Merging 2.2 release branch to master:

commit d77789b087527de75b5b3e0d4411cc85badbf59e
Author: Leyuan <laura@gmail.com>
Date:   Sun Aug 31 13:15:42 2014 -0700

    OS supports added, change sm_21 to OFF by default

commit 71b6d5716ea25f1e76ee4bc9727e50fa84ae7e13
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Fri Aug 29 12:01:16 2014 -0700

    oops compile errors

commit 3067842b8432a90278766bc38f751e536adf2db3
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Fri Aug 29 11:43:07 2014 -0700

    clarified what datatypes merge sort can address, also whitespace/formatting issues

commit ee78694e1a7754bf5cf47731c92a9388f591d333
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Fri Aug 29 11:21:08 2014 -0700

    added Issue 148 to the CUDPP home page

commit c1374422344adca076d8e6beabb763e8f2f8bf0c
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Fri Aug 29 11:12:03 2014 -0700

    added some 2013 and 2014 cites

commit d21224a5ec92f43829a9a226b1a4188c15a5a1ad
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Thu Aug 28 13:54:57 2014 -0700

    removed unnecessary global synchronizations

commit e0540fb89b442bbc7776dc0db0d7c0d7fd62e802
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Thu Aug 28 13:49:01 2014 -0700

    added GENCODE_SM21, per Mark Harris

commit 5a95894a5ae94254cd660e2d535a24be8fb9224c
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Thu Aug 28 13:48:21 2014 -0700

    fixing compile warning size_t->unsigned int

commit c0e5dc8fdbe88c293bd2767e4604d1ccaf9b3eef
Merge: 00e02af 0e373cf
Author: Leyuan <laura@gmail.com>
Date:   Thu Aug 28 13:19:01 2014 -0700

    Merge branch '2.2' of github.com:cudpp/cudpp into 2.2

commit 00e02af2767398a55b929bf6010b1eecb6d0288c
Author: Leyuan <laura@gmail.com>
Date:   Thu Aug 28 12:58:49 2014 -0700

    Deleted all cudaThreadSynchronize() and thanks Andy for correcting memory checking bug

commit 0e373cf9ad761e1082eb28e7e60db2cad8aeb177
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Sun Aug 24 17:20:49 2014 -0700

    OS X/clang

commit 66438b00038f146c4399bf99a77d676ae9c9bfaa
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Sun Aug 24 17:19:34 2014 -0700

    slight edits to changelog

commit dd154aae9916a9375cb266ee4d90e17218b0e8b1
Author: Leyuan <laura@gmail.com>
Date:   Sun Aug 24 14:38:06 2014 -0700

    changed log edited for cudpp 2.2, Readme for MTF limit changed

commit f9b67db615ae44d4d880496772a55db7612e47cc
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Wed Aug 20 19:59:53 2014 -0700

    changed -largeGPU and -smallGPU to -skiplargetests (thanks for the suggestion, Mark)

commit 9448cea0a45e1026aea0607605d1ae770cdf522d
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Tue Aug 19 21:06:37 2014 -0700

    added smallGPU/largeGPU flags (currently only used in MTF)

commit f067bfb8d73190931a33ccca41d135d152bf2a51
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Tue Aug 19 21:06:29 2014 -0700

    checking for enough free memory to run large tests

commit d9e00540bcf51903460911f0746c7a7271dee69a
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Tue Aug 19 20:55:25 2014 -0700

    this is fixing whitespace/indentation only

commit fa9f3d335288ffc240212fb4f2cd43ee7cdbd73d
Author: Andrew Davidson <aaldavidson.ucdavis@gmail.com>
Date:   Mon Aug 18 17:55:08 2014 -0700

    fix to make compatible for cc < 2.0

commit e6e7a11eb9d64acf12d509c0404dc43bdde5a794
Author: Andrew Davidson <aaldavidson.ucdavis@gmail.com>
Date:   Sat Aug 16 17:06:39 2014 -0700

