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.
from alphafold.
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.
from alphafold.
Here is a another one. https://github.com/kuixu/alphafold
from alphafold.
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
from alphafold.
@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
from alphafold.
@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.
from alphafold.
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.
from alphafold.
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.
from alphafold.
Hi, how should I output five models instead of only one as shown in the example? Thanks
from alphafold.
Hi @AlvinHew, please refer to our repo's readme.
from alphafold.
Hi @AlvinHew, please refer to our repo's readme.
Do you mean by specifying model_1, model_2, ... etc. in the flag -m ?
from alphafold.
Yes, but make sure you do not have spaces (e.g., -m model_1,model_2,model_3,model_4,model_5
)
from alphafold.
Thanks for the reminder!
from alphafold.
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.
from alphafold.
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.
from alphafold.
Related Issues (20)
- prediction results are not consistent HOT 2
- Getting more than 25 predicted models for multimer mode HOT 4
- Does it cost money to download the dataset or not?
- ValueError: Could not find CIFs
- The proper way to find the maximum subbatch_size?
- Fatal Python error: Segmentation fault
- AlphaFold uses the wrong resolution field during structure parsing HOT 2
- --model_preset=multimer: command not found
- How do I know when to update my local database?
- Issue with missing templates during Multimer Mode running
- RuntimeError: HHblits failed. Unrecognized HMM file format in '468479486'
- Minimizing failing due to CUDA error
- 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
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from alphafold.