google-deepmind / google-deepmind/alphafold

run_docker.py failure caused by module not found error

Ouverte
#653 1 commentaire 0 réactions 0 personnes assignées Voir sur GitHub
docker setup
Langage dominant
Python
Étoiles
14.9k
Forks
2.9k
Métriques de merge des PR
Aucune PR mergée en 30 j

Description

When I run the run_docker.py with the following command,
python3 docker/run_docker.py \
--fasta_paths=/data/xiaoai/alphafold2_software/alphafold-main/T1082.fasta \
--max_template_date=2020-05-14 \
--model_preset=monomer \
--db_preset=full_dbs \
--data_dir=/data/xiaoai/alphafold2_software/download_file
I got this error message:
I1210 22:19:52.657300 139724585183040 run_docker.py:113] Mounting /data/xiaoai/alphafold2_software/alphafold-main -> /mnt/fasta_path_0
I1210 22:19:52.657422 139724585183040 run_docker.py:113] Mounting /data/xiaoai/alphafold2_software/download_file/uniref90 -> /mnt/uniref90_database_path
I1210 22:19:52.657488 139724585183040 run_docker.py:113] Mounting /data/xiaoai/alphafold2_software/download_file/mgnify -> /mnt/mgnify_database_path
I1210 22:19:52.657539 139724585183040 run_docker.py:113] Mounting /data/xiaoai/alphafold2_software/download_file -> /mnt/data_dir
I1210 22:19:52.657588 139724585183040 run_docker.py:113] Mounting /data/xiaoai/alphafold2_software/download_file/pdb_mmcif/mmcif_files -> /mnt/template_mmcif_dir
I1210 22:19:52.657644 139724585183040 run_docker.py:113] Mounting /data/xiaoai/alphafold2_software/download_file/pdb_mmcif -> /mnt/obsolete_pdbs_path
I1210 22:19:52.657705 139724585183040 run_docker.py:113] Mounting /data/xiaoai/alphafold2_software/download_file/pdb70 -> /mnt/pdb70_database_path
I1210 22:19:52.657769 139724585183040 run_docker.py:113] Mounting /data/xiaoai/alphafold2_software/download_file/uniclust30/uniclust30_2018_08 -> /mnt/uniclust30_database_path
I1210 22:19:52.657833 139724585183040 run_docker.py:113] Mounting /data/xiaoai/alphafold2_software/download_file/bfd -> /mnt/bfd_database_path
I1210 22:19:53.050984 139724585183040 run_docker.py:255] Traceback (most recent call last):
I1210 22:19:53.051107 139724585183040 run_docker.py:255] File "/app/alphafold/run_alphafold.py", line 26, in
I1210 22:19:53.051178 139724585183040 run_docker.py:255] from absl import app
I1210 22:19:53.051237 139724585183040 run_docker.py:255] ModuleNotFoundError: No module named 'absl'

but I find that absl-py already exist in conda list and python
I import absl in python without any error

Guide de contribution

Ouvrir le guide de contribution

Piste de recherche

Start with docker/run_docker.py and the container entry point /app/alphafold/run_alphafold.py, using the command and traceback in the report to trace which Python environment runs inside the container. Check the reported absl import failure against the container's runtime environment rather than the host conda environment. Done means the command starts without the ModuleNotFoundError.

Rédigé par le modèle d'indexation à partir du texte de l'issue.

Évaluation

Stack technique
docker, python
Domaine
devops
Type d'issue
Bug
Difficulté
3/5
Temps estimé
1-2 jours
Activité
À l'abandon
Clarté
Plutôt claire
Accessibilité débutants
35/100

Recevez les nouvelles issues par e-mail

Un résumé court des issues GitHub adaptées aux débutants.