(xstack-intel) TG x86 multiblock

- Fixed magic offsets.
- MODULE_STATE mechanism ensures an
  allocator does not get re-initialized
  multiple times when it is shared across
  multiple policy domains.
- TAKE protocol is explained in a detailed
  comment inside ce-policy.c.

[Fixes bug #74]

Change-Id: I5efff5f0ab40624f4723943b2472c3e0ec2fa444
(xstack-intel) ocrAbort with error code

- Added ocrAbort test case.
  The test aborts with code OCR_ECANCELED (125).
  The ocrTests script checks if the return code
  matches the one in testname.res, and if it does,
  then test run is marked as a success.

[Fixes bug #79]

Change-Id: Iea820312ac8d40733a17b9ff26d55adfa8ef6f22
(xstack-intel) Apps: Reorganize apps directory (first step)

Cholesky, fft, fib and smithwaterman are example applications
that now follow the new apps directory structure

More clean-up will be required. Some obviously old
kernels moved out of the way

[See feature #176]

Change-Id: I310f51c227866674e79a9f4fe5973ba490974bb8
(xstack-intel) OCR: Removed hacky task pool for the XEs

This code path should never be used anyways.
[Fixes bug #186]

Change-Id: I7a4aed2f15cbd64ae97d44b34310b44bf8e19f9b
(xstack-intel) Apps: Added a skeleton directory to help in application porting

Also:
  - Cleaned up the makefiles in particular with regards to input files
  - Updated the Wiki documentation (not in this commit obviously)
  - Added documentation to the Makefile themselves
  - Added a DEBUGMAKE option. If set to yes (like DEBUGMAKE=yes make -f ...),
    it will print additional information about the arguments for the app
  - Fixed-up cholesky and smithwaterman to use getArgc and getArgv
  - Changed the order of the program arguments to smithwaterman to put
    the files last

[Closes feature #176]

Change-Id: I8fd4ed0650567619d2472c6e88ab197f698ddc02
(xstack-intel) Apps: Fixups to the app structure

Thanks to Roger for pointing these flaws out:
  - Renamed anything 'fsim' to 'tg' to make it clearer
  - Removed the need for ocr-wrapper.sh by using a relative path
    that works from both locations
  - Moved LDFLAGS for TG to *after* the .o (not much use otherwise)
  - Fixed FFT's makefiles (missing CFLAGS and LDFLAGS)
  - Differentiated ARCH and OCR_TYPE:
    - OCR_TYPE is the "version" of OCR you want to build (tg, x86-pthread-x86, ...)
    - ARCH is x86 or TG depending on what machine you are running on
  - Fixed an issue in cholesky that caused it to not run on TG
  - Moved rmd-bin-files.h to the proper location
  - Minor other fixes

[See feature #176]

Change-Id: I6b7979a9b53c2650fcd841c32206d344bdefb9da
(xstack-intel) Few more cleanups following previous fix

- Fixed fsim/tg confusions in a few places
- Got rid of a couple of warning messages during build

[See feature #176]

Change-Id: I0e0a545ca4997ed19f54e13e39795ed07a20c3c5
(xstack-intel) Improved build system to better track changed files

The build system in ss/ did not properly pick up changes to
things like configuration files and linker scripts. This is
now fixed.

Also made the same changes to the OCR build to pick up
changes to include files and machine configurations.

Change-Id: I144d5b7907fa9b1fb9df8bf1e42a2019d1169bb4
(xstack-intel) OCR: Merge MPI branch into runtime/master

Issues fixed:
  - Shutdown protocol was screwed up in the merge
  - Re-added Single Assignment DBs as some of the tests still
    use it (is it still relevant, maybe remove in a follow-up
    change)
  - Initialization of the allocators in TGEmul
  - Other minor things
  - db containing mainEdt arguments must be released by XE
    do not use ocrDbRelease to avoid WARN message interpreted
    by jenkins as a failure (release outside EDT)
  - Add code in CE PD to manage a busy DB acquire request/response
  - x86-pthread-x86 change default CFG file to a lockableDB one

[Closes issue #137]
[Closes issue #163]
[References issue #195]