    Changing to extern smem declaration instead. should fix cc 2.0 issues

commit 6365b02485fed434e528b432c1beb3b3552b7fb0
Author: Leyuan <laura@gmail.com>
Date:   Thu Aug 14 18:43:45 2014 -0700

    Cudpp2.2 compilation pass when compute version is less than 2.0

commit fd5074a4a96d3f92d755f5d6caab25c0fa20adb3
Author: Leyuan <laura@gmail.com>
Date:   Tue Aug 12 01:06:48 2014 -0700

    Thanks Andy for including mgpu, make suffix array compiled with compute version less than 2.0

commit a7763c7c4b71768b0eae38140dd0f02b8bb20a43
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Thu Aug 7 16:29:50 2014 -0700

    Leyuan found the out-of-bounds error: h_hist needed to be allocated as NUM_CHARS (257) not 256. This fixed CPU regression. Might revoke Ritesh's degree for this.

commit 0abf31e539130d8d73e3a6bccd6b28397b5c8d46
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Thu Aug 7 10:45:19 2014 -0700

    added check for CUDA 6.0/OS X -ccbin (does not add -ccbin to command line if it's already there)

commit 877898ddf4e25056259c8161a202a792d01714d8
Author: Leyuan <laura@gmail.com>
Date:   Tue Jul 29 12:02:59 2014 -0700

    compression memory leak error solved

commit febd37db4339446c4202b4890c4cb1c21a0f0e84
Merge: 7b3e04a 1a88503
Author: Leyuan <laura@gmail.com>
Date:   Thu Jul 24 15:01:29 2014 -0700

    Merge branch '2.2' of github.com:cudpp/cudpp into 2.2
    Added suffix array test memory bound, removed the test bound for compression

commit 7b3e04a3872674d41fa11278c4a0ccad0696e98c
Author: Leyuan <laura@gmail.com>
Date:   Thu Jul 24 14:58:13 2014 -0700

    out of memory bound added, compression test limitation removed

commit 1a88503bdb2ed89891183cf0a4e03b3d832f6723
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Thu Jul 24 14:12:38 2014 -0700

    integrated CUDA-6-not-6.5-on-OS-X-with-clang fixes

commit 81a1d001f0e2a368527a1abe493d5bdc0bdc971c
Author: John Owens <jowens@ece.ucdavis.edu>
Date:   Thu Jul 24 13:37:07 2014 -0700

    Both apps and the CUDPP library need to use libstdc++ when compiling for OS X Mavericks

commit bc0d63fde8f6d47cbd3044f9c5bfe1f114bfc559
Author: Leyuan <laura@gmail.com>
Date:   Wed Jul 23 17:32:09 2014 -0700

    CMakeLists changed by John

commit 93740e1623f794f8ed9877c4f0b2af399a836539
Author: Leyuan <laura@gmail.com>
Date:   Wed Jul 23 15:52:41 2014 -0700

    All tests passed on totoro(K20c), doc with no warnings

commit f442cefd87b95151f50bc7284915343dbb649c62
Author: Leyuan <laura@gmail.com>
Date:   Mon Jul 21 11:45:50 2014 -0700

    documentation changed no warnings

commit 13502942d0a903767835ca8c9827f3a55c6aed81
Author: Leyuan <laura@gmail.com>
Date:   Fri Jul 18 14:28:55 2014 -0700

    compression test passed

commit 792eeb32e618df379fce127f90545bbdd0c5429d
Author: Leyuan <laura@gmail.com>
Date:   Mon Jul 7 16:28:03 2014 -0700

    mtf bug solved

commit 315b5f332e4ebec15cab093ffa56ce41784735f8
Author: Leyuan <laura@gmail.com>
Date:   Tue Jun 10 12:03:50 2014 -0700

    solved mtf out of bounds bug but there are some gpu outputs in conflict with cpu outputs

commit 0da21feed1660302d51a6cc7ce31ab7c35c65c6f
Author: Leyuan <laura@gmail.com>
Date:   Sun Jun 8 15:03:00 2014 -0700

