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adding slurm script (DO NOT MERGE) #9

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adding slurm script (DO NOT MERGE) #9

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442da76
adding slurm script
Nov 14, 2023
a675696
add czi extenstion in the list
Apr 17, 2023
9965b7c
add excel dependencies
Apr 18, 2023
62cb99e
first commit
May 2, 2023
6c1b18d
rm readme
May 2, 2023
f6bc398
add ome.tiff and image read logic
sayatmimar Oct 17, 2023
81599b1
allow bandcount of 3 or 4
sayatmimar Oct 17, 2023
1de0015
add f-string
sayatmimar Nov 6, 2023
6673c77
fix f_string
sayatmimar Nov 8, 2023
68dfc19
Merge branch 'main' into training_slurm
Nov 14, 2023
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36 changes: 36 additions & 0 deletions histomicstk/deeplab/slurm_cript.sh
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#!/bin/sh
#SBATCH --account=pinaki.sarder
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=7000mb
#SBATCH --partition=gpu
#SBATCH --gpus=geforce
#SBATCH --time=72:00:00
#SBATCH --output=./slurm_log.out
#SBATCH --job-name="segmentation_frozen"
echo "SLURM_JOBID="$SLURM_JOBID
echo "SLURM_JOB_NODELIST="$SLURM_JOB_NODELIST
echo "SLURM_NNODES="$SLURM_NNODES
echo "SLURMTMPDIR="$SLURMTMPDIR

echo "working directory = "$SLURM_SUBMIT_DIR
ulimit -s unlimited
module load singularity
ls
ml

# Add your userid here:
USER=sayat.mimar
# Add the name of the folder containing WSIs here
PROJECT=segmentation

CODESDIR=/blue/pinaki.sarder/sayat.mimar/segmentation_test/Histo-cloud/histomicstk/deeplab

DATADIR=/$CODESDIR/training_data
MODELDIR=$CODESDIR/trained_model

CONTAINER=$CODESDIR/myhistorepo_histo_img.sif

singularity exec --nv -B $(pwd):/exec/,$DATADIR/:/data,$MODELDIR/:/model/ $CONTAINER python3 /exec/train.py --model_variant xception_65 --atrous_rates 6 --atrous_rates 12 --atrous_rates 18 --output_stride 16 --decoder_output_stride 4 --train_crop_size 400 --train_batch_size 2 --training_number_of_steps 5000 --slow_start_step 1000 --augment_prob 0.01 --slow_start_learning_rate 1e-05 --base_learning_rate 0.0005 --tf_initial_checkpoint /model/model.ckpt-400000 --dataset_dir /data/ --train_logdir $CODESDIR/log_dir --save_interval_secs 600 --num_clones 1 --global_step 0 --end_learning_rate 0.0 --learning_power 0.9 --ignore_label 2 --decay_steps 0 --last_layer_gradient_multiplier 10.0 --wsi_downsample 1 --wsi_downsample 2 --wsi_downsample 3 --wsi_downsample 4 --initialize_last_layer=false --fine_tune_batch_norm=false --last_layers_contain_logits_only=false --upsample_logits=true