fixed bugs for running docker in docker.

THU-ATOM · Mar 6, 2024 · da6b1d0 · da6b1d0
1 parent 7bacffa
commit da6b1d0
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Showing 9 changed files with 21 additions and 22 deletions.
diff --git a/api/api.py b/api/api.py
@@ -82,24 +82,8 @@ async def analysis_task(requests: List[Dict[str, Any]]):
     return {"task_id": task.id}
 
 @app.post(f"/submit")
-async def submit_task(
-    request: Request,
-    pdb_path: Union[str, Path] = None,
-    plddt: float = 0.0,
-    target_addresses: str = "",
-):
-    _params = request.json()
-    print("Request: ", _params)
-    HASH_ID = "hash_id"
-    if _params is None or HASH_ID not in _params:
-        return json.dumps([])
-    hash_ids = _params[HASH_ID]
-    if not isinstance(hash_ids, list):
-        hash_ids = [hash_ids]
-
-    task = celery_client.send_task(
-        "submit", args=[pdb_path, plddt, target_addresses], queue="queue_submit"
-    )
+async def submit_task(requests: List[Dict[str, Any]]):
+    task = celery_client.send_task("submit", args=[requests], queue="queue_submit")
     return {"task_id": task.id}
 
 

diff --git a/docker-compose.yaml b/docker-compose.yaml
@@ -118,6 +118,7 @@ services:
       - CELERY_BROKER_URL=amqp://rabbitmq:5672
       - CELERY_RESULT_BACKEND=redis://redis
     volumes:
+      - /var/run/docker.sock:/var/run/docker.sock # run docker in docker
       - ./services/searchtpl:/worker
       - /data:/data
       - ./lib:/worker/lib

diff --git a/gui/stats.html b/gui/stats.html
diff --git a/services/analysis/Dockerfile b/services/analysis/Dockerfile
@@ -4,6 +4,7 @@ ENV CELERY_BROKER_URL pyamqp://guest:guest@localhost:5672/
 ENV CELERY_RESULT_BACKEND rpc://
 ENV C_FORCE_ROOT true
 
+# RUN apk add build-base linux-headers   # very slow
 COPY requirements.txt /tmp/requirements.txt
 
 RUN pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple

diff --git a/services/analysis/worker.py b/services/analysis/worker.py
@@ -300,4 +300,4 @@ def run(self, *args, dry=False, **kwargs):
         )
         result_path = os.path.join(dirname, "plddt_results.json")
         dtool.write_json(result_path, data=model2plddts)
-        return True
+        # return True
diff --git a/services/searchtpl/Dockerfile b/services/searchtpl/Dockerfile
@@ -10,6 +10,16 @@ RUN pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
 RUN pip install -U setuptools pip
 RUN pip install --no-cache-dir -r /tmp/requirements.txt
 
+# Install docker (to make docker in docker work)
+RUN curl -fsSL https://download.docker.com/linux/ubuntu/gpg \
+    | gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg \
+    && echo \
+    "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu focal stable" 
+    | tee /etc/apt/sources.list.d/docker.list > /dev/null \
+    && apt-get update \
+    && apt-get install -y docker-ce docker-ce-cli containerd.io docker-compose-plugin \
+    && rm -rf /var/lib/apt/lists/*
+
 WORKDIR /worker
 
 # Specify the command to run on container start

diff --git a/services/submit/Dockerfile b/services/submit/Dockerfile
@@ -1,4 +1,5 @@
 FROM python:3.9
+
 ENV CELERY_BROKER_URL pyamqp://guest:guest@localhost:5672/
 ENV CELERY_RESULT_BACKEND rpc://
 ENV C_FORCE_ROOT true

diff --git a/services/submit/worker.py b/services/submit/worker.py
@@ -336,4 +336,4 @@ def init_runners(self, groups):
     def run(self, dry=False, *args, **kwargs):
         for runner in self.runners:
             runner.run(dry=dry)
-        return True
+        # return True
diff --git a/services/tplfeature/requirements.txt b/services/tplfeature/requirements.txt
@@ -9,4 +9,6 @@ py3Dmol
 psutil
 gpustat
 absl-py
-docker
+docker
+ray
+dm-tree
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,4 +9,6 @@ py3Dmol @@
     psutil
     gpustat
     absl-py
-    docker
+    docker
+    ray
+    dm-tree