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executable file
·541 lines (468 loc) · 23.1 KB
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#!/bin/bash
PS3='Please enter your choice: '
options=("Run Galactica"
"Run LLaMA"
"Run Alpaca"
"Run LLaMA-2"
"Run LLaMA-3"
"Run LLaMA-3.1"
"Run Mistral"
"Run Solar"
"Run Falcon"
"Run MPT"
"Run RST"
"Run BioGPT"
"Run BioMedLM"
"Run Gemini"
"Quit")
select opt in "${options[@]}"
do
export DATA_REPO_PATH=/home/ac.gpark/BioIE-LLM-WIP/data
export OUTPUT_DIR=/home/ac.gpark/BioIE-LLM-WIP/result
export LORA_OUTPUT_DIR=/scratch/ac.gpark/LoRA_finetuned_models
case $opt in
"Run Galactica")
echo "you chose Run Galactica."
export MODEL_NAME=Galactica
export MODEL_TYPE=facebook/galactica-6.7b
# export MODEL_TYPE=facebook/galactica-30B
# export MODEL_TYPE=facebook/galactica-120b
export DATA_NAME=kbase # string, kegg, indra, kbase, lll
export TASK=entity_type # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase), entity_and_entity_type (kbase)
export TRAIN_BATCH_SIZE=2 # used in finetuning
export VALIDATION_BATCH_SIZE=8 # used in finetuning
export TEST_BATCH_SIZE=8
export N_SHOTS=0
# export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/meta-llama/Llama-2-7b-chat-hf/string/entity/final_checkpoint
# python ~/BioIE-LLM-WIP/src/run_model.py \
# torchrun --nproc_per_node=4 ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--train_batch_size $TRAIN_BATCH_SIZE \
--validation_batch_size $VALIDATION_BATCH_SIZE \
--test_batch_size $TEST_BATCH_SIZE \
--n_shots $N_SHOTS \
--lora_finetune \
--use_quantization \
--lora_output_dir $LORA_OUTPUT_DIR
: '
--parallelizm
'
break
;;
"Run LLaMA")
echo "you chose Run LLaMA."
export MODEL_NAME=LLaMA
export MODEL_TYPE=/scratch/ac.gpark/LLaMA_HF/7B
export DATA_NAME=string # string, kegg, indra, kbase
export TASK=entity # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase)
export TEST_BATCH_SIZE=32
export TRAIN_BATCH_SIZE=32 # used in finetuning
export N_SHOTS=1
python ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--test_batch_size $TEST_BATCH_SIZE \
--train_batch_size $TRAIN_BATCH_SIZE \
--n_shots $N_SHOTS
break
;;
"Run Alpaca")
echo "you chose Run Alpaca."
export MODEL_NAME=Alpaca
export MODEL_TYPE=/scratch/ac.gpark/LLaMA_HF/7B # decapoda-research/llama-7b-hf
export DATA_NAME=kegg # string, kegg, indra, kbase
export TASK=entity # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase)
export TEST_BATCH_SIZE=8
export TRAIN_BATCH_SIZE=32 # used in finetuning
export N_SHOTS=3
export LORA_WEIGHTS=tloen/alpaca-lora-7b
# python ~/BioIE-LLM-WIP/src/run_model.py \
accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--test_batch_size $TEST_BATCH_SIZE \
--train_batch_size $TRAIN_BATCH_SIZE \
--n_shots $N_SHOTS
: '
--load_8bit
'
break
;;
"Run LLaMA-2")
echo "you chose Run LLaMA-2."
