Need to fix generated conf files in destination directory not install directory

Commit-type: bug-fix
Reported-by: Drew Parsons

Issue 208 Set PETSC_DIR appropriately in petscconf.h for --prefix installs

Commit-type: bug-fix

Merge branch 'maint'

Merge branch 'balay/fix-uninstall-rm/maint' into maint

Merge branch 'barry/improve-installer'

Cleanup the installer a abit, no longer install some unneeded items, accomplish some of the TODO

Commit-type: bug-fix, style-fix
Reported-by: Jed Brown

Merge branch 'barry/fix-bin-install'

Revert "unstall now deletes petsc specific directories created by PETSc"

There should never be 'rmtree' in uninstall script - as prefix is
usually a common location shared by multiple packages.

Thi

Revert "unstall now deletes petsc specific directories created by PETSc"

There should never be 'rmtree' in uninstall script - as prefix is
usually a common location shared by multiple packages.

This reverts commit e22ab8e6ea0e27378051f3cece371df7452c4e2f.

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Remove/move all items from $PETSC_DIR/bin so that package maintainers don't have to deal with non-standard usage.

Commit-type: style-fix

Merge branch 'scott/test-harness-installfixes'

Improvements for the install

The test harness has to operate in 3 modes:
1. Normal development mode
2. Test install from source dir (make allgtests)
3. Test install from install dir
See config

Improvements for the install

The test harness has to operate in 3 modes:
1. Normal development mode
2. Test install from source dir (make allgtests)
3. Test install from install dir
See config/gmakegentest.py documentation for how these differs.
This sorts out the paths for all 3 cases.

A big change is making gmakefile.test use absolute paths
rather than the relative paths used originally and in the normal
gmakefile. This simplifies a lot of the development, including the
previous method of doing a lot of modifications for the installs.

`make test` is still not hooked up to the new test system so testing was
done with allgtest.

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Merge branch 'barry/tao-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'barry/move-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warni

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warning
Plex ex26: Protect ExodusII stuff
DM: DMCreateSubDM() field argument should be const
TS ex46: Newlines and some numerical jitter
TS ex45: Newlines and some numerical jitter
TS ex11: Fixed indentation and time step numbering
SNES ex12: Update for DM view changes
Plex tests: Update to new DM output
Plex ex23: Use Nc not dim for vector fields
Plex: Default section now ignores cells hanging off boundary meshes
Plex: Viewer now reports the cell Height
Increase patchlevel to 3.8.3
Plex: Fixed DMPlexInterpolate() bugs - Do not copy associated data if we are not interpolating - Do not interpolate if we already have full depth
fix valgrind errors with using PetscObjectGetName()/SetName() with the same object - resulting in a free() before copy.
ex4: fix compile warning and update makefile
Minor fixes
Improving report_tests
PetscDS: Must initialize the default adjacency
...

Conflicts:
include/petsc/private/dmimpl.h
include/petscdm.h
include/petscis.h
src/dm/impls/plex/plexcreate.c

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Merge remote-tracking branch 'origin/scott/test-harness-report_tests_fix'

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if m

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if malloc is already set
Plex: Fixed array initialization
pgi: compile fix
knl: update test to use memkind and remove option that worked arround a bug with intel 17
Check the return value for memkind_posix_memalign
Change the default behavour for -malloc_hbw
Bib: More refs
test: remove runex13f90 as its now converted to new test suite
fix win32 crash. This test was previously run with '-n 4' - so restoring it
Fix petscsfgetgraph_ to work for all Fortran compilers by directly using array of PetscSFNodes
bugfix for MatDuplicate_MPIAIJ_PtAP Reported-by: Samuel Lanthaler <s.lanthaler@gmail.com>
strip out dead sundials usage code; change sundials test to only run 5 timesteps to prevent different number of steps on different systems.
Remove extra lines of output file
Example uses C99 constructs so must mark with requires: c99
fix const missmatch for DMDAVecRestoreArrayRead()
remove conflict between function name in example and new PETSc TS function
builds: attempt to do maint/master/next test builds in separate clones
ex62: it turned out that CHACO partioning is not deterministic. Use a prescribed partition instead
...

