To connect to CURC Open OnDemand, visit https://ondemand.igbmc.fr.
The first page of IGBMC Open OnDemand will bring you to a login prompt. Use your IGBMC IT account to login.
Features
When you have successfully logged into IGBMC Open OnDemand, you will see the landing page with the following features broken into tabs along the top of the page: Files, Jobs, Clusters (shell access), Interactive Apps, and My Interactive Sessions.
When you have successfully logged into IGBMC Open OnDemand, you will see the landing page with the following features broken into tabs along the top of the page: Files, Jobs, Clusters (shell access), Interactive Apps, and My Interactive Sessions.
In the center of the page you can see direct links to some popular interactives apps.
Files
The File menu allows you to view and operate on files in different file spaces: your home directory, mendel and space2
Selecting one of the file spaces will open a separate browser window which will allow you to navigate the space in a graphical setting similar to a file browser on a personal computer. From here you can download, upload, create, delete, and open files.
Jobs
Jobs can be monitored, created, edited and scheduled with the job management tools under the Jobs menu.
- Active Jobs: Under the “Active Jobs” tab you can view active jobs. You can choose to view your jobs or all jobs. From this menu you can also cancel your own jobs.
- Job Composer: Create and edit job scripts and schedule jobs under this menu.
Clusters (Shell Access)
The Clusters menu provides shell access to the login node on IGBMC cluster. The shell terminal is similar to many other tools that provide terminal access.
When starting the Terminal, you will be prompted for your IGBMC IT account password. After your password has been entered successfully (no characters is appearing on screen) your shell session on the login node will start.
From here, you can work on the cluster using command line to run SLURM commands. If you are new to SLURM, please go through our documentations :
SLURM user guide and SLURM advanced guide
Interactive Apps
The Interactive Apps menu contains options to launch certain applications that have graphical user interfaces (GUIs) for interactive use on IGBMC cluster. Each application is running in a dedicated SLURM jobs with the resources (RAM, CPU, GPU) you request.
Current supported applications include :
- CryoSPARC : CryoSPARC is a web platform fro cryo-electron microscopy (cryo-EM) images analysis
- Desktop : an XFCE environment letting your run any graphical application available on the cluster (Matlab, Relion, Chimerax, etc.)
- Icarus : Icarus is a web application for single cell RNA-seq analysis using the Seurat scRNA-seq analysis toolkit
- JupyterLab : JupyterLab is a web-based interactive development environment for notebooks, code and data
- RStudio Server : RStudio Server is web based version of the RStudio integrated development envrionment (IDE) for R
To find out more about using apps, please consult the following documents :