rapids/docs/setup/execution.md

# Execution

After you have [installed](../installation) and [configured](../configuration) RAPIDS, use the following command to execute it.

```bash
./rapids -j1
```

!!! done "Ready to extract behavioral features"
    If you are ready to extract features head over to the [Behavioral Features Introduction](../../features/feature-introduction/)

!!! hint "We wrap Snakemake" 
    The script `#!bash ./rapids` is a wrapper around Snakemake so you can pass any parameters that Snakemake accepts (e.g. `-j1`). 
    
!!! hint "Updating RAPIDS output after modifying `config.yaml`"
    Any changes to the `config.yaml` file will be applied automatically and only the relevant files will be updated. This means that after modifying the features list for `PHONE_MESSAGE` for example, RAPIDS will execute the script that computes `MESSAGES` features and update its output file.

!!! hint "Multi-core"
    You can run RAPIDS over multiple cores by modifying the `-j` argument (e.g. use `-j8` to use 8 cores). **However**, take into account that this means multiple sensor datasets for different participants will be loaded in memory at the same time. If RAPIDS crashes because it ran out of memory reduce the number of cores and try again.

    As reference, we have run RAPIDS over 12 cores and 32 Gb of RAM without problems for a study with 200 participants with 14 days of low-frequency smartphone data (no accelerometer, gyroscope, or magnetometer).

!!! hint "Deleting RAPIDS output"
    If you  want to delete all the output files RAPIDS produces you can execute the following command:

    ```bash
    ./rapids -j1 --delete-all-output
    ```

!!! hint "Forcing a complete rerun"
    If you want to update your raw data or rerun the whole pipeline from scratch run the following commands:

    ```bash
    ./rapids -j1 --delete-all-output
    ./rapids -j1
    ```
Update minimal workflow example docs 2020-11-04 19:27:58 +01:00			`# Execution`

Links and CI updates to work with mike versioning 2020-11-09 19:34:02 +01:00			`After you have [installed](../installation) and [configured](../configuration) RAPIDS, use the following command to execute it.`
Update minimal workflow example docs 2020-11-04 19:27:58 +01:00
			```bash
			`./rapids -j1`
			```

Separate device data configuration and update docs 2020-11-26 01:42:11 +01:00			`!!! done "Ready to extract behavioral features"`
			`If you are ready to extract features head over to the [Behavioral Features Introduction](../../features/feature-introduction/)`

Update docs to support Empatica 2021-02-21 23:30:30 +01:00			`!!! hint "We wrap Snakemake"`
Update minimal workflow example docs 2020-11-04 19:27:58 +01:00			The script `#!bash ./rapids` is a wrapper around Snakemake so you can pass any parameters that Snakemake accepts (e.g. `-j1`).

Add FAQ 2020-11-04 22:41:39 +01:00			!!! hint "Updating RAPIDS output after modifying `config.yaml`"
Update docs to support Empatica 2021-02-21 23:30:30 +01:00			Any changes to the `config.yaml` file will be applied automatically and only the relevant files will be updated. This means that after modifying the features list for `PHONE_MESSAGE` for example, RAPIDS will execute the script that computes `MESSAGES` features and update its output file.
Update minimal workflow example docs 2020-11-04 19:27:58 +01:00
			`!!! hint "Multi-core"`
Update docs to support Empatica 2021-02-21 23:30:30 +01:00			You can run RAPIDS over multiple cores by modifying the `-j` argument (e.g. use `-j8` to use 8 cores). However, take into account that this means multiple sensor datasets for different participants will be loaded in memory at the same time. If RAPIDS crashes because it ran out of memory reduce the number of cores and try again.
Update minimal workflow example docs 2020-11-04 19:27:58 +01:00
Add FAQ 2020-11-04 22:41:39 +01:00			`As reference, we have run RAPIDS over 12 cores and 32 Gb of RAM without problems for a study with 200 participants with 14 days of low-frequency smartphone data (no accelerometer, gyroscope, or magnetometer).`

Update docs to support Empatica 2021-02-21 23:30:30 +01:00			`!!! hint "Deleting RAPIDS output"`
			`If you want to delete all the output files RAPIDS produces you can execute the following command:`
Add FAQ 2020-11-04 22:41:39 +01:00
			```bash
Update docs to support Empatica 2021-02-21 23:30:30 +01:00			`./rapids -j1 --delete-all-output`
Add FAQ 2020-11-04 22:41:39 +01:00			```

Update docs to support Empatica 2021-02-21 23:30:30 +01:00			`!!! hint "Forcing a complete rerun"`
			`If you want to update your raw data or rerun the whole pipeline from scratch run the following commands:`
Add FAQ 2020-11-04 22:41:39 +01:00
			```bash
Refactor day segments to time segments 2020-12-03 00:41:03 +01:00			`./rapids -j1 --delete-all-output`
Update docs to support Empatica 2021-02-21 23:30:30 +01:00			`./rapids -j1`
			```