Due to the unavailability of NFS-based filesystems at this stage, PERM is temporarily setup on Lustre.
The filesystems available are HOME, PERM, HPCPERM and SCRATCH, and are completely isolated from those in other ECMWF platforms in Reading such as ECGATE or the Cray HPCF.
Filesystems from those platforms are not cross-mounted either. This means that if you need to use data from another ECMWF platform such as ECGATE or the Cray HPCF, you will need to so transfer it first using scp or rsync. See HPC2020: File transfers for more information.
File System | Suitable for ... | Technology | Features | Quota |
|---|---|---|---|---|
| HOME | permanent files, e. g. .profile, utilities, sources, libraries, etc. | NFS | It is backed up. Limited I/O performance | 20GB |
| PERM | permanent files without the need for automated backups, smaller input files for serial or small processing, std output, etc. | NFS | It is backed up. Limited I/O performance | 1 TB |
| HPCPERM | permanent files without the need for automated backups, bigger input files for parallel model runs, climate files, etc. | NFS | No Backup No automatic deletion | 10TB |
| SCRATCH | all temporary (large) files. Main storage for your jobs and experiments input and output files. | Lustre | Automatic deletion to be configured at a later stage No backup | 50TB |
SCRATCHDIR | Big temporary data for an individual session or job, not as fast as TMPDIR but higher capacity. Files accessible from all cluster. | Lustre | Deleted at the end of session or job Created per session/ job as a subdirectory in SCRATCH | part of SCRATCH quota |
TMPDIR | Fast temporary data for an individual session or job, small files only. Local to every node. | SSD on shared nodes (*f QoSs) | Deleted at the end of session or job Created per session/ job | 3 GB per session/job by default. Customisable up to 40 GB with
|
RAM on exclusive compute nodes (*p QoSs) | no limit (maximum memory of the node) |
Environment variables
Those filesystems can be conveniently referenced from your session and scripts using the environment variables of the same name: $HOME, $PERM, $HPCPERM, $SCRATCH, $SCRATCHDIR and $TMPDIR.
$TEMP, which in the past was an alias to $SCRATCH, has been deprecated and is no longer defined. Please use $SCRATCH instead
More capacity for $TMPDIR?
When running on the shared nodes (*f QoSs), you may request a bigger space in the SSD-backed TMPDIR with the extra SBATCH option:
#SBATCH --gres=ssdtmp:<size>G
With <size> being a number up to 40 GB. If that is still not enough for you, you may point your TMPDIR to SCRATCHDIR:
export TMPDIR=$SCRATCHDIR
How much have I used?
You can check your current usage and limits with the "quota" command
New filesystem structure
You will notice your filesystems have now a flatter and simpler name structure. If you port any scripts or code that had paths to filesystems hardcoded from older platforms, please make sure you update them. Where possible, try and use the environment variables provided, which should work on both sides pointing to the right location in each case:
| Before | After |
|---|---|
| /home/group/user or /home/ms/group/user | /home/user |
| /perm/group/user or /perm/ms/group/user | /perm/user |
| - | /hpcperm/user |
| /scratch/group/user or /scratch/ms/group/user | /scratch/user |
Special directories on RAM
Some special directories are not disk-based but actually mapped into the node's main memory. There are no limits set on exclusive nodes running on parallel queues. However, when running on shared nodes (GPILs) on fractional or interactive queues, this could lead to a single application or user exhausting all the memory of the node and thus impacting others. This is why the following limits are set:
| Directory | New limit |
|---|---|
| /tmp | 428 GB (80% of available memory) per user's session |
| /var/tmp | 428 GB (80% of available memory) per user's session |
| /dev/shm | 428 GB (80% of available memory) per user's session |
| $XDG_RUNTIME_DIR | 64 MB per user's session |
Users should instead use the general purpose file systems available, and in particular, $TMPDIR or $SCRATCHDIR for temporary storage per session or job. See HPC2020: Filesystems.
Automatic cleanup
Any data left on those spaces will be automatically deleted at the end of the job or session.