Merge branch 'main' into gpu-model

.github/CONTRIBUTING.md

@@ -0,0 +1,63 @@
+# Contribution Guidelines
+
+Thank you for your interest in contributing to Uni-Dock! We value your time and effort, and aim to make the contribution process enjoyable and efficient. To ensure consistency and maintainability, please follow these guidelines when submitting your contributions.
+
+## Troubleshooting
+
+If you encountered problems using Uni-Dock, please refer to our GitHub [issue tracker](https://github.com/dptech-corp/Uni-Dock/issues), and check if it is a known problem.
+If you found a bug, you can help us improve by [submitting a new issue](https://github.com/dptech-corp/Uni-Dock/issues/new) to our GitHub Repository. Provide a clear and concise title and description, including steps to reproduce the issue (if applicable) and any relevant context.
+Even better, you can submit a Pull Request with a patch.
+
+## Feature requests
+
+We highly appreciate your contributions, and would like to help you crafting the changes and making contributions to the community.
+If you would like to implement a new feature, please **submit a feature requesting issue with a proposal for your work first**. 
+This help fitting your ideas and work with the development road map well, coordinating our efforts, and avoiding duplication of work.
+
+## Submitting a Pull Request
+
+**Please fork your own copy of the Uni-Dock repository, and draft your changes there.** Once the modified codes work as expected, please submit a pull request to merge your contributions.
+
+1. [Fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) the [Uni-Dock repository](https://github.com/dptech-corp/Uni-Dock). If you already had an existing fork, [sync](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork) the fork to keep your modification up-to-date.
+
+2. Pull your forked repository, create a new git branch, and make your changes in it:
+
+     ```shell
+     git checkout -b bug-fix
+     ```
+
+3. Coding your patch and commit the changes.
+
+4. Push your branch to GitHub:
+
+    ```shell
+    git push origin my-fix-branch
+    ```
+
+5. On GitHub, create a pull request (PR) from your bug-fix branch targeting `dptech-corp/Uni-Dock`.
+
+6. After your pull request is merged, you can safely delete your branch and sync the changes from the main (upstream) repository:
+
+- Delete the remote branch on GitHub either [through the GitHub web UI](https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/managing-branches-in-your-repository/deleting-and-restoring-branches-in-a-pull-request#deleting-a-branch-used-for-a-pull-request) or your local shell as follows:
+
+    ```shell
+    git push origin --delete my-fix-branch
+    ```
+
+- Check out the master branch:
+
+    ```shell
+    git checkout develop -f
+    ```
+
+- Delete the local branch:
+
+    ```shell
+    git branch -D my-fix-branch
+    ```
+
+- Update your master with the latest upstream version:
+
+    ```shell
+    git pull --ff upstream develop
+    ```

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,26 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior.
+Please provide necessary information including input file, running commands, error log, etc.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Environment (please complete the following information):**
+ - CUDA version
+ - GPU model
+ - Uni-Dock version
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/custom.md

@@ -0,0 +1,10 @@
+---
+name: Custom issue template
+about: Describe this issue template's purpose here.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is.
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/ci_tools.yml

@@ -1,9 +1,7 @@
 name: Uni-Dock Tools CI/CD
 on:
   push:
-    branches: [ main ]
   pull_request:
-    branches: [ main ]
 
 jobs:
   flake8:
@@ -15,7 +13,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python  ${{ matrix.python-version }}
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
@@ -83,15 +81,15 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.9"]
-    container: 
+    container:
       image: docker.io/dptechnology/unidock:latest
       options: --gpus all
     steps:
     - name: checkout repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Setup conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         miniconda-version: "latest"
         python-version: ${{ matrix.python-version }}
@@ -107,9 +105,9 @@ jobs:
       working-directory: ./unidock_tools
       run: |
         export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH
-        python setup.py install
+        conda run -n test python setup.py install
 
     - name: perform unit-test
       run: |
         export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH
-        pytest unidock_tools/tests/ut -v
+        conda run -n test pytest unidock_tools/tests/ut -v

.github/workflows/ci_unidock.yml

@@ -1,14 +1,14 @@
 name: Uni-Dock CI/CD
 on:
   push:
-    branches: [ main ]
+    branches: []
   pull_request:
     branches: [ main ]
 
 jobs:
   unidock_test:
     runs-on: nvidia
-    container: 
+    container:
       image: nvidia/cuda:12.2.0-devel-ubuntu22.04
       options: --gpus all
     steps:
@@ -19,7 +19,7 @@ jobs:
       run: |
         apt-get update
         apt-get install -y build-essential cmake libboost-all-dev ninja-build
-    
+
     - if: ${{ env.ACT }}
       name: Hack container for local development
       run: |
@@ -42,32 +42,29 @@ jobs:
         nvidia-smi
         unidock --version
 
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: 3.8
+        python-version: '3.10'
 
     - name: perform unit-test
       run: |
         python -m pip install --upgrade pip
-        pip install pytest coverage
-        coverage run -m pytest unidock/test/ut -v
-        coverage xml
+        pip install pytest>=8.0.0 pytest-cov
+        pytest unidock/test/ut -vv --doctest-modules --junitxml=junit/test-results.xml --cov --cov-report term
 
   build_docker_image:
     needs: unidock_test
     runs-on: ubuntu-latest
     steps:
 
     - name: log in to docker hub
-      uses: docker/login-action@v2
+      uses: docker/login-action@v3
+      if: github.event_name == 'push'
       with:
         username: dptechnology
         password: ${{ secrets.DOCKERHUB_PAT }}
 
