# FAQ on lab storage
This page lists frequently asked questions related to lab storage.
- General archiving
- Iaas and blue storage
- What storage do I get on iaas and blue machines?
- Where is my data?
- How can I transfer data to my iaas and blue machines?
- Where should I store my data on iaas and blue machines?
- Do iaas and blue machines have backup?
- What happens to my data when iaas and blue machines are destroyed?
- My scripts require data storage outside of the /home folder
# What storage does my lab have?
You will find the following storage volumes inside your home machine in your lab:
|home|| ||Private space for lab users||None|
|work|| ||Workspace for all lab users||Nightly snapshots*|
|scratch|| ||Temporary files||None|
|archive|| ||Long term archiving||Nightly snapshots*|
(*) The nightly snapshot for file changes are intended to protect against accidental deletion and accidental overwrites.
# How can I see the sizes of my lab volumes?
Log into your home machine in your lab with your favourite terminal and type:
df -h | grep -E '(^Filesystem|/dev/vd)'. This will give you an overview of the storage resources (volumes) that are allocated to your lab machine. Example output that list attached volumes:
$ df -h | grep -E '(^Filesystem|/dev/vd)' Filesystem Size Used Avail Use% Mounted on /dev/vda1 9.7G 7.2G 2.6G 74% / /dev/vdb1 99G 60M 94G 1% /home /dev/vdc1 197G 61M 187G 1% /mnt/work /dev/vdd1 493G 71M 467G 1% /mnt/archive /dev/vde1 197G 60M 187G 1% /mnt/scratch /dev/vdf1 99G 60M 94G 1% /mnt/cargo
# How can I find out what is taking the most space on volume?
# How can I move my tmp out of the root?
Log into your home machine in your lab with your favorite terminal and type:
echo "export TMPDIR=/mnt/scratch/tmp" >> ~/.profile source ~/.profile mkdir -p $TMPDIR
Move tmp on blue and iaas machines
To move tmp for the default ubuntu user on blue and iaas machines:
# Move tmp folder out of the system disk echo "export TMPDIR=/home/ubuntu/tmp/" >> ~/.profile source ~/.profile mkdir -p $TMPDIR
# Why is home only 100G?
The intention behind HUNT Cloud is to establish collaborative lab environments where people become stronger together by sharing data, code, results and knowledge. We have therefore kept the private
home volume to a minimum to encourage lab users to move their activities into collaborative volumes such as work, archive and scratch. Order a volume expansion in our service desk of these volumes if you are in need of space.
There is -no- restore (backup) on your home-folder. All data in
home may be lost in case of unexpected events. We strongly recommend that you keep the scientific data that your care about on the
archive folders. Click here to read more about restore.
See our data management FAQ in our Coordination section for information on volume expansions.
# Can other lab users access my data?
Yes. HUNT Cloud is a collaborative computing platform where mutually trusted people work together in dedicated lab environments. Therefore, all lab users inside your lab may by access data that you store in work, archive, scratch and cargo. This may include both your scripts and your results. Contact us if you have data that need further protections, as we are happy to establishing dedicated labs in such circumstances.
# Can anyone access my home folder?
Yes. More precise, other lab users will not be able do access data in your home folder direclty. However, data in your lab is under the control of your data controller. This includes data that you upload and generate, also data in your private home folder. This is stated in our user agreement. Thus, your data controller or lab leader may request us to transfer data from your home folder into other folders that are accessible for other lab users or for compliance archiving, for example if you leave your lab. We will not expose your system keys during such moves.
# How can other lab users edit my files by default?
Depending on your lab configuration, the files you generate may be read-only for other users. You may relax these permissions to read-write for any new files you create by adding
umask 002 to your
~/.profile file (more on umask (opens new window)), for example by running this snippet in the command line inside your home machine:
echo " # -- set default file permissions for user and group to read-write umask 002" >> ~/.profile; source ~/.profile
# Can I restrict permissions to files within my lab?
Yes. Sometimes you might want to restrict write permissions to avoid accidental overwrites or accidental deletions of valuable data in your
home-machine. You may restrict the write access to files with the
# -- restrict write privileges for individual file chmod 600 <filename> # -- Restrict write privileges for all files in a folder chmod 600 -R <foldername>
Log into your lab and test the privileges settings:
# move to scratch cd /mnt/scratch # Make a test file touch test.txt # Restrict write privileges to you only chmod 600 test.txt # Check privileges ls -lh test.txt
We do -not- recommend using
chmod to restrict access to data within your lab for confidentiality purposes. All data within a lab will principally be accessible for all lab users in our agreement framework. Contact us for a dialogue on heightened security measures if you need increased data confidentiality.
See our Data coordinator FAQ for questions regarding backup and restore.
# General archiving
# How do I zip and unzip files in my lab?
We recommend using the 7z software to compress and decompress files and folders. Read our 7z guide to get going.
# Iaas and blue storage
This section list commonly asked questions for storage our unmanaged iaas and blue machine types that you maintain yourself.
# What storage do I get on iaas and blue machines?
Default iaas and blue machines comes with a 1TB empty volume attached to your
/home folder. That is the same folder as you log into with the default user (
/home/ubuntu). You can request other storage sizes according to your need before deployment.
# Where is my data?
Your data is located on your home machine. You will need to (1) transfer data to your iaas and blue machine for analysis, and (2) transfer your your results back to your home machine for long term preservation afterwards.
# How can I transfer data to my iaas and blue machines?
rsync for data transfers between your home machine and iaas and blue machines. This will sync up your data and only transfer files that has changed since your last transfer.
# -- Principal example rsync <options> <source> <destination> # -- Principal example from your home machine to your iaas machine rsync -avhP <home-folder> ubuntu@<iaas-macine-name>:<iaas-folder> # -- Practical example from your home machine to your iaas machine: rsync -avhP /mnt/scratch/data/ ubuntu@demolab-blue-sarga:~/data/
# Where should I store my data on iaas and blue machines?
You are free to create the directory structure that fits your needs under the
/home folder in your iaas and blue machines. For example, under the default login folder (
# Do iaas and blue machines have backup?
Your iaas and blue machines have NO backup installed by default. You will need to transfer your results back to your
/mnt/work folders on your
home machine for restore provided by us.
# What happens to my data when iaas and blue machines are destroyed?
All data on iaas and blue machines will be lost when your machine is reclaimed. It is your sole responsibility to ensure that you transfer the data that your care about from your iaas and blue machines back to your home machine for long term preservation.
# My scripts require data storage outside of the /home folder
When you need to store larger chunks of data outside of your
bind mounts is a handy tool. With a bind mount you can create whatever path you need on the file system and map it back to a suitable location under your
/home folder. Such trick might be handy if you want to transfer the exact same scripts from your
home machine (not to be confused with the
/home folder on your iaas and blue machines, sorry...) to your new iaas and blue machines:
# -- Principal example: sudo mkdir -p /path/outside/home sudo mount --bind /home/directory/stucture /path/outside/home # -- Working example: sudo mkdir -p /home/ubuntu/workflow sudo mkdir -p /mnt/work/workflow sudo mount --bind /home/ubuntu/workflow /mnt/work/workflow ls /mnt/work/workflow