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rookie experience (2019)

Rookie experience with the cluster (from 2019)#

Here the CECI documentation for creating an account and accessing the cluster. But please do check in the folder where this google doc is saved for quick tips for creating an account.

  1. Access the cluster: things have changed after august 2020, if you had an account before this date you need to follow all the steps explained here again. It is very important that you follow all the steps in this link (e.g. get a private ceci key, configure ssh, …) They also provide troubleshooting tips.

  2. Avoiding providing password/passphrase all the time you access to the cluster:

Doing ssh clustername does not work in a vanilla way as before, you may need to insert the pss every time or try this:

ssh-add -k ~/.ssh/id_rsa.ceci ssh-add -l ssh clustername

clutername should be replaced by the cluster you want to join, e.g. lemaitre3

Finally, if everything is working, the next time one logs in, the following should be fine:

ssh lemaitre3
  1. Troubleshooting: (26/04/2021 onwards)

Issues with connecting with the cluster.(even after following steps 1 and 2.)

Solution: Since CISM changed the server gwceci.cism.ucl.ac.be .

Go to: /Users/your_local_username/.ssh/known_hosts

Warning

In your local machine, you need to go to the folder where you keep the .ssh folder. And in that folder you need to navigate to known_hosts. You can type as follow in the terminal

atom ~/.ssh/known_hosts

Remove or comment line 4 as shown below. According to your known_hosts file, the line number can vary. !

Tip#1: Used Atom, as evident from above, easy to edit, and save.

Tip#2: While using OpenConnectVPN from home, set preferences to IPV4 (and not IPV6).

Then repeat the step2. You should log in. And if you can log in, that’s all! This action will add another line in knownhosts document, starting with gwceci.cism.ucl.ac.be as can be seen in above _line 6.

  1. Although one ssh to the cluster, the main folder is the root (cd ~). One can also find which folder you have access to, e.g. if you are under IPSY like most CPP-members, by navigating to:
cd /home/ucl/irsp/ cd $HOME cd $GLOBALSCRATCH
  1. You can check where you are - which folder is your home in the cluster- with below command
pwd
  1. Move file to the cluster and back:
scp -r mydir/ clustername:cluster/dir/

scp -r clustername:cluster/dir/ mydir/

Note: The commands above need to be entered in a terminal that is logged into the local machine not in the cluster-logged terminal.

Example to load a file:

scp sub-x001_ses-001_T1w.nii
lemaitre3:/home/ucl/cosy/battal/RhythmCateg/RhythmCateg_Anat

Running FreeSurfer recon all stuff#

First one would need to create scripts, which should be under this format.

Then follow the above examples for carrying your folder of input into the cluster folder.

Copy from your local to the cluster:

scp -r MovieBlind_Anatomicals lemaitre3:/home/ucl/irsp/morezk/MovieBlind

Copy from the cluster to the local

scp -r
lemaitre3:/home/ucl/irsp/morezk/MovieBlind/MovieBlind_Anatomicals/fs_output
~/Desktop/

Copy scripts

scp -r run_reconall.slurm lemaitre3:/home/ucl/irsp/morezk/MovieBlind
scp -r run_reconall_batch.slurm lemaitre3:/home/ucl/irsp/morezk/MovieBlind

Lastly, when running scripts use sbatch instead of sh

This is wrong:

sh ./

Try:

sbatch submit.slurm

How to check if the job is working/submitted successfully?#

For more general information please see this link.

Some quick and helpful guides: slurm workload manager

One can type to check if their job is R: RUNNING, PD:PENDING

squeue

If one uses this website to generate their bash script, they will also get a notification email when the job is started and done including the job-id.

How to read the slurm<jobID>.out files?

.out are error /log files.

cat slurm $jobID>.out

Running container stuff, example with mriQC#

To create the singularity image:

singularity pull --name ~/sing_images/mriqc_0.15.2.sif
docker://poldracklab/mriqc:0.15.2

To run singularity:

    singularity run --cleanenv \
    --bind ~/data/V5_high-res_pilot-1/raw:/data \
    --bind ~/data/V5_high-res_pilot-1/derivatives/mriqc:/out \
    ~/sing_images/mriqc_0.15.2.sif \
    /data /out participant \
    --participant_label pilot001

Resources#

Lecture slides on singularity : Packaging software in portable containers with Singularity

Recorded Event(lecture) : on Teams

Tips#

Command to navigate the folders and open text files in a terminal “gui”

mc

Other#

  • There is Cloud computing (what Remi was suggesting, virtual machines) and Cluster computing. UCL only supports cluster computing for the moment.

  • To install new software:

  • They can install it

  • They can be installed in the home directory of the user by the user. (At our own risk)

CPPlab software#

  • Matlab
  • SPM
  • Conn
  • PyMVPA (Python compatible) -installed in Lemaitre 3
  • Freesurfer -installed in Lemaitre 3
  • FSL
  • Mrtrix -installed in HMEM

https://nl.mathworks.com/products/compiler/matlab-runtime.html https://en.wikibooks.org/wiki/SPM/Standalone