Request for configuring a different version of Cytosim

IFB Core Cluster Tool or data bank request
1

I recently requested a project under the name 'bcpolarity'. Everything is fine but I need to configure a specific version of "Cytosim" that's different from the two versions in the module currently.
I tried configuring it manually but it didn't allow me to do so as I am not a pseudo user. I totally understand this, so if you could configure it for us that will be a great help. The version we want can be found here: Cytosim codebase extensions for a 3D T cell model

Thanks in advance.

Kind regards,
Mostafa

2

Hello @mostafa_elraies,
ok, I will try and deploy this particular cytosim version.
Regards,
Loraine

3

Dear Loraine,

Thank you so much. That will be of great help.

Best regards,
Mostafa

4

This is installing: Add cytosim 20210129-t_cell_model (!1444) · Merge requests · Institut Français de Bioinformatique / Cluster / tools · GitLab

5

This is installed: module load cytosim/20210129-t_cell_model

6

Dear Loraine,

Thanks for your effort. I just tried to run some simulations but I got an error as it cannot find a shape I choose. I have the same version on my local computer and it works perfectly.
Maybe the issue is that you configured the 2D version but not the sim/play/report for the 3D? I am not sure.

Thanks for your understanding and help.

Kind regards,
Mostafa

7

Yes I did, you can test with sim3, play3, report3

Could you please send me your error message ? (and the command run)

8

I didn't know that I had to call it using sim3, report3. I think that was the problem. Now it seems that the simulation is running.
Thanks a lot.
I will let you know in case I received an error.

Kind regards,
Mostafa

9

Indeed, instructions do not appear as they should, I am fixing this: Add instructions for cytosim (!1445) · Merge requests · Institut Français de Bioinformatique / Cluster / tools · GitLab

Cytosim is compiled for 1D, 2D and 3D dimensionality, accessible with sim1/play1, sim2/play2 and sim3/play3. Default is 2D (sim/play).

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10

Dear Loraine,

Thanks a lot for your assistance. Now it works perfectly.
I have an inquiry I think you might know the answer for. So after running the simulation we usually use the play attribute to build images that we then use to make a video.
When I tried doing this before it give me the error that it cannot open display. How I solved this on my computer was by configuring XLaunch which solved this problem. May I know which module do people usually use for such cases?

Thanks in advance.

Kind regards,
Mostafa

11

Dear Mostafa,
Do not forget to connect to the cluster with the -Y option to enable the display ssh -Y <username>@core.cluster.france-bioinformatique.fr. This should be enough to use the play command of cytosim.
Regards,
Loraine

12

Dear Loraine,

I hope you are doing well.
So I was already putting -Y before, but still it didn't work. I tried connecting via MobaXterm instead and it seems that when I go to the directory of simulation and run the play3 it works, however, when I use sbatch it doesn't work.

Could you please help me solve this issue?

Kind regards,
Mostafa

13

Could you try with SLURM Running interactive jobs - IFB Core Cluster Documentation ?

14

I tried doing so, but when I go to the new node and try module load, it says module: command not found.

Regards,

15

Can you try to load the module BEFORE entering sinteractive mode ?