Tutorials

Tutorials and how-to guides on a wide range of topics relating to the DCSR.

DCSR NAS

How to access the DCSR NAS

If you don't have a DCSR NAS (Network Attached Storage) storage yet and you would like one, the PI (Principal Investigator) of your project needs to fill up a request application form on the following web interface:

https://conference.unil.ch/research-resource-requests/

Once the DCSR has accepted the request and the access has been granted to you by your PI, you will be able to access your DCSR NAS storage by one of the following method:

Access from a laptop

laptop <-> NAS instructions

Access from the cluster

If you have access to the compute clusters of the DCSR, the data stored on the NAS is directly accessible under /nas. See:

cluster <-> NAS instructions

In case you have asked for the "sensitive data" special option for your storage, please follow the specific instructions to access RECHERCHE-S on the following page:

How to manage sensitive data on UNIL NAS

General structure of the NAS

The general structure of the directories on the DCSR NAS (Network Attached Storage) is:

nasdcsr.unil.ch/RECHERCHE/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project>

On mac

smb://nasdcsr.unil.ch/RECHERCHE/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project>

On Windows

\\nasdcsr.unil.ch\RECHERCHE\FAC\<your_faculty>\<your_department>\<your_PI>\<your_project>

 

In case you have asked for the "personal data" special option for your storage, please use RECHERCHE-P with:

nasdcsr.unil.ch/RECHERCHE-P/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project>

On mac

smb://nasdcsr.unil.ch/RECHERCHE-P/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project>

On Windows

\\nasdcsr.unil.ch\RECHERCHE-P\FAC\<your_faculty>\<your_department>\<your_PI>\<your_project>

 

In case you have asked for the "sensitive data" special option for your storage, please follow the specific instructions to access RECHERCHE-S on the following page:

How to manage sensitive data on UNIL NAS

What are the /D1c, /D2c, and /LTS subdirectories?

In your project directory you will see at least a D2c and a LTS directory, with the following meanings/purposes:

<your_project>/D2c

D2c means "data 2 copies". This directory has an off-site backup. This is where you can put your research data during the life time of your project. Please note that in case you are using the HPC cluster and perform computations on this data, your are advised to copy this data to a fast storage (i.e. /scratch or /work) to speed up computations (see this page).

<your_project>/LTS

LTS means "Long Term Storage". This data will be kept for a very long time on the UNIL storage (a decade, on tapes). This is where you should put the part of your data that needs to be archived e.g. at the end of your project. When you reach this point, you will then be asked to make a description of your data ("meta-data"). See "Long-term storage of research data" section here: 

https://www.unil.ch/openscience/en/home/menuinst/open-research-data/gerer-les-donnees-de-recherche-research-data-management/stockage--securite.html

Users who explicitly asked for it will also have a D1c directory:

<your_project>/D1c

D1c means "data 1 copy". This data has no backup (and may be lost). This is where you can put e.g. some reference data that you downloaded from an external source, and that can easily be recovered again from the same external source, in case the data get lost in /D1c.

Long term storage at DCSR and other data repositories

 

Data management

This page presents the way to move data between the different locations used for either processing or storing data. The three main locations are hereafter referred to as: laptop, cluster, and NAS.

Laptop <-> Cluster

Note: If you work from home, you first need to connect to Unil's VPN using Pulse Secure (see VPN instructions).

To copy data between your laptop and a cluster you will have to use scp (secure copy).

Linux/Mac

Linux and Mac users simply have to open a terminal.

From laptop to cluster: $ scp /path/to/fileToCopy <username>@<server>:/path/to/dest

From cluster to laptop: $ scp <username>@<server>:/path/to/fileToCopy /path/to/dest

Where:

<username> your UNIL username
<cluster> wally or axiom
<server> <cluster>-front1.unil.ch

Examples

To copy file "file.txt" to your home directory:

scp file.txt ulambda@wally-front1.unil.ch:~

To copy the entire directory "dirA" to your home directory:

scp -r dirA ulambda@wally-front1.unil.ch:~

Windows

Windows users can use WinSCP.

Step 1: create a new session

image-1591861598320.png

Step 2: enter the configuration elements (SCP file protocol, hostname, and credentials). Finally, save the session details

 

image-1591861942154.png

Step 3: enter an explicit session name

image-1591862150318.png

Step 4: login

image-1591862176391.png

Step 5: enter your password

image-1591862202616.png

Step 6: navigate through folders (1 is for local files, 2 is for cluster files) and copy the files in one way or the other

image-1591862220621.png

 

Laptop <-> NAS

Note: If you work from home, you first need to connect to Unil's VPN using Pulse Secure (see VPN instructions).

Samba server

Windows

Step 1: right click on Network in File explorer and choose "Map network drive…"

image-1591798613766.png

Step 2: enter the address of the Samba server and click to finish

Ie9map01.PNG

Step 3: enter your Unil credentials and clikc "OK"

map02.PNG

Step 4: click on "This PC" and then on the new network drive

map03.PNG

 

Linux

It is possible to use a GUI but there are as much solutions as desktop managers. So here is a way to mount the NAS using command line interface. Don't forget to adapt the username= field in the sudo mount command!

# First install the packages
# Debian/Ubuntu version
$ sudo apt install samba cifs-utils
# Fedora/RedHat version
$ sudo dnf install cifs-utils

# In the following, ~/nas is chosen as a mountpoint, but it could be elsewhere
$ mkdir ~/nasdcsr
$ sudo mount -t cifs -o username=unil_username,domain=ad,rw,iocharset=utf8,dir_mode=0700,file_mode=0700,uid=$(id -u) //nasdcsr.unil.ch/RECHERCHE ~/nasdcsr

# Perform the reauired operations
$ cd ~/nasdcsr
…

# When finished, don't forget to umount it
$ sudo umount ~/nasdcsr

 

Mac

Step 1: open the Finder, in Go menu, select "Connect to Server"

image-1591856270964.png

Step 2: enter the NAS url (smb://nasdcsr.unil.ch/RECHERCHE), you also may add this server as a favourite by clicking on + symbol

image-1605528817646.png

Step 3: enter your credentials

image-1605528837404.png

Step 4: navigate through the directories to find your working directory and push/fetch files as you see fit

image-1605528863048.png

Cluster <-> NAS

Note: If you work from home, you first need to connect to Unil's VPN using Pulse Secure (see VPN instructions).

From the login nodes the NAS is available under /nas. The folder hierarchy is:

/nas/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project>

Cluster -> NAS

To copy a file to the new NAS:

cp /path/to/file /nas/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project>

To copy a folder to the new NAS:

cp -r /path/to/folder /nas/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project>

For more complex operations, consider using rsync. For the documentation see the man page:

man rsync

or check out this link.

NAS -> cluster

As above, just swapping the source and destination:

cp /nas/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project>/file /path/to/dest
cp -r /nas/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project>/folder /path/to/dest

Accessing DCSR NAS from CHUV network

Windows and Mac users can install the graphical desktop client from DataExpedition as well if they wish so:

Download Expedat from here, installation instruction from here, and product documentation from there.

Here is an example of ExpeDat session: