In this page:
| Table of Contents |
|---|
...
Data Storage architecture
All HPC systems share the same logical disk structure and file systems definition.
...
Important: It is the user's responsibility to backup your important data. We only guarantee a daily backup of data in the $HOME area.
$HOME: permanent/backed up, user specific, local
$HOME is a local area where you are placed after the login procedure. It is where system, and user applications store their dot-files and dot-directories (.nwchemrc, .ssh, ...) and where users keep initialization files specific for the systems (.cshrc, .profile, ...). There is a $HOME area for each username on the machine.
This area is conceived to store programs and small personal data. It has a quota of 50 GB. Files are never deleted from this area. Moreover, they are guaranteed by daily backups: if you delete or accidentally overwrite a file, you can ask our Help Desk (superc@cineca.it) to restore it. A maximum of 3 versions of each file is stored as a backup. The last version of the deleted file is kept for two months, then definitely removed from the backup archive. File retention is related to the life of the username; data are preserved until the username remains active.
$WORK: permanent, project specific, local
$WORK is a scratch area for collaborative work within a given project. File retention is related to the life of the project. Files in $WORK will be conserved up to 6 months after the project end, and then they will be cancelled. Please note that there is no back-up in this area.
...
The (chprj - change project) command makes it easier to manage the different WORK areas for different projects, see here for details.
...
$FAST:
...
permanent,
...
project specific, local
...
(LEONARDO ONLY)
$FAST is a scratch area for collaborative work within a given project. File retention is related to the life of the project. Files in $FAST will be conserved up to 6 months after the project end, and then they will be cancelled. Please note that there is no back-up in this area.
This area is conceived for hosting working data files whenever the I/O operations constitute the bottleneck for your applications. It behaves well both when I/O is performed accessing large blocks of data, and for frequent and small I/O operations. Due to the limited size of the area, the main space for maintaining the data resulting from batch processing is the corresponding $WORK area.
There is one $FAST area for each active project on the machine. The fixed quota is 1 TB per project, and due to the total dimension of the storage, extensions cannot be considered. The owner of the main directory is the PI (Principal Investigator) of the project. All collaborators are allowed to read/write in there. Collaborators are advised to create a personal directory in $FAST for storing their personal files. By default, the personal directory will be protected (only the owner can read/write), but protection can be easily modified, for example by allowing write permission to project collaborators through chmod command. This second approach does not affect global files security.
The (chprj - change project) command makes it easier to manage the different FAST areas for different projects, see here for details.
$CINECA_SCRATCH: temporary , user specific, local
This is a local temporary storage conceived for temporary files from batch applications. There are important differences with respect to $WORK area. It is user specific (not project specific). By default, file access is closed to everyone, in case you need less restrictive protections, you can set them with chmod command.
On this area, a periodic cleaning procedure could be applied, with a normal retention time of 40 days: files are daily cancelled by an automatic procedure if not accessed for more than 40 days. In each user's home directory ($HOME) a file lists all deleted files for a given day. Please notice that on G100 the variable is $SCRATCH.
CLEAN_<yyyymmdd>.log
<yyyymmdd> = date when files were cancelled
There is one $CINECA_SCRATCH area for each username on the machine.
$CINECA_SCRATCH does not have any disk quota. Please be aware that on Galileo100 and Marconi100 clusters, to prevent a very dangerous filling condition, a 20TB disk quota will be temporarily imposed to all users when the global quota area reaches 88% of occupancy; this disk quota will be removed when the global occupancy lowers back to normal.
To verify if and how the cleaning procedure is active on a given cluster, check the Mott-of-the-Day.
$TMPDIR: temporary, user specific, local
Each compute node is equipped with a local area whose dimension differs depending on the cluster (please look at the specific page of the cluster for more details).
When a job starts, a temporary area is defined on the storage local to each compute node. On MARCONI and GALILEO100:
TMPDIR=/scratch_local/slurm_job.$SLURM_JOB_ID
Differently from the other CINECA clusters, on LEONARDO the job's temporary area is managed by the slurm job_container/tmpfs plugin, which provides an equivalent job-specific, private temporary file system space, with private instances of /tmp and /dev/shm in the job's user space:
TMPDIR=/tmp
visible via the command "df -h /tmp". If more jobs share one node, each one will have a private /tmp in the job's user space. The tmpfs are removed at the end of the job (and all data will be lost).
Whatever the mechanism, the TMPDIR can be used exclusively by the job's owner. During your jobs, you can access the area with the (local) variable $TMPDIR. In your sbatch script, for example, you can move the input data of your simulations to the $TMPDIR before the beginning of your run and also write on $TMPDIR your results. This would further improve the I/O speed of your code.
However, the directory is removed at the job's end; hence always remember to save the data stored in such area to a permanent directory in your sbatch script at the end of the run. Please note that the area is located on local disks, so it can be accessed only by the processes running on the specific node. For multinode jobs, if you need all the processes to access some data, please use the shared filesystems $HOME, $WORK, $CINECA_SCRATCH.
Differently from the other CINECA clusters, thanks to the job_container/tmpfs plugin the local storage is considered a "resource" on LEONARDO, and can be explicitly asked on the diskful nodes only (DCGP and serial nodes) via the sbatch directive or srun option "-gres=tmpfs:XX" (see the specific Disks and Filesystems section on LEONARDO's User Guide for the allowed maximum values). For the same reason, the requested amount of gres/tmpfs resource contributes to the consumed budget, changing the number of accounted equivalent core hours, see the dedicated section on the Accounting on CINECA clusters
This is local temporary storage, like $WORK, conceived for temporary files from batch applications. There are important differences with respect to $WORK area. It is user specific (not project specific), and it can be used for sharing data with people outside your project. By default, file access is open to everyone, in case you need more restrictive protections, you can set them with chmod command.
