This is an automated email from the ASF dual-hosted git repository.
dimuthuupe pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata.git
The following commit(s) were added to refs/heads/master by this push:
new f7fc547d1b Jupyter image changes
f7fc547d1b is described below
commit f7fc547d1b85064d0ecb51462b03be651df6faa5
Author: Dimuthu Wannipurage <[email protected]>
AuthorDate: Mon Jul 22 05:50:00 2024 -0400
Jupyter image changes
---
.../airavata-agent/build-container.sh | 4 +
.../airavata-agent/jupyter/Dockerfile | 14 +-
.../airavata-agent/jupyter/labconfig/__init__.py | 0
.../jupyter/labconfig/airavata_magics.py | 234 ++++++++++++++
.../airavata-agent/jupyter/labconfig/bootstrap.sh | 2 +
.../airavata-agent/jupyter/magic.ipynb | 340 ++++++++++++++++++---
6 files changed, 554 insertions(+), 40 deletions(-)
diff --git a/modules/agent-framework/airavata-agent/build-container.sh
b/modules/agent-framework/airavata-agent/build-container.sh
new file mode 100755
index 0000000000..411d222405
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/build-container.sh
@@ -0,0 +1,4 @@
+env GOOS=linux GOARCH=amd64 go build
+cp airavata-agent airavata-agent-linux
+docker build --platform linux/x86_64 -t dimuthuupe/airavata-agent .
+docker push dimuthuupe/airavata-agent
\ No newline at end of file
diff --git a/modules/agent-framework/airavata-agent/jupyter/Dockerfile
b/modules/agent-framework/airavata-agent/jupyter/Dockerfile
index af6904add9..cd2f044471 100644
--- a/modules/agent-framework/airavata-agent/jupyter/Dockerfile
+++ b/modules/agent-framework/airavata-agent/jupyter/Dockerfile
@@ -4,10 +4,22 @@ RUN apt update
RUN apt install fuse -y
RUN pip install notebook
RUN apt install kmod -y
+RUN apt install git -y
+RUN pip install PyJWT
+RUN pip install --upgrade cybershuttle-tune
+RUN pip install scipy
+RUN pip install numpy
+RUN pip install matplotlib
+
COPY labconfig/jupyter_lab_config.py /jupyter_lab_config.py
+COPY labconfig/airavata_magics.py /airavata_magics.py
+COPY labconfig/__init__.py /__init__.py
+RUN git clone https://github.com/cyber-shuttle/jupyter-notebook-examples
/home/jupyter-notebook-examples
+COPY labconfig/bootstrap.sh /bootstrap.sh
+RUN chmod +x /bootstrap.sh
COPY fuse/client /client
EXPOSE 8888
WORKDIR /home
-ENTRYPOINT ["jupyter", "lab", "--config=/jupyter_lab_config.py",
"--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root",
"--NotebookApp.token=''"]
+ENTRYPOINT ["sh", "/bootstrap.sh"]
diff --git
a/modules/agent-framework/airavata-agent/jupyter/labconfig/__init__.py
b/modules/agent-framework/airavata-agent/jupyter/labconfig/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git
a/modules/agent-framework/airavata-agent/jupyter/labconfig/airavata_magics.py
b/modules/agent-framework/airavata-agent/jupyter/labconfig/airavata_magics.py
new file mode 100644
index 0000000000..c3cf49c204
--- /dev/null
+++
b/modules/agent-framework/airavata-agent/jupyter/labconfig/airavata_magics.py
@@ -0,0 +1,234 @@
+from IPython.core.magic import register_cell_magic
+from IPython.core.magic import register_line_magic
+
+from IPython.display import display, Image
+import base64
+import requests
+import json
+import jwt
+import time
+from pathlib import Path
+import os
+
+current_agent_info = None
+
+EXPLICIT_TOKEN_FILE = (
+ Path(os.path.expanduser("~")) / "csagent" / "token" / "keys.json"
+)
+
+def read_explicit_token_file():
