alphafold: failed to build docker

Wonderful repo !!! Thanks so much for the Alphafold2 Team. And I have a problem in building alphafold docker. Error information is shown below. It seems that the related cuda resource is not found. Thanks all.

$ docker build -f docker/Dockerfile -t alphafold .

Sending build context to Docker daemon  12.69MB
Step 1/19 : ARG CUDA=11.0
Step 2/19 : FROM nvidia/cuda:${CUDA}-base
 ---> 2ec708416bb8
Step 3/19 : ARG CUDA
 ---> Using cache
 ---> 076eace7d488
Step 4/19 : SHELL ["/bin/bash", "-c"]
 ---> Using cache
 ---> b57b88dc2b9a
Step 5/19 : RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y       build-essential       cmake       cuda-command-line-tools-${CUDA/./-}       git       hmmer       kalign       tzdata       wget     && rm -rf /var/lib/apt/lists/*
 ---> Running in 52e953f25c2b
...
...


E: Failed to fetch https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64/by-hash/SHA256/27b2dbb347d54776dec155d98e1eefbde6c10a3fd1295007c3e836cfd9b98522  404  Not Found [IP: 58.205.210.80 443]
E: Some index files failed to download. They have been ignored, or old ones used instead.

About this issue

Original URL
State: closed
Created 3 years ago
Reactions: 1
Comments: 16

Most upvoted comments

Alphafold2 Team Hello Alphafold2 Team, 1>I’m using docker build -f docker/Dockerfile -t alphafold. According to your method, ping developer.download.nvidia.com and the IP obtained by adding /etc/hosts still reports an error, and every time you ping developer. Download.nvidia.com gets different ips, please help，Thank you

docker build -f docker/Dockerfile -t alphafold . Sending build context to Docker daemon 13.04MB Step 1/19 : ARG CUDA=11.0 Step 2/19 : FROM nvidia/cuda:${CUDA}-base —> 2ec708416bb8 Step 3/19 : ARG CUDA —> Using cache —> a1f524bee0b4 Step 4/19 : SHELL [“/bin/bash”, “-c”] —> Using cache —> 09dc16b21719 Step 5/19 : RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential cmake cuda-command-line-tools-${CUDA/./-} git
hmmer kalign tzdata wget && rm -rf /var/lib/apt/lists/* —> Running in 2433b949ee79 Get:1 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB] Get:3 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB] Ign:2 https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64 InRelease Get:4 https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64 Release [697 B] Get:5 https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64 Release.gpg [836 B] Ign:6 https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64 Packages Ign:6 https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64 Packages Ign:6 https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64 Packages Err:6 https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64 Packages 404 Not Found [IP: 124.132.138.69 443] Get:7 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB] Get:8 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [782 kB] Get:9 http://archive.ubuntu.com/ubuntu focal-backports InRelease [101 kB] Get:10 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB] Get:11 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [33.4 kB] Get:12 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB] Get:13 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [930 kB] Get:14 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [27.6 kB] Get:15 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [368 kB] Get:16 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1275 kB] Get:17 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [32.0 kB] Get:18 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [1367 kB] Get:19 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [416 kB] Get:20 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1053 kB] Get:21 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [2668 B] Get:22 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [6303 B] Fetched 18.4 MB in 1min 44s (176 kB/s) Reading package lists… E: Failed to fetch https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64/by-hash/SHA256/27b2dbb347d54776dec155d98e1eefbde6c10a3fd1295007c3e836cfd9b98522 404 Not Found [IP: 124.132.138.69 443]E: Some index files failed to download. They have been ignored, or old ones used instead.

[root@fat03 alphafold]# ping developer.download.nvidia.com PING developer.download.nvidia.com.zengslb.com (192.254.94.202) 56(84) bytes of data. 64 bytes from 192.254.94.202 (192.254.94.202): icmp_seq=1 ttl=53 time=46.0 ms 64 bytes from 192.254.94.202 (192.254.94.202): icmp_seq=2 ttl=53 time=45.7 ms 64 bytes from 192.254.94.202 (192.254.94.202): icmp_seq=3 ttl=53 time=45.9 ms ^C — developer.download.nvidia.com.zengslb.com ping statistics — 3 packets transmitted, 3 received, 0% packet loss, time 2003ms rtt min/avg/max/mdev = 45.774/45.906/46.036/0.205 ms [root@fat03 alphafold]# vim /etc/hosts [root@fat03 alphafold]# ping developer.download.nvidia.com PING developer.download.nvidia.com.zengslb.com (45.43.32.210) 56(84) bytes of data. 64 bytes from 45.43.32.210 (45.43.32.210): icmp_seq=1 ttl=53 time=46.8 ms 64 bytes from 45.43.32.210 (45.43.32.210): icmp_seq=2 ttl=53 time=46.7 ms ^C — developer.download.nvidia.com.zengslb.com ping statistics — 2 packets transmitted, 2 received, 0% packet loss, time 1001ms rtt min/avg/max/mdev = 46.759/46.786/46.813/0.027 ms [root@fat03 alphafold]# vim /etc/hosts [root@fat03 alphafold]# vim /etc/hosts [root@fat03 alphafold]# ping developer.download.nvidia.com PING developer.download.nvidia.com.zengslb.com (129.227.48.133) 56(84) bytes of data. 64 bytes from 129.227.48.133 (129.227.48.133): icmp_seq=1 ttl=45 time=72.4 ms 64 bytes from 129.227.48.133 (129.227.48.133): icmp_seq=2 ttl=45 time=73.6 ms

I use docker pull fanxuezhe/alphafold_test The download is also wrong [root@fat03 alphafold]# docker pull fanxuezhe/alphafold_test Using default tag: latest Error response from daemon: manifest for fanxuezhe/alphafold_test:latest not found: manifest unknown: manifest unknown

wangyanmin123 on Jul 16, 2021

Try this: Modify the Dockerfile like this if you are in China:

.................  # some command

RUN echo deb https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu2004/x86_64 / | tee /etc/apt/sources.list.d/cuda.list    # HERE! Add this before apt-get update

RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
.................  # some command

And you may also unable to access the github depository. So you can modify the website of https://github.com/soedinglab/hh-suite.git to https://github.com.cnpmjs.org/soedinglab/hh-suite.git

FizzerYu on Jul 18, 2021

Here is the no docker version: https://github.com/kuixu/alphafold

kuixu on Jul 18, 2021

I think this might be a location issue, rather than an issue with Docker.

It should download the following: https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-command-line-tools-11-0_11.0.3-1_amd64.deb. However, your network is trying to use the developer.download.nvidia.cn domain. Maybe it’s not available in China?

Perhaps you can try the following:

On your host computer, obtain the IPv4 address for the domain developer.download.nvidia.com by using ping developer.download.nvidia.com (use ctrl+c to stop sending pings). For example, the IP address can be 152.195.19.142.
Open your host machine’s hosts file. For Linux/Unix-like operating systems, it should be /etc/hosts.
Add the following line to the bottom of the hosts file (replace the IP address with the one obtained from the pings):

152.195.19.142       developer.download.nvidia.cn

This will tell your computer to translate the developer.download.nvidia.cn domain to the 152.195.19.142 IP address. Note that you may need escalated privileges to modify that file.

tjrana on Jul 16, 2021

docker build —add-host “developer.download.nvidia.com:152.195.19.142 -f docker/Dockerfile -t alphafold .

meecle on Jul 24, 2021