From 17a8ba44335ccbef356c0fc04dfbb854acb49062 Mon Sep 17 00:00:00 2001
From: Sayat Mimar <sayat.mimar@login8.ufhpc>
Date: Tue, 14 Nov 2023 14:10:41 -0500
Subject: [PATCH] adding testing slurm script

---
 histomicstk/deeplab/slurm_test.sh | 35 +++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 histomicstk/deeplab/slurm_test.sh

diff --git a/histomicstk/deeplab/slurm_test.sh b/histomicstk/deeplab/slurm_test.sh
new file mode 100644
index 00000000..f600fa4a
--- /dev/null
+++ b/histomicstk/deeplab/slurm_test.sh
@@ -0,0 +1,35 @@
+#!/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_test.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/test_data
+MODELDIR=$CODESDIR/log_dir
+
+CONTAINER=$CODESDIR/myhistorepo_histo_img.sif
+
+singularity exec --nv -B $(pwd):/exec/,$DATADIR/:/data $CONTAINER python3 /exec/vis.py --model_variant xception_65 --atrous_rates 6 --atrous_rates 12 --atrous_rates 18 --output_stride 16 --decoder_output_stride 4 --checkpoint_dir $MODELDIR/model.ckpt-5000 --dataset_dir /data/ --vis_crop_size 2000 --wsi_downsample 2 --tile_step 1000 --min_size 2000 --vis_batch_size 1 --vis_remove_border 100 --simplify_contours 0.005 --num_classes 2 --class_names 'gloms' --save_heatmap=False --heatmap_stride 2 --gpu 0