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Update BULDING.md for the yi-src-multi #1

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b0c0bd4
Removed deprecated code from PipelineManager
WillianJunior Jun 15, 2016
91da898
Bug fixes
WillianJunior Jun 18, 2016
674a787
Bug fix
WillianJunior Jun 18, 2016
f8cc34f
Bug fix
WillianJunior Jun 18, 2016
70e68df
Bug fixes
WillianJunior Jun 20, 2016
b679c0f
Removed free on PìpelineComponentBase.cpp:46 due to SIGABRT. Memory c…
WillianJunior Jun 20, 2016
fbf1141
Still buggy code. Attempting to get the output id to retrieve the wor…
WillianJunior Jun 20, 2016
cbf7957
Output Argument on workflow generator now has updated id from the sta…
WillianJunior Jun 20, 2016
366637a
Bug Fix
WillianJunior Jun 21, 2016
e9a4f5f
Bug fix
WillianJunior Jun 25, 2016
7b9d1ac
Bug Fix:
WillianJunior Jul 13, 2016
77b2ae6
Bug Fix:
WillianJunior Jul 13, 2016
797b951
Expanded the PCB class to have a list of ReusableTask.
WillianJunior Aug 2, 2016
3a70395
Included fine-grain merging algorithm. Fine-grain merging algorithm s…
WillianJunior Aug 2, 2016
ad5ca2d
Segmentation now implements ReusableTask. All serialization
WillianJunior Aug 2, 2016
73dd542
Updated Segmentation constructor to generate the task desc list and a…
WillianJunior Aug 2, 2016
1d3e373
All base structure (so far) for task reuse implemented and tested.
WillianJunior Aug 4, 2016
dfa16e0
Bug fix: system wasn't working with more than a value for the same va…
WillianJunior Aug 4, 2016
ac3669c
Serialization bug fixed:
WillianJunior Aug 8, 2016
adc4d3a
Stage fine-grain merging partially working:
WillianJunior Aug 10, 2016
6f57bb8
Basic structure for task reuse now working:
WillianJunior Aug 10, 2016
0ba23a4
Task reuse structure implemented and working with one
WillianJunior Aug 17, 2016
cdf2512
Task reuse partially working:
WillianJunior Aug 17, 2016
9750998
Bug fix:
WillianJunior Aug 17, 2016
70c7a1a
Reimplemented Task merging. Now FGO is fully functional with naive me…
WillianJunior Aug 22, 2016
ec300f2
Task code generator implemented. Still need to do Stage generation.
WillianJunior Aug 30, 2016
80633e5
Source code generation implementation finished.
WillianJunior Aug 30, 2016
ba6ca30
Generated code working with any np value but still buggy:
WillianJunior Aug 31, 2016
6901fe3
Bug fix:
WillianJunior Sep 5, 2016
5768b82
Stoer-Wagner min-cut algorithm implemented.
WillianJunior Sep 7, 2016
62f0b28
Fixed cut weight calculation and namespace interface to min-cut module.
WillianJunior Sep 7, 2016
5f18a87
Integration of mincut with PipelineManager 50% complete.
WillianJunior Sep 8, 2016
c26d759
Mincut algorithm fully integrated and, as far as it was tested, working.
WillianJunior Sep 8, 2016
adf673d
Milenium bug fixed
WillianJunior Sep 8, 2016
a06bb55
Non-recursive version of new merge-cut algorithm.
WillianJunior Sep 13, 2016
ea3023c
Recursive version of merge-cut algorithm implemented and partially wo…
WillianJunior Sep 13, 2016
247b409
Getting rid of memory leaks.
WillianJunior Sep 13, 2016
39e6895
All memory leaks fixed. The execution part of the application, howeve…
WillianJunior Sep 14, 2016
1bb4958
Application fully working.
WillianJunior Sep 14, 2016
f5fc3f6
Recursive montecarlo implementation created.
WillianJunior Sep 14, 2016
552a224
Recursive Montecarlo algorithm implemented and tested.
WillianJunior Sep 14, 2016
5810c93
Changed intertask arguments to smart pointers in order to fix the mem…
WillianJunior Sep 19, 2016
b875411
Started new values input implementation.
WillianJunior Sep 19, 2016
1970df8
Dakota input file added and partial implementation on PipelineManager.
WillianJunior Sep 21, 2016
f4cbf75
Stage creation implemented. Still need to add interstage arguments.
WillianJunior Sep 22, 2016
65f9c73
Workflows generation almost complete:
WillianJunior Sep 23, 2016
aaa1b2e
The workflows are executing, but the manager is finishing before all …
WillianJunior Sep 24, 2016
77c9183
Bug Fixes:
WillianJunior Sep 26, 2016
6843928
Fixed np > 2 bug.
WillianJunior Sep 26, 2016
40aa440
Changed the format of the dakota input
WillianJunior Sep 26, 2016
5aa2b21
Fixed non-enforced task dependency bug:
WillianJunior Sep 26, 2016
74b43b5
Stage-task code generation:
WillianJunior Sep 26, 2016
e929216
Finished and tested the stage-task code generator.
WillianJunior Sep 26, 2016
071068a
Fixed the workflow outputs and added a file output to the fine grain …
WillianJunior Sep 26, 2016
8859fac
Fixed the missing stage on merge bug.
WillianJunior Sep 27, 2016
ac732b1
Used OpenMP to speed the merging part of the montecarlo recursive cut…
WillianJunior Sep 27, 2016
1078ccb
Fixed all (serious) memory leaks.
WillianJunior Sep 27, 2016
b0ee75a
Changed MPI_Init strategy
WillianJunior Sep 29, 2016
f7e1dcc
Added outputs for testing purposes.
WillianJunior Oct 7, 2016
71f8341
Fixed the test output files naming.
WillianJunior Oct 8, 2016
af4d732
Most severe memory leaks fixed.
WillianJunior Oct 10, 2016
3715b79
Merge branch 'FGO' of https://github.com/SBU-BMI/region-templates int…
WillianJunior Oct 10, 2016
3dc14d4
First implementation of reuse tree finished
WillianJunior Oct 11, 2016
e8dd98d
First reuse tree optimization (now ~30% reuse).
WillianJunior Oct 11, 2016
368d60a
Removed cout's form merging algorithm
WillianJunior Oct 11, 2016
e7bb37c
Implemented and tested the second pass of pruning operation.
WillianJunior Oct 12, 2016
fd94657
Fixed the application args input.
WillianJunior Oct 13, 2016
82b6558
Fixed application file outputs to ease testing.
WillianJunior Oct 13, 2016
44a0531
A new interface to access all FGO merging algorithms was created
WillianJunior Oct 13, 2016
7587c88
Reuse-tree merging now has the option to turn the double-prune optimi…
WillianJunior Oct 13, 2016
420d0b5
Added stage shuffling option.
WillianJunior Oct 18, 2016
20350c6
Added a 'no coarse grain merging' option.
WillianJunior Oct 18, 2016
981bc36
Added profiling cout's.
WillianJunior Feb 7, 2017
1858dad
Worker time profiler added to stdout.
WillianJunior Feb 21, 2017
2f8c595
Merge branch 'FGO-bucket-star' of github.com:SBU-BMI/region-templates…
WillianJunior Feb 21, 2017
9258b86
Dependency test.
WillianJunior Feb 21, 2017
30b704a
More manager profiling.
WillianJunior Feb 22, 2017
257d676
Removed unused cout's and started workflow-clustered stages generatio…
WillianJunior Apr 7, 2017
9162d65
Solved the '1 RT per pipeline' problem. Found out that the dependenci…
WillianJunior Apr 10, 2017
d108998
The dependency problem isn't really a problem. Just don't use cluster…
WillianJunior Apr 11, 2017
0e54b3a
Update BULDING.md for the yi-src-multi
Pedroagaponto Apr 17, 2017
4c9b25d
TaskSegmentation5 memory leak fixed.
WillianJunior Apr 19, 2017
acef0df
Fixed the Diff memory leak
WillianJunior Apr 20, 2017
672ad2b
Fixed Segmentation DDR2D memory leaks (updateDR would make new DDR2Ds…
WillianJunior Apr 21, 2017
050e76b
Some further memory leaks fixed on workflow generation.
WillianJunior Apr 21, 2017
eb6a7bf
Reworked the input agruments to something somewhat more professional.
WillianJunior Apr 26, 2017
844086f
Reworked the directory structure of FGO and cleaned some PipelineMana…
WillianJunior Apr 27, 2017
29f8eb7
Updated the stage generator to match the current needs and fixed a mi…
WillianJunior Apr 27, 2017
d9b5d25
Forgot to add the jsoncpp source and to update the generator makefile.
WillianJunior Apr 27, 2017
2ac70fb
Merge pull request #3 from SBU-BMI/FGO-bucket-star
scartezini Apr 27, 2017
fae0175
Merge remote-tracking branch 'sbu/master'
scartezini Mar 9, 2018
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21 changes: 15 additions & 6 deletions BUILDING.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@