+ if not EXPLICIT_TOKEN_FILE.exists():
+ return None
+ else:
+ with open(EXPLICIT_TOKEN_FILE, "r") as f:
+ return json.load(f)
+
+def get_access_token():
+ expl_token_data = read_explicit_token_file()
+ if expl_token_data:
+ return expl_token_data["access_token"]
+
+def get_agent_status():
+ global current_agent_info
+
+ if not current_agent_info:
+ print("No agent was scheduled yet. Please run %init_remote
cluster=<cluster> cpu=<cpu> memory=<memory mb> queue=<queue> walltime=<walltime
minutes>")
+ return
+
+ url = 'http://scigap02.sciencegateways.iu.edu:18880/api/v1/agent/' +
current_agent_info['agentId']
+ response = requests.get(url)
+ if response.status_code == 202:
+ return response.json()
+ else:
+ print('Invalid response reveived. Status code:', response.status_code)
+ print('Response:', response.text)
+
+def submit_agent_job(experiment_name, cluster, queue, cpus, memory, wallTime,
access_token, gateway_id='testdrive'):
+
+ global current_agent_info
+ # URL to which the POST request will be sent
+ url = 'http://scigap02.sciencegateways.iu.edu:18880/api/v1/exp/launch'
+
+ # Data to be sent in the POST request
+ data = {
+ 'experimentName': experiment_name,
+ 'remoteCluster': cluster,
+ 'cpuCount': cpus,
+ 'nodeCount': 1,
+ 'memory': memory,
+ 'wallTime': wallTime,
+ 'queue': queue
+ }
+
+ # Convert the data to JSON format
+ json_data = json.dumps(data)
+
+ decode = jwt.decode(access_token, options={"verify_signature": False})
+ user_id = decode['preferred_username']
+ claimsMap = {
+ "userName": user_id,
+ "gatewayID": gateway_id
+ }
+
+ # Headers
+ headers = {
+ 'Content-Type': 'application/json',
+ 'Authorization': 'Bearer ' + access_token,
+ 'X-Claims': json.dumps(claimsMap)
+ }
+
+ # Send the POST request
+ response = requests.post(url, headers=headers, data=json_data)
+
+ # Check if the request was successful
+ if response.status_code == 200:
+ # Parse the JSON response
+ response_data = response.json()
+ print('Response:', response_data)
+ current_agent_info = response_data
+ else:
+ print('Failed to send POST request. Status code:',
response.status_code)
+ print('Response:', response.text)
+
+def terminate_agent(access_token, gateway_id='testdrive'):
+
+ global current_agent_info
+
+ expId = current_agent_info['experimentId']
+ url = 'http://scigap02.sciencegateways.iu.edu:18880/api/v1/exp/terminate/'
+ expId
+
+ decode = jwt.decode(access_token, options={"verify_signature": False})
+ user_id = decode['preferred_username']
+ claimsMap = {
+ "userName": user_id,
+ "gatewayID": gateway_id
+ }
+
+ # Headers
+ headers = {
+ 'Content-Type': 'application/json',
+ 'Authorization': 'Bearer ' + access_token,
+ 'X-Claims': json.dumps(claimsMap)
+ }
+
+ # Send the POST request
+ response = requests.get(url, headers=headers)
+
+ if response.status_code == 200:
+ # Parse the JSON response
+ response_data = response.json()
+ print('Agent terminated:', response_data)
+ current_agent_info = None
+ else:
+ print('Failed to send termination request. Status code:',
response.status_code)
+ print('Response:', response.text)
+
+
+@register_cell_magic
+def run_remote(line, cell):
+
+ global current_agent_info
+ if not current_agent_info:
+ print("No agent was scheduled yet. Please run %init_remote
cluster=<cluster> cpu=<cpu> memory=<memory mb> queue=<queue> walltime=<walltime
minutes>")
+
+ url =
'http://scigap02.sciencegateways.iu.edu:18880/api/v1/agent/executejupyterrequest'
