Singularity Definition

[jdhayes]

Here is a singularity definition dirived from your Dockerfile:
https://github.com/jdhayes/alphafold/blob/main/docker/Singularity.def
Do you think you could integrate this with your codebase, should I make a pull request?

[jdhayes]

Moved to:
https://github.com/jdhayes/alphafold/blob/main/singularity/Singularity.def

[EricDeveaud]

Hello in order to tun the downlaod scripts from the container
aria2 and rsync should be installed
esay fix, see above diff. not sure it worth providing a patch ;-)

packbuilder:alphafold/alphafold-v2.0.0 > diff -u Singularity.def alphafold-v2.0.0.recipe
--- Singularity.def     2021-09-23 17:13:49.019136000 +0200
+++ alphafold-v2.0.0.recipe     2021-09-23 17:13:29.162525000 +0200
@@ -41,6 +41,8 @@
kalign \
tzdata \
wget \
+aria2 \
+rsync \
&& rm -rf /var/lib/apt/lists/*

# Get code base

regards

Eric

[tomgreen66]

Did a run_docker.py-like script get written? I converted Python to bash since we didn't need any Python API - see: /ARCCA/alphafold/tree/singularity/docker/run_singularity.sh

[EricDeveaud]

see bottom of the singularity defintion file.
a shell script is generated.

echo '#!/bin/bash
#ldconfig
source /opt/conda/etc/profile.d/conda.sh
conda activate base
python /app/alphafold/run_alphafold.py "$@"' > /app/run_alphafold.sh

this is the launcher you should use

singularity run <singulariy arguments> <alphafold arguments>

[Augustin-Zidek]

Unfortunately we don't have the capacity to maintain and support Singularity. We added a link in the README to the two AlphaFold issues that have links to third party repositories with Singularity definition files (#10 and #24).

[SomePersonSomeWhereInTheWorld]

Looks like the link to the cuda download is broken:

FATAL: While performing build: conveyor failed to get: Error reading manifest 11.1-cudnn8-runtime-ubuntu18.04 in docker.io/nvidia/cuda: manifest unknown: manifest unknown