[Wien] Problem in x-optic
Peeyush kumar kamlesh
peeyush.physik.rku at gmail.com
Sat Feb 15 20:03:40 CET 2020
Dear Sir,
Last time when I was calculation optical properties using hf potential then
i got some error. Then Peter Blaha sir suggested to remove that /. And
problem was solved by doing this. Thats why this / is not here.
Best Regards
On Sat, Feb 15, 2020 at 11:52 PM Peeyush kumar kamlesh <
peeyush.physik.rku at gmail.com> wrote:
> Dear Gavin Sir,
> opticpara_lapw file is as follows:
>
> #!/bin/tcsh -f
> #
> # Run optic in parallel mode
> #
> # $Author: M.Lee $
> #
>
> touch .lock_
> foreach i (.lock_*)
> rm $i
> end
>
> onintr exit
> set name = $0
> set bin = $name:h #default directory for WIEN-executables
> if !(-d $bin) set bin = .
> set name = $name:t
>
> unalias rm
> alias testinput 'if (! -e \!:1 || -z \!:1) goto \!:2'
> alias testerror 'if (! -z \!:1.error) goto error'
>
> set t = time
> set cmplx
> set log = :parallel
> set defmach = `hostname`
> set updn # spinpolarization switch
> set dnup = 'dn' # spinpolarization switch
> set sc # semicore-switch
> set hf # hybrid-switch
> set so # spinorbit-switch
> set remote = ssh
> set tmp_dir = /tmp
> set init = init:
> set res = residue:
> set taskset0
> set taskset='no'
>
> set scratch =
>
> if ( $?SCRATCH && $SCRATCH != '') then
> set scratch=`echo $SCRATCH | sed -e 's/\/$//'` # we are afraid
> # different settings in different
> # computing centers
> #use global variable for scratch if set
> endif
>
>
>
> ############################################################################
> # In this section use 0 to turn of an option, 1 to turn it on,
> # respectively choose a value
>
> set useremote = 1 # using remote shell to launch processes
> setenv DELAY 0.1 # delay launching of processes by n
> seconds
> set debug = 0 # set verbosity of debugging output
>
>
> ############################################################################
> # and now we look if we should override the defaults
> if (-e $bin/parallel_options) then
> source $bin/parallel_options
> endif
> if ( $?TASKSET ) then
> set taskset="$TASKSET"
> endif
> if ( $?USE_REMOTE ) then
> set useremote = $USE_REMOTE
> endif
>
> ############################################################################
>
> set tmp = $tmp_dir/opticpara.$user.$$
> set tmp2 = $tmp_dir/opticpara.$user.$$_2
>
> if ($#argv < 1) then
> echo usage: $0 deffile
> exit
> endif
>
> while ($#argv)
> switch ($1)
> case -h:
> case -H:
> set help
> shift; breaksw
> case -c:
> set cmplx = c
> shift; breaksw
> case -up:
> set updn = 'up'
> set dnup = 'dn'
> shift; breaksw
> case -dn:
> set updn = 'dn'
> set dnup = 'up'
> shift; breaksw
> case -hf:
> set hf = 'hf'
> shift; breaksw
> case -so:
> set so = 'so'
> shift; breaksw
> case -sc:
> set sc = 's'
> shift; breaksw
> default:
> set def = $1:r
> shift; breaksw
> endsw
> end
>
> set exe = $bin/optic$cmplx
> set exe = optic$cmplx
>
> #are we running parallel?
> testinput .processes single
> echo "running OPTIC in parallel mode"
> echo "RUNNING" >.opticpara
>
> #before we start, we wipe away all parallel error files
> if ( -e optic_1.error ) rm *optic_*.error
> if ( -e .timeop_1) rm .timeop_*
>
> if (-e .machines.help) rm .machines.help
>
> grep -v $init .processes|grep : | grep -v $res >$tmp2
> set mist = `wc $tmp2 `
> set maxproc = $mist[1]
> #set machine = `grep $init .processes |cut -f2 -d: | xargs`
> set machine = `grep -v $init .processes |grep : | grep -v $res | cut -f2
> -d: | xargs`
>
> set lockfile = `cut -f2 -d: $tmp2 | awk '{print $1 NR}'|xargs`
> set residue = `grep $res .processes|cut -f2 -d:`
> if ($residue == "") unset residue
>
> if ($debug > 0) echo machines: $machine
>
> echo "** " Error in Parallel OPTIC >$def.error
> #bounding cpus
> set p_cpu_bound = ($machine)
> set i=1
> set cpu=0
> set old=old
> while ($i <= $#p_cpu_bound)
> if($old != $p_cpu_bound[$i]) then
> set cpu=0
> endif
