Storage spaces - Atos HPCF and ECS Introduction Tutorial

Reference documentation

HPC2020: Filesystems

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?
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.
There are 3 more main storage spaces. Create an empty file called del.me on each one of them. Then, 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

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       -

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.
For long term archival purposes, most users 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.
Cooperating State access to ECFS
Users from Cooperating States do not have full access to the ECFS service, but only to a temporary storage domain on tape for 90 days. They should therefore not use ECFS for longer term archival.
For users with full access to the ECFS service, you can use the ec: permanent domain where files are stored indefinitely:
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
Cooperating State users can only use the ectmp: temporary domain where files are stored for 90 days, after which they are automatically deleted. For completeness, here is the same exercise using ectmp:
echo "hello world" > test_file.txt ecp test_file.txt ectmp: els -l ectmp:test_file.txt ecp ectmp:test_file.txt retrieved_test_file.txt diff test_file.txt retrieved_test_file.txt erm ectmp: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/.
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?
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
HOME would be the preferred choice. They are typically small but important files, so convenience of backups, snapshots and availability on all computing platforms is more important than parallel performance.
Store Climate Files to be used by your model runs on Atos HPCF.
HPCPERM is the right choice for big files that are going to be used concurrently by parallel applications such as NWP models.
Working directory for your jobs.
SCRATCH is the go to place for your daily work. Plenty of space, good parallel performance for output data that is transient by nature. Remember to move the data you want to keep after your job somewhere else, since files not used for 30 days will be automatically deleted.
Store data that that you use frequently, which is considerable in size.
PERM if accessibility from other computing platforms or the need of snapshots is important. You can see PERM as an extension to your HOME space.
HPCPERM, if I/O performance is more important than, especially if they are going to be used in parallel jobs on Atos HPCF.
Store data for longer term which is considerable in size, such as experiment results. You are not going to use it often.
ECFS would be the right place for longer term archival or storing backups. This is by far the place where you can store However, data on tapes needs to be retrieved to another disk space before it can be used, so it is costly in terms of time.
In order to use ECFS efficiently, remember to store fewer but bigger files, so it is a good idea to use tools like tar or zip to bundle together big directories with lots of files.
Temporary files that you don't need beyond the end of the session or job
$TMPDIR if performance is important and size is small, since TMPDIR is either in memory (for parallel jobs on HPCF), or on SSD disk.
$SCRATCHDIR if size of the files is big and does not fit TMPDIR.

Recovering Deleted files