alphafold3 installation

[rakabari]

I am writing to request the installation of AlphaFold 3 on CCR, as the source code for the latest version is now available -
https://github.com/google-deepmind/alphafold3/blob/main/docs/installation.md
This tool will be valuable for various ongoing projects at UB, supporting advanced research across departments. Please let me know if there are any prerequisites or additional information needed from our end to facilitate this installation.

[dsajdak]

@rakabari thank you for your request! As you may be aware, we have AlphaFold installed. We will be waiting until there is an available Easybuild recipe to install AlphaFold3 as this is a complicated piece of software to build. We'll keep an eye out on the Easybuild repository for that.

[rakabari]

@dsajdak thank you for the update. The use of AlphaFold3 is very timely for projects currently underway at UB. If there’s a way for our group (rams) to get involved to expedite the installation, I’d be happy to help. The instructions are straightforward if followed carefully, I just built a Docker image and converted it to Singularity outside of CCR. Slightly off-topic, but is there any possibility of CCR supporting Docker? I’ve noticed some HPCs are supporting it, potentially through a rootless version.

[gy2025]

Strongly support this installation request, I was about to make this request and saw @rakabari just opened the request 3 days ago. In fact, I need alphafold3 (not alphafold2) right now to perform DNA/Protein/Protein analyses (alphafold2 is unable to do). Hope the installation can be expedited as @rakabari requested.

[gy2025]

@rakabari, if you have one running locally, is there any possibility that I run a dataset of about 4000 proteins when your system is not in use? Thanks, Guojun

[rakabari]

@gy2025 I am still testing it on CCR using the GPU nodes. I built the Docker image outside CCR due to the lack of Docker support. I can provide you with the built Singularity image if you’d like to run it yourself.

[gy2025]

@rakabari, Appreciate the offer, that will be great, probably also need your knowhow after your successful testing.

[dsajdak]

@rakabari We are working on a rootless docker service but it is not in production yet. For now, you have to use Apptainer/Singularity for containers.

@gy2025 what group are you working with/for?

We appreciate that you are both interested in this and would ask for your patience as we manage an incredible amount of requests that are critical to over 400 research groups and several thousand users at UB and beyond. Our small team works through them as quickly as possible in as fair of a way as possible while balancing the rest of our workload.

[rakabari]

@gy2025 I successfully ran a test sequence on CCR. Let me know the directory (with sufficient space and write permission) where I should place the Singularity image. After cloning alphafold3.git, you will need to download the database by running fetch_databases.py (refer to the guide). Then, execute the Singularity command from the installation guide, ensuring you update the paths to point to your directories. You will also need to get the model parameters from DeepMind (check the guide for the form). It will take a few days to get it.

[rakabari]

@dsajdak we truly appreciate the incredible effort your team puts into supporting so many research groups and users. I’m happy to assist in any way I can to help streamline the process. Thank you again for starting this discussion.

[gy2025]

@rakabari @dsajdak Sounds great, I'm in the Yan group, my directory is /projects/academic/zhenyan/Yang currently we have only 0.3TB available, let me know if more is needed. Thanks a lot.

[rakabari]

@rakabari @dsajdak Sounds great, I'm in the Yan group, my directory is /projects/academic/zhenyan/Yang currently we have only 0.3TB available, let me know if more is needed. Thanks a lot.

You need to adjust the permissions so that I can copy it to your directory. The image is about 5 GB, but the database is >600 GB.

[dsajdak]

@gy2025 Rather than changing project directory permissions, I recommend creating a subdirectory for this container to be put in and then create Globus share for @rakabari to copy the image and database. Instructions for Globus can be found here

[gy2025]

@dsajdak @rakabari Thanks for the info. I will let you know when it's set up on my side and make enough space.

[gy2025]

@rakabari, looks a bit of hassle to go through Globus, anyway my own directory /user/gyang24 is basically empty with about 20G space available. You can put the Singularity image there now (write allowed temporarily). I will download the database myself. Thanks a lot!

[dsajdak]

@gy2025 Globus is very simple to use and you can create a share easily. You should never change the permissions on your home directory of a shared system. This will cause you problems with logging in via SSH. It is also insecure to have access open to everyone on our systems. Worse, we're discussing this in an open forum on the internet. If Globus is not going to work for you, please submit a ticket to CCR Help and I'll connect you both and provide an alternative. I am changing the permissions back on your home directory

[gy2025]

@dsajdak OK, I will submit a ticket. I looked at the Globus instructions and seems a bit too much to set it up just to do this once in probably years.

[rakabari]

@dsajdak OK, I will submit a ticket. I looked at the Globus instructions and seems a bit too much to set it up just to do this once in probably years.

Shared via UB dropbox. You can scp the image to your directory. Also shared on Globus

[gy2025]

@rakabari, Saw it, Thanks a lot!

[gy2025]

@dsajdak, Thank you too for facilitating!