7. Using Taito-shell for running interactive jobs in Taito

7.1 What is Taito-shell

The Taito-shell environment is intended for interactive use of scientific applications maintained by CSC, serial jobs and usage of graphical application interfaces. The Taito-shell computing environment is part of the Taito cluster.

Taito-shell emulates normal application server like behavior. For the user, it appears very much like a normal Linux server: you can log in and run applications interactively with Linux commands. Taito-shell uses the same the disk environment, software stack and module system as the normal Taito cluster. The difference to the Taito login nodes is, that Taito-shell does not have the 1 hour time limit for jobs, that are executed interactively. Instead, a job started in Taito-shell can run as long as the Taito-shell session remains open.

From the technical point of view, Taito-shell is an oversubscribed interactive batch queue on the Taito super cluster. When you log in to taito-shell.csc.fi, you are automatically connected to an interactive batch job running in this unlimited partition.

Using this kind or approach has the following advantages over a traditional application server:

  • Taito-shell uses the same resources as Taito, like home directory, $WRKDIR directory and installed software. You can easily switch between interactive working and batch jobs based working.
  • Better scalability: In case of high demand, more Taito nodes can be assigned to Taito-shell and vice versa.
  • Improved load balancing: The number of users per Taito-shell node can be better controlled.

Taito-shell is, however, not a separate Linux server and it has two important exceptions compared to traditional Linux application servers:

  • No direct node access. "ssh taito-shell.csc.fi" logs in to the next free Taito-shell node on Taito. You cannot determine on which node you will end up. We are aware that specific node access is sometimes necessary, please see the FAQ section below on how to achieve this.
  • screen/nohup does not work in Taito-shell. Logging out of Taito-shell kills all processes of the user in question, also background jobs. For long running jobs you can use Taito's batch job system, or, for smaller scale jobs, consult the FAQ.

The features of Taito-Shell environment in a nutshell:

  • Direct login with the address: taito-shell.csc.fi
  • Offers no-queuing interactive use of software installed on Taito
  • Uses the same file system and network shares as Taito.
  • Enables seamless switching between quick interactive use and batch jobs.
  • Computing capacity up to 4 cores per user
  • Shared memory of up to 128 GB per user

Jobs that utilize more than 4 cores or that require more than 128 GB memory usage should be executed as batch jobs in Taito or in Sisu.

7.2 Using Taito-shell

7.2.1 Obtaining a user id

If you have a user account for Taito, you can use it to login to Taito-shell too.

If you are a new customer for CSC's computing and application software services, see first instructions for new customers below. The application procedure depends on whether your are an academic user or not.

https://research.csc.fi/csc-guide-getting-access-to-cscs-resources

New CSC users get access to Taito and Taito-Shell per default. After registration, users not assigned to any project, get a small default quota ( 5000 bu) to run small jobs on Taito-shell.

7.2.2 Logging in

There are two ways to login:shell login (ssh, Putty etc.)  and NoMachine for graphical logins.

7.2.2.1 Logging in via ssh

To log in, normally one has to first access a local workstation (at university or some other site on the Internet) and then use an SSH program to connect to Taito-shell (taito-shell.csc.fi) with your CSC user_id:

ssh -X csc_user_id@taito-shell.csc.fi

After you have provided your password, you will see a prompt similar to the one below, the number might be different:

[user_id@c305 ~]

Taito-shell is now ready to execute your commands. For more information on connecting to CSC's servers via SSH please consult the general guide on how to use SSH at CSC.

7.2.2.2. Logging in via NoMachine

Graphical logins to Taito-shell are possible via NoMachine. You need to download and install a NoMachine client and configure it to use the server nxkajaani.csc.fi. Please consult the NoMachine documentation on how to get graphical access. To start Taito-Shell in NoMachine, right click with the mouse in the Desktop area, choose Taito-shell from the pull-down menu, add your password, and you are logged in. You can now type in the commands to launch the software you want to use, eg. for Rstudio commands would be

module load r-env
module load rstudio
rstudio

 

7.2.3 Submitting batch jobs from Taito-shell

Taito-shell.csc.fi environment is configured for running commands interactively. You can submit batch jobs from Taito-shell to taito.csc.fi cluster. However to do that, you need to add definition -M csc either top the batch job commands or to the #SBATCH lines of the batch job files.

For example to submit a batch job command you should use command:

sbatch -M csc batch_job_file.sh

In the same way, the status of the jobs , running in Taito cluster, can be checked with command

squeue -M csc -l

(Running squeue command without -M csc would list the current taito-shell.csc.fi sessions)

 

 

7.3 Taito-shell FAQ

How do I start long-running jobs in Taito-shell?

Taito's batch job system is the preferred way of starting long running jobs. It gives you guaranteed CPU and memory access. However, if you have long running interactive jobs that you want to run...

My job runs out of memory in taito-shell.csc.fi

In taito-shell.csc.fi each user is allowed to use up to 128 GB of memory. However, the memory is over-subscribed and there is no session specific memory allocations (like in normal batch jobs)....

I have already a taito-shell session open and would like to open another session on the same node. How?

If you need to open a second shell on the same taito-shell node, for example to check the node's load or memory usage while your process is already running, here's how you do it: Take note...

How do I reserve a large memory node for interactive use on Taito?

If you need significantly more memory than the 128 GB provided on Taito-shell nodes, please proceed as follows: Login to Taito: ssh -X taito.csc.fi (-X being optional) Reserve a node with the...