script to do icon processing

cluster/indivICONGPU_v3.slurm

+#!/bin/bash
+#SBATCH -J iconGPU-reconst     # the job's name
+#SBATCH -t 30:00:00       # max. wall clock time 5s
+#SBATCH -n 1          # number of tasks
+#SBATCH -N 1
+#SBATCH -c 2
+#SBATCH -o /projects/project-nieverge/logs/iconGPU-reconst_%j.out  # output file
+#SBATCH --partition=gpu
+#SBATCH --gres=gpu:2
+
+#module load cuda/10 #make cuda available to this session's environemt
+
+numNodes=16
+totalSlices=3837 # zero referenced
+
+module load cuda/9.2.148
+module load fftw/3.3.4
+
+baseDir="/projects/project-nieverge"
+k2correct="${baseDir}/scripts/processing/correctK2Lines.py"
+mcorrBin="${baseDir}/bin/motioncor2/MotionCor2_1.2.3-Cuda100"
+iconGPU="${baseDir}/bin/ICON_GPU_v1.2.9_CentOS64/bin/ICON-GPU"
+iconMask="${baseDir}/bin/ICON_GPU_v1.2.9_CentOS64/bin/ICONMask3"
+
+tomoProc="${baseDir}/tomoProc"
+rawDir="${tomoProc}/raw"
+correctedDir="${tomoProc}/corrected"
+alignedDir="${tomoProc}/aligned"
+stackDir="${tomoProc}/tiltStacks"
+
+baseDir=${1%%.*}
+mkdir -p $baseDir
+
+${iconGPU} -i $1 -t $2 -iter 80,160,80 -thr 0 -o ${baseDir} -s 0,3837 -d 1
+
+${iconMask} -i ${baseDir}/reconstruction -t $2 -th 750 -cf ${baseDir}/crossValidation/crossV.frc -ff ${baseDir}/crossValidation/fullRec.frc -o ${baseDir}_icon.rec -s 0,3837