Commit 1782a015 authored by Wang, Xiao's avatar Wang, Xiao
Browse files

rename the file

parent 8c0fab22

pretrain_pubmed.lsf

deleted100644 → 0
+0 −174
Original line number Diff line number Diff line 
#!/bin/bash



#BSUB -nnodes 2

#BSUB -W 0:30

#BSUB -P med106

#BSUB -alloc_flags "smt4 nvme"

#BSUB -J debug

#BSUB -o debug.%J

#BSUB -q debug



set +x



module load open-ce

conda deactivate

conda activate /gpfs/alpine/med106/world-shared/irl1/rhel8/mytorch

module list



export OMP_NUM_THREADS=1

#export PYTHONPATH=$PYTHONPATH:/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/megatron/fused_kernels

#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/gpfs/alpine/med106/world-shared/irl1/rhel8/mytorch/lib/python3.8/site-packages/torch/lib

#export PATH=$PATH:/gpfs/alpine/med106/world-shared/irl1/rhel8/mytorch/lib/python3.8/site-packages/torch/include



nodes=($(cat ${LSB_DJOB_HOSTFILE} | sort | uniq | grep -v login | grep -v batch))

nnodes=${#nodes[@]}

echo $nnodes



DATASET_0="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm000_abstract_sentence"

DATASET_1="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm001_abstract_sentence"

DATASET_2="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm002_abstract_sentence"

DATASET_3="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm003_abstract_sentence"

DATASET_4="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm004_abstract_sentence"

DATASET_5="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm005_abstract_sentence"

DATASET_6="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm006_abstract_sentence"

DATASET_7="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm007_abstract_sentence"

DATASET_8="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm008_abstract_sentence"

DATASET_9="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm009_abstract_sentence"

DATASET_10="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm010_abstract_sentence"

DATASET_11="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm011_abstract_sentence"

DATASET_12="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm012_abstract_sentence"

DATASET_13="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm013_abstract_sentence"

DATASET_14="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm014_abstract_sentence"

DATASET_15="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm015_abstract_sentence"

DATASET_16="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm016_abstract_sentence"

DATASET_17="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm017_abstract_sentence"

DATASET_18="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm018_abstract_sentence"

DATASET_19="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm019_abstract_sentence"

DATASET_20="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm020_abstract_sentence"

DATASET_21="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm021_abstract_sentence"

DATASET_22="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm022_abstract_sentence"

DATASET_23="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm023_abstract_sentence"

DATASET_24="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm024_abstract_sentence"

DATASET_25="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm025_abstract_sentence"

DATASET_26="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm026_abstract_sentence"

DATASET_27="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm027_abstract_sentence"

DATASET_28="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm028_abstract_sentence"

DATASET_29="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm029_abstract_sentence"

DATASET_30="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm030_abstract_sentence"

DATASET_31="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm031_abstract_sentence"

DATASET_32="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm032_abstract_sentence"

DATASET_33="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm033_abstract_sentence"

DATASET_34="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm034_abstract_sentence"

DATASET_35="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm035_abstract_sentence"

DATASET_36="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm036_abstract_sentence"

DATASET_37="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm037_abstract_sentence"

DATASET_38="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm038_abstract_sentence"

DATASET_39="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm039_abstract_sentence"

DATASET_40="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm040_abstract_sentence"

DATASET_41="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm041_abstract_sentence"

DATASET_42="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm042_abstract_sentence"

DATASET_43="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm043_abstract_sentence"

DATASET_44="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm044_abstract_sentence"

DATASET_45="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm045_abstract_sentence"

DATASET_46="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm046_abstract_sentence"

DATASET_47="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm047_abstract_sentence"

DATASET_48="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm048_abstract_sentence"

DATASET_49="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm049_abstract_sentence"

DATASET_50="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm050_abstract_sentence"

DATASET_51="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm051_abstract_sentence"

DATASET_52="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm052_abstract_sentence"

DATASET_53="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm053_abstract_sentence"

DATASET_54="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm054_abstract_sentence"

DATASET_55="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm055_abstract_sentence"

DATASET_56="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm056_abstract_sentence"

