Ecosyste.ms: Issues

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GitHub / google-deepmind/alphafold issues and pull requests

#1063 - setting `--gpu_device ` is not working for mutiple GPUs

Issue - State: open - Opened by menghaowei 19 days ago - 3 comments

#1061 - Dump unpaired v2

Pull Request - State: closed - Opened by damiano-sg 25 days ago - 1 comment

#1060 - jnp.clip() unknown argument max

Issue - State: closed - Opened by komeil0480 28 days ago - 1 comment

#1057 - Fix CUDA's Docker image version in the README file

Pull Request - State: open - Opened by arminsl about 1 month ago

#1056 - compatible with pytorch and cuda 12.4

Issue - State: open - Opened by collyyang520 about 1 month ago - 1 comment

#1055 - Compatibility question CUDA12, A100/H100

Issue - State: open - Opened by smouilleron about 1 month ago

#1054 - Alphafold v2.3.2 build broken (LibMambaUnsatisfiableError)

Issue - State: closed - Opened by krishors about 2 months ago - 1 comment
Labels: setup

#1052 - Fix Installation Issues

Pull Request - State: closed - Opened by minh-le-q about 2 months ago - 1 comment

#1050 - Fix docker cuda in conda install for docker build

Pull Request - State: closed - Opened by akors 2 months ago - 1 comment

#1048 - CUDA backend failed to initialize

Issue - State: open - Opened by hofmank0 2 months ago - 1 comment

#1047 - ModuleNotFoundError: No module named 'tree'

Issue - State: open - Opened by adokhugi 2 months ago

#1046 - cccccbrvievirrenuvrtivgfruuuceuundhrfldutlrd

Issue - State: closed - Opened by dannf 3 months ago - 1 comment

#1045 - unable to generate User-provided CCD format ligand

Issue - State: closed - Opened by YoavShamir5 3 months ago - 2 comments

#1043 - FTP blocked? Try the rcsb aws bucket

Issue - State: closed - Opened by danpf 3 months ago

#1041 - Alpha fold

Issue - State: closed - Opened by taisom27 3 months ago

#1040 - Alpha fold dependencies plot protein command not executing

Issue - State: closed - Opened by SatyajitMishra1 3 months ago - 1 comment

#1039 - Error in ' install dependencies"

Issue - State: open - Opened by christinapapa 4 months ago - 1 comment

#1038 - Failed to build docker on cuda:11.0.3-base

Issue - State: open - Opened by hyeonLIB 4 months ago - 2 comments

#1037 - Not able to run prediction __ AlphaFold2.ipynb

Issue - State: closed - Opened by asm-cell 4 months ago - 1 comment
Labels: third-party tool

#1036 - does alphafold 2 explicitly model co-evolution?

Issue - State: open - Opened by PatschD 4 months ago

#1035 - Alphafold stopped using GPU after upgrade to Ubuntu 24.04.1 (noble)

Issue - State: open - Opened by hofmank0 4 months ago - 3 comments

#1034 - Update requirements.txt

Pull Request - State: open - Opened by PentesterPriyanshu 4 months ago - 2 comments

#1033 - Add rsync notice

Pull Request - State: open - Opened by MamfTheKramf 4 months ago - 1 comment

#1031 - how is alpha fold 3 trained

Issue - State: open - Opened by joepareti54 4 months ago

#1030 - requirement:tensorflow-cpu

Issue - State: open - Opened by nibingwei123 4 months ago - 1 comment

#1029 - Alphafold runs will not find the GPU

Issue - State: closed - Opened by tuttlelm 4 months ago - 3 comments

#1028 - Updated requirements.txt

Pull Request - State: open - Opened by vignesh1507 4 months ago - 2 comments

#1027 - Hopefully that helps.

Issue - State: closed - Opened by SocialNinjaMaster 4 months ago - 1 comment

#1026 - Installation without docker

Issue - State: open - Opened by fglaser 5 months ago

#1024 - Remove $ROOT_DIR from the argument of gunzip command

Pull Request - State: open - Opened by kojiwell 5 months ago - 1 comment

#1023 - lost some output files

Issue - State: open - Opened by xjhzjucas 5 months ago

#1018 - Could we track how long one AlphaFold program run?

