bugfix save_to_hdf

mlip_arena/tasks/eos_alloy/flow.py

@@ -9,7 +9,7 @@ from huggingface_hub import hf_hub_download
 from prefect import Task, flow, task
 from prefect.client.schemas.objects import TaskRun
 from prefect.futures import wait
-from prefect.states import State
+from prefect.states import State, Failed
 from prefect_dask import DaskTaskRunner
 
 from ase.db import connect
@@ -40,9 +40,15 @@ def save_to_hdf(
     Define a hook on completion of EOS task to save results to HDF5 file.
     """
 
-    if run.state.is_completed():
-        result = run.state.result(raise_on_failure=False)
+    if run.state.is_failed():
+        return
 
+    result = run.state.result(raise_on_failure=False)
+
+    if not isinstance(result, dict):
+        return
+    
+    try:
         atoms = result["atoms"]
         calculator_name = (
             run.task_inputs["calculator_name"] or result["calculator_name"]
@@ -83,6 +89,8 @@ def save_to_hdf(
                 data_columns=True,
                 min_itemsize={"formula": 50, "method": 20},
             )
+    except Exception as e:
+        print(e)
 
 
 @flow

mlip_arena/tasks/eos_alloy/run.ipynb

@@ -107,18 +107,30 @@
       "source ~/.bashrc\n",
       "module load python\n",
       "source activate /pscratch/sd/c/cyrusyc/.conda/mlip-arena\n",
+<<<<<<< Updated upstream
       "/pscratch/sd/c/cyrusyc/.conda/mlip-arena/bin/python -m distributed.cli.dask_worker tcp://128.55.64.37:38383 --name dummy-name --nthreads 1 --memory-limit 59.60GiB --nanny --death-timeout 60\n",
+=======
+      "/pscratch/sd/c/cyrusyc/.conda/mlip-arena/bin/python -m distributed.cli.dask_worker tcp://128.55.64.21:34485 --name dummy-name --nthreads 1 --memory-limit 59.60GiB --nanny --death-timeout 60\n",
+>>>>>>> Stashed changes
       "\n"
      ]
     },
     {
      "data": {
       "text/html": [
+<<<<<<< Updated upstream
        "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">22:51:52.414 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | prefect.engine - Created flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'sly-owl'</span> for flow<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\"> 'run-from-db'</span>\n",
        "</pre>\n"
       ],
       "text/plain": [
        "22:51:52.414 | \u001b[36mINFO\u001b[0m    | prefect.engine - Created flow run\u001b[35m 'sly-owl'\u001b[0m for flow\u001b[1;35m 'run-from-db'\u001b[0m\n"
+=======
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">13:44:10.434 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | prefect.engine - Created flow run<span style=\"color: #800080; text-decoration-color: #800080\"> 'khaki-spider'</span> for flow<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\"> 'run-from-db'</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "13:44:10.434 | \u001b[36mINFO\u001b[0m    | prefect.engine - Created flow run\u001b[35m 'khaki-spider'\u001b[0m for flow\u001b[1;35m 'run-from-db'\u001b[0m\n"
+>>>>>>> Stashed changes
       ]
      },
      "metadata": {},
@@ -127,11 +139,19 @@
     {
      "data": {
       "text/html": [
+<<<<<<< Updated upstream
        "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">22:51:52.419 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | prefect.engine - View at <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/runs/flow-run/d2afea80-afd7-4be2-b734-087f31274217</span>\n",
        "</pre>\n"
       ],
       "text/plain": [
        "22:51:52.419 | \u001b[36mINFO\u001b[0m    | prefect.engine - View at \u001b[94mhttps://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/runs/flow-run/d2afea80-afd7-4be2-b734-087f31274217\u001b[0m\n"
+=======