Assuming:
- You have no previous dependency installed

This guide will go through each of these dependencies:
- ActiveHarmony [4.6.0](http://www.dyninst.org/sites/default/files/downloads/harmony/ah-4.6.0.tar.gz)
- OpenCV [2.4.9](http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/2.4.9/opencv-2.4.9.zip/download)
- InsightToolkit [4.11.0](https://sourceforge.net/projects/itk/files/itk/4.11/InsightToolkit-4.11.0.tar.gz/download)
Expand Down Expand Up @@ -67,7 +69,7 @@ inside `/opencv` folder
unzip opencv-2.4.9.zip
cd build
cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local ../opencv-2.4.9/
make
make -j$(nproc)
sudo make install
```

Expand All @@ -89,12 +91,13 @@ on the interface
- press `t` to toggle advanced mode
- turn on `BUILD_SHARED_LIBS`
- turn on `MODULE_ITKVideoBridgeOpenCV`
- turn on `Module_ITKReview`
- press `c` to configure
- press `g` to generate

then build
```
make
make -j$(nproc)
```

## Installing Nscale
Expand All @@ -121,13 +124,18 @@ on the interface

then build
```
make
make -j$(nproc)
```

NOTE: it may give errors of vars `NSCALE_VERSION_MAJOR` and `NSCALE_VERSION_MINOR`, press `e` to continue and ignore.

## Installing Yi's library

prerequisite
```
sudo apt install libopenslide-dev
sudo ln -s /usr/lib/x86_64-linux-gnu/libopenslide.so /usr/lib/libopenslide.so
```
inside `/workspace` folder
```
cp project/region-templates/runtime/regiontemplates/external-src/yi-src-multi.tar.gz ./libs/yi/
Expand All @@ -147,15 +155,16 @@ on the interface
- press `c` to configure
- press `e` to ignore errors and continue
- fill `ITK_DIR` to your `ITK` installation
- turn off `build_mainTileAndSegmentWSINuclei`
- turn on `build_mainTileAndSegmentWSINuclei`
- press `c` to configure
- fill `OpenSlide_INSTALLATION_PATH` with only `/usr`
- turn on `build_mainSegmentSmallImage`
- press `c` to configure
- press `g` to generate

then build
```
make
make -j$(nproc)
```

## Installing Active Harmony
Expand Down Expand Up @@ -232,5 +241,5 @@ on the interface

then build
```
make
make -j$(nproc)
```