![\"\"](\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F22938014%2F46156076d48614578c8b3d9c7ca3b943%2F1.png?generation=1769225120216584&alt=media\")
Hi all — quick question about Stanford RNA 3D Folding Part 2 notebook submissions.
\nI’m running a notebook that takes ~1–2 hours. I’d like to stop/cancel the run to save GPU time and submit immediately.
\nBut Kaggle reports: “Submission file not found: submission.csv.”
I haven’t hit this in other competitions. Is there any way to submit without waiting for the notebook to finish and commit, or does Kaggle only allow submission from the final committed output in this comp? Thanks!
\n
Add this at the top. It creates a valid all-zeros submission.csv and exits when not running in Kaggle’s competition rerun; during the rerun it will continue normally.
# --- Early-exit guard for local runs (put this as the very first cell) ---\nimport os\nimport sys\nimport pandas as pd\n\nflag = os.environ.get(\"KAGGLE_IS_COMPETITION_RERUN\")\n\n# Kaggle sets this to a truthy value during the submission rerun environment.\n# If not in that environment, write an all-zeros submission and stop.\nif not flag:\n # Try to derive the correct row count / IDs from an available sequences file.\n # (adjust paths if your competition uses different names)\n candidate_seq_paths = [\n \"/kaggle/input/stanford-rna-3d-folding-2/test_sequences.csv\",\n \"/kaggle/input/stanford-rna-3d-folding-2/validation_sequences.csv\",\n \"/kaggle/input/stanford-rna-3d-folding-2/train_sequences.csv\",\n ]\n\n seq_df = None\n for p in candidate_seq_paths:\n if os.path.exists(p):\n seq_df = pd.read_csv(p)\n break\n\n if seq_df is None or \"target_id\" not in seq_df.columns or \"sequence\" not in seq_df.columns:\n raise RuntimeError(\n \"Not in competition rerun, and could not find a sequences file to build a valid zero submission.\\n\"\n \"Make sure test_sequences.csv is available under /kaggle/input/... or adjust candidate_seq_paths.\"\n )\n\n rows = []\n for row in seq_df.itertuples(index=False):\n tid = row.target_id\n seq = row.sequence\n for i, base in enumerate(seq, start=1):\n rec = {\n \"ID\": f\"{tid}_{i}\",\n \"resname\": base,\n \"resid\": i,\n }\n for k in range(1, 6):\n rec[f\"x_{k}\"] = 0.0\n rec[f\"y_{k}\"] = 0.0\n rec[f\"z_{k}\"] = 0.0\n rows.append(rec)\n\n out = pd.DataFrame(rows)\n\n # Enforce official column order\n cols = (\n [\"ID\", \"resname\", \"resid\"] +\n [f\"{ax}_{k}\" for k in range(1, 6) for ax in (\"x\", \"y\", \"z\")]\n )\n out = out[cols]\n out.to_csv(\"submission.csv\", index=False)\n print(\"Not in Kaggle competition rerun. Wrote zero submission.csv and exiting early.\")\n raise SystemExit(0)\n\n# If flag is truthy: do nothing, notebook continues normally.\nprint(\"KAGGLE_IS_COMPETITION_RERUN detected -> continuing normally.\")\nThanks very much — I really appreciate the help! This saved me a lot of time and GPU time 😄
", "rawMarkdown": "Thanks very much — I really appreciate the help! This saved me a lot of time and GPU time 😄", "votes": 3 }, { "id": 3396038, "postDate": "2026-01-24T06:41:34.190Z", "content": "This is a great tip! Didn't know this was even possible.
", "rawMarkdown": "This is a great tip! Didn't know this was even possible." } ] }, { "id": 3395966, "postDate": "2026-01-24T03:24:59.947Z", "content": "Hi all — quick question about Stanford RNA 3D Folding Part 2 notebook submissions.
\nI’m running a notebook that takes ~1–2 hours. I’d like to stop/cancel the run to save GPU time and submit immediately.
\nBut Kaggle reports: “Submission file not found: submission.csv.”
I haven’t hit this in other competitions. Is there any way to submit without waiting for the notebook to finish and commit, or does Kaggle only allow submission from the final committed output in this comp? Thanks!
\n
Add this at the top. It creates a valid all-zeros submission.csv and exits when not running in Kaggle’s competition rerun; during the rerun it will continue normally.
