# VTC (Voice Type Classifier)

{% hint style="warning" %}
Wav files must be already renamed to "AB\_XXX\_YYY.wav" before you start.
{% endhint %}

{% hint style="info" %}
This page is outdated as it was originally written for usage at Duke. I (Kien) am currently working on changing this to the FASRC clusters at Harvard, but the general instructions is still useful.
{% endhint %}

## Prerequisites:

* You have [set up](https://gitbook.bergelsonlab.com/archive/duke-archive/duke-computing-cluster-dcc/..#setup) the connection to the Duke Computing Cluster (DCC). This will require the involvement of Elika so budget your time accordingly.
* On your computer
  * You have a working Python installation with [blabpy](https://gitbook.bergelsonlab.com/data-pipeline/code#blabpy) installed and updated (>=0.15.0). Check with `pip show blabpy`.
* On cluster (connect with `ssh <netid>@dcc-login.oit.duke.edu`)
  * Check that `/hpc/group/bergelsonlab/VTC/VTC_repo` exists and isn't empty. If the folder doesn't exist or it's empty, clone the VTC [repo](https://github.com/MarvinLvn/voice-type-classifier) into that location

{% code lineNumbers="true" %}

````
  ```shell
  cd /hpc/group/bergelsonlab/VTC
  git clone --recurse-submodules https://github.com/MarvinLvn/voice_type_classifier.git VTC_repo
  ```
  
````

{% endcode %}

* Check that you have a conda enironment called "pyannote":

  <pre class="language-shell" data-line-numbers><code class="lang-shell"><strong>conda activate pyannote
  </strong></code></pre>

  If it doesn't exist, create it and check again:

  <pre class="language-shell" data-line-numbers><code class="lang-shell">cd /hpc/group/bergelsonlab/VTC/VTC_repo
  srun --mem=16G --pty bash -i
  # wait until a prompt appears
  <strong>conda env create -f vtc.yml
  </strong>exit
  conda activate pyannote
  </code></pre>
* Make sure you have `sox` installed (check with `which sox`). If you don't, run

{% code lineNumbers="true" %}

````
  ```shell
  conda install -c conda-forge sox
  ```
  
````

{% endcode %}

## General steps

1. Copy wav file(s) to the cluster from your computer's shell. It is necessary because the cluster doesn't have access to PN-OPUS. Use FileZilla or `scp`, see [#copying-files](https://gitbook.bergelsonlab.com/archive/duke-archive/duke-computing-cluster-dcc/..#copying-files "mention")
2. Connect to the cluster in the terminal. Run VTC. Delete wavs, disconnect.
3. Copy `all.rttm` file (VTC output) back to your computer and run a function that will distribute its contents into the individual subjets' folder.

## Detailed version

* Open two terminal windows. Connect to the cluster in one of them:

{% code lineNumbers="true" %}

````
```shell
ssh <netid>@dcc-login.oit.duke.edu
```
````

{% endcode %}

* On the terminal window that is connected to the cluster:
  * Create a **new** folder under `/hpc/group/bergelsonlab/VTC/wavs`

    <pre class="language-shell" data-line-numbers><code class="lang-shell">vtc_dir=/hpc/group/bergelsonlab/VTC
    <strong>wav_dir=$vtc_dir/wavs/&#x3C;my-new-folder>
    </strong><strong>mkdir -p $wav_dir
    </strong></code></pre>

    We'll use `wav_dir` later on, so do define this variable. It's better to create a unique folder each time you do this process.
* On your terminal window that is still local to your computer:
  * Copy the wav files to `wav_dir`. Use FileZilla (by dragging from pn-opus and dropping into the new wav\_dir you just made) or `scp`, see [#copying-files](https://gitbook.bergelsonlab.com/archive/duke-archive/duke-computing-cluster-dcc/..#copying-files "mention")
* On the terminal window that is connected to the cluster:
  1. Activate conda environment "pyannote": `conda activate pyannote`
  2. Check that all the files *are* wav files sampled at 16 KHz:

{% code lineNumbers="true" %}

````
  ```shell
  soxi -t $(find "$wav_dir" -type f)  # file types
  soxi -r $(find "$wav_dir" -type f)  # sampling rate
  ```
  
````

{% endcode %}

3. Change into the `VTC_repo` folder with

   <pre class="language-shell" data-line-numbers><code class="lang-shell"><strong>cd $vtc_dir/VTC_repo
   </strong></code></pre>
4. Switch to a gpu-enabled "computer":

{% code lineNumbers="true" %}

````
  ```shell
  srun -p gpu-common --gres=gpu:1 --mem=32G -c 8 --pty bash -i
  ```
  
````

{% endcode %}

```
  Check that it worked:

  1. Wait for the following to appear (the number will be different):\
     `srun: job 19332600 has been allocated resources`
  2. Check that your prompt now ends with `<net-id>@dcc-core-gpu-<x>` (where `<x>` is some number)
  3. Check that your prompt still starts with `(pyannote)` If it doesn't, activate `pyannote` again with `conda activate pyannote`
  4.  You may also need to remind the cluster of your previously set variables. If you get an "access denied"/ no such directory error when you try to run VTC, rerun these two commands prior to setting the error log and output log variables in the next step:

      <pre><code><strong>vtc_dir=/hpc/group/bergelsonlab/VTC
      </strong><strong>wav_dir=$vtc_dir/wavs/&#x3C;my-new-folder>
      </strong></code></pre>
```