+
+ data = {
+ "sessionId": "session1",
+ "keepAlive": True,
+ "code": cell,
+ "agentId": current_agent_info["agentId"]
+ }
+
+ json_data = json.dumps(data)
+ response = requests.post(url, headers={'Content-Type':
'application/json'}, data=json_data)
+ execution_resp = response.json()
+ execution_id = execution_resp["executionId"]
+ error = execution_resp["error"]
+ if error:
+ print("Cell execution failed. Error: " + error)
+ if execution_id:
+ while True:
+ url =
"http://scigap02.sciencegateways.iu.edu:18880/api/v1/agent/executejupyterresponse/";
+ execution_id
+ response = requests.get(url, headers={'Accept':
'application/json'})
+ json_response = response.json()
+ #print(json_response)
+ if json_response['available']:
+ result_str = json_response['responseString']
+ result = json.loads(result_str)
+ if 'result' in result:
+ print(result['result'])
+ elif 'error' in result:
+ print(result['error']['ename'])
+ print(result['error']['evalue'])
+ print(result['error']['traceback'])
+ elif 'display' in result:
+ display_obj = result['display']
+ if 'data' in display_obj:
+ data_obj = display_obj['data']
+ if 'image/png' in data_obj:
+ image_data = data_obj['image/png']
+ display(Image(data=base64.b64decode(image_data),
format='png'))
+ break
+ time.sleep(1)
+
+@register_line_magic
+def init_remote(line):
+
+ if current_agent_info:
+ status = get_agent_status()
+ if status:
+ if status['agentUp']:
+ print("An agent is already running. Please terminate it first
by running %terminate_remote")
+ return
+ else:
+ print("An agent was scheduled. Please terminate it first by
running %terminate_remote")
+ return
+
+ access_token = get_access_token()
+ pairs = line.split()
+
+ # Initialize variable to store the cluster value
+ cluster_value = None
+ memory_value = None
+ cpu_value = None
+ queue_value = None
+ walltime_value = None
+
+ # Iterate through the pairs to find the cluster value
+ for pair in pairs:
+ if pair.startswith("cluster="):
+ cluster_value = pair.split("=")[1]
+ if pair.startswith("cpu="):
+ cpu_value = pair.split("=")[1]
+ if pair.startswith("memory="):
+ memory_value = pair.split("=")[1]
+ if pair.startswith("queue="):
+ queue_value = pair.split("=")[1]
+ if pair.startswith("walltime="):
+ walltime_value = pair.split("=")[1]
+
+ submit_agent_job('CS Agent', cluster_value, queue_value, cpu_value,
memory_value, walltime_value, access_token)
+
+@register_line_magic
+def status_remote(line):
+ status = get_agent_status()
+ if status:
+ if status['agentUp']:
+ print("Agent", status['agentId'], 'is running')
+ else:
+ print("Agent", status['agentId'], 'is still prepairing. Please
wait')
+
+@register_line_magic
+def terminate_remote(line):
+ global current_agent_info
+ access_token = get_access_token()
+ if current_agent_info:
+ terminate_agent(access_token)
+
+
+def load_ipython_extension(ipython):
+ ipython.register_magic_function(init_remote)
+ ipython.register_magic_function(status_remote)
+ ipython.register_magic_function(terminate_remote)
+ ipython.register_magic_function(run_remote)
diff --git
a/modules/agent-framework/airavata-agent/jupyter/labconfig/bootstrap.sh
b/modules/agent-framework/airavata-agent/jupyter/labconfig/bootstrap.sh
new file mode 100644
index 0000000000..754a6e8f52
--- /dev/null
+++ b/modules/agent-framework/airavata-agent/jupyter/labconfig/bootstrap.sh
@@ -0,0 +1,2 @@
