From e07682c0643881390f59a7696fd91ad0232ea1ea Mon Sep 17 00:00:00 2001 From: mlbileschi <mlbileschi@google.com> Date: Tue, 12 Nov 2024 18:39:19 +0000 Subject: [PATCH] Update singularity instructions (thanks davidecarlson!) PiperOrigin-RevId: 695790186 --- docs/installation.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/installation.md b/docs/installation.md index 0731dc2..70eff71 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -321,7 +321,7 @@ docker push localhost:5000/alphafold3 Then build the Singularity container: ```sh -SINGULARITY_NOHTTPS=1 singularity build alphafold3.simg docker://localhost:5000/alphafold3:latest +SINGULARITY_NOHTTPS=1 singularity build alphafold3.sif docker://localhost:5000/alphafold3:latest ``` You can confirm your build by starting a shell and inspecting the environment. @@ -329,24 +329,25 @@ For example, you may want to ensure the Singularity image can access your GPU. You may want to restart your computer if you have issues with this. ```sh -singularity exec --nv alphafold3.simg sh -c 'nvidia-smi' +singularity exec --nv alphafold3.sif sh -c 'nvidia-smi' ``` You can now run AlphaFold 3! ```sh -singularity exec --nv alphafold3.simg <<args>> +singularity exec --nv alphafold3.sif <<args>> ``` For example: ```sh singularity exec \ - --nv alphafold3.simg \ + --nv \ --bind $HOME/af_input:/root/af_input \ --bind $HOME/af_output:/root/af_output \ --bind <MODEL_PARAMETERS_DIR>:/root/models \ --bind <DATABASES_DIR>:/root/public_databases \ + alphafold3.sif \ python alphafold3/run_alphafold.py \ --json_path=/root/af_input/fold_input.json \ --model_dir=/root/models \ -- GitLab