Storage systems

Introduction

On our cluster, we provide multiple storage systems, which are optimized for different purposes. Since the available storage space on our clusters is limited and shared between all users, we set quotas in order to prevent single users from filling up an entire storage system with their data.

A summary of general questions about file systems, storage and file transfer can be found in our FAQ. If you have questions or encounter problems with the storage systems provided on our clusters or file transfer, then please contact cluster support.

Personal storage (everyone)

Home

On our clusters, we provide a home directory (folder) for every user that can be used for safe long term storage of important and critical data (program source, script, input file, etc.). It is created on your first login to the cluster and accessible through the path

/cluster/home/username

The path is also saved in the variable $HOME. The permissions are set that only you can access the data in your home directory and no other user. Your home directory is limited to 16 GB and a maximum of 100'000 files and directories (inodes). The content of your home is saved every hour and there is also a nightly backup (tape).

Scratch

We also provide a personal scratch directory (folder) for every user, that can be used for short-term storage of larger amounts of data. It is created, when you access it the first time through the path

/cluster/scratch/username

The path is also saved in the variable $SCRATCH. It is visible (mounted), only when you access it. If you try to access it with a graphical tool, then you need to specify the full path as it is might not visible in the /cluster/scratch top-level directory. Before you use your personal scratch directory, please carefully read the usage rules to avoid misunderstandings. The usage rules can also be displayed directly on the cluster with the following command.

cat $SCRATCH/__USAGE_RULES__

Your personal scratch directory has a disk quota of 2.5 TB and a maximum of 1'000'000 files and directories (inodes). There is no backup for the personal scratch directories and they are purged on a regular basis (see usage rules).

Group storage (shareholders only)

Project

Shareholder groups have the option to purchase additional storage inside the cluster. The project file system is designed for safe long-term storage of critical data (like the home directory). Shareholder groups can buy as much space as they need. The path for project storage is

/cluster/project/groupname

Access rights and restriction is managed by the shareholder group. We recommend to use NETHZ groups for this purpose. Backup (tape) is not included, but can be purchase optionally. If you are interested in getting more information and prices of the project storage, then please contact cluster support.

Work

Apart from project storage, shareholder groups also have the option to buy so-called work (high-performance) storage. It is optimized for I/O performance and can be used for short- or medium-term storage for large computations (like scratch, but without regular purge). Shareholders can buy as much space as they need. The path for work storage is

/cluster/work/groupname

Access rights and restriction is managed by the shareholder group. We recommend to use NETHZ groups for this purpose. The directory is visible (mounted), only when accessed. If you are interested in getting more information and prices of the work storage, then please contact cluster support.

Local scratch (on each compute node)

The compute nodes in our HPC clusters also have some local hard drives, which can be used for temporary storing data during a calculation. The main advantage of the local scratch is, that it is located directly inside the compute nodes and not attached via the network. This is very beneficial for serial, I/O-intensive applications. The path of the local scratch is

/scratch

You can either create a directory in local scratch yourself, as part of a batch job, or you can use a directory in local scratch, which is automatically created by the batch system. LSF creates a unique directory in local scratch for every job. At the end of the job, LSF is also taking care of cleaning up this directory. The path of the directory is stored in the environment variable

$TMPDIR

If you use $TMPDIR, then you need to request scratch space from the batch system.

External storage

Central NAS

Groups who have purchased storage on the central NAS of ETH can ask the storage group of IT services to export it to our HPC clusters. There are certain requirements that need to be fullfilled in order to use central NAS shares on our HPC clusters.

• The NAS share needs to be mountable via NFS (shares that only support CIFS cannot be mounted on the HPC clusters).
• The NAS share needs to be exported to the subnet of our HPC clusters (please contact ID Systemdienste, and ask them for an NFS export of your NAS share).
• Please carefully set the permissions of the files and directories on your NAS share if other cluster users should not have read/write access to your data.

