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# Documentation | ||
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### Links | ||
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- [Download datasets](download-datasets.md) | ||
- [Compile the project](compile-project.md) | ||
- [Run speedup analysis notebooks](./speedup_analysis) |
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| Executables | Description | | ||
|:------------|:--------------------------------------| | ||
| `bwtzip` | Original sequential version of bwtzip | | ||
| `bwtunzip` | Decompressor | | ||
| `pbwtzip` | Parallel version (3-stage pipeline) | | ||
| `pbwtzip2` | Parallel version (2-stage pipeline) | | ||
| `tests` | Test to check pbwtzip and pbwtzip2 | | ||
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# Compile project | ||
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## Debug build | ||
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Fast way: | ||
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```bash | ||
$ chmod +x ./script/* | ||
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$ ./script/build_debug.sh | ||
``` | ||
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Manually: | ||
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```bash | ||
$ mkdir cmake-build-debug | ||
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$ cd cmake-build-debug | ||
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$ cmake -DCMAKE_BUILD_TYPE=Debug .. | ||
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$ make -j4 | ||
``` | ||
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## Release build | ||
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Fast way: | ||
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```bash | ||
$ chmod +x ./script/* | ||
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$ ./script/build_release.sh | ||
``` | ||
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Manually: | ||
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```bash | ||
$ mkdir cmake-build-release | ||
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$ cd cmake-build-release | ||
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$ cmake -DCMAKE_BUILD_TYPE=Release .. | ||
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$ make -j4 | ||
``` | ||
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# Speedup analysis of pbwtzip and pbwtzip2 | ||
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- [pbwtzip_speedup_analysis.ipynb](./pbwtzip_speedup_analysis.ipynb) | ||
- [pbwtzip2_speedup_analysis.ipynb](./pbwtzip2_speedup_analysis.ipynb) | ||
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## Run the notebooks | ||
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1. Install Python virtualenv | ||
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```bash | ||
$ pip install virtualenv | ||
``` | ||
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2. Create a new virtual env inside the doc/speedup_analysis folder | ||
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```bash | ||
$ cd doc/speedup_analysis | ||
$ python3 -m venv ./venv | ||
``` | ||
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3. Install Python dependencies | ||
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```bash | ||
# activate virtual env | ||
$ source venv/bin/activate | ||
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# first upgrade pip | ||
(venv) $ pip install --upgrade pip | ||
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(venv) $ pip install --upgrade -r requirements.txt | ||
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# deactivate virtual env | ||
$ deactivate | ||
``` | ||
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4. Activate virtualenv and run Jupiter Notebook | ||
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```bash | ||
$ source venv/bin/activate | ||
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(venv) $ jupyter notebook . | ||
``` | ||
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A new page on your browser should open with Jupyter running. |