+cd /home/jupyter-notebook-examples && git pull && cd -
+jupyter lab --config=/jupyter_lab_config.py --ip=0.0.0.0 --port=8888
--no-browser --allow-root --NotebookApp.token=''
\ No newline at end of file
diff --git a/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
b/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
index c667375f30..d03b63d029 100644
--- a/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
+++ b/modules/agent-framework/airavata-agent/jupyter/magic.ipynb
@@ -18,23 +18,208 @@
},
{
"cell_type": "code",
- "execution_count": 53,
+ "execution_count": 2,
+ "id": "9350833b-5c79-4b7e-9a27-db44db26e98f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "current_agent_info = None"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 54,
+ "id": "eca0c9a6-4771-44b9-94c7-cf931bff4e83",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{'agentId': 'agent_ba91240a-3e3d-4f15-8aac-207ba7f36b8b',\n",
+ " 'experimentId': 'CS_Agent_7c607c7f-c1af-485f-b883-3eff3f54e89e'}"
+ ]
+ },
+ "execution_count": 54,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "current_agent_info"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 115,
+ "id": "d3ef593b-7bdb-4228-9422-3f12cf4c14fd",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Collecting pyjwt\n",
+ " Obtaining dependency information for pyjwt from
https://files.pythonhosted.org/packages/2b/4f/e04a8067c7c96c364cef7ef73906504e2f40d690811c021e1a1901473a19/PyJWT-2.8.0-py3-none-any.whl.metadata\n";,
+ " Using cached PyJWT-2.8.0-py3-none-any.whl.metadata (4.2 kB)\n",
+ "Using cached PyJWT-2.8.0-py3-none-any.whl (22 kB)\n",
+ "Installing collected packages: pyjwt\n",
+ "Successfully installed pyjwt-2.8.0\n",
+ "\n",
+
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
A new release of pip is available:
\u001b[0m\u001b[31;49m23.2.1\u001b[0m\u001b[39;49m ->
\u001b[0m\u001b[32;49m24.1.2\u001b[0m\n",
+
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n"
+ ]
+ }
+ ],
+ "source": [
+ "! pip install pyjwt"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 99,
"id": "c5c591cb-7f0f-47ab-a9fa-4700161439c2",
"metadata": {},
"outputs": [],
"source": [
+ "from IPython.core.magic import register_cell_magic\n",
+ "from IPython.core.magic import register_line_magic\n",
+ "\n",
"from IPython.display import display, Image\n",
"import base64\n",
+ "import requests\n",
+ "import json\n",
+ "import jwt\n",
+ "import time\n",
+ "from pathlib import Path\n",
+ "\n",
+ "current_agent_info = None\n",
+ "\n",
+ "EXPLICIT_TOKEN_FILE = (\n",
+ " Path(os.path.expanduser(\"~\")) / \"csagent\" / \"token\" /
\"keys.json\"\n",
+ ")\n",
+ "\n",
+ "def read_explicit_token_file():\n",
+ " if not EXPLICIT_TOKEN_FILE.exists():\n",
+ " return None\n",
+ " else:\n",
+ " with open(EXPLICIT_TOKEN_FILE, \"r\") as f:\n",
+ " return json.load(f)\n",
+ "\n",
+ "def get_access_token():\n",
+ " expl_token_data = read_explicit_token_file()\n",
+ " if expl_token_data:\n",
+ " return expl_token_data[\"access_token\"]\n",
+ " \n",
+ "def get_agent_status():\n",
+ " global current_agent_info\n",
+ " \n",
+ " if not current_agent_info:\n",
+ " print(\"No agent was scheduled yet. Please run %init_remote
cluster=<cluster> cpu=<cpu> memory=<memory mb> queue=<queue> walltime=<walltime
minutes>\")\n",
+ " return\n",
+ " \n",
+ " url = 'http://scigap02.sciencegateways.iu.edu:18880/api/v1/agent/' +
