# AutoDock-GPU Follow this procedure to run AutoDock, an example of a community project including SYCL support. - Operating system: Ubuntu* 22.04 - Hardware: Intel® Data Center Max GPUs - Software: Intel® oneAPI Base toolkit, Intel® oneAPI HPC toolkit - Time to complete: 15 minutes For more information, see the [AutoDock-GPU repository](https://github.com/emascarenhas/AutoDock-GPU). 1. Check whether the driver stack is installed. ```(bash) $ xpu-smi discovery ``` The command should return at least one Intel® Data Center GPU Max device. 2. Check whether the oneAPI toolkit is installed. Check if oneAPI toolkits are installed: ```(bash) $ apt list intel-basekit intel-hpckit ``` Expected output ```(bash) Listing... Done intel-basekit/all,now 2023.2.0-49384 amd64 [installed] intel-hpckit/all,now 2023.2.0-49438 amd64 [installed] ``` 3. If you previously have not configured your environment, install the Ubuntu 22.04 graphics driver. See [dgpu-docs](https://dgpu-docs.intel.com/) for details. ```{note} Access to Ubuntu repositories, such as https://repositories.intel.com and https://apt.repos.intel.com, is required for installation. If proxy settings involve changes to environment variables such as http_proxy or https_proxy, small modifications are required in the following steps, such as adding -E (preserve environment) to sudo commands. ``` 4. If you previously have not configured your environment, enable access to the Intel repo serving the oneAPI packages and install the oneAPI Base toolkit and HPC toolkit for Ubuntu 22.04. ```bash wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \ | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list sudo apt update ``` ```bash sudo apt install -y intel-basekit intel-hpckit ``` 5. Build AutoDock. ```(bash) git clone https://github.com/emascarenhas/AutoDock-GPU.git cd AutoDock-GPU/ source /opt/intel/oneapi/setvars.sh make DEVICE=XeGPU NUMWI=64 ``` 6. Run AutoDock. ```(bash) ./bin/autodock_xegpu_64wi -ffile ./input/1stp/derived/1stp_protein.maps.fld --lfile ./input/1stp/derived/1stp_ligand.pdbqt ``` For more information, see [usage instructions](https://github.com/emascarenhas/AutoDock-GPU#usage). The following example presents a result snapshot from Intel® Data Center GPU Max 1550: ```bash Running 1 docking calculation XeGPU device: Intel(R) Data Center GPU Max 1550 (#1 / 6) Available memory on device: 131072 MB (total: 131072 MB) xPU Setup time 0.000173s Running Job #1 Using heuristics: (capped) number of evaluations set to 1132076 Local-search chosen method is: ADADELTA (ad) Rest of Setup time 1.110014s Executing docking runs, stopping automatically after either reaching 0.15 kcal/mol standard deviation of the best molecules of the last 4 * 5 generations, 42000 generations, or 1132076 evaluations: Generations | Evaluations | Threshold | Average energy of best 10% | Samples | Best energy ------------+--------------+------------------+------------------------------+---------+------------------- 0 | 150 | 194.55 kcal/mol | 117.36 +/- 20.58 kcal/mol | 4 | 91.69 kcal/mol 5 | 29795 | 194.55 kcal/mol | 7.43 +/- 27.52 kcal/mol | 123 | -9.06 kcal/mol 10 | 56772 | 10.79 kcal/mol | -8.95 +/- 0.21 kcal/mol | 10 | -9.47 kcal/mol 15 | 83098 | -8.65 kcal/mol | -9.43 +/- 0.19 kcal/mol | 8 | -9.63 kcal/mol 20 | 108845 | -9.08 kcal/mol | -9.52 +/- 0.16 kcal/mol | 5 | -9.77 kcal/mol 25 | 134752 | -9.02 kcal/mol | -9.54 +/- 0.16 kcal/mol | 17 | -9.87 kcal/mol 30 | 160782 | -9.40 kcal/mol | -9.59 +/- 0.19 kcal/mol | 7 | -9.91 kcal/mol 35 | 186577 | -9.17 kcal/mol | -9.46 +/- 0.22 kcal/mol | 17 | -9.94 kcal/mol 40 | 212506 | -9.27 kcal/mol | -9.66 +/- 0.16 kcal/mol | 16 | -9.95 kcal/mol 45 | 238004 | -9.51 kcal/mol | -9.78 +/- 0.13 kcal/mol | 7 | -9.95 kcal/mol 50 | 263476 | -9.50 kcal/mol | -9.82 +/- 0.12 kcal/mol | 10 | -9.99 kcal/mol 55 | 289158 | -9.64 kcal/mol | -9.83 +/- 0.09 kcal/mol | 13 | -10.01 kcal/mol 60 | 314687 | -9.73 kcal/mol | -9.91 +/- 0.09 kcal/mol | 14 | -10.01 kcal/mol 65 | 340233 | -9.82 kcal/mol | -9.93 +/- 0.07 kcal/mol | 11 | -10.02 kcal/mol 70 | 365733 | -9.73 kcal/mol | -9.91 +/- 0.09 kcal/mol | 9 | -10.02 kcal/mol 75 | 391608 | -9.76 kcal/mol | -9.90 +/- 0.07 kcal/mol | 13 | -10.02 kcal/mol 80 | 417188 | -9.73 kcal/mol | -9.95 +/- 0.07 kcal/mol | 10 | -10.02 kcal/mol ------------+--------------+------------------+------------------------------+---------+------------------- Finished evaluation after reaching -9.92 +/- 0.08 kcal/mol combined. 43 samples, best energy -10.02 kcal/mol. ... All jobs ran without errors. ```