export MODEL_NAME=LLaMA-2
export MODEL_TYPE=meta-llama/Llama-2-7b-chat-hf
# export MODEL_TYPE=meta-llama/Llama-2-13b-chat-hf
# export MODEL_TYPE=meta-llama/Llama-2-70b-chat-hf
# export MODEL_TYPE=LoftQ/Llama-2-13b-hf-4bit-64rank # LoftQ test
export DATA_NAME=kbase # string, kegg, indra, kbase, lll
export TASK=entity_type # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase), entity_and_entity_type (kbase)
export TRAIN_BATCH_SIZE=2 # used in finetuning
export VALIDATION_BATCH_SIZE=8 # used in finetuning
export TEST_BATCH_SIZE=8
export N_SHOTS=0
# export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/meta-llama/Llama-2-7b-chat-hf/string/entity/final_merged
# export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/meta-llama/Llama-2-7b-chat-hf/string/entity/final_checkpoint/
export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/meta-llama/Llama-2-7b-chat-hf/kegg/entity/final_checkpoint
# export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/meta-llama/Llama-2-70b-chat-hf/string/entity/final_checkpoint
# export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/meta-llama/Llama-2-7b-chat-hf/kbase/entity_type/final_checkpoint/
# python ~/BioIE-LLM-WIP/src/run_model.py \
# torchrun --nproc_per_node=4 ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--train_batch_size $TRAIN_BATCH_SIZE \
--validation_batch_size $VALIDATION_BATCH_SIZE \
--test_batch_size $TEST_BATCH_SIZE \
--n_shots $N_SHOTS
: '
# export MODEL_TYPE=meta-llama/Llama-2-7b-hf
# export MODEL_TYPE=upstage/Llama-2-70b-instruct-v2
--lora_finetune \
--use_quantization \
--lora_output_dir $LORA_OUTPUT_DIR
--lora_weights $LORA_WEIGHTS
'
break
;;
"Run LLaMA-3")
echo "you chose Run LLaMA-3."
export MODEL_NAME=LLaMA-3
# export MODEL_TYPE=meta-llama/Meta-Llama-3-8B
# export MODEL_TYPE=meta-llama/Meta-Llama-3-8B-Instruct
export MODEL_TYPE=meta-llama/Meta-Llama-3-70B
# export MODEL_TYPE=meta-llama/Meta-Llama-3-70B-Instruct
export DATA_NAME=kbase # string, kegg, indra, kbase, lll
export TASK=entity_type # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase), entity_and_entity_type (kbase)
export TRAIN_BATCH_SIZE=2 # used in finetuning
export VALIDATION_BATCH_SIZE=8 # used in finetuning
export TEST_BATCH_SIZE=8
export N_SHOTS=0
export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/meta-llama/Llama-3-8B/kegg/entity/final_checkpoint
# python ~/BioIE-LLM-WIP/src/run_model.py \
# torchrun --nproc_per_node=4 ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
python ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--train_batch_size $TRAIN_BATCH_SIZE \
--validation_batch_size $VALIDATION_BATCH_SIZE \
--test_batch_size $TEST_BATCH_SIZE \
--n_shots $N_SHOTS \
--lora_finetune \
--use_quantization \
--lora_output_dir $LORA_OUTPUT_DIR
: '
# export MODEL_TYPE=meta-llama/Llama-2-7b-hf
# export MODEL_TYPE=upstage/Llama-2-70b-instruct-v2
--lora_finetune \
--use_quantization \
--lora_output_dir $LORA_OUTPUT_DIR
--lora_weights $LORA_WEIGHTS
'
break
;;
"Run LLaMA-3.1")
echo "you chose Run LLaMA-3.1"
export MODEL_NAME=LLaMA-3.1
export MODEL_TYPE=meta-llama/Meta-Llama-3.1-8B-Instruct
# export MODEL_TYPE=meta-llama/Meta-Llama-3.1-70B-Instruct
# export MODEL_TYPE=meta-llama/Meta-Llama-3.1-405B-Instruct
# export MODEL_TYPE=meta-llama/Meta-Llama-3.1-8B
# export MODEL_TYPE=meta-llama/Meta-Llama-3.1-70B
# export MODEL_TYPE=meta-llama/Meta-Llama-3.1-405B
export DATA_NAME=kbase
export TASK=entity_and_entity_type # entity_type (kbase), entity_and_entity_type (kbase)
export TRAIN_BATCH_SIZE=2 # used in finetuning
export VALIDATION_BATCH_SIZE=8 # used in finetuning
export TEST_BATCH_SIZE=1
export N_SHOTS=0
export MAX_NEW_TOKENS=2000 # 500, 2000
# python ~/BioIE-LLM-WIP/src/run_model.py \
# torchrun --nproc_per_node=4 ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
python ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--train_batch_size $TRAIN_BATCH_SIZE \
--validation_batch_size $VALIDATION_BATCH_SIZE \
--test_batch_size $TEST_BATCH_SIZE \
--max_new_tokens $MAX_NEW_TOKENS \
--n_shots $N_SHOTS \
--use_quantization
: '
# if you run into OOM, try quantization.
--use_quantization \
'
break
;;
"Run Mistral")
echo "you chose Run Mistral."