current_agent_info['agentId']\n",
+ " response = requests.get(url)\n",
+ " if response.status_code == 202:\n",
+ " return response.json()\n",
+ " else:\n",
+ " print('Invalid response reveived. Status code:',
response.status_code)\n",
+ " print('Response:', response.text)\n",
+ " \n",
+ "def submit_agent_job(experiment_name, cluster, queue, cpus, memory,
wallTime, access_token, gateway_id='testdrive'):\n",
+ "\n",
+ " global current_agent_info\n",
+ " # URL to which the POST request will be sent\n",
+ " url =
'http://scigap02.sciencegateways.iu.edu:18880/api/v1/exp/launch'\n",
+ "\n",
+ " # Data to be sent in the POST request\n",
+ " data = {\n",
+ " 'experimentName': experiment_name,\n",
+ " 'remoteCluster': cluster,\n",
+ " 'cpuCount': cpus,\n",
+ " 'nodeCount': 1,\n",
+ " 'memory': memory,\n",
+ " 'wallTime': wallTime,\n",
+ " 'queue': queue\n",
+ " }\n",
+ " \n",
+ " # Convert the data to JSON format\n",
+ " json_data = json.dumps(data)\n",
+ "\n",
+ " decode = jwt.decode(access_token, options={\"verify_signature\":
False})\n",
+ " user_id = decode['preferred_username']\n",
+ " claimsMap = {\n",
+ " \"userName\": user_id,\n",
+ " \"gatewayID\": gateway_id\n",
+ " }\n",
+ " \n",
+ " # Headers\n",
+ " headers = {\n",
+ " 'Content-Type': 'application/json',\n",
+ " 'Authorization': 'Bearer ' + access_token,\n",
+ " 'X-Claims': json.dumps(claimsMap)\n",
+ " }\n",
+ " \n",
+ " # Send the POST request\n",
+ " response = requests.post(url, headers=headers, data=json_data)\n",
+ " \n",
+ " # Check if the request was successful\n",
+ " if response.status_code == 200:\n",
+ " # Parse the JSON response\n",
+ " response_data = response.json()\n",
+ " print('Response:', response_data)\n",
+ " current_agent_info = response_data\n",
+ " else:\n",
+ " print('Failed to send POST request. Status code:',
response.status_code)\n",
+ " print('Response:', response.text)\n",
+ "\n",
+ "def terminate_agent(access_token, gateway_id='testdrive'):\n",
+ "\n",
+ " global current_agent_info\n",
+ " \n",
+ " expId = current_agent_info['experimentId']\n",
+ " url =
'http://scigap02.sciencegateways.iu.edu:18880/api/v1/exp/terminate/' + expId\n",
+ "\n",
+ " decode = jwt.decode(access_token, options={\"verify_signature\":
False})\n",
+ " user_id = decode['preferred_username']\n",
+ " claimsMap = {\n",
+ " \"userName\": user_id,\n",
+ " \"gatewayID\": gateway_id\n",
+ " }\n",
+ " \n",
+ " # Headers\n",
+ " headers = {\n",
+ " 'Content-Type': 'application/json',\n",
+ " 'Authorization': 'Bearer ' + access_token,\n",
+ " 'X-Claims': json.dumps(claimsMap)\n",
+ " }\n",
+ " \n",
+ " # Send the POST request\n",
+ " response = requests.get(url, headers=headers)\n",
+ "\n",
+ " if response.status_code == 200:\n",
+ " # Parse the JSON response\n",
+ " response_data = response.json()\n",
+ " print('Agent terminated:', response_data)\n",
+ " current_agent_info = None\n",
+ " else:\n",
+ " print('Failed to send termination request. Status code:',
response.status_code)\n",
+ " print('Response:', response.text)\n",
+ "\n",
"\n",
"@register_cell_magic\n",
"def run_remote(line, cell):\n",
- " url =
'http://scigap02.sciencegateways.iu.edu:18880/api/v1/agent/executejupyterrequest'\n",
"\n",
+ " global current_agent_info\n",
+ " if not current_agent_info:\n",
+ " print(\"No agent was scheduled yet. Please run %init_remote
cluster=<cluster> cpu=<cpu> memory=<memory mb> queue=<queue> walltime=<walltime
