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File Systems

A central aspect in the design of HAICORE has been the enormous amount of data generated by scientific research projects. A multi-level data storage concept guarantees high-throughput processing of data using several different storage systems.

The core of this design are two large-scale, parallel file systems based on IBM Spectrum Scale (also known as GPFS) used for globally visible user data. Individual home directories are automatically created for each user on the Spectrum Scale home file system, and the environment variable $HOME points to these directories. Each user can also create so-called workspaces on the Spectrum Scale work file system.

Other storage locations include a temporary directory called $TMPDIR that is is located on the local solid state disks (SSDs) of a node, and is therefore only visible on an individual node while a job is running. In order to create a temporary directory which is visible on all nodes of a batch job, users can request a temporary BeeGFS On Demand (BeeOND) file system. Access to BeeOND file systems is only possible from the nodes of the batch job and while the job is running.

The characteristics of the file systems are shown in the following table.

Property $HOME workspace $TMPDIR BeeOND
Visibility global global local job local
Lifetime permanent limited job walltime job walltime
Disk space 2.5 PB 13.5 PB 800 GB n * 750 GB
Quotas yes yes no no
Snapshot yes yes no no
Backup yes no no no
Total read perf 84 GB/s 196 GB/s 750 MB/s n * 700 MB/s
Total write perf 60 GB/s 140 GB/s 750 MB/s n * 700 MB/s
Read perf/node 10 GB/s 10 GB/s 750 MB/s 10 GB/s
Write perf/node 10 GB/s 10 GB/s 750 MB/s 10 GB/s

global : all nodes see the same file system local : each node has its own local file system job local : only available within the currently running job permanent : data is stored permanently (across job runs and reboots) limited : data is stored across job runs and reboots, but will be deleted at some time job walltime : files are removed at end of the batch job.

Selecting the appropriate file system

In general, you should separate your data and store it on the appropriate file system.

Permanently required data like software or important results should be stored below $HOME, but capacity limits (so-called "quotas") apply. Permanent data which is not needed for months or exceeds the capacity restrictions should be sent to external large scale storage systems and deleted from the home file system.

Temporary data which is only needed on a single node, which does not exceed the disk space shown in the table above and which is only needed during job runtime should be stored below $TMPDIR. Temporary data which is only needed during job runtime and which needs to be accessed from all nodes of a batch job should be stored on BeeOND. Scratch data which can be easily recomputed or which is the result of one job and input for another job should be stored below so-called workspaces. The lifetime of data in workspaces is limited and depends on the lifetime of the workspace.

Backups

If you accidentally deleted data on $HOME or on a workspace, you can usually copy back an older version from a so-called snapshot path. In addition, for $HOME there is also a the possibility to restore files from a backup. Please see the Backup and Archival section for more information.

$HOME

For each user a fixed amount of disk space for the $HOME directory is reserved. The disk space is controlled by so-called quotas. The default quota limit per user is 1 TB and 2 million inodes.

Workspaces

Workspaces are directory trees which are available for a limited amount of time (few months). The corresponding Spectrum Scale work file system has no backup, i.e. you should use workspaces for data which can be recreated, e.g. by running the same batch jobs once again. This is only needed in the very unlikely case that the file system gets corrupt.

Initially workspaces have a maximum lifetime of 60 days. You can extend the lifetime 3 times for another 60 days but you should do this near the end of the lifetime since the new lifetime starts when you execute the command which requests the extension.

If a workspace has inadvertently expired we can restore the data during a limited time (few weeks). In this case you should create a new workspace and report the name of the new and of the expired workspace by opening a support ticket.

For your account (user ID) there is a quota limit for all of your workspaces and for the expired workspaces (as long as they are not yet completely removed). The default quota limit per user is 250 TB and 50 million inodes.

Create workspace

To create a workspace you need to state ''name'' of your workspace and ''lifetime'' in days. Note that maximum integer for ''lifetime'' is 60. Execution of:

$ ws_allocate blah 30

returns:

Info: could not read email from users config ~/.ws_user.conf.
Info: reminder email will be sent to local user account
Info: creating workspace.
/hkfs/work/workspace_haic/scratch/USERNAME-blah
remaining extensions  : 3
remaining time in days: 30

For more information read the program's help, i.e. man ws_allocate.

Reminder for workspace deletion

By default you will get an email about an expiring workspace 7 days before a workspace expires. You can adapt this time by using the option ''-r '' of ''ws_allocate''.

