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Once `oops` is compiled and installed, clone the `git` tree:
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```
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git clone https://forge.uvolante.org/code/salza.git
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mkdir -p salza/build && cd salza/build
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cmake -DCMAKE_BUILD_TYPE=Release ..
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make
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sudo make install
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```
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The last step can be replaced with building a Debian package (type: `cpack`) to be installed with `sudo dpkg -i salza-xxxxx.deb`.
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# Known issues
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`salza` eats a lot of memory. Launch it with the verbose option (`-v`) to monitor its behaviour.
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In case it is too slow, that may be because your machine had to free memory. A suggestion is to kill the process and launch it again.
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That proved useful in LXD containers where the guests do not have the same view of memory as the host.
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In any case, all strings have to fit in memory with their associated search structures.
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# Getting started
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```
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salza -h
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```
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# Reproducing the figures in the preprint
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... | ... | @@ -70,7 +89,7 @@ Download this Jupyter [notebook](https://cloud.uvolante.org/index.php/s/WtepD8fW |
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The NCD distance matrices are provided with the datasets.
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To compute the NSD matrices:
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1. make sure you have installed `drpt` (see above) ;
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1. make sure you have installed [`drpt`](https://forge.uvolante.org/code/drpt/wikis) ;
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2. download the script [compute-nxd-matrices](https://cloud.uvolante.org/index.php/s/gqPCRCKwFKwf887/download) ;
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3. update the variable `DATASET` in `compute-nxd-matrices` with the path to the datasets ;
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4. run the script on the four datasets:
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... | ... | |