On this area, a periodic cleaning procedure could be applied, with a normal retention time of 40 days: files are daily cancelled by an automatic procedure if not accessed for more than 40 days. In each user's home directory ($HOME) a file lists all deleted files for a given day. Please notice that on G100 the variable is $SCRATCH.
CLEAN_<yyyymmdd>.log
<yyyymmdd> = date when files were cancelled
There is one $CINECA_SCRATCH area for each username on the machine.
$CINECA_SCRATCH does not have any disk quota. Please be aware that on Galileo100 and Marconi100 clusters, to prevent a very dangerous filling condition, a 20TB disk quota will be temporarily imposed to all users when the global quota area reaches 88% of occupancy; this disk quota will be removed when the global occupancy lowers back to normal.
To verify if and how the cleaning procedure is active on a given cluster, check the Mott-of-the-Day.
$TMPDIR: temporary, user specific, local
Each compute node is equipped with a local storage whose dimension differs depending on the cluster (please look at the specific page of the cluster for more details).
When a job starts, a temporary area is defined on the storage local to each compute node:
TMPDIR=/scratch_local/slurm_job.$SLURM_JOB_ID
which can be used exclusively by the job's owner. During your jobs, you can access the area with the (local) variable $TMPDIR. In your sbatch script, for example, you can move the input data of your simulations to the $TMPDIR before the beginning of your run and also write on $TMPDIR your results. This would further improve the I/O speed of your code.
However, the directory is removed at the job's end; hence always remember to save the data stored in such area to a permanent directory in your sbatch script at the end of the run. Please note that the area is located on local disks, so it can be accessed only by the processes running on the specific node. For multinode jobs, if you need all the processes to access some data, please use the shared filesystems $HOME, $WORK, $CINECA_SCRATCH.
$DRES: permanent, shared (among platforms and projects)
This is a repository area for collaborative work among different projects and across platforms. You need to explicitly ask for this kind of resource: it does not come as part of a project (mailto: superc@cineca.it).
...
The Data movement is transparent for the user. Only physical support changes, while the logical environment will not be affected (this means that you can reach data stored in tape using the same path you used for storing it in the first place)
...
Backup policies
Daily backups guarantee the $HOME filesystem. In particular cases, a different agreement is possible: contact the HPC support (superc@cineca.it) for further details.
The backup procedure runs daily, and we preserve a maximum of three different copies of the same file. Older versions are kept for 1 month. The last version of deleted files is kept for 2 months, then definitely removed from the backup archive.
Environment variables
$HOME, $WORK,$CINECA_SCRATCH ($SCRATCH on G100) and $DRES environment variables are defined on all HPC Systems, and you can access these areas simply using those names:
...
You are strongly encouraged to use these environment variables instead of full paths to refer to your scripts and codes data.
Summary
| $CINECA_SCRATCH | $WORK | $DRES |
|---|---|---|
Created when username has granted access. | Created when a project is opened. | Created on request. |
A clean-up procedure is active. | Data are preserved up to few months after the end of the project. | Data are preserved up few months after the expiring date No backup. |
No quota. | Default quota of 1 TB. Motivated requests for quota increase will be taken into account. | Quota based on the needs. |
| By default files are public (read only). The user can change the permission (chmod) and make files private. It is not possible to restrict access to the group (all usernames share the same mail unix group). | By default files are private. The user can change the permission (chmod) and make files visible (R o R/W) to project collaborators. | Same as $WORK area. |
Note: the $FAST area is not reported in the Summary since it is defined on Leonardo cluster only.
What to use when...
| Data are critical, not so large, I want to be sure to preserve them. | $HOME is the right place. Pay attention to the 50 GB quota limit for each user on this space. |
| Large data to be shared with collaborators of my project. | $WORK is the right place. Here each collaborator can have his own directory. He can open it for reading or even writing and be sure, at the same time, that data are not public. People not included in the project will not be able to access the data. Moreover, data are preserved up to a few months after the project’s end. |
| Data to be shared with other users, not necessarily participating in common projects | $CINECA_SCRATCH is the right place. |
| Data to be maintained even beyond the end of the project. I'll use the data on different CINECA hosts | $DRES is a better solution. |
| Data to be shared among different platforms | $DRES allows this. |
Monitoring the occupancy
A command is available on all HPC systems to check the status of the occupancy of all the areas accessible by the user and eventually the presence of a quota limit.
...
An additional tool for monitoring the disk occupancy is also available only on GALILEO100 and LEONARDO, since the command is working only on Lustre filesystems
...
The tool is available in the module cintools, which is automatically loaded in your environment. However, the module can be unloaded as all the other modules (Modules).
File permissions
$WORK and $DRES are environmental variables automatically set in the user environment.
...
Since the $WORK/$DRES fileset is closed to non collaborators, the data sharing is active only among the project collaborators.
Pointing $WORK to a different project: the chprj command
The user can modify the project pointed to by the variable $WORK using the "change project" command.
...
More details are in the help page of the command:
chprj -h
chprj --help
On LEONARDO only: The command applies to the $FAST variable as well.
Endianness
Endianness is the attribute of a system that indicates whether integers are represented from left to right or right to left. At present, all CLusters clusters in Cineca are "little-endian".
Managing your data
A comprehensive discussion on how to manage your data can be found in a specific document.
...