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kalininalab / alphafold_non_docker

AlphaFold2 non-docker setup
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FATAL Flags parsing error #34

Closed mingyue80 closed 2 years ago

mingyue80 commented 2 years ago

I'm consistently running into this issue when trying to run the non-docker AP2 install. Followed directions and everything installed just fine. Downloaded run_alphafold.sh and tried to run the script, I consistently got the following error:

FATAL Flags parsing error: flag --use_gpu_relax=None: Flag --use_gpu_relax must have a value other than None. Pass --helpshort or --helpfull to see help on flags.

I don't know where this setting is coming from, since it's not part of the script. I'm running Ubuntu 20.04.3 LTS, cuda version 11.5 v11.5.119, and nvidia-smi returns the following: +-----------------------------------------------------------------------------+ | NVIDIA-SMI 495.29.05 Driver Version: 495.29.05 CUDA Version: 11.5 | |-------------------------------+----------------------+----------------------+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |===============================+======================+======================| | 0 NVIDIA RTX A4000 On | 00000000:19:00.0 Off | Off | | 41% 34C P8 8W / 140W | 13MiB / 16117MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ | 1 NVIDIA RTX A4000 On | 00000000:1A:00.0 Off | Off | | 41% 36C P8 7W / 140W | 13MiB / 16117MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ | 2 NVIDIA RTX A4000 On | 00000000:67:00.0 Off | Off | | 41% 34C P8 6W / 140W | 13MiB / 16117MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ | 3 NVIDIA RTX A4000 On | 00000000:68:00.0 On | Off | | 41% 37C P8 9W / 140W | 352MiB / 16116MiB | 1% Default | | | | N/A | +-------------------------------+----------------------+----------------------+

LukePiszkin commented 2 years ago

I am also receiving this error when trying to use the CPU only mode. (alphafold) [lpiszkin@crcfe01 alphafold]$ bash run_alphafold.sh -d ../alphafolddata/ -o ../ -f beta_gal.fasta -t 2020-05-14 -g false FATAL Flags parsing error: flag --use_gpu_relax=None: Flag --use_gpu_relax must have a value other than None. Pass --helpshort or --helpfull to see help on flags.

sanjaysrikakulam commented 2 years ago

Hi,

It looks like AF2 has made a new release a few days ago which adds new GPU relaxation stuff. The bash script in this repo is not yet updated (I will do this as soon as possible) to adapt to the changes. So, please use AF2's v2.1.1 release (https://github.com/deepmind/alphafold/releases) instead of the latest v2.1.2. This should fix your problems.

mingyue80 commented 2 years ago

rolling back to AF2 v2.1.1 solved the issues for me, thank you.

TaoDFang commented 2 years ago

I also run into this problem . Did anyone figure out how to solve this problem besides rolling back to v2.1.1 ?

g-sutherland commented 2 years ago

Did anyone manage to update the bash script for the GPU relaxation? Thanks in advance!

sanjaysrikakulam commented 2 years ago

Hi All,

Sorry for the delay (too hectic lately), I have updated the bash script along with the documentation in Readme. The bash script now works with AF2 version 2.2.0. If you encounter any problem please create a new ticket.

g-sutherland commented 2 years ago

Works great for me, thanks Sanjay!