This documentation is under active development, meaning that it can change over time as we refine it. Please email email@example.com if you require assistance.
16/08/2018: We have updated instructions on how to access
File Systems on M3¶
The M3 File System is arranged in 3 parts:
- your home directory
- your project directory
- project scratch space
In your home directory you should find a number of symbolic links (
ls -al). These
point to the project space and scratch you have been allocated. You can request
additional space via firstname.lastname@example.org
For example if your project name is “YourProject001” you will see the following two links:
ls -al ~/ YourProject001 -> /projects/YourProject001 YourProject001_scratch -> /scratch/YourProject001
The first link points to your
project data that is backed up weekly (as with
home directory). The second one points to the faster system
space, which is not backed up and is used for temporary data.
What to put on each file system?¶
That is up to you, but as a general guide:
Home directory (~2GB)¶
This should contain all of your hidden files and configuration files. Things like personal settings for editors and other programs can go here.
hard quota limits.
soft limit allows you to have more than your allocated space for a short
period of “grace” time (in days). After the grace time has been exceeded, the
filesystem will prevent further files being added until the excess is removed.
hard limit prevents further files being added.
The quotas on the Project directories are much larger than the space users get in their own Home directories, so it is much better to use the Project space. Also the project space is available for all members of your project, so you can use it to share data with your colleagues.
Default Quotas for New Projects¶
By default, quotas for
/projects directory will be applied as below:
- Default projects for Cryo-Electron Microscopy: 5TB
- Default project for MX: 5TB
- Other projects: 500GB
Default quota for
/scratch directory is 3TB.
Please use the
user_info command to view your usage and quota on all your projects and
Scratch Usage Policies¶
Demand for scratch space is high so the following policies are now in force to ensure fair access to this high performance resource.
- Scratch space is only to be used for data that is actively being processed.
- The system quota (above) will allow data up to 20T to be stored for up to 30 days before new data will be prevented from being created
- Data which is older than 60 days will be targeted for deletion
Due the specialist facility nature of M3, exceptions to the above policies can be catered for and can be requested via email@example.com. We can also help make archival storage (such as RDS) available on M3 for integrating into your workflows directly.
System Backups and File Recovery¶
The data storage on M3 is based on Lustre which distributes data across a number of disks and provides a mechanism to manage disk failures. This means that the M3 file system is fault tolerant and provides a high level of data protection.
In addition to this, the home directories are backed up to tape every night. This means that if you create a file on Tuesday, on the following day there will be a copy of the file stored in the backup system. Backups are kept for 30 days, before the system permanently removes the file to make space for new data.
|File System||Type||Quota||Policy||How long are backups kept?|
|Home Directory||NFS||Yes||Daily Backup||30 days|
|Project Directory||Lustre||Yes||Daily Backup||30 days|
File Recovery Procedure¶
If you delete a file/directory by mistake, you will be able to recover the file by following the following the following procedure:
- Email a request to firstname.lastname@example.org.
- Please include the the full path to the missing data, as well as information on when it was last seen and when it was deleted
- We will be able to restore files modified within the 30 day window. Beyond that time, any changes in the file will be lost.
The project scratch space is not backed up. Files are purged from this space as new space is required.
Information for Desktop Users¶
Desktop users should be aware that many application and Desktop defaults dump data to your home directory. Care must be taken when dealing with large files as these can create large amounts of hidden data and that can cause your home directory to go over quota.
The following is some information for solving common issues:
Thumbnails Generating Too Much Data¶
The act of viewing large amounts of images in a file browser cause the generation of many Gigabytes of thumbnail images. To fix:
- Go to Applications - System Tools - File Browser
- At your File Browser, Go to Edit - Preference
- At preference, Go to Preview
- At Other Previewable files - Show thumbnails - Change to ‘Never’
- Ok .
Remember to empty your trash folder¶
Some users may still encounter disk quota full messages when they have already removed many files from their Home directories.
Files in the trash folder count towards a user’s home directory quota.
Ensure that you clear your trash folder when you exit your MASSIVE Desktop Session.
Already over quota?¶
If you are over quota, and cannot login via the desktop, you can login using a login shell and use the commands described above in “Tools for Helping Manage Files”.
Storage outside of M3¶
With your M3 project, you have an allocation of storage on its high performance Lustre file system. This storage space is intended for data analyses and has a limited capacity. For large-scale, secure, and long-term research data storage, Monash University has the following offerings available through VicNode:
Vault– primarily used as archive, is a tape-based system specifically for long-term storage; this is best used to free up space on your M3 project, allowing for more data to be staged into your project for analyses. For further information, please visit: https://vicnode.org.au/products-4/vault-tape-mon/
Market– is backed-up storage intended for active data sets and is accessible through the Windows, Linux, or Mac desktop environments at your research laboratory for convenient sharing of data files. For further information, please visit: https://vicnode.org.au/products-4/market-mon
Instructions to access Ceph Market¶
Update: 16th August 2018
Issues with connecting with the method below have been resolved. Please note that unmounting is using a different flag.
Market allocation is presented as a CIFS share with a given name,
usually of the form:
RDS-R-<Faculty>-<Name>. This share can be
mounted within an M3 Desktop session as follows:
1. Open a Terminal window within your M3 Desktop session and issue this command:
- Replace the
<sharename>with the one provided by your allocation;
- Enter your Monash ID (previously known as Authcate) username, when prompted;
MONASHwhen prompted to enter the “Domain”; and
- finally your Monash ID password on the “Password” prompt.
gvfs-mount is not available on M3 login nodes, use desktop
(Strudel) to access the share.
2. If successful, the mounted share will be visible through the file browser. If the user is not a member of the group, an “access denied” message will be displayed.
3. It is best to cleanly
unmount the share when it is no longer needed,
by using this command:
gvfs-mount -u smb://storage.erc.monash.edu.au/shares/<sharename>
However, the share will be automatically unmounted once the desktop session terminates.
The collection owner will/should be able to add and/or remove collaborators who
can mount the share; through the eSolution’s Group Management page:
https://groupadmin.monash.edu/ On this page, a list of shares that you have
admin privileges will appear, each of this shares will appear as:
Important Note: It is a known issue that the available storage for the share is incorrectly reported. Users are advised to simply ignore the warning, and allow a copy/move to proceed. We are unable to add non-Monash users to mount a share, since this authenticates against the Monash AD.
Instructions to access Vault¶
In the meantime, please contact: