running vcell on local hpc

[Junhao Gu]

Hi,

I have sent an email to the support address, but I would like to post one here in case others might have similar question.

I would like to run vcell on our local hpc cluster as my model is quite big (large network with 3D reaction diffusion) and running with vcell server does not support with large memory. I have no problem running it with my laptop as it has large memory but the simulation takes days and I would not be able to turn off my laptop. It would be great if someone can give an instruction on how to run vcell with hpc cluster through terminal.

Further, I would like to know whether now vcell supports multicore/multinodes or gpu acceleration as this would be very useful when we assign computing resources for the job. I know that someone else had asked this couple years ago, and vcell did not have such feature, I wonder whether there is any update on this regard.

Normally we need to login with vcell account, if running on local cluster through terminal is possible, would logging problem be an issue, as one might run multiple jobs with hpc with the same account.

Thank you

Best,

Junhao Gu

[Blinov,Michael]

Hi Junhao,

To understand VCell resources utilization, you can check Account -> View Simulation jobs.

You can install VCell at your local hpc server following instructions on Building and Running VCell Client/Server at https://github.com/virtualcell/vcell, but it’s very elaborate multi-strep process. 

Unfortunately, there is no multicore/multinodes or gpu acceleration.

Hope it helps,

Michael

On Sep 28, 2020, at 7:11 PM, Junhao Gu <jun...@uci.edu> wrote:

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