minutes>\")\n",
+ "\n",
+ " url =
'http://scigap02.sciencegateways.iu.edu:18880/api/v1/agent/executejupyterrequest'\n",
+ " \n",
" data = {\n",
" \"sessionId\": \"session1\",\n",
" \"keepAlive\": True,\n",
" \"code\": cell,\n",
- " \"agentId\": \"agent1991\"\n",
+ " \"agentId\": current_agent_info[\"agentId\"]\n",
" }\n",
"\n",
" json_data = json.dumps(data) \n",
@@ -71,32 +256,62 @@
"\n",
"@register_line_magic\n",
"def init_remote(line):\n",
- " print(f\"Your input: {line}\")\n",
+ "\n",
+ " if current_agent_info:\n",
+ " status = get_agent_status()\n",
+ " if status:\n",
+ " if status['agentUp']:\n",
+ " print(\"An agent is already running. Please terminate it
first by running %terminate_remote\")\n",
+ " return\n",
+ " else:\n",
+ " print(\"An agent was scheduled. Please terminate it first
by running %terminate_remote\")\n",
+ " return\n",
+ " \n",
+ " access_token = get_access_token()\n",
" pairs = line.split()\n",
"\n",
" # Initialize variable to store the cluster value\n",
" cluster_value = None\n",
+ " memory_value = None\n",
+ " cpu_value = None\n",
+ " queue_value = None\n",
+ " walltime_value = None\n",
" \n",
" # Iterate through the pairs to find the cluster value\n",
" for pair in pairs:\n",
" if pair.startswith(\"cluster=\"):\n",
" cluster_value = pair.split(\"=\")[1]\n",
- " break\n",
+ " if pair.startswith(\"cpu=\"):\n",
+ " cpu_value = pair.split(\"=\")[1]\n",
+ " if pair.startswith(\"memory=\"):\n",
+ " memory_value = pair.split(\"=\")[1]\n",
+ " if pair.startswith(\"queue=\"):\n",
+ " queue_value = pair.split(\"=\")[1]\n",
+ " if pair.startswith(\"walltime=\"):\n",
+ " walltime_value = pair.split(\"=\")[1]\n",
" \n",
- " # Print the cluster value\n",
- " if cluster_value:\n",
- " print(f\"Cluster value: {cluster_value}\")\n",
+ " submit_agent_job('CS Agent', cluster_value, queue_value, cpu_value,
memory_value, walltime_value, access_token)\n",
"\n",
- " \n",
+ "@register_line_magic\n",
+ "def status_remote(line):\n",
+ " status = get_agent_status()\n",
+ " if status:\n",
+ " if status['agentUp']:\n",
+ " print(\"Agent\", status['agentId'], 'is running')\n",
+ " else:\n",
+ " print(\"Agent\", status['agentId'], 'is still prepairing.
Please wait')\n",
"\n",
"@register_line_magic\n",
"def terminate_remote(line):\n",
- " print(f\"Your input: {line}\")"
+ " global current_agent_info\n",
+ " access_token = get_access_token()\n",
+ " if current_agent_info:\n",
+ " terminate_agent(access_token)"
]
},
{
"cell_type": "code",
- "execution_count": 51,
+ "execution_count": 117,
"id": "9e969c05-fbf9-4eca-9b83-d1c62429a13b",
"metadata": {},
"outputs": [
@@ -104,18 +319,36 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Your input: cluster=jetstream cpu=2 memory=2GB\n",
- "Cluster value: jetstream\n"
+ "Your input: cluster=expanse cpu=2 memory=2024 queue=shared
walltime=60\n",
+ "Response: {'agentId': 'agent_e26bfeb7-f76a-4166-9a21-af76d0a713d4',
'experimentId': 'CS_Agent_dcdd52d1-b5c9-4318-b08f-450fa625e671'}\n"
+ ]
+ }
+ ],
+ "source": [
+ "%init_remote cluster=expanse cpu=2 memory=2024 queue=shared walltime=60"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 118,
+ "id": "fee186a2-a196-4092-ad43-1e3d8b035ac7",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Agent agent_e26bfeb7-f76a-4166-9a21-af76d0a713d4 is running\n"
]
}
],
"source": [
- "%init_remote cluster=jetstream cpu=2 memory=2GB queue=shared walltime=60"
