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nieverge
scripts
Commits
86a4ee80
Commit
86a4ee80
authored
Aug 21, 2019
by
Adrian Nievergelt
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script to do icon processing
parent
25463191
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cluster/indivICONGPU_v3.slurm
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86a4ee80
#!/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
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