#!/bin/bash -l
#
# RELION 4.0 job submission template for SLURM at MRC-LMB cluster
# This script is maintained by Takanori Nakane.
#
#SBATCH --job-name=RELION4.0
#SBATCH --error=Refine3D/job017/run.err
#SBATCH --output=Refine3D/job017/run.out
#SBATCH --open-mode=append
#SBATCH --time=3-00:00:00 # should be enough for most jobs
#SBATCH --mail-type=FAIL
#SBATCH --partition=cpu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=112 # grab a full node
#SBATCH --mem=700G

# This folder is created by the job prolog script.
# For some reason, the environmental variable is not properly set,
# so I do here.
export RELION_SCRATCH_DIR=/ssd/${SLURM_JOB_USER}-${SLURM_JOBID}

source /public/gcc/gcc10_2_0.sh
source /public/compilers/intel-2021.3/setvars.sh # no tcsh version
export OMPI_CC=icc
export OMPI_CXX=icpc
export PATH=/public/EM/OpenMPI/openmpi-4.0.1/build/bin:$PATH
export LANG=en_US.utf8 # Intel compilers require this
export LC_ALL=en_US.utf8

# We cannot source relion-4.0-dev.csh because this is BASH.
export PATH=/public/EM/RELION/relion-4.0-dev/build-cpu/bin:$PATH

# SIDESPLITTER
export RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE=/public/EM/SIDESPLITTER/sidesplitter_wrapper.sh
export SIDESPLITTER=/public/EM/SIDESPLITTER/sidesplitter

echo "* RELION 4.0 CPU JOB ENVIRONMENT *"
echo
echo PATH TO mpiexec: `which mpiexec`
echo PATH TO relion_refine_mpi: `which relion_refine_mpi`
echo LIBRARIES FOR relion_refine_mpi:
ldd  `which relion_refine_mpi`
echo RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE: $RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE
echo SIDESPLITTER: $SIDESPLITTER
echo

STARTTIME=`date +%s`
echo RUN STARTED AT `date -d@${STARTTIME}`
echo TO KILL THIS JOB, RUN: scancel $SLURM_JOB_ID
echo ------------------------------------------------------------------------------------

# --oversubscribe is intentional to allow almost idle rank 0.
# --mca btl_tcp_if_include 10.0.0.0/8 is to prevent crash on multiple nodes.
# See https://github.com/open-mpi/ompi/issues/6240.
mpirun --mca btl_tcp_if_include 10.0.0.0/8 --oversubscribe -n 21 `which relion_refine_mpi` --o Refine3D/job017/run --auto_refine --split_random_halves --i Refine3D/job014/run_data.star --ref Refine3D/job014/run_half1_class001_unfil.mrc --ini_high 10 --dont_combine_weights_via_disc --scratch_dir $RELION_SCRATCH_DIR --pool 30 --pad 2  --skip_gridding  --ctf --particle_diameter 220 --flatten_solvent --zero_mask --solvent_mask MaskCreate/job016/mask.mrc --solvent_correct_fsc  --oversampling 1 --healpix_order 3 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale  --helix --helical_outer_diameter 180 --helical_nr_asu 3 --helical_twist_initial -1.14 --helical_rise_initial 4.75 --helical_z_percentage 0.2 --sigma_tilt 5 --sigma_psi 3.33333 --sigma_rot 0 --helical_keep_tilt_prior_fixed --j 4  --pipeline_control Refine3D/job017/

echo ------------------------------------------------------------------------------------
ENDTIME=`date +%s`
echo RUN FINISHED AT `date -d@${ENDTIME}`
echo ELAPSED WALL CLOCK TIME IN SECONDS: `echo $ENDTIME - $STARTTIME | bc`

exit 0