# --- Early-exit guard for local runs (put this as the very first cell) ---\nimport os\nimport sys\nimport pandas as pd\n\nflag = os.environ.get(\"KAGGLE_IS_COMPETITION_RERUN\")\n\n# Kaggle sets this to a truthy value during the submission rerun environment.\n# If not in that environment, write an all-zeros submission and stop.\nif not flag:\n # Try to derive the correct row count / IDs from an available sequences file.\n # (adjust paths if your competition uses different names)\n candidate_seq_paths = [\n \"/kaggle/input/stanford-rna-3d-folding-2/test_sequences.csv\",\n \"/kaggle/input/stanford-rna-3d-folding-2/validation_sequences.csv\",\n \"/kaggle/input/stanford-rna-3d-folding-2/train_sequences.csv\",\n ]\n\n seq_df = None\n for p in candidate_seq_paths:\n if os.path.exists(p):\n seq_df = pd.read_csv(p)\n break\n\n if seq_df is None or \"target_id\" not in seq_df.columns or \"sequence\" not in seq_df.columns:\n raise RuntimeError(\n \"Not in competition rerun, and could not find a sequences file to build a valid zero submission.\\n\"\n \"Make sure test_sequences.csv is available under /kaggle/input/... or adjust candidate_seq_paths.\"\n )\n\n rows = []\n for row in seq_df.itertuples(index=False):\n tid = row.target_id\n seq = row.sequence\n for i, base in enumerate(seq, start=1):\n rec = {\n \"ID\": f\"{tid}_{i}\",\n \"resname\": base,\n \"resid\": i,\n }\n for k in range(1, 6):\n rec[f\"x_{k}\"] = 0.0\n rec[f\"y_{k}\"] = 0.0\n rec[f\"z_{k}\"] = 0.0\n rows.append(rec)\n\n out = pd.DataFrame(rows)\n\n # Enforce official column order\n cols = (\n [\"ID\", \"resname\", \"resid\"] +\n [f\"{ax}_{k}\" for k in range(1, 6) for ax in (\"x\", \"y\", \"z\")]\n )\n out = out[cols]\n out.to_csv(\"submission.csv\", index=False)\n print(\"Not in Kaggle competition rerun. Wrote zero submission.csv and exiting early.\")\n raise SystemExit(0)\n\n# If flag is truthy: do nothing, notebook continues normally.\nprint(\"KAGGLE_IS_COMPETITION_RERUN detected -> continuing normally.\")\nThanks very much — I really appreciate the help! This saved me a lot of time and GPU time 😄
", "votes": 3, "replies": [] }, { "id": 3396038, "author_name": "dataWr3cker", "author_url": "", "post_date": "2026-01-24T06:41:34.190000", "content": "This is a great tip! Didn't know this was even possible.
", "votes": 0, "replies": [] } ] } ], "raw_markdown_by_id": { "3395969": "Add this at the top. It creates a valid all-zeros `submission.csv` and exits when not running in Kaggle’s competition rerun; during the rerun it will continue normally.\n\n # --- Early-exit guard for local runs (put this as the very first cell) ---\n import os\n import sys\n import pandas as pd\n\n flag = os.environ.get(\"KAGGLE_IS_COMPETITION_RERUN\")\n\n # Kaggle sets this to a truthy value during the submission rerun environment.\n # If not in that environment, write an all-zeros submission and stop.\n if not flag:\n # Try to derive the correct row count / IDs from an available sequences file.\n # (adjust paths if your competition uses different names)\n candidate_seq_paths = [\n \"/kaggle/input/stanford-rna-3d-folding-2/test_sequences.csv\",\n \"/kaggle/input/stanford-rna-3d-folding-2/validation_sequences.csv\",\n \"/kaggle/input/stanford-rna-3d-folding-2/train_sequences.csv\",\n ]\n\n seq_df = None\n for p in candidate_seq_paths:\n if os.path.exists(p):\n seq_df = pd.read_csv(p)\n break\n\n if seq_df is None or \"target_id\" not in seq_df.columns or \"sequence\" not in seq_df.columns:\n raise RuntimeError(\n \"Not in competition rerun, and could not find a sequences file to build a valid zero submission.\\n\"\n \"Make sure test_sequences.csv is available under /kaggle/input/... or adjust candidate_seq_paths.\"\n )\n\n rows = []\n for row in seq_df.itertuples(index=False):\n tid = row.target_id\n seq = row.sequence\n for i, base in enumerate(seq, start=1):\n rec = {\n \"ID\": f\"{tid}_{i}\",\n \"resname\": base,\n \"resid\": i,\n }\n for k in range(1, 6):\n rec[f\"x_{k}\"] = 0.0\n rec[f\"y_{k}\"] = 0.0\n rec[f\"z_{k}\"] = 0.0\n rows.append(rec)\n\n out = pd.DataFrame(rows)\n\n # Enforce official column order\n cols = (\n [\"ID\", \"resname\", \"resid\"] +\n [f\"{ax}_{k}\" for k in range(1, 6) for ax in (\"x\", \"y\", \"z\")]\n )\n out = out[cols]\n out.to_csv(\"submission.csv\", index=False)\n print(\"Not in Kaggle competition rerun. Wrote zero submission.csv and exiting early.\")\n raise SystemExit(0)\n\n # If flag is truthy: do nothing, notebook continues normally.\n print(\"KAGGLE_IS_COMPETITION_RERUN detected -> continuing normally.\")\n", "3395966": "Hi all — quick question about **Stanford RNA 3D Folding Part 2** notebook submissions.\n\nI’m running a notebook that takes ~1–2 hours. I’d like to **stop/cancel the run** to save GPU time and **submit immediately**.\n\nBut Kaggle reports: **“Submission file not found: `submission.csv`.”**\n\nI haven’t hit this in other competitions. Is there **any way to submit without waiting for the notebook to finish and commit**, or does Kaggle only allow submission from the final committed output in this comp? Thanks!\n\n\n" } }