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Interactive Jobs	interactive, X11, X, srun	22 October 2019	This document describes how to run interactive jobs as well as X based software.	merlin6_sidebar	/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.

srun

Is run is used to run parallel jobs in the batch system. It can be used within a batch script (which can be run with sbatch), or within a job allocation (which can be run with salloc). Also, it can be used as a direct command (in example, from the login nodes).

When used inside a batch script or during a job allocation, srun is constricted to the amount of resources allocated by the sbatch/salloc commands. In sbatch, usually these resources are defined inside the batch script with the format #SBATCH <option>=<value>. In other words, if you define in your batch script or allocation 88 tasks (and 1 thread / core) and 2 nodes, srun is constricted to these amount of resources (you can use less, but never exceed those limits).

When used from the login node, usually is used to run a specific command or software in an interactive way. srun is a blocking process (it will block bash prompt until the srun command finishes, unless you run it in background with &). This can be very useful to run interactive software which pops up a Window and then submits jobs or run sub-tasks in the background (in example, Relion, cisTEM, etc.)

Refer to man srun for exploring all possible options for that command.

[Show 'srun' example]: Running 'hostname' command on 3 nodes, using 2 cores (1 task/core) per node

(base) [caubet_m@merlin-l-001 ~]$ srun --clusters=merlin6 --ntasks=6 --ntasks-per-node=2 --nodes=3 hostname
srun: job 135088230 queued and waiting for resources
srun: job 135088230 has been allocated resources
merlin-c-102.psi.ch
merlin-c-102.psi.ch
merlin-c-101.psi.ch
merlin-c-101.psi.ch
merlin-c-103.psi.ch
merlin-c-103.psi.ch

salloc

salloc is used to obtain a Slurm job allocation (a set of nodes). Once job is allocated, users are able to execute interactive command(s). Once finished (exit or Ctrl+D), the allocation is released.

Please, not that salloc is by default a blocking process, and once the resources get allocated user gets the bash prompt back. Once prompt is back, a new bash shell is created, and user can run any srun commands, which will run tasks on the allocated resources. Once finished, exiting the bash shell will release the allocation.

[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node)

(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --ntasks=2 --nodes=2
salloc: Pending job allocation 135087844
salloc: job 135087844 queued and waiting for resources
salloc: job 135087844 has been allocated resources
salloc: Granted job allocation 135087844
(base) [caubet_m@merlin-l-001 ~]$ srun hostname
merlin-c-120.psi.ch
merlin-c-119.psi.ch
(base) [caubet_m@merlin-c-119 ~]$ exit
logout
Connection to merlin-c-119 closed.
(base) [caubet_m@merlin-l-001 ~]$ exit
exit
salloc: Relinquishing job allocation 135087844

Running interactive jobs with X11 support

Requirements

Graphical access

NoMachine is the official supported service for graphical access in the Merlin cluster. This service is running on the login nodes. Check the document {Accessing Merlin -> NoMachine} for details about how to connect to the NoMachine service in the Merlin cluster.

For other non officially supported graphical access (X11 forwarding):

• For Linux clients, please follow {Accessing Merlin -> Accessing from Linux Clients}
• For Windows clients, please follow {Accessing Merlin -> Accessing from Windows Clients}
• For MacOS clients, please follow {Accessing Merlin -> Accessing from MacOS Clients}

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:

   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

   cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys 
   

3. Ensure that ~/.ssh/authorized_keys has proper permissions:

   chmod 600 ~/.ssh/authorized_keys
   

[Show 'ssh-keygen' example]: Generate RSA keys with default key filenames

(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

'srun' with x11 support

Once RSA keys are setup, you can run any windows based application. For that, you need to add the option --x11 to the srun command. In example:

srun --x11 xclock

will popup a X11 based clock.

In the same manner, you can create a bash shell with x11 support. For doing that, you need to add the option --pty to the srun --x11 command. Once resource is allocated, from there you can interactively run X11 and non-X11 based commands.

srun --x11 --pty bash

[Show 'srun' with X11 support examples]

(base) [caubet_m@merlin-l-001 ~]$ srun --x11 xclock
srun: job 135095591 queued and waiting for resources
srun: job 135095591 has been allocated resources
(base) [caubet_m@merlin-l-001 ~]$
(base) [caubet_m@merlin-l-001 ~]$ srun --x11 --pty bash
srun: job 135095592 queued and waiting for resources
srun: job 135095592 has been allocated resources
(base) [caubet_m@merlin-c-205 ~]$ xclock
(base) [caubet_m@merlin-c-205 ~]$ echo "This was an example"
This was an example
(base) [caubet_m@merlin-c-205 ~]$ exit
exit