#!/bin/tcsh
#$ -pe openmpi 1
#$ -l dedicated=24 
#$ -e Extract/job057/run.err
#$ -o Extract/job057/run.out
#$ -N Relion4.0
#$ -cwd
#$ -S /bin/tcsh

source /public/EM/RELION/relion-4.0-dev.csh

echo "* RELION 4.0 JOB ENVIRONMENT *" # csh expands * ...
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

set  STARTTIME = `date +%s`
echo RUN STARTED AT `date -d@${STARTTIME}`
echo -----------------------------------------------------------

# OpenMPI 2.0.1 complains when XXmpinodesXX > number of slots in parallel environment (= XXnodesXX)
# --oversubscribe suppresses this error.

mpiexec --prefix /public/EM/OpenMPI/openmpi-2.0.1/build  -oversubscribe -n 8  `which relion_preprocess_mpi` --i CtfFind/job056/micrographs_ctf.star --reextract_data_star Select/job042/particles.star --part_star Extract/job057/particles.star --pick_star Extract/job057/extractpick.star --pick_star Extract/job057/extractpick.star --part_dir Extract/job057/ --extract --extract_size 256 --float16  --norm --bg_radius 96 --white_dust -1 --black_dust -1 --invert_contrast  --helix --helical_outer_diameter 180 --helical_bimodal_angular_priors --helical_tubes --helical_cut_into_segments --helical_nr_asu 3 --helical_rise 4.75  --pipeline_control Extract/job057/

echo -----------------------------------------------------------
set ENDTIME = `date +%s`
echo RUN FINISHED AT $ENDTIME
echo ELAPSED WALL CLOCK TIME: `echo $ENDTIME - $STARTTIME | bc`

exit 0