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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 or ECS computing platforms.

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:
  • Using the Virtual Desktop Infrastructure (VDI). See the corresponding documentation to get started.
  • Using Teleport SSH from your end user device .

Logging into Atos HPCF and ECS

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

Accessing a login node

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

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ssh hpc-login
hostname

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ssh ecs-login
hostname

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

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?

ssh-key-setup

Interactive session

Standard sessions on login nodes do not guarantee access to dedicated resources such as cpus or memory, and strict limits on those are imposed.

Can you get a dedicated interactive session with 10 GB of memory and 4 cpus for 8 hours?

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You can use ecinteractive. It is installed and available on all the Atos HPCF and ECS nodes, as well as the VDI, so you can run it from there

ecinteractive -c 4 -m 10 -t 8:00

This will create an interactive job with the requested configuration and land you on a shell in a given node.

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• • own computer

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Log out of that interactive session. Can you reattach to it?

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Your job kept running in the background, and there can only be one interactive job per user. You can attach as many concurrent shells to the same interactive session, for example in different terminal tabs, with:

ecinteractive

Cancel your interactive session

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ssh hpc-login
hostname

Storage spaces

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

Main filesystems

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

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

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.

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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

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

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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       -

• • .

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

ls $HOME
ls $PERM

EXTRA: For long term archival purposes, users with access to HPCF may also use ECFS. Files will be stored in ECMWF's Data Handling System on Tape. Create a small text file and copy it to your ECFS space, then ensure it is there, retrieve it and remove it.

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echo "hello world" > test_file.txt
ecp test_file.txt ec:
els -l ec:test_file.txt
ecp ec:test_file.txt retrieved_test_file.txt
diff test_file.txt retrieved_test_file.txt
erm ec:test_file.txt

Temporary spaces

There are a number of temporary spaces you can use in your session or job.

Create a file called testfile on the $TMPDIR, $SCRATCHDIR and /tmp/.

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touch $TMPDIR/testfile
touch $SCRATCHDIR/testfile
touch /tmp/testfile

Open another session in the same login node with ssh $HOSTNAME. Can you find the files you have created earlier?

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ls -l $TMPDIR/testfile
ls -l $SCRATCHDIR/testfile
ls -l /tmp/testfile

You will not see the files you created in any of those locations, since every session or job will have a different location. This includes /tmp, which is also a dedicated ramdisk for session.

Filesystem Usage

Can you decide what would be the best filesystem to use in the following cases? Why would you make that choice?

Store the source code, scripts and configuration of your programs and workflows

Store Climate Files to be used by your model runs on Atos HPCF.

Working directory for your jobs.

Store data that that you use frequently, which is considerable in size.

Store data for longer term which is considerable in size, such as experiment results. You are not going to use it often.

Temporary files that you don't need beyond the end of the session or job

Recovering Deleted files

Imagine you have accidentally deleted ~/.profile in your HOME directory. Can you get back the latest version?

ls -l ~/.snapshot/*/.profile

Imagine you have accidentally deleted a file in your PERM directory. Can you get back the latest version?

perm_snap

Imagine you have accidentally deleted a file in your SCRATCH or HPCPERM directories. Can you get back the latest version?

Managing your software stack environment

Atos HPCF and ECS computing platforms offer a wide range of software, libraries and tools.

Basic software environment management

You want to use CDO, a popular tool to manipulate climate and NWP model data. What do you need to do to get the following result?

$ cdo --version
Climate Data Operators version X.Y.Z (https://mpimet.mpg.de/cdo)
System: x86_64-pc-linux-gnu
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If you run the command without any prior action, you may get:

$ cdo --version
-bash: cdo: command not found

Many software packages and tools are not part of your default environment, and need to be explicitly loaded via modules.

So the following commands would be sufficient to get to the desired result:

module load cdo
cdo --version

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You can also use the ml shortcut to load the module

ml cdo

Note that we did not ask for any specific version. In those cases, you will get the one defined as default.

How many versions of CDO can be used at ECMWF? Can you pick the newest?

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There are hundreds of different packages with their corresponding different versions installed at ECMWF. You can use:

module avail

To see what modules can be loaded at any time.

However, not all modules can be loaded at any time, some will only become available if a certain combination of modules is loaded.

You can also use the following command for an overview or all the packages that are installed, including those that may not be visible in module avail:

module spider

In this case we are only interested in CDO so we can do either:

module avail cdo

or 

module spider cdo

To load the newest, you can either explicitly pick up the latest version explicitly, so assuming that it was "X.Y.Z":

module load cdo/X.Y.Z

But you can also use the module tag "new":

module load cdo/new

or also ask for the latest with:

module --latest load cdo

Load the netcdf4 module. Can you see what modules do you have loaded in your environment now?

module load netcdf4

module list

ml

Remove the netcdf4 module from your environment and check it is gone/

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To unload the netcdf4 module just do:

module unload netcdf4

or with just the shortcut:

ml -netcdf4

Then, you can see what your software environment looks like with:

module list

Can you restore the default environment you had when you logged in? Check that 

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If you log out of your session, next time you log in you will start with a fresh default environment. Modules are only loaded for that specific session.

However, if you don't want to log out, you can also reset your module environment with:

module reset

You can then check the effects with

module list

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