DATASET_57="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm057_abstract_sentence"

DATASET_58="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm058_abstract_sentence"

DATASET_59="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm059_abstract_sentence"

DATASET_60="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm060_abstract_sentence"

DATASET_61="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm061_abstract_sentence"

DATASET_62="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm062_abstract_sentence"

DATASET_63="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm063_abstract_sentence"

DATASET_64="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm064_abstract_sentence"

DATASET_65="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm065_abstract_sentence"

DATASET_66="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm066_abstract_sentence"

DATASET_67="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm067_abstract_sentence"

DATASET_68="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm068_abstract_sentence"

DATASET_69="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm069_abstract_sentence"

DATASET_70="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm070_abstract_sentence"

DATASET_71="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm071_abstract_sentence"

DATASET_72="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm072_abstract_sentence"

DATASET_73="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm073_abstract_sentence"

DATASET_74="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm074_abstract_sentence"

DATASET_75="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm075_abstract_sentence"

DATASET_76="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm076_abstract_sentence"

DATASET_77="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm077_abstract_sentence"

DATASET_78="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm078_abstract_sentence"

DATASET_79="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm079_abstract_sentence"

DATASET_80="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm080_abstract_sentence"

DATASET_81="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm081_abstract_sentence"

DATASET_82="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm082_abstract_sentence"

DATASET_83="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm083_abstract_sentence"

DATASET_84="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm084_abstract_sentence"

DATASET_85="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm085_abstract_sentence"

DATASET_86="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm086_abstract_sentence"

DATASET_87="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm087_abstract_sentence"

DATASET_88="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm088_abstract_sentence"

DATASET_89="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm089_abstract_sentence"

DATASET_90="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm090_abstract_sentence"

DATASET_91="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm091_abstract_sentence"

DATASET_92="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm092_abstract_sentence"

DATASET_93="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm093_abstract_sentence"

DATASET_94="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm094_abstract_sentence"

DATASET_95="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm095_abstract_sentence"

DATASET_96="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm096_abstract_sentence"

DATASET_97="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm097_abstract_sentence"

DATASET_98="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm098_abstract_sentence"

DATASET_99="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm099_abstract_sentence"

DATASET_100="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm100_abstract_sentence"

DATASET_101="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm101_abstract_sentence"

DATASET_102="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm102_abstract_sentence"

DATASET_103="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm103_abstract_sentence"

DATASET_104="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm104_abstract_sentence"

DATASET_105="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm105_abstract_sentence"

DATASET_106="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm106_abstract_sentence"

DATASET_107="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm107_abstract_sentence"

DATASET_108="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm108_abstract_sentence"

DATASET_109="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm109_abstract_sentence"

DATASET_110="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm110_abstract_sentence"

DATASET_111="/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/preprocess_data/pm111_abstract_sentence"

