Data Storage

Add storage to Neurodesktop

Drag and Drop

Uploading files

You can drag-and-drop files into the browser window to get files into Neurodesktop. This will then start a file upload:

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Downloading files

To download files from the desktop using the same mechanism you will need to open the guacamole settings by pressing CTRL-ALT-SHIFT (Control-Command-Shift on Mac). This will open a menu on the side:

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where you can click on “Shared Drive”:

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a click (or double click on Mac) on the file will start the download.

You can browse into folders in the shared drive by clicking (double clicking on Mac) on them. To get back to the base of the shared drive, press on the drive icon in the top left of the side menu (just below the “Shared Drive” title).

To close the side menu, click on CTRL-ALT-SHIFT once more (Control-Command-Shift on Mac).

Note that it is only possible to upload or download one file at a time through this interface. If you have multiple files in a directory we recommend zipping the directory and then transferring one zip archive:

zip files.zip files/

Local storage

If you are running Neurodesktop on your own hardware there will be a direct connection between the “Storage” folder on the Desktop, which is a link between “/neurodesktop-storage” in neurodesktop and the “neurodesktop-storage” folder on your C-drive (Windows) or home directory (Mac/Linux). This connection can be used for data processing and data transfer.

Mounting external storage on your host-computer

The -v C:/neurodesktop-storage:/neurodesktop-storage part of the docker command links the directory “neurodesktop-storage” on the “C drive” of your Windows computer to the directory /neurodesktop-storage inside the Desktop environment. Everything you store in there will be available inside the desktop and on the host computer. You can also mount additional directories by adding another -v parameter set (e.g. -v D:/moredata:/data) - this will mount the directory moredata from your D drive to /data inside neurodesktop. Important: the mountpoint inside neurodesktop needs to be named /data, otherwise the applications will not see the files without modifying the SINGULARITY_BINDPATH variable in your .bashrc.

If you are using the NeurodeskApp, you can set an additional storage location through the settings

If you are starting Neurodesk through the command line, here is an example for Windows adding another storage directory:

docker run --shm-size=1gb -it --privileged --user=root --name neurodesktop -v C:/neurodesktop-storage:/neurodesktop-storage -v D:/moredata:/data -p 8888:8888 -e NEURODESKTOP_VERSION=2024-05-25 vnmd/neurodesktop:2024-05-25

Note for Windows users: Connecting network shares from Windows to Neurodesk can cause problems, so be careful when attempting this. Also, be aware that processing large amounts of files stored on a Windows filesystem inside Neurodesk will come with a performance penality due to the file system translation in the background. One option to get around these problems is to directly accessing your storage infrastructure inside Neurodesk.

Cloud storage

Another way to get your data into Neurodesktop is to use a cloud storage provider like Dropbox, OneDrive, OwnCloud, Nextcloud or more general tools like rclone or davfs2. Another good option could be to utilize Globus for large amounts of data.

Nextcloud and Owncloud desktop clients

Under the menu item “Accessories” you can find “Nextcloud” and “ownCloud” desktop sync clients that you can configure with your cloud service accounts.

Mounting webdav storage using davfs2

Another option is to directly mount webdav storage. Here is an example how to mount OwnCloud Storage into Neurodesktop:

sudo mount -t davfs https://yourOwnCloudInstance.com/plus/remote.php/webdav/ /data/

It then asks you for a username and password, which you can generate in the settings: yourOwnCloudInstance/plus/settings/personal?sectionid=security

Rclone

Rclone is a command line tool that enables interaction with various cloud services. Here is an example how to setup rclone with an OwnCloud account:

  • start the configuration in a terminal window rclone config
  • Create a new remote: n
  • Provide a name for the remote: OwnCloud
  • For the “Storage” option choose: webdav
  • As “url” set: https://yourOwnCloudInstance.com/plus/remote.php/webdav/
  • As “vendor” set OwnCloud: 2
  • Set your OwnCloud username after generating an access token yourOwnCloudInstance/plus/settings/personal?sectionid=security
  • Choose to type in your own password: y
  • Enter the Password / Token from the OwnCloud App passwords page and confirm it again:
  • Leave blank the bearer_token: <hit Enter>
  • No advanced config necessary: <hit Enter>
  • accept the configuration: <hit Enter>
  • Quit the config: q
  • Now we can download data to the HPC easily: rclone copy --progress --transfers 8 OwnCloud:/raw-data-for-science-paper .
  • or upload data to OwnCloud: rclone copy --progress --transfers 8 . OwnCloud:/data-processed

Globus

We also provide the globus client, so you can transfer large amounts of data between globus endpoints and Neurodesktop. You can configure it by running the following commands in the Neurodesktop environment:

ml globus
# First run the setup:
globusconnectpersonal -setup

#Follow the instructions in the terminal: 
#1) copy the URL into a browser and generate the Native App Authorization Code
#2) then copy this code and paste it in the terminal
#3) then name the endpoint, e.g. Neurodesktop

# Then start the GUI:
globusconnectpersonal -gui

# If the connection fails, reset the permissions on the key file:
chmod 600 /home/jovyan/.globusonline/lta/relay-anonymous-key.pem

# If the connection still fails, start the client like this to get more information
globusconnectpersonal -debug

Then add the directories you want to share with globus, by opening File -> Preferences:

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and then add the paths required and hit Save:

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Then you can go to the globus file-manager https://app.globus.org/file-manager and your neurodesktop instance will be an endpoint for globus. You can change the path to any location you specified in the Preferences:

image

Mount volume using SSHFS

It is theoretically possible to mount an SSH target inside Neurodesktop, but it’s not a very reliable way of mounting storage:

sshfs -o allow_root USER@TARGET_HOST:TARGET_PATH SOURCE_PATH

A better option is to use scp and copy data from an SSH endpoint:

scp /neurodesk/myfile user@remoteserver:/data/

An alternative is to mount the SSHFS target into a parent directory on your local machine or VM and then use the -v option in the docker run command to bind the parent directory of the SSHFS mount. NOTE: the SSHFS has to be mounted to a subdirectory inside a parent directory which is then bound to the docker container. If you directly bind to the mounted directory itself, your Neurodesktop container will stop being able to access it if the SSHFS mount disconnects and will not be able to access it again without restarting the Neurodesktop container.

For example, on a local Linux machine or VM:

sshfs -o allow_root USER@TARGET_HOST:TARGET_PATH/MyData SOURCE_PATH/SSHFS_Mounts/MyData

Then add the following line to the docker run command when starting Neurodesktop (note the rshared flag):

-v /SSHFS_Mounts:/data:rshared \

TIP: If you use key pair authentication instead of password for your SSHFS mount, you can use the reconnect flag to reconnect automatically if the connection drops:

sshfs -o IdentityFile=~/.ssh/id_rsa,allow_root,ServerAliveInterval=5,ServerAliveCountMax=3 USER@TARGET_HOST:TARGET_PATH/MyData SOURCE_PATH/SSHFS_Mounts/MyData