Merge pull request #46 from Becksteinlab/develop

NAMD Testing with private image + Docs

.github/workflows/gh-ci.yaml

@@ -123,6 +123,10 @@ jobs:
     if: github.repository == 'Becksteinlab/imdclient'
     runs-on: ubuntu-latest
 
+    permissions:
+      contents: read
+      packages: read
+
     steps:
       - uses: actions/checkout@v4
 
@@ -132,6 +136,13 @@ jobs:
           df -h
           ulimit -a
 
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.NAMD_DOCKER_TOKEN }}
+
       - name: Install conda dependencies
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -161,9 +172,18 @@ jobs:
           python --version
           python -m pip install .  --no-deps 
 
-      - name: Pull container
+      - name: Pull private NAMD container
+        run: |
+          docker pull ghcr.io/becksteinlab/streaming-namd-docker:main-common-cpu
+  
+      # Uses private container
+      - name: Run NAMD tests
+        run: |
+          pytest -v --color=yes imdclient/tests/test_namd.py
+
+      - name: Pull GROMACS + LAMMPS container
         run: |
-          docker pull ghcr.io/becksteinlab/streaming-md-docker:main-Common-CPU
+          docker pull ghcr.io/becksteinlab/streaming-md-docker:main-common-cpu
 
       - name: Run GROMACS tests
         run: |
@@ -172,11 +192,6 @@ jobs:
       - name: Run LAMMPS tests
         run: |
           pytest -v --color=yes imdclient/tests/test_lammps.py
-  
-      # SUSPEND until NAMD permissions are resolved
-      # - name: Run NAMD tests
-      #   run: |
-      #     pytest -v --color=yes imdclient/tests/test_namd.py
 
   pylint_check:
     if: github.repository == 'Becksteinlab/imdclient'

docs/source/usage.rst

@@ -22,19 +22,36 @@ MDAnalysis IMDReader client when this line is printed to the terminal:
 
     IMD: Will wait until I have a connection and IMD_GO orders.
 
+You are now ready to connect to the simulation engine with a client.
+
 NAMD
 ----
-In NAMD, the simulation will wait for a client connection when the  
-``IMDon`` option is set to ``yes`` in the NAMD configuration file. 
-Other options that can be set are detailed 
-`here <https://github.com/amruthesht/namd-3.0/blob/IMDv3-dev/IMDv3-dev.md>`_. 
-This will produce a simulation that is ready for a client connection with the 
+To use IMDv3 with NAMD, add the following lines to your NAMD configuration file:
+
+.. code-block:: none
+
+    IMDon yes
+    IMDport <port, must be the same port used for the client>
+    IMDwait <yes/no>
+    IMDfreq <frequency of sending data to the client>
+
+    IMDsendPositions <yes/no>
+    IMDsendEnergies <yes/no>
+    IMDsendTime <yes/no>
+    IMDsendBoxDimensions <yes/no>
+    IMDsendVelocities <yes/no>
+    IMDsendForces <yes/no>
+    IMDwrapPositions <yes/no>
+
+
+Once the simulation is ready for a client connection, it will print 
 following terminal message:
 
 .. code-block:: none
 
     Info: INTERACTIVE MD AWAITING CONNECTION
 
+You are now ready to connect to the simulation engine with a client.
 
 Using IMDClient with MDAnalysis
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

imdclient/tests/base.py

@@ -64,6 +64,10 @@ def assert_allclose_with_logging(a, b, rtol=1e-07, atol=0, equal_nan=False):
 
 class IMDv3IntegrationTest:
 
+    @pytest.fixture()
+    def container_name(self):
+        return "ghcr.io/becksteinlab/streaming-md-docker:main-common-cpu"
+
     @pytest.fixture()
     def setup_command(self):
         return None
@@ -80,12 +84,13 @@ def docker_client(
         setup_command,
         simulation_command,
         port,
+        container_name,
     ):
         # In CI, container process needs access to tmp_path
         tmp_path.chmod(0o777)
         docker_client = docker.from_env()
         img = docker_client.images.pull(
-            "ghcr.io/becksteinlab/streaming-md-docker:main-Common-CPU"
+            container_name,
         )
         # Copy input files into tmp_path
         for inp in input_files:

imdclient/tests/docker_testing/docker.md

@@ -5,7 +5,7 @@ Ensure [docker](https://www.docker.com/) and the [NVIDIA container toolkit](http
 
 To run the container:
 ```bash
-docker pull ghcr.io/becksteinlab/streaming-md-docker:main-Common-GPU
+docker pull ghcr.io/becksteinlab/streaming-md-docker:main-common-gpu
 
 docker run -v $PWD/imdclient/data:/home/conda:rw -it --runtime=nvidia --gpus=all \
     ghcr.io/becksteinlab/streaming-md-docker:main-Common-GPU

imdclient/tests/test_namd.py

@@ -26,6 +26,10 @@
 
 class TestIMDv3NAMD(IMDv3IntegrationTest):
 
+    @pytest.fixture()
+    def container_name(self):
+        return "ghcr.io/becksteinlab/streaming-namd-docker:main-common-cpu"
+
     @pytest.fixture(params=[NAMD_CONF_NST_1, NAMD_CONF_NST_8])
     def inp(self, request):
         return request.param
@@ -87,10 +91,8 @@ def test_compare_imd_to_true_traj(self, imd_u, true_u, first_frame):
                 imd_u.trajectory[i - first_frame].dt,
                 atol=1e-03,
             )
-            assert_allclose(
-                true_u.trajectory[i].data["step"],
-                imd_u.trajectory[i - first_frame].data["step"],
-            )
+            # step in DCDReader is frame index, not integration step
+            # don't compare step
             assert_allclose_with_logging(
                 true_u.trajectory[i].dimensions,
                 imd_u.trajectory[i - first_frame].dimensions,
@@ -103,12 +105,11 @@ def test_compare_imd_to_true_traj(self, imd_u, true_u, first_frame):
             )
 
     # Compare velocities
-    def test_compare_imd_to_true_traj_vel(
-        self, imd_u, true_u_vel, first_frame
-    ):
+    def test_compare_imd_to_true_traj_vel(self, imd_u, true_u_vel, first_frame):
         for i in range(first_frame, len(true_u_vel.trajectory)):
             assert_allclose_with_logging(
-                true_u_vel.trajectory[i].positions,
+                # Unit conversion
+                true_u_vel.trajectory[i].positions * 20.45482706,
                 imd_u.trajectory[i - first_frame].velocities,
                 atol=1e-03,
             )