    bwt_test passed, mtf has bugs, compression won't pass

commit 92869bd7c51bbc5142038a9a22744077f37857fb
Author: Leyuan <laura@gmail.com>
Date:   Sun Jun 8 13:13:02 2014 -0700

    suffix array added to bwt, bwt test file re-write, bwt test passed but there's cudaFree error for suffix array plan

commit 5c5d6b58b394817cfd7d123d874d966591744059
Merge: 42f31c0 efa2e61
Author: Leyuan <laura@gmail.com>
Date:   Thu Jun 5 19:37:31 2014 -0700

    merging from Edmund's code review

commit 42f31c063145c9f0b373449a07fc39d84dc3e3ed
Author: Leyuan <laura@gmail.com>
Date:   Thu Jun 5 17:41:55 2014 -0700

    sa added to bwt some comments changed

commit efa2e6169676f176415700692f508de8e25577b6
Author: Edmund Yan <edmundhyan@gmail.com>
Date:   Wed Jun 4 20:11:14 2014 -0700

    Code review with comments.  Mostly indents and fixing a bad merge for
    stringsort

commit b1d9ae0aa541f97cd9ea079327c55b047ee1bc8e
Merge: 33e7ae2 4f22044
Author: Leyuan <laura@gmail.com>
Date:   Tue Jun 3 16:41:32 2014 -0700

    merge cudpp_plan for suffix array into branch 2.2

commit 4f2204499e3a900b3eef9c6aed9c08ec666439e9
Author: Leyuan <laura@gmail.com>
Date:   Tue Jun 3 15:15:21 2014 -0700

    Cherry-picking line endings commit to suffix_array

commit 0befc2175432bbd8aa2a2e78c067fd843b3d8115
Author: Edmund Yan <edmundhyan@gmail.com>
Date:   Tue Jan 21 15:47:34 2014 -0800

    Cherry-picking line endings commit to suffix_array

    Adding gitattribute

commit 6d6b1f71fb05c4a5b4e6d32f61d43771b412fdb2
Author: Leyuan <laura@gmail.com>
Date:   Mon Jun 2 09:28:01 2014 -0700

    Documentation for suffix array added and no warn in doxygen for suffix array

commit 8d70e34ac2d9140e3983553a58ed00ac2ea20f81
Author: Leyuan <laura@gmail.com>
Date:   Sat May 31 16:03:00 2014 -0700

    All tests passed

commit 230ae8df95c22d34b5445d4476341adcd1b37295
Author: Leyuan <laura@gmail.com>
Date:   Wed May 28 21:43:02 2014 -0700

    cpu_sa added combine skew and sa to sa

commit 507c103254f52661577d4d5f6de44d67e782be55
Author: Leyuan <laura@gmail.com>
Date:   Tue May 27 15:10:40 2014 -0700

    simpleCUDPP test passed

commit 9db3d956ee9aabdabc10c73e4639165cbf1d1fbf
Author: Leyuan <laura@gmail.com>
Date:   Tue May 27 14:23:14 2014 -0700

    compiled

commit a3e9e0d73437db28866684914afa7e7d41fd3ece
Author: Edmund Yan <edmundhyan@gmail.com>
Date:   Mon May 26 23:05:13 2014 -0700

    Fixing the submodules url.  Should work for https clones now.

commit 7bbe13eb9bb15a9adaa64f2c0d79f9ac6514eafb
Author: Leyuan <laura@gmail.com>
Date:   Fri May 23 22:02:31 2014 -0700

    test code added

commit 41a57dbb43d591b8462cad3af5c431bba7a77727
Author: Leyuan <laura@gmail.com>
Date:   Tue May 20 01:29:38 2014 -0700

