votca-csg-scripts 1.3.0-3 / usr / share / votca / scripts / inverse / inverse.sh

#! /bin/bash
#
# Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

show_help () {
  cat << eof
${0##*/}, version %version%

Start the script to run ibi, imc, etc. or clean out current dir

Usage: ${0##*/} [OPTIONS] --options settings.xml [clean]

Allowed options:
-h, --help                    show this help
-N, --do-iterations N         only do N iterations (ignoring settings.xml)
    --wall-time SEK           Set wall clock time
    --options FILE            Specify the options xml file to use
    --debug                   enable debug mode with a lot of information
    --nocolor                 disable colors

Examples:
* ${0##*/} --options cg.xml
* ${0##*/} -6 --options cg.xml
eof
}

#--help should always work so leave it here
if [[ $1 = "--help" ]]; then
  show_help
  exit 0
fi

#do all start up checks option stuff
source "${VOTCASHARE}/scripts/inverse/start_framework.sh"  || exit 1

#defaults for options
do_iterations=""
waittime=10

#unset stuff from enviorment
unset CSGXMLFILE CSGENDING CSGDEBUG

### begin parsing options
shopt -s extglob
while [[ ${1#-} != $1 ]]; do
 if [[ ${1#--} = $1 && -n ${1:2} ]]; then
    #short opt with arguments here: fc
    if [[ ${1#-[fc]} != ${1} ]]; then
       set -- "${1:0:2}" "${1:2}" "${@:2}"
    else
       set -- "${1:0:2}" "-${1:2}" "${@:2}"
    fi
 fi
 case $1 in
   --do-iterations)
    do_iterations="$2"
    is_int "$do_iterations" || die "inverse.sh: --do-iterations need a number as argument, but I got $do_iterations"
    shift 2 ;;
   --wall-time)
    is_int "$2" || die "inverse.sh: --wall-time need a number as argument, but I got $2"
    export CSGENDING=$(( $(get_time) + $2 ))
    shift 2 ;;
   -[0-9]*)
    do_iterations=${1#-}
    is_int "$do_iterations" || die "inverse.sh: $1 need a number in its argument, but I got $do_iterations"
    shift ;;
   --options)
    CSGXMLFILE="$2"
    [[ -f $CSGXMLFILE ]] || die "options xml file '$CSGXMLFILE' not found"
    export CSGXMLFILE="$(globalize_file "${CSGXMLFILE}")"
    shift 2;;
   --nocolor)
    export CSGNOCOLOR="yes"
    shift;; 
   --nowait)
    waittime=0
    shift;;
   --debug)
    export CSGDEBUG="yes"
    shift;; 
   -h | --help)
    show_help
    exit 0;;
  *)
   die "Unknown option '$1'";;
 esac
done
### end parsing options

#old style, inform user
[[ -z ${CSGXMLFILE} ]] && die "Please add your setting xml file behind the --options option (like for all other votca programs) !"

[[ $1 = "clean" ]] && { csg_inverse_clean "$waittime"; exit $?; }

enable_logging
[[ -n $CSGDEBUG ]] && set -x
check_for_obsolete_xml_options

echo "Sim started $(date)"

method="$(csg_get_property cg.inverse.method)"
msg "We are doing Method: $method"

scriptpath="$(csg_get_property --allow-empty cg.inverse.scriptpath)"
[[ -n $scriptpath ]] && echo "Adding $scriptpath to csgshare" && add_to_csgshare "$scriptpath"

#after scriptpath to allow overwrite
sim_prog="$(csg_get_property cg.inverse.program)"
echo "We are using Sim Program: $sim_prog"
source_function $sim_prog

show_csg_tables

#main script
[[ -f done ]] && { msg "Job is already done (remove the file named 'done' if you want to go on)"; exit 0; }

######## BEGIN STEP 0 ############
update_stepnames 0
restart_file="$(get_restart_file)"
this_dir=$(get_current_step_dir --no-check)
if [[ -d $this_dir &&  -f "$this_dir/done" ]]; then
  msg "step 0 is already done - skipping"
else
  echo ------------------------
  msg --color blue "Prepare (dir ${this_dir##*/})"
  echo ------------------------
  if [[ -d $this_dir ]]; then
    msg "Incomplete step 0"
    [[ -f "${this_dir}/${restart_file}" ]] || die "No restart file found (remove stepdir '${this_dir##*/}' if you don't know what to do - you will lose the prepare step)"
  else
    mkdir -p $this_dir || die "mkdir -p $this_dir failed"
  fi
  cd $this_dir || die "cd $this_dir failed"
  mark_done "stepdir"

  if is_done "Prepare"; then
    msg "Prepare of potentials already done"
  else
    filelist="$(csg_get_property --allow-empty cg.inverse.filelist)"
    #get need files (leave the " " unglob happens inside the function)
    [[ -n ${filelist} ]] && cp_from_main_dir "$filelist"

    do_external prepare $method
    mark_done "Prepare"
  fi

  touch "done"
  msg "step 0 done"
  cd $(get_main_dir)
fi
######## END STEP 0 ############

begin=1
trunc=$(get_stepname --trunc)
for i in ${trunc}*; do
  [[ -d $i ]] || continue
  nr=${i#$trunc}
  if [[ -n $nr && -z ${nr//[0-9]} ]]; then
    #convert to base 10, otherwise 008 is interpreted as octal
    nr=$((10#$nr))
    [[ $nr -gt $begin ]] && begin="$nr"
  fi
done
unset nr trunc
[[ $begin -gt 1 ]] && msg "Jumping in at iteration $begin"