export MODEL_NAME=Mistral
export MODEL_TYPE=mistralai/Mistral-7B-Instruct-v0.2
# export MODEL_TYPE=mistralai/Mixtral-8x7B-Instruct-v0.1
export DATA_NAME=kbase # string, kegg, indra, kbase
export TASK=entity_and_entity_type # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase), entity_and_entity_type (kbase)
export TRAIN_BATCH_SIZE=2 # used in finetuning
export VALIDATION_BATCH_SIZE=8 # used in finetuning
export TEST_BATCH_SIZE=2
export N_SHOTS=0
export MAX_NEW_TOKENS=2000 # 500, 2000
export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/mistralai/Mistral-7B-Instruct-v0.2/kbase/entity_type
# export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/mistralai/Mixtral-8x7B-Instruct-v0.1/kbase/entity_type
# python ~/BioIE-LLM-WIP/src/run_model.py \
# torchrun --nproc_per_node=4 ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
python ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--train_batch_size $TRAIN_BATCH_SIZE \
--validation_batch_size $VALIDATION_BATCH_SIZE \
--test_batch_size $TEST_BATCH_SIZE \
--max_new_tokens $MAX_NEW_TOKENS \
--n_shots $N_SHOTS \
--use_quantization
: '
# export MODEL_TYPE=meta-llama/Llama-2-7b-hf
# export MODEL_TYPE=upstage/Llama-2-70b-instruct-v2
--lora_finetune \
--use_quantization \
--lora_output_dir $LORA_OUTPUT_DIR
--lora_weights $LORA_WEIGHTS
'
break
;;
"Run Solar")
echo "you chose Run Solar."
export MODEL_NAME=Solar
# export MODEL_TYPE=upstage/SOLAR-10.7B-v1.0
export MODEL_TYPE=upstage/SOLAR-10.7B-Instruct-v1.0
export DATA_NAME=kbase # string, kegg, indra, kbase
export TASK=entity_type # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase), entity_and_entity_type (kbase)
export TRAIN_BATCH_SIZE=2 # used in finetuning
export VALIDATION_BATCH_SIZE=8 # used in finetuning
export TEST_BATCH_SIZE=8
export N_SHOTS=0
export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/tiiuae/falcon-7b/kbase/entity_type/final_checkpoint/
# python ~/BioIE-LLM-WIP/src/run_model.py \
# torchrun --nproc_per_node=4 ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
python ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--train_batch_size $TRAIN_BATCH_SIZE \
--validation_batch_size $VALIDATION_BATCH_SIZE \
--test_batch_size $TEST_BATCH_SIZE \
--n_shots $N_SHOTS \
--lora_finetune \
--use_quantization \
--lora_output_dir $LORA_OUTPUT_DIR
: '
# export MODEL_TYPE=meta-llama/Llama-2-7b-hf
# export MODEL_TYPE=upstage/Llama-2-70b-instruct-v2
--lora_finetune \
--lora_output_dir $LORA_OUTPUT_DIR
--use_quantization \
--lora_weights $LORA_WEIGHTS
'
break
;;
"Run Falcon")
echo "you chose Run Falcon."
export MODEL_NAME=Falcon
# export MODEL_TYPE=tiiuae/falcon-7b
export MODEL_TYPE=tiiuae/falcon-40b
# export MODEL_TYPE=tiiuae/falcon-7b-instruct
# export MODEL_TYPE=tiiuae/falcon-40b-instruct
export DATA_NAME=kbase # string, kegg, indra, kbase
export TASK=entity_type # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase), entity_and_entity_type (kbase)
export TRAIN_BATCH_SIZE=2 # used in finetuning
export VALIDATION_BATCH_SIZE=8 # used in finetuning
export TEST_BATCH_SIZE=8
export N_SHOTS=0
export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/tiiuae/falcon-7b/kbase/entity_type/final_checkpoint/
# python ~/BioIE-LLM-WIP/src/run_model.py \
# torchrun --nproc_per_node=4 ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
python ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--train_batch_size $TRAIN_BATCH_SIZE \
--validation_batch_size $VALIDATION_BATCH_SIZE \
--test_batch_size $TEST_BATCH_SIZE \
--n_shots $N_SHOTS \
--lora_finetune \
--use_quantization \
--lora_output_dir $LORA_OUTPUT_DIR
break
;;
"Run MPT")
echo "you chose Run MPT."