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">13:44:10.439 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | prefect.engine - View at <span style=\"color: #0000ff; text-decoration-color: #0000ff\">https://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/runs/flow-run/1acc1e4f-4cbc-49d7-964d-a132abd28d08</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "13:44:10.439 | \u001b[36mINFO\u001b[0m    | prefect.engine - View at \u001b[94mhttps://app.prefect.cloud/account/f7d40474-9362-4bfa-8950-ee6a43ec00f3/workspace/d4bb0913-5f5e-49f7-bfc5-06509088baeb/runs/flow-run/1acc1e4f-4cbc-49d7-964d-a132abd28d08\u001b[0m\n"
+>>>>>>> Stashed changes
       ]
      },
      "metadata": {},
@@ -140,11 +160,19 @@
     {
      "data": {
       "text/html": [
+<<<<<<< Updated upstream
        "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">22:51:53.100 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | prefect.task_runner.dask - Connecting to existing Dask cluster SLURMCluster(f5a25e18, 'tcp://128.55.64.37:38383', workers=0, threads=0, memory=0 B)\n",
        "</pre>\n"
       ],
       "text/plain": [
        "22:51:53.100 | \u001b[36mINFO\u001b[0m    | prefect.task_runner.dask - Connecting to existing Dask cluster SLURMCluster(f5a25e18, 'tcp://128.55.64.37:38383', workers=0, threads=0, memory=0 B)\n"
+=======
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">13:44:11.086 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | prefect.task_runner.dask - Connecting to existing Dask cluster SLURMCluster(58a52fcd, 'tcp://128.55.64.21:34485', workers=0, threads=0, memory=0 B)\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "13:44:11.086 | \u001b[36mINFO\u001b[0m    | prefect.task_runner.dask - Connecting to existing Dask cluster SLURMCluster(58a52fcd, 'tcp://128.55.64.21:34485', workers=0, threads=0, memory=0 B)\n"
+>>>>>>> Stashed changes
       ]
      },
      "metadata": {},
@@ -153,11 +181,19 @@
     {
      "data": {
       "text/html": [
+<<<<<<< Updated upstream
        "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">22:52:10.768 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Task run 'get_atoms_from_db-f27' - Created task run 'get_atoms_from_db-f27' for task 'get_atoms_from_db'\n",
        "</pre>\n"
       ],
       "text/plain": [
        "22:52:10.768 | \u001b[36mINFO\u001b[0m    | Task run 'get_atoms_from_db-f27' - Created task run 'get_atoms_from_db-f27' for task 'get_atoms_from_db'\n"
+=======
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">13:45:41.275 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Task run 'get_atoms_from_db-8e2' - Created task run 'get_atoms_from_db-8e2' for task 'get_atoms_from_db'\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "13:45:41.275 | \u001b[36mINFO\u001b[0m    | Task run 'get_atoms_from_db-8e2' - Created task run 'get_atoms_from_db-8e2' for task 'get_atoms_from_db'\n"
+>>>>>>> Stashed changes
       ]
      },
      "metadata": {},
@@ -166,11 +202,19 @@
     {
      "data": {
       "text/html": [
+<<<<<<< Updated upstream
        "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">22:52:41.782 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Task run 'get_atoms_from_db-f27' - Finished in state <span style=\"color: #008000; text-decoration-color: #008000\">Completed</span>()\n",
        "</pre>\n"
       ],
       "text/plain": [
        "22:52:41.782 | \u001b[36mINFO\u001b[0m    | Task run 'get_atoms_from_db-f27' - Finished in state \u001b[32mCompleted\u001b[0m()\n"
+=======
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">13:46:12.488 | <span style=\"color: #008080; text-decoration-color: #008080\">INFO</span>    | Task run 'get_atoms_from_db-8e2' - Finished in state <span style=\"color: #008000; text-decoration-color: #008000\">Completed</span>()\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "13:46:12.488 | \u001b[36mINFO\u001b[0m    | Task run 'get_atoms_from_db-8e2' - Finished in state \u001b[32mCompleted\u001b[0m()\n"
+>>>>>>> Stashed changes
       ]
      },
      "metadata": {},