AlphaFold 3 container docs #32
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Fix pagination Tony
apptainer shell -B /util:/util,/scratch:/scratch,/projects:/projects ./AlphaFold-3-$(arch).sif change the command to: |
Monishnd
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Sep 30, 2025
| # Example AlphaFold 3 container | ||
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| NOTE: | ||
| AlphaFold 3 requeres a model parameters file. |
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| AlphaFold 3 requeres a model parameters file. | |
| AlphaFold 3 requires a model parameters file. |
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| 3. Build your container | ||
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| Building the AlphaFold-3 container taks about half an hour |
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| Building the AlphaFold-3 container taks about half an hour | |
| Building the AlphaFold-3 container takes about half an hour |
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| [AlphaFold 3 Slurm Data Pipeline example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_AlphaFold-3_Data_Pipeline_example.bash) | ||
| [AlphaFold 3 Slurm Inference example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_AlphaFold-3_Inference_example.bash) | ||
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| ### Grace Hopper (GH200) GPU example | ||
| [AlphaFold 3 Slurm (x86_64) Data Pipeline example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_GH200_AlphaFold-3_Data_Pipeline_example.bash) | ||
| [AlphaFold 3 Slurm Grace Hopper Inference example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_GH200_AlphaFold-3_Inference_example.bash) |
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| [AlphaFold 3 Slurm Data Pipeline example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_AlphaFold-3_Data_Pipeline_example.bash) | |
| [AlphaFold 3 Slurm Inference example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_AlphaFold-3_Inference_example.bash) | |
| ### Grace Hopper (GH200) GPU example | |
| [AlphaFold 3 Slurm (x86_64) Data Pipeline example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_GH200_AlphaFold-3_Data_Pipeline_example.bash) | |
| [AlphaFold 3 Slurm Grace Hopper Inference example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_GH200_AlphaFold-3_Inference_example.bash) | |
| [AlphaFold 3 Slurm Data Pipeline example](https://raw.githubusercontent.com/ubccr/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_AlphaFold-3_Data_Pipeline_example.bash) | |
| [AlphaFold 3 Slurm Inference example](https://raw.githubusercontent.com/ubccr/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_AlphaFold-3_Inference_example.bash) | |
| ### Grace Hopper (GH200) GPU example | |
| [AlphaFold 3 Slurm (x86_64) Data Pipeline example](https://raw.githubusercontent.com/ubccr/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_GH200_AlphaFold-3_Data_Pipeline_example.bash) | |
| [AlphaFold 3 Slurm Grace Hopper Inference example](https://raw.githubusercontent.com/ubccr/ccr-examples/refs/heads/AlphaFold-3/containers/2_ApplicationSpecific/AlphaFold-3/slurm_GH200_AlphaFold-3_Inference_example.bash) |
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| Copy the sample Slurm scripts "slurm_AlphaFold-3_Data_Pipeline_example.bash" | ||
| and "slurm_AlphaFold-3_Inference_example.bash" to this directory then modify | ||
| for your use case. | ||
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| You should change the SLURM cluster, partition, qos and account; then change | ||
| the "[YourGroupName]" in the cd command: |
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| Copy the sample Slurm scripts "slurm_AlphaFold-3_Data_Pipeline_example.bash" | |
| and "slurm_AlphaFold-3_Inference_example.bash" to this directory then modify | |
| for your use case. | |
| You should change the SLURM cluster, partition, qos and account; then change | |
| the "[YourGroupName]" in the cd command: | |
| Copy the sample Slurm scripts [slurm_AlphaFold-3_Data_Pipeline_example.bash](./slurm_AlphaFold-3_Data_Pipeline_example.bash) | |
| and [slurm_AlphaFold-3_Inference_example.bash](./slurm_AlphaFold-3_Inference_example.bash) to this directory then modify | |
| for your use case. | |
| You should change the SLURM cluster, partition, qos and account; then change | |
| the `[YourGroupName]` in the cd command. | |
| Use the `slimits` command to see what accounts and QOS settings you have access to. |
| Note that the partition/qos combination does not have to be the same for the | ||
| Data Pipeline and Inference scripts. | ||
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| NOTE: You can add other Slurm options to eiher script. |
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| NOTE: You can add other Slurm options to eiher script. | |
| NOTE: You can add other Slurm options to either script. |
| > -rw-rw-r-- 1 [CCRusername] nogroup 7301275 Aug 1 11:12 ./af_output/2PV7/2PV7_data.json | ||
| > ``` | ||
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| The "./af_output/2PV7" directory will be used as the input directory for the Inference run |
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| The "./af_output/2PV7" directory will be used as the input directory for the Inference run | |
| The `./af_output/2PV7` directory will be used as the input directory for the Inference run |
| > ``` | ||
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| Note from the about output the location of the AlphaFold run output files |
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| Note from the about output the location of the AlphaFold run output files | |
| Note from the above output the location of the AlphaFold run output files |
| cd /projects/academic/[YourGroupName]/AlphaFold-3 | ||
| ``` | ||
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| Then create the sample fold_input.json from [here](https://github.com/google-deepmind/alphafold3?tab=readme-ov-file#installation-and-running-your-first-prediction) |
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| Then create the sample fold_input.json from [here](https://github.com/google-deepmind/alphafold3?tab=readme-ov-file#installation-and-running-your-first-prediction) | |
| Then create the sample `fold_input.json` from [here](https://github.com/google-deepmind/alphafold3?tab=readme-ov-file#installation-and-running-your-first-prediction) |
| ``` | ||
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| ## Buid the ARM64 container image |
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| ## Buid the ARM64 container image | |
| ## Build the ARM64 container image |
| for ARM64 | ||
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| # Slurm batch job |
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Not sure if level 1 heading is required here.
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AlphaFold 3 container build & run examples.
Tony