+ "%status_remote"
]
},
{
"cell_type": "code",
- "execution_count": 59,
+ "execution_count": 119,
"id": "4e60d84a-2a81-4b04-9dcb-dea48c4228b8",
"metadata": {},
"outputs": [
@@ -137,7 +370,7 @@
},
{
"cell_type": "code",
- "execution_count": 60,
+ "execution_count": 120,
"id": "ebd549f1-3a5d-47e3-876d-beb91d971ac2",
"metadata": {},
"outputs": [
@@ -174,7 +407,7 @@
},
{
"cell_type": "code",
- "execution_count": 57,
+ "execution_count": 121,
"id": "a946bee5-384b-4883-9753-e5d2bf162d39",
"metadata": {},
"outputs": [
@@ -182,33 +415,61 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Requirement already satisfied: matplotlib in
/usr/local/lib/python3.12/site-packages (3.9.1)\n",
- "Requirement already satisfied: contourpy>=1.0.1 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (1.2.1)\n",
- "Requirement already satisfied: cycler>=0.10 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (0.12.1)\n",
- "Requirement already satisfied: fonttools>=4.22.0 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (4.53.1)\n",
- "Requirement already satisfied: kiwisolver>=1.3.1 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (1.4.5)\n",
- "Requirement already satisfied: numpy>=1.23 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (2.0.0)\n",
- "Requirement already satisfied: packaging>=20.0 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (24.1)\n",
- "Requirement already satisfied: pillow>=8 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (10.4.0)\n",
- "Requirement already satisfied: pyparsing>=2.3.1 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (3.1.2)\n",
- "Requirement already satisfied: python-dateutil>=2.7 in
/usr/local/lib/python3.12/site-packages (from matplotlib) (2.9.0.post0)\n",
- "Requirement already satisfied: six>=1.5 in
/usr/local/lib/python3.12/site-packages (from python-dateutil>=2.7->matplotlib)
(1.16.0)\n",
- "\u001b[33mWARNING: Running pip as the 'root' user can result in broken
permissions and conflicting behaviour with the system package manager. It is
recommended to use a virtual environment instead:
https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n";,
- "\u001b[0m\n",
-
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
A new release of pip is available:
\u001b[0m\u001b[31;49m24.0\u001b[0m\u001b[39;49m ->
\u001b[0m\u001b[32;49m24.1.2\u001b[0m\n",
-
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n",
+ "total 412\n",
+ "drwxr-x--- 22 scigap uot111 42 Jul 20 23:52 .\n",
+ "drwxr-xr-x 1 scigap uot111 60 Jul 21 15:38 ..\n",
+ "-rw------- 1 scigap uot111 1908 Jul 19 11:48 .Xauthority\n",
+ "-rw------- 1 scigap uot111 20517 Jul 20 23:52 .bash_history\n",
+ "-rw-r--r-- 1 scigap uot111 18 Nov 8 2019 .bash_logout\n",
+ "-rw-r--r-- 1 scigap uot111 141 Nov 8 2019 .bash_profile\n",
+ "-rw-r--r-- 1 scigap uot111 1227 Sep 20 2023 .bashrc\n",
+ "drwx------ 7 scigap uot111 7 Jun 6 14:05 .cache\n",
+ "drwxrwsr-x 4 scigap uot111 5 Jun 9 2023 .conda\n",
+ "drwxr-xr-x 3 scigap uot111 3 Sep 7 2022 .config\n",
+ "drwx------ 3 scigap uot111 3 Jun 6 12:17 .dbus\n",
+ "-rw-r--r-- 1 scigap uot111 334 May 11 2019 .emacs\n",
+ "-rw-r--r-- 1 scigap uot111 18 Sep 20 2023 .gitconfig\n",
+ "drwxr-xr-x 3 scigap uot111 3 Jul 19 15:53 .ipython\n",
+ "-rw-r--r-- 1 scigap uot111 172 Apr 23 2020 .kshrc\n",
+ "-rw------- 1 scigap uot111 38 Jun 23 12:39 .lesshst\n",
+ "drwxr-xr-x 3 scigap uot111 3 May 15 2023 .lmod.d\n",
