#!/bin/csh
### CPU
### Yong Zi
### Edited 18 June 2017
### Queue name
#PBS -q shortq
### Specify the number of nodes and thread (ppn) for your job.
#PBS -l nodes=6:ppn=23
### Log Files
#PBS -o MotionCorr/job011/run.out
#PBS -e MotionCorr/job011/run.err
#PBS -m bea
#PBS -M carlatnysbc@gmail.com
#################################

module unload relion
module unload relion
module unload relion
module unload relion
module unload relion
module load relion/3-beta/CPU-Cluster
module load cuda/8.0

cd $PBS_O_WORKDIR

mpiexec -mca orte_forward_job_control 1 -n 138 -bynode `which relion_run_motioncorr_mpi` --i Import/job005/movies.star --o MotionCorr/job011/ --first_frame_sum 1 --last_frame_sum -1 --use_own  --j 1 --bin_factor 1 --bfactor 500 --angpix 1.0961 --voltage 300 --dose_per_frame 1.33 --preexposure 0 --patch_x 5 --patch_y 5 --gainref ../../../../kzhou/19feb16b/ddstack/ddstack1/norm-buffer2-1.mrc --gain_rot 0 --gain_flip 1 --dose_weighting