

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elemental: update to v0.87.4 and fix interface

Thanks-to: Hong Zhang <hzhang@mcs.anl.gov>
Thanks-to: Jack Poulson <jack.poulson@gmail.com>

elemental: add complex tests and organize wrt complex/datafilespath

tests: add elemental to complex, 64idx testbuilds.

Update ex145 diff for linux-cxx-cmplx-pkgs-64idx build

Thanks-to: Hong Zhang

elemental: add complex tests and organize wrt complex/datafilespath

tests: add elemental to complex, 64idx testbuilds.

Update ex145 diff for linux-cxx-cmplx-pkgs-64idx build

Thanks-to: Hong Zhang <hzhang@mcs.anl.gov>

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configure: add -fstack-protector to default CFLAGS for a debug build

Merge branch 'balay/update-mpich-3.3a2-squashed'

Merge branch 'balay/update-hdf5-netcdf-squashed'

Merge remote-tracking branch 'origin/balay/update-MUMPS_5.0.2'

mpich: update to version 3.3a2

However use mpich-3.2 on linux/PGI and on OSX due to the following issues:

https://github.com/pmodels/mpich/issues/2354
https://github.com/pmodels/mpich/issues/2436

mpich: update to version 3.3a2

However use mpich-3.2 on linux/PGI and on OSX due to the following issues:

https://github.com/pmodels/mpich/issues/2354
https://github.com/pmodels/mpich/issues/2436

valgrind: (for mpich-3.3a2) add new suppression entry runex2_window in src/vec/is/sf/examples/tutorials

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hdf5: update to version 1.8.18
netcdf: update to version 4.4.1

Notes:

* netcdf changed default of dynamic-loading option resluting in '-ldl' error. Hence using --disable-dynamic-loading option

* T

hdf5: update to version 1.8.18
netcdf: update to version 4.4.1

Notes:

* netcdf changed default of dynamic-loading option resluting in '-ldl' error. Hence using --disable-dynamic-loading option

* Tried using hdf5-1.10.0-patch1 - and it has a few issues.
- Does not work with ubuntu-12.04 default compilers. [fix is in git]
- requires gnumake for 'fortran/test/Makefile' as it uses .NOTPARALLEL directive [so has issues with bsdmake]
- requires F2003 compiler for fortran interface [so has issues on opensolaris]

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Merge branch 'barry/fix-fortran-interfaces-matsetvalues'

Merge remote-tracking branch 'origin/barry/fix-chaco-from-trilinos'

Merge branch 'jose/matlrc'

MUMPS: update to version 5.0.2-p1

petsc4py: use snapshot with MatCreateLRC change