How to run specific tools on GPU?

As the Galaxy tools use the CPU, but some of the tools (GROMACS) and similar are able to use the GPU for better performance as well.

Is it possible to run the galaxy or specific tools on GPU?

Kindly suggest some tutorials or help to run GROMACS on GPU through Galaxy.

@vmevada102 yes this is in theory possible. However, at least the European Galaxy server has way more CPUs than GPUs. This means while a single user can maybe profit from GPU support we can run more jobs in parallel on CPUs at the moment. So overall all users profit currently more from CPU-Gromacs.

If you really need GPU because you are running a bigger project please get in contact with us and we can find a solution. The crucial part is to setup a container with GPU support and GROMACS that can run on the given infrastructure. This is not really a Galaxy problem.

Hope that helps a little bit,

Thanks for your reply,

Sometimes, GROMACS required 1 day or more than that to run the job on CPU. If we can process it using GPU, we might be reducing the time period to run such jobs.

There are serveral users having their own system with more GPU. They might be also benfited like me.


Hi bjoern.gruening,

We discussed the usage of the Gromacs on GPU.

If you have found some resolution. Kindly share with me to run this on my server as well.

We have dedicated NVIDIA GPU card for the calculations.

Can you submit jobs to your GPU host? We have created VMs ontop of our GPUs, so that every VM just get one GPU. Then we simply submit jobs into those VMs.