04-Bash.Rmd

# BASH
On this section we will write some hints on the Bourne Again Shell (BASH), a command interpreter used in several *nix systems, such as Linux, Unix, MacOS and recently incorporated into Windows through PowerShell. This will be more of a collection of hints, and not substituting a full knowledge of BASH and the Operating System in which is running.

## Screen
Screen is a tool you can use to keep a ssh session run through BASH alive. Why it is useful(?):

1. When you have unreliable internet connections connections (ex.: Wifi, cellphone);
2. Power outages;
3. Your local machine freezes, or have any other issue, and your connection is killed;
4. Any random reason that blocks your local terminal to access the remote ssh session.

### How to use it
Some useful description is available in [this website](https://web.archive.org/web/20230606181644/https://www.networkworld.com/article/3441777/how-the-linux-screen-tool-can-save-your-tasks-and-your-sanity-if-ssh-is-interrupted.html), and on the app documentation. But you can proceed as follows:

### Creating a session
You create a new session, named _session_01_ as:

```{bash, eval=FALSE}
screen -S session_01
```

### See all available sessions
```{bash, eval=FALSE}
screen -ls
```

You probably will see something like this:
```
There are screens on:
        6617.session_00      (09/26/2019 04:35:30 PM)    (Detached)
        1946.session_01         (09/26/2019 02:51:50 PM)    (Detached)
2 Sockets in /run/screen/S-shs
```

### Reattach to a previously established session
Let's say you want to attach to _session_00_:
```{bash, eval=FALSE}
screen -r session_00
```

### Finishing a session
Let's say you want to finish _session_01_. You first enter in another session, and:
```{bash, eval=FALSE}
screen -XS 1946 quit
```

If the session you are aiming to finish is the last one, then:

* **ctrl + A**;
* **k**;
* and **y**.

## Watch
Watch is a program that runs commands using a clock. In our case, watch is kind
of useful when needing to monitor an application shell output. Common cases in HPC
are when you need to see updates in `nvidia-smi` or slurm `squeue` command.

The base syntax is:
```{bash, eval=FALSE}
watch -n XX command
```

In which:

* **XX** is the refresh rate in seconds;
* **command** is the bash command you want to refresh the output

### Slurm queue example
The base syntax is:
```{bash, eval=FALSE}
watch -n 5 squeue -u username
```

In which:

* **username** is the username in the slurm cluster;

### NVIDIA card output
The base syntax is:
```{bash, eval=FALSE}
watch -n 5 nvidia-smi
```

It refreshes every 5 seconds the running info from the NVIDIA card in the node (this will fail on CPU-only nodes)