Comments (15)
Thank you for sharing your tips! My solution was very similar to yours, I was about to share mine. :)
For the record, in my case, the NVIDIA driver installed on our system supports cuda/cudatoolkits up to 11.0. In this case, I was able to create a non-docker environment with jaxlib==0.1.68+cuda110, jax==0.2.17
UPDATE: according to #20, jaxlib==0.1.69 is required to be able to use CUDA unified memory for running long sequences.
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for those who prefers singularity container (such as HPC environment), I wrapped the instructions from @sanjaysrikakulam and made a singularity definition files. https://github.com/hyoo/alphafold_singularity
hope this helps.
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Here is a another one. https://github.com/kuixu/alphafold
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Hi, all. I have recently been organizing a recent fork of AlphaFold (with multimer support) that removes all Docker dependencies. If you find it helpful, please feel free to give it a try and let me know what you think: https://github.com/amorehead/alphafold_non_docker
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@sanjaysrikakulam and @kuixu
following both ur examples, on Ubuntu 20.0 LTS on VirtualMachine/VMware and WSL2 (windows 10 host)
always missing simtk/openmm in site-packages ?
i have cuda 10.1 installed on my windows PC, will upgrade to 11
~/miniconda3/envs/alphafold/lib/python3.8/site-packages
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@lydonchandra Sorry I don't have a windows system to test this.
Update: if you get missing simtk/openmm issues, it means the openmm installation was not through properly. I would suggest reinstalling this package alone and check if it gets installed.
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thanks for confirming @sanjaysrikakulam , it runs flawlessly on ubuntu 20 baremetal.
windows 10 WSL does not support cuda yet (windows 10 insider does) which i haven't tried.
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Is it possible that we run a non-Docker version AF2 in a Docker container?
Consumes a lot of time to configure the environment on a host.
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Hi, how should I output five models instead of only one as shown in the example? Thanks
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Hi @AlvinHew, please refer to our repo's readme.
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Hi @AlvinHew, please refer to our repo's readme.
Do you mean by specifying model_1, model_2, ... etc. in the flag -m ?
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Yes, but make sure you do not have spaces (e.g., -m model_1,model_2,model_3,model_4,model_5
)
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Thanks for the reminder!
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Unfortunately we don't have the capacity to maintain and support Singularity. We added a link in the README to this issue and issue #10 that have links to third party repositories with Singularity definition files. I am going to close this issue as it is directly accessible from the README.
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I am maintaining a Singularity port of AlphaFold's Docker stuff. It makes no change to the AlphaFold code (or even its Docker code): it merely adds a new directory for the Singularity stuff. It also has an example Slurm job script.
It has just been updated for AlphaFold 2.2.2. Please see https://github.com/prehensilecode/alphafold_singularity
Feel free to fork and submit issues or pull requests there.
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Related Issues (20)
- AttributeError: module 'haiku' has no attribute 'custom_creator' HOT 1
- ValueError: Minimization failed after 100 attempts. HOT 3
- AttributeError: module 'jax' has no attribute 'linear_util' HOT 4
- I am unable to run the fourth step normally, the following is the error code HOT 5
- Problem with step four in colabpro
- Database Installation
- How to get iPAE
- The definition of bins in Predicted Aligned Error Head(PAE) may be wrong
- Can I use a custom PDB file for multimer prediction
- An error free installation package HOT 1
- FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpzszd_m92/output.a3m'
- Open Access
- Downloaded cif file from open access doesn't have secondary structure assignments HOT 2
- Specifying Disulphide bonds to AlphaFold HOT 1
- mmCIF much larger than stated
- The request and urllib3 version dependency conflict problem occurs, and the error ocker.errors.DockerException: Error while fetching server API version: request() got an unexpected keyword argument 'chunked' appears
- Using rotamers for mutations HOT 1
- JSON upload to AF3 server saves drafts without running, then gives remaining jobs is 0
- InvalidSpec: The package "nvidia/linux-64::cuda-compiler==12.5.0=0" is not available for the specified platform HOT 4
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