export MODEL_NAME=MPT
# export MODEL_TYPE=mosaicml/mpt-7b-chat
export MODEL_TYPE=mosaicml/mpt-30b-chat
export DATA_NAME=kbase # string, kegg, indra, kbase
export TASK=entity_type # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase), entity_and_entity_type (kbase)
export TRAIN_BATCH_SIZE=2 # used in finetuning
export VALIDATION_BATCH_SIZE=8 # used in finetuning
export TEST_BATCH_SIZE=8
export N_SHOTS=0
export LORA_WEIGHTS=/scratch/ac.gpark/LoRA_finetuned_models/mosaicml/mpt-7b-chat/kbase/entity_type/final_checkpoint/
# python ~/BioIE-LLM-WIP/src/run_model.py \
# torchrun --nproc_per_node=4 ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--train_batch_size $TRAIN_BATCH_SIZE \
--validation_batch_size $VALIDATION_BATCH_SIZE \
--test_batch_size $TEST_BATCH_SIZE \
--n_shots $N_SHOTS \
--lora_finetune \
--use_quantization \
--lora_output_dir $LORA_OUTPUT_DIR
: '
# export MODEL_TYPE=meta-llama/Llama-2-7b-hf
# export MODEL_TYPE=upstage/Llama-2-70b-instruct-v2
--lora_finetune \
--lora_output_dir $LORA_OUTPUT_DIR
--lora_weights $LORA_WEIGHTS
'
break
;;
"Run RST")
echo "you chose Run RST."
export MODEL_NAME=RST
export MODEL_TYPE=XLab/rst-all-11b
export DATA_NAME=string # string, kegg, indra, kbase
export TASK=entity # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase)
export TEST_BATCH_SIZE=16
export TRAIN_BATCH_SIZE=32 # used in finetuning
export N_SHOTS=5
python ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--test_batch_size $TEST_BATCH_SIZE \
--train_batch_size $TRAIN_BATCH_SIZE \
--n_shots $N_SHOTS
break
;;
"Run BioGPT")
echo "you chose Run BioGPT."
export MODEL_NAME=BioGPT
export MODEL_TYPE=microsoft/BioGPT-Large # microsoft/biogpt, microsoft/BioGPT-Large, microsoft/BioGPT-Large-PubMedQA
export DATA_NAME=string # string, kegg, indra, kbase
export TASK=entity # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase)
export TEST_BATCH_SIZE=32
export TRAIN_BATCH_SIZE=32 # used in finetuning
export N_SHOTS=5
# python ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--test_batch_size $TEST_BATCH_SIZE \
--train_batch_size $TRAIN_BATCH_SIZE \
--n_shots $N_SHOTS
break
;;
"Run BioMedLM")
echo "you chose Run BioMedLM."
export MODEL_NAME=BioMedLM
export MODEL_TYPE=stanford-crfm/BioMedLM
export DATA_NAME=kegg # string, kegg, indra, kbase
export TASK=entity # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase)
export TEST_BATCH_SIZE=32
export TRAIN_BATCH_SIZE=32 # used in finetuning
export N_SHOTS=1
# python ~/BioIE-LLM-WIP/src/run_model.py \
# accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
accelerate launch ~/BioIE-LLM-WIP/src/run_model.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--test_batch_size $TEST_BATCH_SIZE \
--train_batch_size $TRAIN_BATCH_SIZE \
--n_shots $N_SHOTS
break
;;
"Run Gemini")
echo "you chose Run Gemini."
export MODEL_NAME=Gemini
export MODEL_TYPE=gemini-pro
export DATA_NAME=kegg # string, kegg, indra, kbase
export TASK=entity # entity (string, kegg), relation (string, kegg), relation_type (indra), entity_type (kbase)
export TEST_BATCH_SIZE=1
export N_SHOTS=2
python ~/BioIE-LLM-WIP/src/run_gemini.py \
--model_name $MODEL_NAME \
--model_type $MODEL_TYPE \
--data_repo_path $DATA_REPO_PATH \
--output_dir $OUTPUT_DIR \
--data_name $DATA_NAME \
--task $TASK \
--test_batch_size $TEST_BATCH_SIZE \
--n_shots $N_SHOTS
break
;;
"Quit")
break
;;
*) echo "invalid option $REPLY";;
esac
done