5\. Start VTC and wait (\~15 minutes per file but can vary a lot):

{% code lineNumbers="true" %}

````
  ```shell
  error_log=$wav_dir/error.log
  output_log=$wav_dir/output.log
  ./apply.sh $wav_dir --device=gpu 2> $error_log 1> $output_log &
  ```
  
````

{% endcode %}

6. Check that everything went well. Either open `error.log` and `output.log` files in FileZilla (right click and click "View or edit"-- don't double click which may be your instinct) or use `less` on `$error_log` and `$output_log` to view the log files in the terminal window (run `less $error_log` to open, press \[Q] to exit the viewer).\
   Here is what your `error.log` should look like:

   <pre><code><strong>Test set: &#x3C;N>it [07:06, 426.16s/it]
   </strong>Test set: &#x3C;N>it [01:14, 74.71s/it]
   Test set: &#x3C;N>it [01:14, 74.95s/it]
   Test set: &#x3C;N>it [01:15, 75.11s/it]
   Test set: &#x3C;N>it [01:15, 75.93s/it]
   Test set: &#x3C;N>it [01:15, 75.00s/it]
   </code></pre>

   Where \<N> is the number of files you were processing. And here is `output.log`:

   ```
   Creating config for pyannote.
   Done creating config for pyannote. 
   Took 3430 sec on <wav_dir>.
   ```

   :warning: <mark style="color:green;background-color:red;">Continue only if all is good!</mark> :warning:
7. Once the job is finished and if there were no errors:
   1. Copy the output to `$wav_dir`.

{% code lineNumbers="true" %}

````
     ```shell
     wav_dir_name=$(basename $wav_dir)
     vtc_output_dir=$vtc_dir/VTC_repo/output_voice_type_classifier
     cp -a $vtc_output_dir/$wav_dir_name/. $wav_dir
     ```
     
````

{% endcode %}

```
 2.  Delete wav files from DCC:

     
```

{% code lineNumbers="true" %}

````
     ```shell
     rm $wav_dir/*.wav
     ```
     
````

{% endcode %}

* Back on your computer:
  1. Make an empty folder and copy `all.rttm` file from `wav_dir` to it (use `scp` or [FileZilla](https://gitbook.bergelsonlab.com/archive/duke-archive/duke-computing-cluster-dcc/filezilla))
  2. `cd` into that folder in the terminal.
  3. Run `vihi distribute-all-rttm` from your command line (this is a function in blabpy) and check the output.

## In short

* Set a few variables and make a new folder on the cluster.

{% hint style="warning" %}
If not on a Duke computer: substitute your Net ID for `$USER` in the first line.
{% endhint %}

<pre class="language-shell" data-line-numbers><code class="lang-shell">net_id=$USER
ssh $net_id@dcc-login.oit.duke.edu
<strong>vtc_dir=/hpc/group/bergelsonlab/VTC
</strong>wav_dir=$vtc_dir/wavs/$(date +%Y-%m-%d)_$net_id
mkdir $wav_dir
echo "Copy wav files to:"
echo $wav_dir
</code></pre>

* Copy the wav files (<mark style="background-color:orange;">with VIHI-formatted names!</mark>) to the folder printed (use `scp`/FileZilla).
* Check filetypes (must be "wav") and sampling rates (must be 16000)

{% code lineNumbers="true" %}

```shell
conda activate pyannote
soxi -t $(find "$wav_dir" -type f)  # file types must be "wav"
soxi -r $(find "$wav_dir" -type f)  # sampling rates must be 16000
```

{% endcode %}

* Start VTC

{% code lineNumbers="true" %}

```shell
error_log=$wav_dir/error.log
output_log=$wav_dir/output.log
cd $vtc_dir/VTC_repo
srun -p gpu-common --gres=gpu:1 --mem=32G -c 8 --pty bash -i
# wait for allocation
./apply.sh $wav_dir --device=gpu 2> $error_log 1> $output_log &
```

{% endcode %}

* After \~15 minutes per file, check `error.log` (should have six rows with "\<N>it") and `output.log` (look for "Took X sec ...").
* If all is good, copy the output and delete the wavs:

{% code lineNumbers="true" %}

```shell
wav_dir_name=$(basename $wav_dir)
vtc_output_dir=$vtc_dir/VTC_repo/output_voice_type_classifier
cp -a $vtc_output_dir/$wav_dir_name/. $wav_dir
rm $wav_dir/*.wav
```

{% endcode %}

* Copy (`scp`/FileZilla) `all.rttm` from `wav_dir` to a new folder on your local computer (not on PN-OPUS) and `cd` into that folder.
* Run `vihi distribute-all-rttm`.

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