Conflicts resolved:
	ocr/build/common.mk
	ocr/build/tg-null-tg-xe/Makefile
	ocr/ocr-apps/fib/fib.c
	ocr/runtime/ocr-x86/src/api/ocr.c
	ocr/runtime/ocr-x86/src/comm-platform/comm-platform-all.c
	ocr/runtime/ocr-x86/src/inc/ocr-runtime-types.h
	ocr/runtime/ocr-x86/src/policy-domain/ce/ce-policy.c
	ocr/runtime/ocr-x86/src/policy-domain/hc/hc-policy.c
	ocr/runtime/ocr-x86/src/task/hc/hc-task.c
	ocr/runtime/ocr-x86/src/worker/xe/xe-worker.c

Change-Id: I5dbdfbbdaf94bc61942fa9ebbb48bbb740499859
(xstack-intel) Add app makefiles for ocr-distributed

Change-Id: I119cb2ce0894fec733119c9161aea6d05b7abc7b
(xstack-intel) Fix issue in request/response matching code for helper-mode

Change-Id: I44a05838af3f9ccb3223d63fc708942de1c8c129
(xstack-intel) Latch and Finish EDT support for distributed OCR

[Fixes bug #205]
[See bug #204]

Change-Id: Ibf6fb8a408ffadcc9ede31b6dc146edc0846fe79
(xstack-intel) Revisit distributed shutdown implementation

Temporary fix to avoid race conditions when shutting
down distributed policy-domain.

- In distributed, ocrShutdown sets a flag in the PD and
let subsequent calls to 'take' to try and detect quiescence
of the local node. Once the shutdown master node has reached
it, it sends shutdown msg to other nodes. Others will do the
same, detect local quiescence and send a shutdown ack to all
other nodes. Once a node got a ack from every other PD it
calls stop. This is a race hasty fix that should be handle
much more cleanly when we implement runlevels.

- Fix a number of incorrect non-regression tests

[closes bug #200]
[references bug #134]
[references enhancement #80]
[references bug #194]

Change-Id: I93dd684fbec0caf5cca627deb65364b8b82ebb03
(xstack-intel) Remove 0xdead used as DB/EDT properties

[closes bug #203]

Change-Id: Ifeec18bd7ee2797165a1fa4afaadbc5390c7aa0e
(xstack-intel) OCR: Extended ocrWait to FSim

[Closes bug #126]

The API has also been moved to ocr-legacy.h and configuration files
have been appropriately modified

Change-Id: Ifc33a9403728af52a94336c3ac34143e4ba184f0
(xstack-intel) OCR Applications: Make system cleanups

Specifically:
  - Allowed the possibility to extend PATH (for example)
  - Added OCR_CE_CONFIG and OCR_XE_CONFIG to allow the user
    to override the default configuration on FSim
  - Added -frmd-extensions for TG
  - Made sure that a change in OCR source would trigger a
    rebuild of the OCR library when building an app
  - Added a step in TG that collects all XE console messages
    to a single file (console.out in the execution directory)
  - Minor other small fixes

[See feature #176]

Change-Id: Ie7b0c830a1bf717c733d2f242a0eb5a210e3232d
(xstack-intel) OCR MPI: Several fixes in the handling of data blocks

There were several issues with the way data block write backs
were handled (among other things). Specifically:
 - Fixed a race between an ITW write-back and a concurrent
   acquire from the same node
 - Fixed an erroneous Lockable DB destroy check
 - Fixed issues in DB proxy flags when a DB transitioned from RO
   to ITW

This fixes issues in Fibonnacci [closes bug #211]

Change-Id: I3b1c542e823c88eee4d35259f3ce0afe76e3daf8
(xstack-intel) Adding HLL CnC-OCR for TG App Workshop 3.

Change-Id: I1ea0d6214415c1e8407652f084742c0cf47fa219
(xstack-intel) OCR Apps: Built all apps on all platforms and added to Jenkins

Specifically:
 - Refactored smith-waterman to be OCR API compliant
 - Moved affinitized version of cholesky
 - Verified that all tests work well and added to Jenkins
 - Improved Jenkins run (now uses make run for everything)
 - Improved Cholesky to get the text output so
   we can verify it

[Closes bug #212]
Still need to add:
 - Figure out verification for SW [See bug #220]

Change-Id: I49181512f465cfaf6888dd89e4e4b81f314f092e
(xstack-intel) OCR: Cleaned up doxygen

Cleaned up the doxygen documentation in the public API for release
with the specification.

Change-Id: I6b3bcf2594f2fae025b616021a67fc790de47eb3