You can also send yourself a calender entry which reminds you when a workspace will be automatically deleted:

$ ws_send_ical <workspace> <email>

List all your workspaces

To list all your workspaces, execute:

$ ws_list

which will return you:

  • Workspace ID
  • Workspace location
  • creation date, remaining time and expiration date
  • available extensions

Find workspace location

Workspace location/path can be prompted for any workspace ''ID'' using ws_find, in case of workspace ''blah'':

$ ws_find blah

returns the one-liner:

/hkfs/work/workspace_haic/scratch/USERNAME-blah

Extend lifetime of your workspace

Any workspace's lifetime can be only extended three times. There two similar commands to extend workspace lifetime:

  • ws_extend blah 40 which extends workspace ID ''blah'' by ''40'' days from now,
  • ws_allocate -x blah 40 which extends workspace ID ''blah'' by ''40'' days from now.

Delete a workspace

$ ws_release blah # Manually erase your workspace blah

$TMPDIR

The environment variable $TMPDIR contains the name of a directory which is local to each node. This means that different tasks of a parallel application use different directories when they do not utilize the same node. Although $TMPDIR points to the same path name for different nodes of a batch job, the physical location and the content of this directory path on these nodes is different.

This directory should be used for temporary files being accessed from the local node during job runtime. It should also be used if you read the same data many times from a single node, e.g. if you are doing AI training. In this case you should copy the data at the beginning of your batch job to $TMPDIR and read the data from there.

The $TMPDIR directory is located on an extremely fast 960 GB NVMe SSD disk. This means that performance on small files is much better than on the parallel file systems.

Each time a batch job is started, a subdirectory is created on the SSD of each node and assigned to the job. $TMPDIR is set to the name of the subdirectory and this name contains the job ID so that it is unique for each job. At the end of the job the subdirectory is removed.

On login nodes $TMPDIR also points to a fast directory on a local NVMe SSD disk but this directory is not unique. It is recommended to create your own unique subdirectory on these nodes. This directory should be used for the installation of software packages. This means that the software package to be installed should be unpacked, compiled and linked in a subdirectory of $TMPDIR. The real installation of the package (e.g. make install) should be made into the $HOME folder.

Usage example for $TMPDIR

We will provide an example for using $TMPDIR and describe efficient data transfer to and from $TMPDIR.

If you have a data set with many files which is frequently used by batch jobs you should create a compressed archive on a workspace. This archive can be extracted on $TMPDIR inside your batch jobs. Such an archive can be read efficiently from a parallel file system since it is a single huge file. On a login node you can create such an archive with the following steps:

## Create a workspace to store the archive
$ ws_allocate data-ssd 60
## Create the archive from a local dataset folder (example)
$ tar -cvzf $(ws_find data-ssd)/dataset.tgz dataset/

Inside a batch job extract the archive on $TMPDIR, read input data from $TMPDIR, store results on $TMPDIR and save the results on a workspace:

#!/bin/bash
# very simple example on how to use local $TMPDIR
#SBATCH -N 1
#SBATCH -t 24:00:00

# Extract compressed input dataset on local SSD
tar -C $TMPDIR/ -xvzf $(ws_find data-ssd)/dataset.tgz

# The application reads data from dataset on $TMPDIR and writes results to $TMPDIR
myapp -input $TMPDIR/dataset/myinput.csv -outputdir $TMPDIR/results

# Before job completes save results on a workspace
rsync -av $TMPDIR/results $(ws_find data-ssd)/results-${SLURM_JOB_ID}/

BeeOND (BeeGFS On-Demand)

Users of the cluster HoreKa can request a private BeeOND (BeeGFS) parallel filesystem for each job. The file system is created during job startup and purged after your job. This means that all data on the private BeeOND filesystem will be deleted after your job. Make sure you have copied your data back within your job to the global filesystem, e.g. $HOME, $PROJECT, any workspace or the LSDF.

BeeOND/BeeGFS can be used like any other parallel file system. Tools like cp or rsync can be used to copy data in and out.

A BeeOND file system is only created if your batch job requests this creation. For details see here.

Snapshots and backup

In case you inadvertently deleted some of your data, want to go back to a previous version or compare your data with a previous version you can use so-called snapshot. Snapshots are a point in time copy of your data. For the home file system there are snapshots of the last 7 days, of the last 4 weeks and of the last 6 months. For the workspaces there are snapshots of the last 7 days and of the last 4 weeks. For the home file system snapshots will be located below /home/<group>/.snapshots. For the work (workspace) file system snapshots will be located below /hkfs/work/.snapshots.

There are also regular backups of all data of the project directories, whereas ACLs and extended attributes will not be saved by the backup. Please open a support ticket if you need us to restore backup data.

Quotas

To display your used quotas and quota limits of $HOME just execute the following command on a login node:

$ /usr/lpp/mmfs/bin/mmlsquota -u $USER  --block-size G -C hkn.scc.kit.edu hkfs-home:$PROJECT_GROUP

The current quota usage and limits of your account on the workspace file system can be displayed with the command

$ /usr/lpp/mmfs/bin/mmlsquota -u $(whoami) --block-size G -C hkn.scc.kit.edu hkfs-work

File system performance tuning

Hints on file system performance tuning can be found here.

Last update: September 28, 2023