Conflicts:
src/dm/interface/dm.c
src/snes/examples/tutorials/ex13.c

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Minor fixes

Generalize to include example files that are not in tests and tutorials.
Start examples tree traversal at the 'src' level which simplifies some
logic and avoids some potential problems

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with updated 17.10 compilers
Fix for test dirs that are not tutorials/tests
fix use of double in PetscAbsReal() which produces compiler warnings with single precision build
elemental: remove info on conflict of -with-cxx-dialect=C++11 on osx - it works now.
Cleanup .bib files
Fix allfortranstubs rule to rm generated files from correct directory, not outdated location
ierr set but not checked
Remove initial refine so test runs faster and does not time out on some machines
Gail's copyedits for bibtex items
Docs: manual: add further description of 3 different current testing options
DM: check for ops->localtolocalbegin/end before calling
PetscSF: fix typo in tutorial ex1
Vec+HDF5: Fix output for complex - Need to check for empty group name
SNES: SNESDestroy() can be called with snes->dm == NULL
SNES: SNESDestroy() can be called with snes->dm == NULL
Vec+HDF5: Fix output for complex - Need to check for empty group name
Docs: Manual: Update tests section
gmakegentest: also exclude .#filenames created by emacs
DMPlex: Fix output of test ex1 after changes to Gmsh reader
...

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Merge remote-tracking branch 'origin/scott/test-harness-installtest'

Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Bug fixes based on previous reports to PR

Various bug fixes to improve the robustnesses:
- Giving full path of testsrcs dependency enables invoking it from outside
of its source directory (removes

Bug fixes based on previous reports to PR

Various bug fixes to improve the robustnesses:
- Giving full path of testsrcs dependency enables invoking it from outside
of its source directory (removes reported infinite loop)
- Adding a dependency to the TESTDIR/.DIR uses Jed's previously
defined sentinel file rules fixes some inconsistent behavior
*and* enables fullpath TESTDIR specification (as in Satish's report)
- Install.py was accidently adding an extraneous 'all' target
- gmakegentest.py was using inInstallDir inconsistently in a few places

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Refactoring to clean up coding and minor bug fixes.

Per discussion on last commit, this is refactored to simplify
the coding and hopefully make it less obtuse.

Also found some minor errors as devel

Refactoring to clean up coding and minor bug fixes.

Per discussion on last commit, this is refactored to simplify
the coding and hopefully make it less obtuse.

Also found some minor errors as development and testing occurred on some
of the install testing.

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Remove redundant info from gmakefile.

Per discussion, gmakefile.examples has been changed to
gmakefile.test. It is now included in gmakefile to enable
the removal of redundant information. Tests o

Remove redundant info from gmakefile.

Per discussion, gmakefile.examples has been changed to
gmakefile.test. It is now included in gmakefile to enable
the removal of redundant information. Tests on whether
gmakefile or gmakefile.test is invoked is used to print
out the appropriate help information for that file (i.e.,
do not print out test info for basic compiles).

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Enable tests to run from install directories.

Previous incarnations of the test harness did not run from installation
(prefix) directories. To enable this feature, the make part of the test
harness

Enable tests to run from install directories.

Previous incarnations of the test harness did not run from installation
(prefix) directories. To enable this feature, the make part of the test
harness was separated from the build gmakefile to create
gmakefile.examples. Install.py then installs the harness, and fixes up
the gmakefile.examples to make it work robustly in the installation dir.
The install paths are:
```
<prefix_dir>/share/petsc/examples/gmakefile.example
<prefix_dir>/share/petsc/examples/config/*
```

Example usage:
```
cd <prefix_dir>
make -f share/petsc/examples/gmakefile.example
```
will run tests in ```<prefix_dir>/tests```.

Another example:
```
cd <prefix_dir>/share/petsc/examples/
make -f gmakefile.example TESTDIR=$PWD/mytests
```
will run tests in ```<prefix_dir>/share/petsc/examples/mytests```.

For developers, other than ```gmakefile``` -> ```gmakefile.examples```,
it should remain the same.

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Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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