Issue - State: open - Opened by WenWu-Bio 5 months ago - 1 comment

#958 - Running AlphaFold on models larger than AMD GPU available memory

Issue - State: open - Opened by dipietrantonio 7 months ago - 4 comments

#955 - ValueError: Minimization failed after 100 attempts.

Issue - State: open - Opened by zcswnm 8 months ago - 5 comments

#954 - Fix deprecation warning / error from BioPython

Pull Request - State: closed - Opened by edawson 8 months ago - 2 comments

#949 - Bulk download from AlphaFold3 server

Issue - State: closed - Opened by johnnytam100 8 months ago - 1 comment

#919 - Issue with missing templates during Multimer Mode running

Issue - State: open - Opened by monojun 11 months ago - 1 comment

#914 - Fatal Python error: Segmentation fault

Issue - State: open - Opened by ghost 11 months ago - 1 comment

#885 - ImportError: cannot import name 'SCOPData' from 'Bio.Data'

Issue - State: open - Opened by lx19930 about 1 year ago - 7 comments

#810 - Titin sequences causing alphafold warning and exit without result

Issue - State: closed - Opened by dhan1004 over 1 year ago - 5 comments

#805 - Unable to find image 'nvidia/cuda:11.0-base' locally

Issue - State: open - Opened by jimchen1551 over 1 year ago - 4 comments

#757 - Alphafold-multimer fails trying to create features file

Issue - State: closed - Opened by Casih almost 2 years ago - 2 comments

#737 - no module named openmm

Issue - State: open - Opened by DrJesseHansen almost 2 years ago - 4 comments

#605 - Add conda lib path to LD_LIBRARY_PATH

Pull Request - State: closed - Opened by gabrielctn over 2 years ago - 2 comments

#475 - ValueError: Could not find Jackhmmer database /mnt/uniprot_database_path/uniprot.fasta

Issue - State: closed - Opened by Pharmacy-student almost 3 years ago - 14 comments
Labels: setup

#340 - RESOURCE_EXHAUSTED: Out of memory

Issue - State: closed - Opened by arneelof about 3 years ago - 4 comments
Labels: error report

#288 - Fetch prediction using bash or python

Issue - State: closed - Opened by DDudka9 about 3 years ago - 2 comments

#282 - HHblits query Running Time

Issue - State: closed - Opened by kdpan about 3 years ago - 7 comments
Labels: third-party tool

#267 - RuntimeError: hmmsearch failed:

Issue - State: closed - Opened by wangyanmin123 about 3 years ago - 7 comments
Labels: third-party tool

#187 - Side chain Frame constrcution

Issue - State: closed - Opened by wangleiofficial over 3 years ago - 2 comments
Labels: usage question

#175 - ModuleNotFoundError: No module named 'simtk.openmm.app.internal'

Issue - State: closed - Opened by archana433 over 3 years ago - 6 comments
Labels: third-party tool

#104 - docker build

Issue - State: closed - Opened by jianhaoc over 3 years ago - 5 comments
Labels: setup

#103 - Alphafold raises an error when it is predicting protein structure

Issue - State: closed - Opened by psp3dcg over 3 years ago - 2 comments

#102 - How to use？

Issue - State: closed - Opened by genomicsgroup over 3 years ago - 6 comments

#101 - ERROR: Could not find a version that satisfies the requirement numpy==1.19.5 (from versions: none)

Issue - State: closed - Opened by Rusfell over 3 years ago - 3 comments
Labels: error report, docker, setup

#100 - Unable to download pdb_mmcif database due to some recurring error.

