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protein structure prediction
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Creating singularity image on Raptor #1

Closed markcoletti closed 3 years ago

markcoletti commented 3 years ago

We need to run AlphaFold in Singularity on the Raptor. This entails taking the original Dockerfile and creating a Singularity image from a Dockerfile/recipe derived from it.

proutrc commented 3 years ago

We currently have a working JAX build in the container. We built the container on a Raptor machine, then transferred the .sif file to Peak and ran it there. The container does not currently contain all the necessary pieces, but JAX was a big dependency to get working first.

After the Summit upgrade, we will be able to test there. We can't currently run the container on Summit due to Summit's older Nvidia driver.

markcoletti commented 3 years ago

Can we not have the same older driver version in the container?

proutrc commented 3 years ago

We could potentially look at this path if we need to. It's not the typical path to do that, but it looks possible. I have always grabbed from the base system.

We did try and do a CUDA10 build with JAX, in the same fashion we did with CUDA11, but it quickly started to spin out. We would need to use CUDA10 on Summit at the moment. Perhaps we can get it to work, but not sure it's worth too much effort.

Further, We still have more packages to get integrated into the container, now that we are successful with JAX and CUDA11. That was the initial hurdle, now we can work on other packages.

Having said all that, I would advocate for us to stay on the CUDA11 train, working towards the full container we need on that base. Especially since we can run tests and work out kinks on Peak with CUDA11. Peak has the CUDA11 base. Then, when Summit upgrades, we should be able to use the same container as is.

markcoletti commented 3 years ago

@proutrc completed this a while back.

markcoletti commented 3 years ago

Even though this is done, assigned to Subil since I think he had a hand in making the final Singularity image we're now using. :D