"/app/alphafold/docker/openmm.patch: No such file or directory" or "can't open file '/app/alphafold/run_alphafold.py': [Errno 2] No such file or directory"

[MaKangYao]

when i build docker image in the docker folder "docker build -t alphafold ."
and then
report error
Step 14/18 : RUN patch -p0 < /app/alphafold/docker/openmm.patch
---> Running in f507715f75d9
/bin/bash: /app/alphafold/docker/openmm.patch: No such file or directory
The command '/bin/bash -c patch -p0 < /app/alphafold/docker/openmm.patch' returned a non-zero code: 1

then i modify the dockerfile
#73 RUN patch -p0 < /app/alphafold/openmm.patch

then the docker image successful build
Step 14/18 : RUN patch -p0 < /app/alphafold/openmm.patch
---> Running in e17ea0d47b4d
patching file simtk/openmm/app/topology.py
Hunk #1 succeeded at 353 (offset -3 lines).
Removing intermediate container e17ea0d47b4d
---> ce77a4895544
Step 15/18 : RUN chmod u+s /sbin/ldconfig.real
---> Running in 71924dd71397
Removing intermediate container 71924dd71397
---> e1c43b3cc4fc
Step 16/18 : WORKDIR /app/alphafold
---> Running in 0d81f85886dc
Removing intermediate container 0d81f85886dc
---> 4c16bc524dd8
Step 17/18 : RUN echo $'#!/bin/bash\nldconfig\npython /app/alphafold/run_alphafold.py "$@"' > /app/run_alphafold.sh && chmod +x /app/run_alphafold.sh
---> Running in dce02456db5b
Removing intermediate container dce02456db5b
---> 4ce1b8b476b5
Step 18/18 : ENTRYPOINT ["/app/run_alphafold.sh"]
---> Running in ca2af0632d71
Removing intermediate container ca2af0632d71
---> ca5a3d381436
Successfully built ca5a3d381436
Successfully tagged alphafold:latest

but when i run the docker

❯ python3 docker/run_docker.py
--fasta_paths=s.fas
--max_template_date=2020-05-14
--data_dir=/home/mky/Data/alphafold_data/
I0216 09:40:52.541118 140714467206976 run_docker.py:107] Mounting /home/mky/Videos/alphafold-main -> /mnt/fasta_path_0
I0216 09:40:52.541209 140714467206976 run_docker.py:107] Mounting /home/mky/Data/alphafold_data/uniref90 -> /mnt/uniref90_database_path
I0216 09:40:52.541244 140714467206976 run_docker.py:107] Mounting /home/mky/Data/alphafold_data/mgnify -> /mnt/mgnify_database_path
I0216 09:40:52.541273 140714467206976 run_docker.py:107] Mounting /home/mky/Data -> /mnt/data_dir
I0216 09:40:52.541300 140714467206976 run_docker.py:107] Mounting /home/mky/Data/alphafold_data/pdb_mmcif -> /mnt/template_mmcif_dir
I0216 09:40:52.541326 140714467206976 run_docker.py:107] Mounting /home/mky/Data/alphafold_data/pdb_mmcif -> /mnt/obsolete_pdbs_path
I0216 09:40:52.541353 140714467206976 run_docker.py:107] Mounting /home/mky/Data/alphafold_data/pdb70 -> /mnt/pdb70_database_path
I0216 09:40:52.541379 140714467206976 run_docker.py:107] Mounting /home/mky/Data/alphafold_data/uniclust30/uniclust30_2018_08 -> /mnt/uniclust30_database_path
I0216 09:40:52.541405 140714467206976 run_docker.py:107] Mounting /home/mky/Data/alphafold_data/bfd -> /mnt/bfd_database_path
I0216 09:40:54.052704 140714467206976 run_docker.py:247] python: can't open file '/app/alphafold/run_alphafold.py': [Errno 2] No such file or directory

it report this error

I'm looking for a way to solve my problem
Want to know if you can give the official docker image
thank you very much!!!

[MaKangYao]

and it give me warning in step 12
Step 12/18 : RUN pip3 install --upgrade pip && pip3 install -r /app/alphafold/requirements.txt && pip3 install --upgrade jax==0.2.14 jaxlib==0.1.69+cuda${CUDA/./} -f https://storage.googleapis.com/jax-releases/jax_releases.html
---> Running in c3a9bc845ac9
Requirement already satisfied: pip in /opt/conda/lib/python3.7/site-packages (22.0.3)
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
Collecting absl-py==0.13.0
Downloading absl_py-0.13.0-py3-none-any.whl (132 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.1/132.1 KB 10.4 kB/s eta 0:00:00
Collecting docker==5.0.0
Downloading docker-5.0.0-py2.py3-none-any.whl (146 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 147.0/147.0 KB 6.9 kB/s eta 0:00:00
Requirement already satisfied: six in /opt/conda/lib/python3.7/site-packages (from absl-py==0.13.0->-r /app/alphafold/requirements.txt (line 2)) (1.16.0)
Collecting websocket-client>=0.32.0
Downloading websocket_client-1.2.3-py3-none-any.whl (53 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.5/53.5 KB 14.7 kB/s eta 0:00:00
Requirement already satisfied: requests!=2.18.0,>=2.14.2 in /opt/conda/lib/python3.7/site-packages (from docker==5.0.0->-r /app/alphafold/requirements.txt (line 3)) (2.27.1)
Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.7/site-packages (from requests!=2.18.0,>=2.14.2->docker==5.0.0->-r /app/alphafold/requirements.txt (line 3)) (2021.10.8)
Requirement already satisfied: charset-normalizer~=2.0.0 in /opt/conda/lib/python3.7/site-packages (from requests!=2.18.0,>=2.14.2->docker==5.0.0->-r /app/alphafold/requirements.txt (line 3)) (2.0.4)
Requirement already satisfied: idna<4,>=2.5 in /opt/conda/lib/python3.7/site-packages (from requests!=2.18.0,>=2.14.2->docker==5.0.0->-r /app/alphafold/requirements.txt (line 3)) (3.3)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/conda/lib/python3.7/site-packages (from requests!=2.18.0,>=2.14.2->docker==5.0.0->-r /app/alphafold/requirements.txt (line 3)) (1.26.8)
Installing collected packages: websocket-client, absl-py, docker
Successfully installed absl-py-0.13.0 docker-5.0.0 websocket-client-1.2.3
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
Looking in links: https://storage.googleapis.com/jax-releases/jax_releases.html
warning: missing-index-doctype

