Refine CodonTranslator docs and public scripts

slurm/rebuild_data_v3_cpu.sbatch

@@ -12,8 +12,10 @@
 
 set -euo pipefail
 
-REPO_ROOT=${REPO_ROOT:-/beacon-projects/codon-lm/HE-DLM}
-PYTHON_BIN=${PYTHON_BIN:-/beacon-projects/codon-lm/miniconda3/envs/dna/bin/python}
+SCRIPT_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
+DEFAULT_REPO_ROOT=$(cd "${SCRIPT_DIR}/.." && pwd)
+REPO_ROOT=${REPO_ROOT:-${DEFAULT_REPO_ROOT}}
+PYTHON_BIN=${PYTHON_BIN:-python}
 MMSEQS_BIN=${MMSEQS_BIN:-$REPO_ROOT/MMseqs2/build/bin/mmseqs}
 INPUT_GLOB=${INPUT_GLOB:-data_v2/*/*.parquet}
 HELDOUT_GLOB=${HELDOUT_GLOB:-data_v2/test/*.parquet}

slurm/submit_train_v3_h200_8x_chain.sh

@@ -2,7 +2,9 @@
 
 set -euo pipefail
 
-cd /beacon-projects/codon-lm/HE-DLM
+SCRIPT_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
+REPO_ROOT=$(cd "${SCRIPT_DIR}/.." && pwd)
+cd "${REPO_ROOT}"
 
 SEGMENTS=${SEGMENTS:-3}
 SBATCH_SCRIPT=${SBATCH_SCRIPT:-slurm/train_v3_h200_8x_single.sbatch}

slurm/train_v3_h200_8x_single.sbatch

@@ -2,13 +2,13 @@
 # Single-node 8x H200 training entrypoint.
 # Reserved single-node smoke-run example:
 #   sbatch --time=00:45:00 \
-#     --export=ALL,OUT_DIR=/beacon-projects/codon-lm/HE-DLM/outputs_v3_rep_h200_8x_reserved_smoke,MAX_STEPS=20,SAVE_STEPS=0,EVAL_INTERVAL=0 \
+#     --export=ALL,OUT_DIR=/path/to/outputs_codontranslator_smoke,MAX_STEPS=20,SAVE_STEPS=0,EVAL_INTERVAL=0 \
 #     slurm/train_v3_h200_8x_single.sbatch
 # Full-run example:
 #   sbatch slurm/train_v3_h200_8x_single.sbatch
 #
 # Suggested W&B overrides:
-#   sbatch --export=ALL,WANDB_PROJECT=he-dlm-v3-h200-8x,WANDB_NAME=he-dlm-v3-h200-8x-run1 \
+#   sbatch --export=ALL,WANDB_PROJECT=codontranslator,WANDB_NAME=codontranslator-run1 \
 #     slurm/train_v3_h200_8x_single.sbatch
 # If the environment is still configured for offline logging, override at submit time:
 #   sbatch --export=ALL,WANDB_MODE=online slurm/train_v3_h200_8x_single.sbatch
@@ -35,14 +35,16 @@ source ~/.bashrc
 conda activate dna
 set -u
 
-cd /beacon-projects/codon-lm/HE-DLM
+SCRIPT_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
+REPO_ROOT=$(cd "${SCRIPT_DIR}/.." && pwd)
+cd "${REPO_ROOT}"
 
-TRAIN_DATA=${TRAIN_DATA:-/beacon-projects/codon-lm/HE-DLM/data_v3_rebuild/train}
-VAL_DATA=${VAL_DATA:-/beacon-projects/codon-lm/HE-DLM/data_v3_rebuild/val}
-EMBED_DIR=${EMBED_DIR:-/beacon-projects/codon-lm/HE-DLM/embeddings_v2}
-OUT_DIR=${OUT_DIR:-/beacon-projects/codon-lm/HE-DLM/outputs_v3_rep_h200_8x_single_wd1e-4_bs48ga4}
+TRAIN_DATA=${TRAIN_DATA:-${REPO_ROOT}/data_v3_rebuild/train}
+VAL_DATA=${VAL_DATA:-${REPO_ROOT}/data_v3_rebuild/val}
+EMBED_DIR=${EMBED_DIR:-${REPO_ROOT}/embeddings_v2}
+OUT_DIR=${OUT_DIR:-${REPO_ROOT}/outputs_codontranslator_h200_8x_bs48ga4}
 
-WANDB_PROJECT=${WANDB_PROJECT:-he-dlm-v3-h200-8x}
+WANDB_PROJECT=${WANDB_PROJECT:-codontranslator}
 WANDB_NAME=${WANDB_NAME:-$(basename "${OUT_DIR}")}
 WANDB_RUN_ID=${WANDB_RUN_ID:-$(basename "${OUT_DIR}")}
 WANDB_RESUME=${WANDB_RESUME:-allow}