-    - name: set up QEMU
-      uses: docker/setup-qemu-action@v2
-
     - name: set up docker buildx
       id: buildx
       uses: docker/setup-buildx-action@v2
@@ -86,4 +83,4 @@ jobs:
         tags: dptechnology/unidock:${{ steps.short-sha.outputs.sha }},dptechnology/unidock:latest
         file: Dockerfile
         context: "{{defaultContext}}:unidock"
-        push: true
+        push: ${{ github.event_name == 'push' }}

.gitignore

@@ -5,6 +5,7 @@ build/
 test/ligands
 test/results
 .vscode
+.idea
 unidock/build/
 unidock/example/screening_test/indata
 unidock/example/screening_test/result

unidock/src/main/main.cpp

@@ -237,6 +237,8 @@ bug reporting, license agreements, and more information.      \n";
         std::string score_file("scores.txt");
 
         positional_options_description positional;  // remains empty
+        // GPU Device id to use
+        int device_id = 0;
 
         options_description inputs("Input");
         inputs.add_options()("receptor", value<std::string>(&rigid_name),
@@ -281,7 +283,9 @@ bug reporting, license agreements, and more information.      \n";
             "output filename (directory + prefix name) for maps. Option --force_even_voxels may be "
             "needed to comply with .map format");
         options_description advanced("Advanced options (see the manual)");
-        advanced.add_options()("score_only", bool_switch(&score_only),
+        advanced.add_options()("device_id", value<int>(&device_id)->default_value(0), 
+            "GPU device id to use (default 0)")
+            ("score_only", bool_switch(&score_only),
                                "score only - search space can be omitted")(
             "score_file", value<std::string>(&score_file)->default_value(score_file),
             "score only output file in batch mode, with 'score_only' option")(
@@ -498,7 +502,8 @@ bug reporting, license agreements, and more information.      \n";
 
             std::vector<double> box_size = {size_x, size_y, size_z};
             simulation_container sc(seed, num_modes, refine_step, out_dir,
-                ligand_index, paired_batch_size, box_size, local_only, max_step, verbosity, exhaustiveness);
+                ligand_index, paired_batch_size, box_size, local_only, max_step, 
+                verbosity, exhaustiveness, device_id);
 
             int res = sc.prime();
             if (res <= 0)
@@ -766,7 +771,9 @@ bug reporting, license agreements, and more information.      \n";
             if (sf_name.compare("ad4") == 0) ad4 = true;
             cudaGetDeviceCount(&deviceCount);
             if (deviceCount > 0) {
-                cudaSetDevice(0);
+                checkCUDA(cudaSetDevice(device_id));
+
+                printf("Set GPU device id to %d\n", device_id);
                 cudaMemGetInfo(&avail, &total);
                 printf("Available Memory = %dMiB   Total Memory = %dMiB\n",
                        int(avail / 1024 / 1024), int(total / 1024 / 1024));

unidock/src/main/simulation_container.h

@@ -59,6 +59,7 @@ struct simulation_container
     int m_seed = 5;
     int m_num_modes = 9;
     int m_refine_steps = 3;
+    int m_device_id = 0;
 
     std::vector<std::string> m_complex_names;
     std::string m_config_json_path;
@@ -79,7 +80,8 @@ struct simulation_container
         int local_only,
         int max_step,
         int verbosity,
-        int exh):
+        int exh,
+        int device_id):
 
         m_seed(seed),
         m_num_modes(num_modes),
@@ -93,7 +95,8 @@ struct simulation_container
         m_verbosity(verbosity),
         m_exhaustiveness(exh),
         m_isGPU(true),
-        m_successful_property_count (0)
+        m_successful_property_count (0),
+        m_device_id(device_id)
      {
         //m_out_phrase = util_random_string(5);
      }
@@ -490,7 +493,7 @@ struct simulation_container
                     vina_cuda_worker vcw(m_seed, m_num_modes, m_refine_steps, props[i].center_x, props[i].center_y, 
                             props[i].center_z, props[i].protein_name,props[i].ligand_name,
                             local_only, std::vector<double>{props[i].box_x, props[i].box_y, props[i].box_z}, m_max_global_steps, m_verbosity,
-                            m_exhaustiveness, workdir, input_dir, out_phrase);
+                            m_exhaustiveness, workdir, input_dir, out_phrase, m_device_id);
                     try
                     {
                         int ret = vcw.launch();

unidock/src/main/vina_cuda_worker.h

@@ -80,6 +80,7 @@ class vina_cuda_worker : public Vina
     double center_z; 
     std::string protein_name;
     std::string ligand_name;
+    int m_device_id = 0;
     void init(std::string out_phrase)
     {
         out_dir = workdir + "/" + out_phrase;
@@ -88,6 +89,7 @@ class vina_cuda_worker : public Vina
             boost::filesystem::create_directory(out_dir);
         }
 	    m_seed = seed;
+        checkCUDA(cudaSetDevice(m_device_id));
     }
 public:            
     vina_cuda_worker(
@@ -106,7 +108,8 @@ class vina_cuda_worker : public Vina
             int exh,
             std::string workdir,
             std::string input_dir,
-            std::string out_phrase):
+            std::string out_phrase,
+            int device_id):
 
             seed(seed),
             num_modes(num_modes),
@@ -125,6 +128,7 @@ class vina_cuda_worker : public Vina
             ligand_name(ligand_name),
             local_only(local_only),
             out_dir(out_phrase),
+            m_device_id(device_id),
             Vina{"vina", 0, seed, verbosity, false, NULL}
     {
         init(out_phrase);