#!/bin/bash -l
#
#SBATCH -o polish2_gautoALL_from_3dref7-noalign.out%j
#SBATCH -e polish2_gautoALL_from_3dref7-noalign.err%j
#SBATCH --job-name=polish2_gautoALL_from_3dref7-noalign
#SBATCH --mem-per-cpu=3150M
#SBATCH --ntasks=40
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=16
#SBATCH --qos=emcpu
#SBATCH --partition=emcpu

export LMOD_DISABLE_SAME_NAME_AUTOSWAP=no

ml purge
ml load CMake/3.9.1-goolf-1.7.20
ml load OpenMPI/3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1

RELION_PATH="/scicore/projects/scicore-p-structsoft/relion/relion-3.0_stable/cpu_gcc"
export PATH="${RELION_PATH}/bin:$PATH"
export LD_LIBRARY_PATH="${RELION_PATH}/lib:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH="${RELION_PATH}/../external/fftw/lib:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH="${RELION_PATH}/../external/fltk/lib:$LD_LIBRARY_PATH"

export RELION_QSUB_EXTRA1="Job Name"
export RELION_QSUB_EXTRA2="CPU: Rank per node, GPU: No. gpu"

time srun `which relion_motion_refine_mpi` --i Refine3D/job290/run_data.star --f PostProcess/job291/postprocess.star --corr_mic JoinStar/job152/join_mics.star --first_frame 1 --last_frame -1 --o Polish/job292/ --params_file Polish/job260/opt_params.txt --combine_frames --bfac_minfreq 20 --bfac_maxfreq -1 --j 16