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This is a series of exercises that will walk you through the basic tasks as you get on board the Atos HPCF.

Prerequisites

In order to follow this tutorial, these are the prerequisites you must fulfil before starting:

  • You must have a valid ECMWF account with privileges to access HPCF or ECS. If you only have access to ECS, you may need to skip certain exercises involving HPCF.
  • You must have 2 Factor Authentication enabled with TOTP.
  • You must be able to connect with at least one of the following methods:

Logging into Atos HPCF and ECS

Reference: HPC2020: How to connect

First of all, let's try to connect to the computing services via SSH:

  1. Access the default login node of the ATOS HPCF or ECS and take note of what node you are in 

    ssh hpc-login
hostname
    ssh ecs-login
hostname

  2. Open a new tab in your terminal and connect again. Did you get the same hostname? Why is that?

    hpc-login hostname is an alias to a load-balanced service of login nodes. You may land on a different one every time you connect.

    ecs-login is an alias to a specific login node of the ECS virtual cluster. It is not automatically load-balanced, so you will typically land on the same node on consecutive connections.

    Both aliases will always point to a working login node, and the actual node and complex behind it may change depending on the load, system sessions or outages.

  3. Now, from your open SSH session on Atos HPCF or ECS, connect to the main login alias again. Did it ask for a password? Can you set your account up so jumps between hosts are done without a password?

    Password-less SSH between ECMWF hosts such as Atos HPCF or ECS nodes, or VDI hosts is not set up by default. If you were asked for a password, you can run the following command from your Atos HPCF, ECS or VDI session to set up  key-based authentication:

    ssh-key-setup

    After this you should be able to jump between hosts without having to introduce your password.

    Besides being convenient, this setup is also necessary for other tools such as ECACCESS or ecinteractive to work properly.

Storage spaces

Reference: HPC2020: Filesystems

We will now explore the different options when it comes to storing your data.

Main filesystems

  1. Connect to Atos HPCF or ECS main login node. What is your default filesystem? Can you try 4 different ways to accessing that space?

    The default directory is your HOME directory, which is /home/$USER. It is a dedicated personal space for you, and you can always come back to that with either of the following commands:

    cd
cd ~
cd $HOME
cd /home/$USER

    Your HOME directory is accessible across all Atos HPCF, ECS, VDI and EcFlow services.

  2. There are 3 more main storage spaces. Create an empty file called del.me on each one of them? Check that they have been created with ls, and then remove them with rm.

    Besides HOME, you also have also access to PERM, HPCPERM and SCRATCH. Like HOME, they are all dedicated personal spaces with their corresponding environment variable. Using those environment variables over hardcoded paths is strongly recommended.

    You can use touch to create the test files:

    touch $PERM/del.me
touch $HPCPERM/del.me
touch $SCRATCH/del.me

    Check they exist with:

    ls -l $PERM/del.me
ls -l $HPCPERM/del.me
ls -l $SCRATCH/del.me

    Remove them with:

    rm $PERM/del.me
rm $HPCPERM/del.me
rm $SCRATCH/del.me

  3. How much space have you used in each of your main 4 filesystems? How much can you store?

    All the filesystems have quotas enforced. You can check them with the quota command

    quota

    For HOME and PERM, the snippet should look similar to:

    Quota for $HOME:
home_b             user    1234        <space used>   <space limit>       <number of files stored>       -   *

Quota for $PERM
POSIX User      1234    <space used>   <space limit>       <number of files stored>       none

    For SCRATCH and HPCPERM the format is slightly different:

    Project quota for $SCRATCH and $SCRATCHDIR:
Disk quotas for prj 1000001798 (pid 1000001798):
     Filesystem    used   quota   limit   grace   files   quota   limit   grace
       /ec/res4     XXX     YYY     YYY       -     ZZZ     WWW     WWW       -

Project quota for $HPCPERM:
Disk quotas for prj 2000001798 (pid 2000001798):
     Filesystem    used   quota   limit   grace   files   quota   limit   grace
       /ec/res4     XXX     YYY     YYY       -     ZZZ     WWW     WWW       -
  4. Can you decide what would be the best filesystem to use in the following cases? Why would you make that choice?
    1. Store the source code, scripts and configuration of your programs and workflows
    2. Store Climate Files to be used by your model runs on Atos HPCF
    3. Working directory for your jobs
    4. Store data that that you use frequently, which is considerable in size.

  5. If you are on the VDI, open a new terminal there. Can you access your HOME, PERM, SCRATCH and HPCPERM ?

    HOME and PERM are NFS-based Filesystems, which are mounted on all user computing platforms at ECMWF. You may access them with $HOME and $PERM environment variables:

    ls $HOME
ls $PERM

    However, SCRATCH and HPCPERM  are Lustre Based filesystem only available on the Atos HPCF, so  they are not available on other computing platforms such as VDI or ecFlow VMs and the corresponding environment variables are therefore not defined.

Temporary spaces

There are 



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