#
# DESCRIPTION namd Molecular dynamics simulation in NAMD
#

# software_usage [optional]

# software_parse_cmd_options [optional]

set_software_environment () {
    NAMD_GPU=${NAMD_GPU:-if_any}
    NAMD_LOG=${NAMD_LOG:-namd.log}
    JOBNAME=mds_namd_$(date +%s)
    [ -n "$NAMD_CONFIG" -a -f "$NAMD_CONFIG" ] || exit_error "Cannot find NAMD configuration file. Job submission aborted"
}

set_software_grid_environment () {
    NAMD_RUNTIME=${NAMD_RUNTIME:-NAMD-2.10}
    NAMD_VERSION=${NAMD_RUNTIME##*-}
    if [ "$BUILD_RUNTIME" = "yes" ]; then
        next_idx_var INPUT_FILES_NAME_ INPUT_FILES_LOCATION_ \
                     "namd_install.sh" "${MDS_SOFT_INSTALLS_PATH%/}/NAMD/namd_install.sh"
        next_idx_var INPUT_FILES_NAME_ INPUT_FILES_LOCATION_ \
                     "NAMD_${NAMD_VERSION}_Linux-x86_64-multicore.tar.gz" "${MDS_SOFT_INSTALLS_PATH%/}/NAMD/NAMD_${NAMD_VERSION}_Linux-x86_64-multicore.tar.gz"
        [ "$NAMD_GPU" = "no" ] || next_idx_var INPUT_FILES_NAME_ INPUT_FILES_LOCATION_ \
                     "NAMD_${NAMD_VERSION}_Linux-x86_64-multicore-CUDA.tar.gz" "${MDS_SOFT_INSTALLS_PATH%/}/NAMD/NAMD_${NAMD_VERSION}_Linux-x86_64-multicore-CUDA.tar.gz"
    else
        next_idx_var RUNTIME_CONDITION_ RUNTIME_VALUE_ "=" "${NAMD_RUNTIME}"
    fi

    if [ -z "$CPUS" -a "$NODES" != "1" ]; then
        echo_bad "WARNING: MolDynSub NAMD submission is not designed to run in multi-node mode. Number of nodes reduced to 1."
        NODES=1
    fi
}

software_gen_params () {
cat <<END
###############################################################
#           NAMD SOFTWARE PARAMETERS                          #
###############################################################

# NAMD release (according to MolDynGrid runtime specification)
NAMD_RUNTIME="NAMD-2.10"

# Install NAMD in runtime instead or requesting pre-installed one
BUILD_RUNTIME=yes

# NAMD configuration file
NAMD_CONFIG=ionized.namd

# GPU Acceleration
# Possible values are:
#   no     - always use CPU only
#   if_any - use GPU if any available (default)
#   force  - compute only if GPU present, fail otherwise
#NAMD_GPU=if_any

# Custom job name (redefine moldynsub autogenerated one)
#JOBNAME=my_namd_job

END
}

create_executable () {
cat << END
#!/bin/bash

# defines from moldynsub job params
BUILD_RUNTIME=${BUILD_RUNTIME}
NAMD_CPUS=${CPUS:-${PPN:-1}}
NAMD_GPU=${NAMD_GPU}
NAMD_CONFIG=${NAMD_CONFIG}
NAMD_LOG=${NAMD_LOG}

# GPU-detection functions
gpus_list () {
    type nvidia-smi >/dev/null 2>&1
    [ \$? -ne 0 ] && return 1
    nvidia-smi -L | sed 's/^GPU\s*\([0-9]\+\):.*/\1/' | sed -e :a -e N -e 's/\n/,/' -e ta
}

gpus_info () {
    echo "INFO: Enabling GPU acceleration. Following Nvidia GPU accelerator(s) has been found on target machine:"
    nvidia-smi -L 
}