Issue - State: closed - Opened by Comp-era over 3 years ago - 2 comments

#99 - /opt/conda/lib/python3.7/site-packages/absl/flags Issue while runnning alphafold

Issue - State: closed - Opened by Comp-era over 3 years ago - 2 comments

#98 - python3 docker/run_docker.py error: requests.exceptions.HTTPError: 400 Client Error

Issue - State: closed - Opened by mglgc over 3 years ago - 12 comments
Labels: error report, docker, setup

#97 - RuntimeError: HHblits failed

Issue - State: closed - Opened by huangjk1103 over 3 years ago - 20 comments
Labels: error report

#96 - Added singularity file and README

Pull Request - State: closed - Opened by davidhemp over 3 years ago - 5 comments
Labels: cla: yes

#95 - max connections (25) reached -- try again later

Issue - State: closed - Opened by mabingqi1 over 3 years ago

#94 - Download speed of database pdb_mmcif is very slow, about 80 KB/s

Issue - State: closed - Opened by liuboeo over 3 years ago - 2 comments

#93 - How to predict homo-oligomer's and hetero-oligomer's structure?

Issue - State: closed - Opened by RodenLuo over 3 years ago - 7 comments

#92 - How to visualize the result?

Issue - State: closed - Opened by RodenLuo over 3 years ago - 12 comments

#91 - Run prediction jobs in background

Issue - State: closed - Opened by siwei-deng over 3 years ago - 1 comment

#90 - Switch setup.py to Tensorflow CPU-only.

Pull Request - State: closed - Opened by chrisroat over 3 years ago - 1 comment
Labels: cla: yes

#88 - tensorflow-cpu

Issue - State: closed - Opened by akhoroshev over 3 years ago - 1 comment

#87 - run_docker.py: Run as non-root user by default, allow setting the user via flag

Pull Request - State: closed - Opened by akors over 3 years ago - 3 comments
Labels: cla: yes

#86 - meet problem in path -p openmm.patch

Issue - State: closed - Opened by Luanxins over 3 years ago - 3 comments

#85 - out of memory w/ colab notebook

Issue - State: closed - Opened by ttianchen over 3 years ago - 4 comments
Labels: error report, colab

#84 - Building wheel for dm-tree (setup.py) ... error

Issue - State: closed - Opened by ZQiangdeng over 3 years ago - 3 comments

#83 - tensorflow issue

Issue - State: closed - Opened by ajian-he over 3 years ago - 3 comments

#82 - high RAM usage w reduced_dbs

Issue - State: closed - Opened by biohegedus over 3 years ago - 3 comments
Labels: error report, third-party tool

#81 - /usr/local/nvidia not found

Issue - State: closed - Opened by cyclicdiamp over 3 years ago - 1 comment

#80 - how to compile alphafold with multiple CPUs

Issue - State: closed - Opened by ZengTao-hub over 3 years ago - 7 comments

#79 - Confusing wording/procedure in the Colab notebook

Issue - State: closed - Opened by josephrocca over 3 years ago - 1 comment
Labels: feature request, colab

#78 - ModuleNotFoundError: No module named 'py3Dmol'

Issue - State: closed - Opened by Leon-HXL over 3 years ago - 3 comments

#77 - Supplement/source code discrepancy in TriangleMultiplicationIncoming

Issue - State: closed - Opened by gahdritz over 3 years ago - 3 comments

#76 - Add flags: download_dir, docker_image_name, output_dir

Pull Request - State: closed - Opened by chrisroat over 3 years ago - 1 comment
Labels: cla: yes

#75 - Flag for output directory, write to current working directory by default

Pull Request - State: closed - Opened by akors over 3 years ago - 3 comments
Labels: cla: yes

#74 - [Question] Speed up prediction speed on GPUs with large memory?

Issue - State: closed - Opened by ashrafgt over 3 years ago - 2 comments

#73 - RuntimeError: HHblits failed

Issue - State: closed - Opened by LuGarfield over 3 years ago - 14 comments
Labels: error report, third-party tool

#72 - CUDA / Tensorflow version mismatch in Dockerfile

Issue - State: closed - Opened by chrisroat over 3 years ago - 9 comments

#71 - Getting "ValueError: Cannot create a tensor proto whose content is larger than 2GB." for smaller sequences

Issue - State: closed - Opened by DavidB256 over 3 years ago - 26 comments
Labels: error report