    ScanInc added

commit 2d6e3edb51f2e92444ac6cc4fbc14cca4517a1cf
Author: Leyuan <laura@gmail.com>
Date:   Mon May 19 17:03:12 2014 -0700

    delete some files

commit 232b2236c602bf3d76ea8d95798f55a96e4fb386
Author: Leyuan <laura@gmail.com>
Date:   Mon May 19 16:58:08 2014 -0700

    added some files for skew

commit 3252275ab676bf7adf3ce91f75da88d198284675
Author: Edmund Yan <edmundhyan@gmail.com>
Date:   Mon May 19 16:20:46 2014 -0700

    Removing cmake files from repo.

commit 5d9a4eb6cc014ebc9ab2a94a10f9a5151eda7f60
Author: Leyuan <laura@gmail.com>
Date:   Mon May 19 01:27:23 2014 -0700

    compiled and tested SA

commit ddf8c2ec8ac9c44d34e9615496faad44acaa68ed
Author: Leyuan <laura@gmail.com>
Date:   Mon May 19 01:22:03 2014 -0700

    add suffix array to cudppPlan, instead of malloc memory in each recursive iteration, malloc one whole piece of memory in CUDPPSkewPlan and access based on certain pattern

commit 96e7ca62543b6406264a3d0d5fe4cf3aab3e8b74
Merge: 389352a 9bc9c4e
Author: Laurawly <laurawly@gmail.com>
Date:   Mon May 12 19:38:39 2014 -0700

    Merge pull request #134 from edmundyan/suffix_array

    Creating git submodules of cub and mgpu

commit 9bc9c4e43a4462890e73df9eff124ab7f3e70048
Author: Edmund Yan <edmundhyan@gmail.com>
Date:   Mon May 12 19:09:35 2014 -0700

    Creating git submodules of cub and mgpu

commit 389352af83d3e23eb2dbd101f90da7c99fc50be1
Author: Leyuan <laura@gmail.com>
Date:   Thu May 8 17:46:26 2014 -0700

    updated suffix_array from Owensgroup_suffix_array

commit d203e6e1aaf6d2f59c626eeb665f8aed94267692
Author: Leyuan <laura@gmail.com>
Date:   Sat Jan 18 00:00:54 2014 -0800

    speed up to deal with data as large as 100MB

commit 5bc9f0e219ff30d5f42618c2f05c3f5adde90f14
Author: Leyuan <laura@gmail.com>
Date:   Fri Jan 17 12:57:12 2014 -0800

    sa_gpu speed up

commit f5bdf6596c01882eba93cc90e5208bce44c5e233
Author: Leyuan <laura@gmail.com>
Date:   Fri Nov 8 13:11:41 2013 -0800

    sa added

commit 1b722729c076dd949d34edeeb0f5ab5c0bd72ac6
Author: Leyuan <laura@gmail.com>
Date:   Tue Oct 29 12:05:41 2013 -0700

    add sa

    add sa]

commit 7dd6379bb7776235cb2afc390cc39f7d53a70104
Author: Leyuan <laura@gmail.com>
Date:   Tue Oct 29 11:55:51 2013 -0700

    Remved sa

commit 7796e1e7c6de0e3232d68c03c19d6632c3a3e10a
Author: Leyuan <laura@gmail.com>
Date:   Fri Oct 25 16:19:35 2013 -0700

    uploading

commit 60bfc21ccacbde6aaa297ec134dfd90836d8f79b
Author: Leyuan <laura@gmail.com>
Date:   Fri Oct 25 16:17:01 2013 -0700

    add sa

commit c06062ae334f11ae9d272931614bc5284b125afe
Author: Leyuan <laura@gmail.com>
Date:   Fri Oct 25 16:07:13 2013 -0700

    remove the lib

commit a8fdb635304df3dafaabc51b076dcdf2ceb63353
Author: Leyuan <laurawly@gmail.com>
Date:   Thu Oct 24 19:01:18 2013 -0700

    add suffix array
Merge branch 'master' of github.com:cudpp/cudpp

Conflicts:
	doc/changelog.txt
	src/cudpp/CMakeLists.txt
	src/cudpp_hash/CMakeLists.txt