# Handle GPU acceleration
if [ "\$NAMD_GPU" != "no" ]; then
  GPUS=\$( gpus_list )

  if [ "\$NAMD_GPU" = "if_any" ]; then
    if [ -n "\$GPUS" ]; then
      export ENABLE_GPU=1
      gpus_info
    else
      echo "INFO: Nvidia GPU accelerator is not found on target machine. CPU-only computing will be performed."
    fi
  elif [ "\$NAMD_GPU" = "force" ]; then
    if [ -n "\$GPUS" ]; then
      export ENABLE_GPU=1
      gpus_info
    else
      echo "ERROR: GPU is explicitly requested (NAMD_GPU=force) but not found on target machine. Job execution aborted."
      exit 1
    fi
  fi
fi

# Install NAMD in runtime if requested
if [ "\$BUILD_RUNTIME" = "yes" ]; then
  echo "INFO: Installing NAMD as a part of job lifecycle"
  if [ -f "namd_install.sh" ]; then
    source namd_install.sh
  else
    echo "ERROR: There is no NAMD install script found. Skipping."
  fi
else
  echo "INFO: Relying on pre-installed NAMD software"
fi

# Invoke NAMD
type namd2 >/dev/null 2>&1
if [ \$? -ne 0 ]; then
  echo "FATAL: There is no namd2 executable found. It seams NAMD installation is broken."
  exit 1
fi

[ -n "\${ENABLE_GPU}" ] && NAMD_DEVICES="+devices \$GPUS"
namd2 +p\${NAMD_CPUS} \${NAMD_DEVICES} "\${NAMD_CONFIG}" ++verbose | tee \$NAMD_LOG

END
}

create_input_files_list () {
    # input files defined within parametrized NAMD_CONFIG 
    # eval variables in NAMD_CONFIG
    eval $( cat $NAMD_CONFIG | sed -n '/^set/s/set\s*\([a-zA-Z]\+\)\s*\(.*\)$/\1=\2/p' )
    # get input files
    eval $( cat $NAMD_CONFIG | sed -n '/^\(coordinates\|structure\|parameters\)/I s/^\([a-z]\+\)\s*\(.*\)$/\L\1=\E\2/pI' )
    # pass files to stage-in/jobdescription
    [ -n "$coordinates" ] && next_idx_var INPUT_FILES_NAME_ INPUT_FILES_LOCATION_ "$coordinates" ""
    [ -n "$structure" ] && next_idx_var INPUT_FILES_NAME_ INPUT_FILES_LOCATION_ "$structure" ""
    [ -n "$parameters" ] && next_idx_var INPUT_FILES_NAME_ INPUT_FILES_LOCATION_ "$parameters" ""
    # pass NAMD_CONFIG itself
    next_idx_var INPUT_FILES_NAME_ INPUT_FILES_LOCATION_ "$NAMD_CONFIG" ""
    return 0
}

create_output_files_list () {
    local stageout_uri=$1
    # output files defined within parametrized NAMD_CONFIG 
    # eval variables in NAMD_CONFIG
    eval $( cat $NAMD_CONFIG | sed -n '/^set/s/set\s*\([a-zA-Z]\+\)\s*\(.*\)$/\1=\2/p' )
    # get output files
    eval $( cat $NAMD_CONFIG | sed -n '/^\(dcdfile\|xstfile\)/I s/^\([a-z]\+\)\s*\(.*\)$/\L\1=\E\2/pI' )
    # pass files to jobdescription
    [ -n "$dcdfile" ] && next_idx_var OUTPUT_FILES_NAME_ OUTPUT_FILES_LOCATION_ "$dcdfile" "${stageout_uri:+$stageout_uri/$dcdfile}"
    [ -n "$xstfile" ] && next_idx_var OUTPUT_FILES_NAME_ OUTPUT_FILES_LOCATION_ "$xstfile" "${stageout_uri:+$stageout_uri/$xstfile}"
    # namd.log should be saved also
    next_idx_var OUTPUT_FILES_NAME_ OUTPUT_FILES_LOCATION_ "$NAMD_LOG" "${stageout_uri:+$stageout_uri/$NAMD_LOG}"
    return 0
}