DATASET="1.0 ${DATASET_0} 1.0 ${DATASET_1} 1.0 ${DATASET_2} 1.0 ${DATASET_3} 1.0 ${DATASET_4} 1.0 ${DATASET_5} 1.0 ${DATASET_6} 1.0 ${DATASET_7} 1.0 ${DATASET_8} 1.0 ${DATASET_9} 1.0 ${DATASET_10} 1.0 ${DATASET_11} 1.0 ${DATASET_12} 1.0 ${DATASET_13} 1.0 ${DATASET_14} 1.0 ${DATASET_15} 1.0 ${DATASET_16} 1.0 ${DATASET_17} 1.0 ${DATASET_18} 1.0 ${DATASET_19} 1.0 ${DATASET_20} 1.0 ${DATASET_21} 1.0 ${DATASET_22} 1.0 ${DATASET_23} 1.0 ${DATASET_24} 1.0 ${DATASET_25} 1.0 ${DATASET_26} 1.0 ${DATASET_27} 1.0 ${DATASET_28} 1.0 ${DATASET_29} 1.0 ${DATASET_30} 1.0 ${DATASET_31} 1.0 ${DATASET_32} 1.0 ${DATASET_33} 1.0 ${DATASET_34} 1.0 ${DATASET_35} 1.0 ${DATASET_36} 1.0 ${DATASET_37} 1.0 ${DATASET_38} 1.0 ${DATASET_39} 1.0 ${DATASET_40} 1.0 ${DATASET_41} 1.0 ${DATASET_42} 1.0 ${DATASET_43} 1.0 ${DATASET_44} 1.0 ${DATASET_45} 1.0 ${DATASET_46} 1.0 ${DATASET_47} 1.0 ${DATASET_48} 1.0 ${DATASET_49} 1.0 ${DATASET_50} 1.0 ${DATASET_51} 1.0 ${DATASET_52} 1.0 ${DATASET_53} 1.0 ${DATASET_54} 1.0 ${DATASET_55} 1.0 ${DATASET_56} 1.0 ${DATASET_57} 1.0 ${DATASET_58} 1.0 ${DATASET_59} 1.0 ${DATASET_60} 1.0 ${DATASET_61} 1.0 ${DATASET_62} 1.0 ${DATASET_63} 1.0 ${DATASET_64} 1.0 ${DATASET_65} 1.0 ${DATASET_66} 1.0 ${DATASET_67} 1.0 ${DATASET_68} 1.0 ${DATASET_69} 1.0 ${DATASET_70} 1.0 ${DATASET_71} 1.0 ${DATASET_72} 1.0 ${DATASET_73} 1.0 ${DATASET_74} 1.0 ${DATASET_75} 1.0 ${DATASET_76} 1.0 ${DATASET_77} 1.0 ${DATASET_78} 1.0 ${DATASET_79} 1.0 ${DATASET_80} 1.0 ${DATASET_81} 1.0 ${DATASET_82} 1.0 ${DATASET_83} 1.0 ${DATASET_84} 1.0 ${DATASET_85} 1.0 ${DATASET_86} 1.0 ${DATASET_87} 1.0 ${DATASET_88} 1.0 ${DATASET_89} 1.0 ${DATASET_90} 1.0 ${DATASET_91} 1.0 ${DATASET_92} 1.0 ${DATASET_93} 1.0 ${DATASET_94} 1.0 ${DATASET_95} 1.0 ${DATASET_96} 1.0 ${DATASET_97} 1.0 ${DATASET_98} 1.0 ${DATASET_99} 1.0 ${DATASET_100} 1.0 ${DATASET_101} 1.0 ${DATASET_102} 1.0 ${DATASET_103} 1.0 ${DATASET_104} 1.0 ${DATASET_105} 1.0 ${DATASET_106} 1.0 ${DATASET_107} 1.0 ${DATASET_108} 1.0 ${DATASET_109} 1.0 ${DATASET_110} 1.0 ${DATASET_111}"



export VOCAB_FILE=/gpfs/alpine/world-shared/med106/g8o/pubmed_bert-vocab.txt

export CHECKPOINT_PATH=/gpfs/alpine/med106/world-shared/irl1/rhel8/fork-megatron/2N6D2T1P



jsrun --smpiargs="-disable_gpu_hooks" -n $nnodes -r 1 -g 6 -a 6 -c 42 python pretrain_bert.py \

       --tensor-model-parallel-size 2 \

       --pipeline-model-parallel-size 1 \

       --num-layers 24 \

       --hidden-size 1024 \

       --num-attention-heads 16 \

       --micro-batch-size 2 \

       --global-batch-size 12 \

       --seq-length 512 \

       --max-position-embeddings 512 \

       --train-iters 2000 \

       --lr-decay-iters 990 \

       --save $CHECKPOINT_PATH \

       --data-path $DATASET \

       --vocab-file $VOCAB_FILE \

       --data-impl mmap \

       --split 949,50,1 \

       --distributed-backend nccl \

       --lr 0.0001 \

       --min-lr 0.00001 \

       --lr-decay-style linear \

       --lr-warmup-fraction .01 \

       --weight-decay 1e-2 \

       --clip-grad 1.0 \

       --log-interval 100 \

       --save-interval 10000 \

       --eval-interval 1000 \

       --eval-iters 10 \

       --fp16 

       #--DDP-impl torch \