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lahirujayathilake pushed a commit to branch agent-framewok-refactoring
in repository https://gitbox.apache.org/repos/asf/airavata.git
The following commit(s) were added to refs/heads/agent-framewok-refactoring by
this push:
new 6093d54a8e changes to the jupyter notebook
6093d54a8e is described below
commit 6093d54a8ef275c657aa992b9df9667a2bf6b0da
Author: lahiruj <[email protected]>
AuthorDate: Wed Dec 18 02:49:15 2024 -0500
changes to the jupyter notebook
---
.../jupyterhub/user-container/MD/poc.ipynb | 34 +++++++++++++---------
1 file changed, 20 insertions(+), 14 deletions(-)
diff --git a/dev-tools/deployment/jupyterhub/user-container/MD/poc.ipynb
b/dev-tools/deployment/jupyterhub/user-container/MD/poc.ipynb
index f0e015c53f..858f473622 100644
--- a/dev-tools/deployment/jupyterhub/user-container/MD/poc.ipynb
+++ b/dev-tools/deployment/jupyterhub/user-container/MD/poc.ipynb
@@ -144,7 +144,7 @@
"outputs": [],
"source": [
"exp = md.NAMD.initialize(\n",
- " name=\"yasith_namd_experiment\",\n",
+ " name=\"SMD\",\n",
" config_file=\"data/pull_cpu.conf\",\n",
" pdb_file=\"data/structure.pdb\",\n",
" psf_file=\"data/structure.psf\",\n",
@@ -199,8 +199,8 @@
"metadata": {},
"outputs": [],
"source": [
- "plan.save() # this will save the plan in DB\n",
- "plan.save_json(\"plan.json\") # save the plan state locally"
+ "plan.save() # this will save the plan in DB\n",
+ "plan.save_json(\"plan.json\") # save the plan state locally"
]
},
{
@@ -298,7 +298,7 @@
"outputs": [],
"source": [
"# plan.stop()\n",
- "plan.wait_for_completion()"
+ "# plan.wait_for_completion()"
]
},
{
@@ -323,16 +323,22 @@
"source": [
"for task in plan.tasks:\n",
" print(task.name, task.pid)\n",
- " # display files\n",
- " display(task.ls())\n",
- " # upload a file\n",
- " task.upload(\"data/sample.txt\")\n",
- " # preview contents of a file\n",
- " display(task.cat(\"sample.txt\"))\n",
- " # download a specific file\n",
- " task.download(\"sample.txt\", f\"./results_{task.name}\")\n",
- " # download all files\n",
- " task.download_all(f\"./results_{task.name}\")"
+ " display(task.ls()) # list files\n",
+ " task.upload(\"data/sample.txt\") # upload
sample.txt\n",
+ " display(task.ls()) # list files
AFTER upload\n",
+ " display(task.cat(\"sample.txt\")) # preview
sample.txt\n",
+ " task.download(\"sample.txt\", f\"./results_{task.name}\") # download
sample.txt"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "plan.wait_for_completion() # wait for plan
to complete\n",
+ "for task in plan.tasks:\n",
+ " task.download_all(f\"./results_{task.name}\") # download
plan outputs"
]
},
{
