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Updated documentation

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caubet_m
2020-01-23 16:43:12 +01:00
parent 6169b7a8dc
commit b12846e82a
8 changed files with 551 additions and 292 deletions
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pages/merlin6/03 Job Submission/interactive-jobs.md
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@@ -1,8 +1,8 @@
---
title: Interactive Jobs
title: Running Interactive Jobs
#tags:
keywords: interactive, X11, X, srun
last_updated: 22 October 2019
last_updated: 23 January 2020
summary: "This document describes how to run interactive jobs as well as X based software."
sidebar: merlin6_sidebar
permalink: /merlin6/interactive-jobs.html
@@ -11,7 +11,10 @@ permalink: /merlin6/interactive-jobs.html
## Running interactive jobs
There are two different ways for running interactive jobs in Slurm. This is possible by using
the ``srun`` or the ``salloc`` commands.
the ``salloc`` and ``srun`` commands:
* **``salloc``**: to obtain a Slurm job allocation (a set of nodes), execute command(s), and then release the allocation when the command is finished.
* **``srun``**: is used for running parallel tasks.
### srun
@@ -143,65 +146,9 @@ For other non officially supported graphical access (X11 forwarding):
* For Windows clients, please follow [{Accessing Merlin -> Accessing from Windows Clients}](/merlin6/connect-from-windows.html)
* For MacOS clients, please follow [{Accessing Merlin -> Accessing from MacOS Clients}](/merlin6/connect-from-macos.html)
#### Enable SSH Keys authentication
For running ``srun`` with **X11** support (``srun --x11``) , you need to setup RSA keys properly.
1. Generate the RSA keys as follows:
```bash
ssh-keygen -t rsa
```
You will be requested for an *optional* passphrase. Entering it, provides more security (if somebody steals your private key he will
need to know the passphrase, however every time you use RSA keys you will need to type it). Whether to set a passphrase or not is up
to the users.
2. Add the public key to the ``~/.ssh/authorized_keys`` file
```bash
cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
```
3. Ensure that ``~/.ssh/authorized_keys`` has proper permissions:
```bash
chmod 600 ~/.ssh/authorized_keys
```
<details>
<summary>[Show 'ssh-keygen' example]: Generate RSA keys with default key filenames</summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-l-001 .ssh]$ ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter file in which to save the key (/psi/home/caubet_m/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /psi/home/caubet_m/.ssh/id_rsa.
Your public key has been saved in /psi/home/caubet_m/.ssh/id_rsa.pub.
The key fingerprint is:
SHA256:AMvGhBWxXs1MXHvwTpvXCOpjUZgy30E+5V38bcj4k2I caubet_m@merlin-l-001.psi.ch
The key's randomart image is:
+---[RSA 2048]----+
| o*o ...o . ...|
| .+ + =. O o .o|
| * o * + Xo..+|
| o . . + B.*oo+|
| . S + =.oo.|
| . .E.+ |
| +. . . |
| . . |
| |
+----[SHA256]-----+
(base) [caubet_m@merlin-l-001 .ssh]$ cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
(base) [caubet_m@merlin-l-001 .ssh]$ chmod 600 ~/.ssh/authorized_keys
</pre>
</details>
### 'srun' with x11 support
Once RSA keys are setup, you can run any windows based application. For that, you need to
Merlin5 and Merlin6 clusters allow running any windows based applications. For that, you need to
add the option ``--x11`` to the ``srun`` command. In example:
```bash
@@ -243,7 +190,7 @@ exit
### 'salloc' with x11 support
Once RSA keys are setup, you can run any windows based application. For that, you need to
**Merlin5** and **Merlin6** clusters allow running any windows based applications. For that, you need to
add the option ``--x11`` to the ``salloc`` command. In example:
```bash