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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
author galaxy-australia
date Tue, 01 Mar 2022 02:53:05 +0000
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2 # Alphafold compute setup 2 # Alphafold compute setup
3 3
4 ## Overview 4 ## Overview
5 5
6 Alphafold requires a customised compute environment to run. The machine needs a GPU, and access to a 2.2 Tb reference data store. 6 Alphafold requires a customised compute environment to run. The machine needs a GPU, and access to a 2.2 Tb reference data store.
7 7
8 This document is designed to provide details on the compute environment required for Alphafold operation, and the Galaxy job destination settings to run the wrapper. 8 This document is designed to provide details on the compute environment required for Alphafold operation, and the Galaxy job destination settings to run the wrapper.
9 9
10 For full details on Alphafold requirements, see https://github.com/deepmind/alphafold. 10 For full details on Alphafold requirements, see https://github.com/deepmind/alphafold.
11 11
12 <br> 12 <br>
13 13
14 ### HARDWARE 14 ### HARDWARE
15 15
16 The machine is recommended to have the following specs: 16 The machine is recommended to have the following specs:
17 - 12 cores 17 - 12 cores
18 - 80 Gb RAM 18 - 80 Gb RAM
19 - 2.5 Tb storage 19 - 2.5 Tb storage
20 - A fast Nvidia GPU. 20 - A fast Nvidia GPU.
21 21
22 As a minimum, the Nvidia GPU must have 8Gb RAM. It also requires ***unified memory*** to be switched on. <br> 22 As a minimum, the Nvidia GPU must have 8Gb RAM. It also requires ***unified memory*** to be switched on. <br>
23 Unified memory is usually enabled by default, but some HPC systems will turn it off so the GPU can be shared between multiple jobs concurrently. 23 Unified memory is usually enabled by default, but some HPC systems will turn it off so the GPU can be shared between multiple jobs concurrently.
24 24
25 <br> 25 <br>
29 This wrapper runs Alphafold as a singularity container. The following software are needed: 29 This wrapper runs Alphafold as a singularity container. The following software are needed:
30 30
31 - [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html) 31 - [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html)
32 - [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html) 32 - [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html)
33 33
34 As Alphafold uses an Nvidia GPU, the NVIDIA Container Toolkit is needed. This makes the GPU available inside the running singularity container. 34 As Alphafold uses an Nvidia GPU, the NVIDIA Container Toolkit is needed. This makes the GPU available inside the running singularity container.
35 35
36 To check that everything has been set up correctly, run the following 36 To check that everything has been set up correctly, run the following
37 37
38 ``` 38 ```
39 singularity run --nv docker://nvidia/cuda:11.0-base nvidia-smi 39 singularity run --nv docker://nvidia/cuda:11.0-base nvidia-smi
77 77
78 # download ref data 78 # download ref data
79 bash scripts/download_all_data.sh /data/alphafold_databases 79 bash scripts/download_all_data.sh /data/alphafold_databases
80 ``` 80 ```
81 81
82 This will install the reference data to `/data/alphafold_databases`. To check this has worked, ensure the final folder structure is as follows: 82 This will install the reference data to `/data/alphafold_databases`. To check this has worked, ensure the final folder structure is as follows:
83 83
84 ``` 84 ```
85 data/alphafold_databases 85 data/alphafold_databases
86 ├── bfd 86 ├── bfd
87 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata 87 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
126 126
127 <br> 127 <br>
128 128
129 ### JOB DESTINATION 129 ### JOB DESTINATION
130 130
131 Alphafold needs a custom singularity job destination to run. 131 Alphafold needs a custom singularity job destination to run.
132 The destination needs to be configured for singularity, and some 132 The destination needs to be configured for singularity, and some
133 extra singularity params need to be set as seen below. 133 extra singularity params need to be set as seen below.
134 134
135 Specify the job runner. For example, a local runner 135 Specify the job runner. For example, a local runner
136 136
137 ``` 137 ```
138 <plugin id="alphafold_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> 138 <plugin id="alphafold_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
152 152
153 <br> 153 <br>
154 154
155 ### Closing 155 ### Closing
156 156
157 If you are experiencing technical issues, feel free to write to help@genome.edu.au. We may be able to provide comment on setting up Alphafold on your compute environment. 157 If you are experiencing technical issues, feel free to write to help@genome.edu.au. We may be able to provide advice on setting up Alphafold on your compute environment.