#!/bin/bash

#################################################################
#                                                               #
#    MolDynGrid CLI job submittion                              #
#                                                               #
#    Written by Andrii Salnikov a.k.a Manf                      #
#    E-mail: manf@grid.org.ua                                   #
#    Parallel Computing Lab, Inforamtion and Computer Center,   #
#    Kyiv National Taras Schevchenko University                 #
#                                                               #
#################################################################

#
# CHANGELOG
#

# 2.3.1  - ability to disable auto results upload to SE
#        - npme mdrun option for MD
#        - SAVE_INPUTS_AS_OUTPUTS for input .mdp files
#        - client side input files check
# 2.4    - empty JOBNAME fix
#        - portal required files fix
#        - g_tune_pme intergarion for gromacs 4.5.x (MD_NPME="g_tune_pme")
# 3.0    - completely new modular architecture
#        - modules for gromacs/oldngclients/xrsl/oldportal
# 3.1    - staging data to storage before submission (MDS_JOBS_STAGING)
#        - staging output files to job dir
#        - defaults are changed to new interfaces usage
#        - processing of CPUs moved to jobdescription processing from software
#        - NAMD (with optional GPU acceleration) support
#        - GROMACS mdrun-only computation support
#        - Proxy generation parameters now in 'params'
# 3.2    - Bugfixes for chekpointing
# 4.0    - Staging on WN (for FedCloud and HTCondor cases)
# 5.0    - PBS and HTCondor support

VERSION="5.0"
MDS_CONFIG_LOCATION=${MDS_CONFIG_LOCATION:-/opt/moldynsub/etc/moldynsub.conf}

# source moldynsub configuration file
if [ -f "$MDS_CONFIG_LOCATION" ]; then
    source "$MDS_CONFIG_LOCATION"
else
    echo "ERROR: Cannot find MolDynSyb CLI configuration file $MDS_CONFIG_LOCATION"
    exit 1
fi

# necessary defaults in case of not defined in the configuration file
MDS_LIBEXEC_PATH=${MDS_LIBEXEC_PATH:-/usr/libexec/moldynsub/}
MDS_DEFAULT_SOFTWARE=${MDS_DEFAULT_SOFTWARE:-gromacs-md-mdrun}
MDS_DEFAULT_INFRASTRUCTURE=${MDS_DEFAULT_INFRASTRUCTURE:-arc}
MDS_DEFAULT_PORTAL=${MDS_DEFAULT_PORTAL:-moldyngrid}

# common modules source
source "${MDS_LIBEXEC_PATH}/colors.sh"
source "${MDS_LIBEXEC_PATH}/common.sh"

# parse command line options and source software/infrastructure/protal modules
parse_cmd_options $@

# source params file
source_params

# set necessary software-specific environment variables
set_software_environment
set_software_grid_environment

# define some project filenames to be created
SUBMITDATE=$( date +%Y%m%d%H%M%S )
EXECUTABLE="moldynsub.${SUBMITDATE}.script"
SUBMITLOG="moldynsub.${SUBMITDATE}.submit.log"
JDESCFILE="moldynsub.${SUBMITDATE}.$(get_jobdescription_type)"
JOBIDFILE="moldynsub.${SUBMITDATE}.jobid"

# create grid-proxy 
generate_proxy

# contact portal before job submission
[ -z "${DISABLEPORTAL}" -a -z "${DRYRUN}" ] && portal_connect_pre

# create input files list for software 
create_input_files_list

# if defined run pre-stages of exec generation
[ -n "$(type -t create_pre_exec)" ]  && create_pre_exec > $EXECUTABLE

# generate main executable to be run on worker node
create_executable >> $EXECUTABLE

# opptionally apply wrapper function if defined
[ -n "$(type -t job_wrap)" ] && job_wrap

# create output files list for software
create_output_files_list ${STAGEOUT_URL}

# if defined run post-stages of exec generation
[ -n "$(type -t create_post_exec)" ]  && create_post_exec >> $EXECUTABLE

# generate grid job-description file for choosen infrastructure
gen_job_description $JDESCFILE

# and optionally upload job files to storage
[ -n "$MDS_JOBS_STAGING" -a -z "${DRYRUN}" ] && stage_in_files

# submit job to choosen grid-infrastructure
[ -z "${DRYRUN}" ] && grid_job_submit $JDESCFILE $JOBIDFILE $EXECUTABLE

# connect portal after submission
[ -z "${DISABLEPORTAL}" -a -z "${DRYRUN}" ] && portal_connect_post