NAS shares are then mounted automatically when you access them. The mount-point of such a NAS share is

/nfs/servername/sharename

a typical NFS export file for the Euler cluster could look like:

# cat /etc/exports
/export 129.132.71.59/32(rw,root_squash,secure) 10.205.0.0/19(rw,root_squash,secure)

If you ask the storage group to export your share to the Euler cluster, then please provide them the above-shown information. When a NAS share is mounted on our HPC clusters, then it is accessible from all the compute nodes in the cluster.

Local NAS

Groups who are operating their own NAS, can export a shared file system via NSF to our HPC clusters. In order to use an external NAS on our HPC clusters, the following requirements need to be fullfilled

• NAS needs to support NFSv3 (this is currently the only NFS version that is supported from our side).
• The user and group ID's on the NAS needs to be consistent with NETHZ user names and group.
• The NAS needs to be exported to the subnet of our HPC clusters.
• Please carefully set the permissions of the files and directories on your NAS share if other cluster users should not have read/write access to your data.

You external NAS can then be accessed through the mount-point

/nfs/servername/sharename

A typical NFS export file to export a share to the Euler cluster would look like

# cat /etc/exports
/export 129.132.71.59/32(rw,root_squash,secure) 10.205.0.0/19(rw,root_squash,secure)

The share is automatically mounted, when accessed.

Comparison

In the table below, we try to give you an overview of the available storage categories/systems on our HPC clusters as well as a comparison of their features.

Category	Mount point	Life span	Backup	Purged	Max. size	Small files	Large files
Home	/cluster/home	permanent	yes	no	16 GB	+	o
Scratch	/cluster/scratch	4 years	no	yes (files older than 15 days)	2.5 TB	o	++
Project	/cluster/project	4 years	optional	no	flexible	+	+
Work	/cluster/work	4 years	no	no	flexible	++	o
Central NAS	/nfs/servername/sharename	flexible	optional	no	flexible	+	+
Local scratch	/scratch	duration of job	no	end of job	800 GB	++	+

File transfer

In order to run your jobs on a HPC cluster, you need to transfer some data or input files from/to the cluster. For smaller and medium amounts of data, you can use some standard command line/graphical tools. If you need to transfer very large amounts of data (on the order of several TB), then please contact the [support] and we will help you to set up the optimal strategy to transfer your data in a reasonable amount of time.

Command line tools

For transferring files from/to the cluster, we recommend to use standard tools like secure copy (scp) or rsync. The general syntax for using scp is

scp [options] source destination

For copying a file from your PC to an HPC cluster (to your home directory), you would the command

scp file username@hostname:

Where username is your NETHZ username and hostname is the hostname of the cluster. Please note the colon after the hostname. For copying a file from the cluster to your PC (current directory), you would use the command

scp username@hostname:file .

For copying an entire directory, you would need to add the option -r. Therefore you would use the following command to transfer a directory from your PC to an HPC cluster (to your home directory).

scp -r directory username@hostname:

The general sytnax for rsync is

rsync [options] source destination

Quotas

The home and scratch directories on our clusters are subject to a strict user quota.

home directories: 16 GB (soft) / 20 GB (hard) / 100K files (hard) per user [aneeser@euler01 ~]$ quota -s Disk quotas for user aneeser (uid 16201):

    Filesystem  blocks   quota   limit   grace   files   quota   limit   grace

eu-ne-home6:/home6

                12549M  16384M  20480M             328   80000    100k       

scratch directories: 2.5 TB (hard) / 800K files (soft) / 1M files (hard) per user [aneeser@euler02 ~]$ pan_quota /cluster/scratch/aneeser

 <GB>  <soft>  <hard> : <files> <soft>  <hard> :         <path to volume> <pan_identity(name)>
45.27 2000.00 2500.00 :      37 800000 1000000 : /cluster/scratch/aneeser uid:16201(aneeser)