+ "drwx------ 5 scigap uot111 5 Jun 6 12:56 .local\n",
+ "-rw------- 1 scigap uot111 21 Jul 19 12:33 .python_history\n",
+ "drwx------ 2 scigap uot111 2 Jun 10 16:53 .screen\n",
+ "drwx------ 4 scigap uot111 5 Jun 13 18:06 .singularity\n",
+ "drwx------ 2 scigap uot111 11 Jul 19 11:56 .ssh\n",
+ "drwxr-xr-x 2 scigap uot111 3 Mar 31 2023 .vim\n",
+ "-rw------- 1 scigap uot111 39749 Jul 20 16:03 .viminfo\n",
+ "drwxr-xr-x 2 scigap uot111 3 Jun 17 17:32 .vnc\n",
+ "-rw-r--r-- 1 scigap uot111 658 Mar 20 2020 .zshrc\n",
+ "drwxr-xr-x 6 scigap uot111 7 Jun 9 2023 AllenTest\n",
+ "drwxr-xr-x 3 scigap uot111 6 Oct 24 2022 NAMD_Test\n",
+ "drwxr-xr-x 9 scigap uot111 22 Jul 20 15:10 NeuroTest\n",
+ "drwxr-xr-x 3 scigap uot111 6 Jul 1 12:34 Neuron\n",
+ "lrwxrwxrwx 1 scigap uic151 55 Jun 6 12:54 containers ->
/expanse/lustre/scratch/scigap/temp_project/containers/\n",
+ "lrwxrwxrwx 1 scigap uic151 52 Jun 11 08:01 dcdfiles ->
/expanse/lustre/scratch/scigap/temp_project/dcdfiles\n",
+ "drwxr-xr-x 2 scigap uot111 2 Oct 21 2022 devseagrid-workdirs\n",
+ "drwxr-xr-x 5 scigap uot111 5 Sep 7 2022 eht-codes\n",
+ "lrwxrwxrwx 1 scigap uot111 52 Sep 7 2022 eht-workdirs ->
/expanse/lustre/projects/ind123/scigap/eht-workdirs/\n",
+ "lrwxrwxrwx 1 scigap uot111 55 Nov 8 2023 md-workdirs ->
/expanse/lustre/scratch/scigap/temp_project/md-workdirs\n",
+ "drwxr-xr-x 2 scigap uot111 4 Mar 25 04:26 mpi-class-tests\n",
+ "lrwxrwxrwx 1 scigap uot111 58 Nov 8 2023 neuro-workdirs ->
/expanse/lustre/scratch/scigap/temp_project/neuro-workdirs\n",
+ "-rw------- 1 scigap uot111 808 Jun 13 14:35 nohup.out\n",
+ "lrwxrwxrwx 1 scigap uot111 38 Jun 17 12:06 projects ->
/expanse/lustre/projects/ind123/scigap\n",
+ "drwxr-xr-x 3 scigap uot111 3 Oct 24 2022 scratch\n",
+ "-rw-r--r-- 1 scigap uot111 349923 Jun 17 16:20 vnchelp\n",
"\n"
]
}
],
"source": [
"%%run_remote\n",
- "!pip3 install matplotlib\n"
+ "!ls -al "
]
},
{
"cell_type": "code",
- "execution_count": 38,
+ "execution_count": 97,
"id": "01b350f1-dc56-4434-86c1-0ff024cc589d",
"metadata": {},
"outputs": [
@@ -216,22 +477,23 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Requirement already satisfied: numpy in
./jupyter/venv/lib/python3.11/site-packages (2.0.0)\n",
+ "Defaulting to user installation because normal site-packages is not
writeable\n",
+ "Requirement already satisfied: numpy in
./.local/lib/python3.12/site-packages (2.0.0)\n",
"\n",
-
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
A new release of pip is available:
\u001b[0m\u001b[31;49m23.2.1\u001b[0m\u001b[39;49m ->
\u001b[0m\u001b[32;49m24.1.2\u001b[0m\n",
+
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
A new release of pip is available:
\u001b[0m\u001b[31;49m24.0\u001b[0m\u001b[39;49m ->
\u001b[0m\u001b[32;49m24.1.2\u001b[0m\n",
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m
To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n",
"\n"
]
}
],
"source": [
- "%%run_remote cluster=jetstream cpu=2 memory=2GB\n",
+ "%%run_remote\n",
"!pip install numpy"
]
},
{
"cell_type": "code",
- "execution_count": 43,
+ "execution_count": 122,
"id": "4acff051-2148-45d6-bb4e-c3cabb1a162c",
"metadata": {},
"outputs": [
@@ -239,7 +501,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Your input: \n"
+ "Agent terminated: {'experimentId':
'CS_Agent_dcdd52d1-b5c9-4318-b08f-450fa625e671', 'terminated': True}\n"
]
}
],
