Closed GoogleCodeExporter closed 9 years ago
Next thing, I will have a look at it myself!
Sorry, did not see where to set the owner, obviously it's me :)
Original comment by abruk...@googlemail.com
on 1 Mar 2014 at 11:56
This looks very brittle to me. Could you just check if the simulation is not
finished (REVCON don't exist) and if a checkpoint exists and run dl_poly again?
If dlpoly runs, great, if not, the user has to do some work by hand anyway.
And the check should be split into checkpoint_exist() and simulation_finish()
(see inverse.sh line 250 for the logic).
Technically:
- readlink, why?
- basename $0 -> ${0##*/}
- grep XXX file | awk '{..}'-> awk '/XXX/{..}' file
Original comment by christop...@gmail.com
on 2 Mar 2014 at 1:39
REVCON and REVIVE are periodically created during the simulation run, and are
needed for restarting an abnormally stopped simulation job. So, these two files
are the "checkpoint" for DL_POLY, and do not tell if the job went all the way
to the end.
The only way to be sure that the simulation has been actually finished is to
check the contents of OUTPUTm as I have shown in that extract (from a working
self-resubmission script).
I agree certain things there can be simplified, or done in a more compact way.
Original comment by abruk...@googlemail.com
on 3 Mar 2014 at 1:25
Correction: REVCON and REVIVE are periodically updated...
Original comment by abruk...@googlemail.com
on 3 Mar 2014 at 1:26
Christoph, what purpose is the code below supposed to serve?
My understanding is that finding HISTORY is considered as a "simulation
finished" flag. But why "touch .dlph/.dlpf", do you check them anywhere later?
simulation_finish() { #checks if simulation is finished
local traj topol
if [[ -f "HISTORY" ]]; then
#hacky workaround as topol/traj is called '.dlph/.dlpf'
traj=$(csg_get_property cg.inverse.dlpoly.traj)
critical touch $traj
topol=$(csg_get_property cg.inverse.dlpoly.topol)
critical touch $topol
return 0
fi
return 1
}
Original comment by abruk...@googlemail.com
on 3 Mar 2014 at 1:46
The following functions should be sufficient (?).
===
simulation_finish() { #checks if simulation is finished
local nneeded npassed
[[ ! -f "HISTORY" ]] && return 1
[[ ! -s "OUTPUT" ]] && return 1
nneeded=$(awk '/selected number of timesteps/{print $'5'}' OUTPUT)
npassed=$(awk '/run terminated after/{print $'4'}' OUTPUT)
[[ $npassed -lt $nneeded ]] && return 1
return 0
}
export -f simulation_finish
checkpoint_exist() { #check if a checkpoint exists (REVIVE _and_ REVCON - both
are needed!)
#support for checkpoint
local checkpoint check
checkpoint="($(csg_get_property --alow-empty cg.inverse.dlpoly.checkpoint))"
[[ -n $checkpoint ]] && checkpoint="REVIVE REVCON"
checkpoint=($checkpoint)
for check in "${checkpoint[@]}"; do
[[ ! -f ${check} ]] && return 1
done
return 0
}
export -f checkpoint_exist
===
Original comment by abruk...@googlemail.com
on 3 Mar 2014 at 3:04
Looks not too bad, but I have the following comments:
1.) touching of .dlph/.dlpf is needed as many update script check the existence
of the topology and trajectory file.
2.) simulation_finish(): only if cg.inverse.dlpoly.traj == .dlph, HISTORY
should be used
3.) simulation_finish(): what is the point of quoting 4 outside of the string?
$variable isn't expanded in single quotes. (echo '$HOME' vs echo "$HOME")
4.) simulation_finish(): return code is automatically the result of the last
command, so "[[ $npassed -ge $nneeded ]]" would do it.
5.) checkpoint_exist(): defaults should do into csg_defaults.xml, also putting
it into an array make not much sense (would help with spaces in the filename,
but csg_get_property doesn't handle space in filename).
We could improve the .dlp* hackery by moving HISTORY to HISTORY.dlph etc. in
run_dlpoly.sh, but then we loss dlpoly's naming scheme.
Original comment by christop...@gmail.com
on 4 Mar 2014 at 1:08
1/2) OK, I see now how "touch .dlph/.dlpf" works (actually encountered an error
when not doing it). So I simply reinsert those commands after the initial
checks on HISTORY and OUTPUT. I think having zero-size "hidden" files as
"finished" flags for checking by votca scripts is alright.
3) OK, removed the quotes.
4) I did not know that the return statement is auto-assumed by the last
command, but I would still use "return" for clarity (not that any user is going
to look into it, though).
5) yep, I put "REVIVE REVCON" in csg_defaults.xml, then the test [[-n
$checkpoint]] won't be needed. Did you mean we can also remove:
checkpoint=($checkpoint)?
Original comment by abruk...@googlemail.com
on 4 Mar 2014 at 1:31
checkpoint_exist() { #check if REVIVE REVCON exist - from in csg_defaults.xml
#support for checkpoints
local checkpoint check
checkpoint="($(csg_get_property cg.inverse.dlpoly.checkpoint))"
for check in $checkpoint; do
[[ ! -f ${check} ]] && return 1
done
echo "DL_POLY checkpoint present (REVIVE REVCON found)"
return 0
}
export -f checkpoint_exist
Original comment by abruk...@googlemail.com
on 4 Mar 2014 at 1:42
Checked its working fine and committed/pushed along with some earlier bug fixes
(see my clone)
Original comment by abruk...@googlemail.com
on 4 Mar 2014 at 4:29
fixed
How do I close or discard it?
Original comment by abruk...@googlemail.com
on 21 Mar 2014 at 12:51
You were missing the "EditIssue" permission.
Original comment by christop...@gmail.com
on 21 Mar 2014 at 2:55
Original issue reported on code.google.com by
abruk...@googlemail.com
on 1 Mar 2014 at 11:51