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iPOP-UP community forum is available at https://discourse.rpbs.univ-paris-diderot.fr/c/ipop-up. Please register in order to stay updated and use the forum to ask for help or new reference files.
Please see the complete documentation.
The slides of the training we gave in November 2022 are available here, as well as exemplary sbatch scripts as corrections of the exercices.
The presentation, exercices and corrections of the 2nd session (June 2023) are available here.
Below are the specificities of the iPOP-UP cluster.
If you had an account on the “old” RPBS cluster, your login and password are unchanged. Otherwise we’ll create a new account for you. In any case you have to ask for a project.
To create an account and/or a project, write an email to ipop-up-account-request@rpbs.univ-paris-diderot.fr with the following information:
We’ll create your account and/or project in the following hours/days. Once your account is ready, you’ll receive an email with your password.
Server : ipop-up.rpbs.univ-paris-diderot.fr
You can connect to iPOP-UP server only via ssh
for now. To do so, use your terminal and type the following command replacing username
by your iPOP-UP username (last name in lower case usually).
You@YourComputer:~/PathTo/RNAseqProject$ ssh username@ipop-up.rpbs.univ-paris-diderot.fr
You will have to enter your password and then you’ll be connected.
You@YourComputer:~/PathTo/RNAseqProject$ ssh username@ipop-up.rpbs.univ-paris-diderot.fr
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# |_|_| \____/|_| \____/|_| #
# #
# Hosted by: #
# Ressource Parisienne en Bioinformatique Structurale #
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# All connections are monitored and recorded. #
# Disconnect IMMEDIATELY if you are not an authorized user! #
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username@ipop-up.rpbs.univ-paris-diderot.fr's password:
Last login: Tue Jan 25 15:21:45 2022 from 172.28.18.162
Bienvenue sur le cluster iPOP-UP.
Pour toute question ou demande de support, rejoignez-nous sur le forum de RPBS : https://discourse.rpbs.univ-paris-diderot.fr
Pour changer le compte projet par défaut : sacctmgr update user $USER set defaultaccount=<project-name>
project1 [--------------------] 3 / 1024 GB
project2 [#-------------------] 913 / 10240 GB
Update: 2022-01-21 16:00 - default account in bold - More info: status_bars --help
[username@ipop-up ~]$
Once your project is created you will see it in the list, with the used and available disk space. You can access it at /shared/projects/YourProjectName
using the cd
command.
[username@ipop-up ~]$ cd /shared/projects/YourProjectName
The scheduler is Slurm. You’ll find some examples of scripts in IFB cluster quick start guide.
The only difference is that you have to use the ipop-up
partition when starting a job. You can define it using srun
:
srun -p ipop-up my_commande
or sbatch
:
sbatch -p ipop-up my_sbatch_script.sh
or directly in your sbatch script adding the line :
#SBATCH --partition=ipop-up
In order to avoid having dozens of copies of the human or mouse genome on the cluster, shared reference files are available in /shared/banks
. This folder contains :
Before running your analysis, please check if your reference is available in shared/banks
. If not, let us know what you need by email or on the community forum and we’ll add it quickly.
BiBs
2023 parisepigenetics
https://github.com/parisepigenetics/bibs |
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