Introduction

ALICE is the new university-wide HPC cluster that is currently in development. In addition to research, Alice can also be used for courses and by students. Currently ALICEdoes not yet support all the features that Shark does (e.g.: hardware accelerated graphics), however implementation of these is planned for the near future. We would advice potential HPC users (who are not working on the LUMC Shark cluster already) to start on ALICE right away, so that a switch later on will not be necessary.

https://wiki.alice.universiteitleiden.nl/images/8/82/Alice.png

Resources

General information:  The best source of information on ALICE is the official New ALICE Wiki (Old ALICE Wiki.)

FSW specific issues:  For FSW specific topics, i.e. fMRI analysis, Matlab usage, data-transfer etc, we will provide additional information on the page below.

Accounts & Contact: to request an account, please see here. For all questions about ALICE usage and accounts please contact ALICE helpdesk: helpdesk@alice.leidenuniv.nl

FSL

To use FSL on the ALICE cluster, do not use the default FSL module. Instead load the following (in order):

  • module load Mesa/20.0.2-GCCcore-9.3.0
  • module load LUMC
  • module load neuroImaging/fsl/6.0.4

fMRIPrep

fMRIprep is a pipeline of fMRI processing tools that allows for highly reproducible analyses. Usage of fMRIPrep on ALICE is possible using Singularity containers. Please note that Singularity itself is just a container technology, and you still need an fMRIPrep image.

Available versions

There are two standard fMRIPrep images already on ALICE that you can use. You can find them in:

/cm/shared/singularity_images/f/

To use them, first load the Singularity module (for the default version use):

module load Singularity

Then run one of the singularity images and specify the required paths. Note that if you want to read/write data to either /data1/ or /scratchspace/ folders these need to be mounted explicitly to the container (Home is mounted by default), e.g.

$ singularity run --cleanenv -B /data1/path_to_your_folder,/scratchdata/path_to_your_folder  /cm/shared/singularity_images/f/fmriprep-20.2.3.simg \
    path/to/data/dir path/to/output/dir \
    participant \
    --participant-label label

For pointers on how to run fMRIPrep with SLURM sbatch scripts, please see here.

Freesurfer

The use of freesurfer in fMRIprep requires a freesurfer license, the path to this license needs to be specified in the singularity call.

Custom containers

Alternatively, you can download an image to your home folder and use that (follow the instructions here). Keep in mind that fMRIPrep may not be specifically optimized for the SLURM scheduler on ALICE and may either need custom adjustments or may submit jobs in a sub-optimal way.

SPM

SPM software package for Matlab allows for the analysis of brain imaging data sequences. For now, SPM is not offered on ALICE as a module, instead you can install it yourself in your home directory. See here for information on installing SPM.

MRIcron

MRIcron is a cross-platform NIfTI format image viewer. You can download it to your home directory. To use it, we recommand using X2Go to connect to ALICE.

X2Go

For instruction on how to use X2Go with ALICE see here.

Known issues:

  • Copy-Paste from local to remote: sometimes the copy-paste functionality from the local machine to the X2Go client stops working. In most cases this is fixed by copy-pasting some text on the remote machine, e.g.: in a terminal or text-editor on the X2Go client copy and then paste some text. Afterward, the copy-paste from the local machine should work again. 

XRDP

An alternative to X2Go for remote desktop sessions, is XRDP which follows the microsoft RDP protocol. With this u can connect to ALICE using of the the default windows RDP apps or by using a third party RDP client. Please see here for detailed instructions. For some users XRDP may prove more stable (especially with regards to copy-past operations) as compared to X2Go.

Data Transfer

SFTP directly to/from scratch drive

As mentioned in the ALICE wiki, the sftp-gateway (sftp-gw.alice.universiteitleiden.nl) does not support direct access to the scratch folders (/Data1). 

To circumvent this and use Cyberduck / Filezilla to get to /Data1, involves going through the regular ssh gateway and one of the login nodes.

FileZilla/Cyberduck

So what you would do is:

  1. Set up an ssh tunnel to a local port. You do this in the terminal (or powershell on windows) with the following command:
  2. ssh -L 3111:login2.alice.universiteitleiden.nl:22 [YOUR-USER-NAME]@ssh-gw.alice.universiteitleiden.nl
  3. Open Cyberduck or Filezilla and for the connection details use:
    Sftp (select from the dropdown in cyberduck, or in Filezilla by adding sftp://)
    Host= localhost
    Port: 3111
    Username = ulcn username
    Pass = ALICE password
  4. You should see all the folders in you home dir, including the symlink to /data1/ , and you should be able to open the symlink.

image-20221006152734-1.png

image-20221006152734-2.png

MobaXterm

Alternatively, if you use MobaXterm to log into ALICE (via the ssh gateway), it will give you an sftp window automatically as well.

F.A.Q.

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