× The package index page being used does not have a proper HTML doctype declaration.
╰─> Problematic URL: https://storage.googleapis.com/jax-releases/jax_releases.html

note: This is an issue with the page at the URL mentioned above.
hint: You might need to reach out to the owner of that package index, to get this fixed. See pypa/pip#10825 for context.
Collecting jax==0.2.14
Downloading jax-0.2.14.tar.gz (669 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 669.2/669.2 KB 15.4 kB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting jaxlib==0.1.69+cuda111
Downloading https://storage.googleapis.com/jax-releases/cuda111/jaxlib-0.1.69%2Bcuda111-cp37-none-manylinux2010_x86_64.whl (196.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 196.5/196.5 MB 8.6 MB/s eta 0:00:00
Requirement already satisfied: numpy>=1.12 in /opt/conda/lib/python3.7/site-packages (from jax==0.2.14) (1.21.1)
Requirement already satisfied: absl-py in /opt/conda/lib/python3.7/site-packages (from jax==0.2.14) (0.13.0)
Collecting opt_einsum
Downloading opt_einsum-3.3.0-py3-none-any.whl (65 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.5/65.5 KB 17.3 kB/s eta 0:00:00
Collecting flatbuffers<3.0,>=1.12
Downloading flatbuffers-2.0-py2.py3-none-any.whl (26 kB)
Collecting scipy
Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.1/38.1 MB 176.2 kB/s eta 0:00:00
Requirement already satisfied: six in /opt/conda/lib/python3.7/site-packages (from absl-py->jax==0.2.14) (1.16.0)
Building wheels for collected packages: jax
Building wheel for jax (setup.py): started
Building wheel for jax (setup.py): finished with status 'done'
Created wheel for jax: filename=jax-0.2.14-py3-none-any.whl size=771352 sha256=58bfb994bf2d5491280383e2162cbd5b64fb251165b1361e115ba3a09539195a
Stored in directory: /root/.cache/pip/wheels/ec/bd/25/923906d87d262ee0be5c68b248d1a8249d028603582a256266
Successfully built jax
Installing collected packages: flatbuffers, scipy, opt_einsum, jaxlib, jax
Successfully installed flatbuffers-2.0 jax-0.2.14 jaxlib-0.1.69+cuda111 opt_einsum-3.3.0 scipy-1.7.3
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
Removing intermediate container c3a9bc845ac9
---> 5f460eb181f9

[Wolf-Z]

Edit:
Nevermind - My problem happens, when running docker under a different docker group, and having a docker user (with this legitimate docker group) running your container - but not, when running the container as root. Because the permissions underneath /app/alphafold/* are mostly zero for "others/World". No problem when running as root, but when running as user, this is not enough. I'll rebuild the image with an extra permission setting step for /app/alphafold/*
I leave this here in case someone else stumbles across this.

Original text:

I didn't observe problems with building the image - however, when starting it by running this on RHEL7.9 / latest docker-ce with python3 coming from a venv (python 3.6) with all the things from docker/requirements.txt inside like this:

 python3 /somewhere/alphafold/docker/run_docker.py --fasta_paths=T1050.fasta \
--max_template_date=2020-05-14 --data_dir=/somewhere/db/alphafold2/alldata

I get almost the same error:

[...]
I0309 13:52:36.921424 139926426507072 run_docker.py:107] Mounting /somewhere/db/alphafold2/alldata/bfd -> /mnt/bfd_database_path
I0309 13:52:37.488527 139926426507072 run_docker.py:247] python: can't open file '/app/alphafold/run_alphafold.py': [Errno 13] Permission denied

Note, that /somewhere is a NFS mount on the host, however "root" as well as docker users can access i.e. /somewhere/alphafold/run_alphafold.py but I doubt it is mounted this way but part of the image itself, right?
Also it's a proxy environment, do I need proxy-credentials within the container (i.e I could setup my ~/.docker/config.json) ?

If my bug is something different I'm sorry for polluting this issue and would open another issue instead. Thanks

[tomwardio]

Hello!

I think the original issue is todo with where you run docker build from: it looks like this was being run from the docker/ sub-directory, rather than from the root of the repository. As @Wolf-Z mentioned, Docker will need to have access to this root directory in order to build the image correctly.