avg_steptime=0
steps_done=0
i="$(( $begin - 1 ))"
while true; do
  ((i++))
  if [[ -z ${do_iterations} ]]; then
    iterations_max="$(csg_get_property cg.inverse.iterations_max)"
    is_int "$iterations_max" || die "inverse.sh: cg.inverse.iterations_max needs to be a number, but I got $iterations_max"
    echo "We are doing $i of $iterations_max iterations (0=inf)."
    [[ $iterations_max -ne 0 && $i -gt $iterations_max ]] && break
  fi
  step_starttime="$(get_time)"
  update_stepnames $i
  last_dir=$(get_last_step_dir)
  this_dir=$(get_current_step_dir --no-check)
  echo -------------------------------
  msg --color blue "Doing iteration $i (dir ${this_dir##*/})"
  echo -------------------------------
  if [[ -d $this_dir ]]; then
    if [[ -f "$this_dir/done" ]]; then
      msg "step $i is already done - skipping"
      continue
    else
      msg "Incomplete step $i"
      [[ -f ${this_dir}/${restart_file} ]] || die "No restart file found (remove stepdir '${this_dir##*/}' if you don't know what to do - you will lose one iteration)"
    fi
  else
    echo "Step $i started at $(date)"
    mkdir -p $this_dir || die "mkdir -p $this_dir failed"
  fi

  cd $this_dir || die "cd $this_dir failed"
  mark_done "stepdir"

  filelist="$(csg_get_property --allow-empty cg.inverse.filelist)"
  if is_done "Filecopy"; then
    echo "Filecopy already done"
    for f in $filelist; do
      [[ -f $f ]] || cp_from_main_dir "$f"
      echo Comparing "$(get_main_dir)/$f" "$f"
      [[ -z $(type -p cmp) ]] && echo "program 'cmp' not found, comparision skipped" && continue
      cmp "$(get_main_dir)/$f" "$f" && echo "Unchanged" || \
	msg --color blue --to-stderr "WARNING: file '$f' in the main dir was changed since the last execution, this will have no effect on the current iteration, to take effect remove the current iteration ('${this_dir##*/}')"
    done
  else
    #get need files (leave the " " unglob happens inside the function)
    [[ -n ${filelist} ]] && cp_from_main_dir "$filelist"

    mark_done "Filecopy"
  fi

  if is_done "Initialize"; then
    echo "Initialization already done"
  else
    #get files from last step, init sim_prog and ...
    do_external initstep $method

    mark_done "Initialize"
  fi

  if is_done "Simulation"; then
    echo "Simulation is already done"
  else
    msg "Simulation with $sim_prog"
    do_external run $sim_prog
  fi

  if simulation_finish; then
    mark_done "Simulation"
  elif [[ "$(csg_get_property cg.inverse.simulation.background)" = "yes" ]]; then
    msg "Simulation is suppose to run in background, which we cannot check."
    msg "Stopping now, resume csg_inverse whenever the simulation is done."
    exit 0
  elif [[ -n ${CSGENDING} ]] && checkpoint_exist; then
    msg "Simulation is not finished, but a checkpoint was found, so it seems"
    msg "walltime is nearly up, stopping now, resume csg_inverse whenever you want."
    exit 0
  else
    die "Simulation is in a strange state, it has no checkpoint and is not finished, check ${this_dir##*/} by hand"
  fi

  do_external pre_update $method

  msg "Make update for $method"
  do_external update $method

  do_external post_update $method
  do_external add_pot $method

  msg "Post add"
  do_external post add

  do_external clean $sim_prog

  step_time="$(( $(get_time) - $step_starttime ))"
  msg "\nstep $i done, needed $step_time secs"
  ((steps_done++))

  touch "done"

  convergence_check="$(csg_get_property cg.inverse.convergence_check.type)"
  if [[ $convergence_check = none ]]; then
    echo "No convergence check to be done"
  else
    msg "Doing convergence check: $convergence_check"
    [[ -f stop ]] && rm -f stop #just in case a script created a stop file
    do_external convergence_check "$convergence_check"
    if [[ -f stop ]]; then
      msg "Iterations are converged, stopping"
      break
    else
      msg "Iterations are not converged, going on"
    fi
  fi

  if [[ -n $CSGENDING ]]; then
    avg_steptime="$(( ( ( $steps_done-1 ) * $avg_steptime + $step_time ) / $steps_done + 1 ))"
    echo "New average steptime $avg_steptime"
    if [[ $(( $(get_time) + $avg_steptime )) -gt ${CSGENDING} ]]; then
      msg "We will not manage another step due to walltime, stopping"
      exit 0
    else
      msg "We can go for another $(( ( ${CSGENDING} - $(get_time) ) / $avg_steptime - 1 )) steps until walltime is up."
    fi
  fi

  if [[ -n $do_iterations ]]; then
    if [[ $do_iterations -eq $steps_done ]] ; then
      msg "Stopping at step $i, user requested to take some rest after this amount of iterations"
      exit 0
    else
      msg "Going on for another $(( $do_iterations - $steps_done )) steps"
    fi
  fi
  cd $(get_main_dir) || die "cd $(get_main_dir) failed"
done

touch "done"
echo "All done at $(date)"
exit 0