> set old=$p_cpu_bound[$i]
> set p_cpu_bound[$i] = $cpu
> @ cpu ++
> @ i ++
> end
> #echo $machine
> #echo $p_cpu_bound
>
> #get name of case
> setenv PWD `pwd|sed "s/tmp_mnt\///"`
> #echo $PWD
> setenv PWD $cwd
> set case = $PWD
> set case = $case:t
> if ($case == "") then
> echo "ERROR: cannot detect working directory $cwd -> exit"
> exit 1
> endif
> ####set case = $case:r #head of file-names
> if ($debug > 0) echo Setting up case $case for parallel execution
> if ($debug > 0) echo of OPTIC
> if ($debug > 0) echo " "
> #
>
> #creating def files
> if ($debug > 0) echo " "
> if ($debug > 0) echo -n "creating "$def"_*.def: "
> set i = 1
> while ($i <= $maxproc)
> if ($debug > 0) echo -n "$i "
> cp $def.def .tmp
> #subsituting in files:
> cat <<theend >.script
> s/vector$hf$so$dnup/&_$i/w .mist
> s/vector$hf$so$updn/&_$i/w .mist
> s/outputop/&_$i/w .mist
> s/symmat/&_$i/w .mist
> s/symma1/&_$i/w .mist
> s/symma2/&_$i/w .mist
> s/mommat2/&_$i/w .mist
> s/mat_diag/&_$i/w .mist
> s/mme/&_$i/w .mist
> s/symop/&_$i/w .mist
>
> theend
>
> sed -f .script .tmp > .tmp1
> sed "s/vector_${i}_$i\&dn/vectordn_$i/" .tmp1>.tmp2
> sed "s/vector_${i}_$i\&up/vectorup_$i/" .tmp2>.tmp1
> sed "s/vector_${i}dn_$i/vectordn_$i/" .tmp1>.tmp2
> sed "s/vector_${i}_$i/vector_$i/" .tmp2>.tmp1
> sed "s/vectorhf_${i}dn_$i/vectorhfdn_$i/" .tmp1> .tmp2
> sed "s/vectorso_${i}dn_$i/vectorsodn_$i/" .tmp2> "$def"_$i.def
> #similar fix for SO necessary
>
> @ i ++
> end
> if ($debug > 0) echo " "
>
>
> #starting processes
> if ($debug > 0) echo " "
> if ($debug > 0) echo "starting process: "
>
> echo "-> "starting parallel optic at `date` >>$log
>
> set loop = 0
> set endloop = 0
> set runmach = ""
> echo "files:$maxproc" >.processes2
> # change working dir because of problems with automounted directories
> # cd $cwd
> while ($loop < $maxproc)
> set p = 1
> if ($?residue && $?resok) set p = 2
> while ($p <= $#machine)
> if ($loop < $maxproc) then
> if !(-e .lock_$lockfile[$p]) then
> @ loop ++
> echo "${loop}:${maxproc} : $p_cpu_bound[$p]" >.processes2
> if ($debug > 0) echo prepare $loop on $machine[$p]
> set runmach = ($runmach $machine[$p])
> echo $runmach >>.processes2
> if ($debug > 1) echo " > $exe ${def}_${loop}.def on $machine[$p]"
> if ($debug > 1) echo " > $exe ${def}_${loop}.def on
> $machine[$p]">>$log
> if ($useremote == 1) then
> if ($debug > 1) echo use remote
> touch .lock_$lockfile[$p]
> echo -n "$runmach[$loop] ">.timeop_$loop
> if("$taskset" != 'no') set taskset0="$taskset
> $p_cpu_bound[$p]"
> ($remote $machine[$p] "cd $PWD;$t $taskset0 $exe ${def}_${loop}.def;rm -f
> .lock_$lockfile[$p]") >>.timeop_$loop &
> else
> if ($debug > 1) echo not using remote shell
> touch .lock_$lockfile[$p]
> echo -n "$runmach[$loop] " >.timeop_$loop
> (cd $PWD;$t $exe ${def}_${loop}.def;rm -f .lock_$lockfile[$p])
> >>.timeop_$loop &
> endif
> endif
> if ($debug > 1) echo sleeping for $DELAY seconds
> sleep $DELAY
> jobs -l >.optic${cmplx}para.$$.`hostname`
> endif
> @ p ++
> end
> end
>
> #wait for execution to be completed
> if ($debug > 0) echo " "
> if ($debug > 0) echo "waiting for processes: "
> wait
>
>
> set i = 1
> while ($i <= $maxproc)
> testerror "$def"_$i
> @ i ++
> end
>
> #cpu summary:
> set i = 1
> while ($i <= $maxproc)
> # echo " "`cat .timeop_$i`
> #fix for bash timing
> bashtime2csh.pl_lapw .timeop_$i > .time_tmp
> mv .time_tmp .timeop_$i
> echo " "`cat .timeop_$i` >>$log
> @ i ++
> end
>
> # postanalysis
> echo " Summary of opticpara:" >$tmp
> set p = 1
> while ($p <= $#machine)
> set m = $runmach[$p]
> cat .timeop_* | grep $m | tr "():" " " | \
> awk '{u += $2; cl += 60*$4+$5} \
> END {print " '$m'\t user=" u "\t wallclock=" cl}' >>$tmp
> @ p ++
> end
>
> uniq < $tmp |tee -a $log
>
> echo "<- "done at `date` >>$log
>
> # concatenating the case.symmat files and case.mommat files
>
> if (-e $case.symop) rm $case.symop
> if (-e ${scratch}$case.mme$updn) rm ${scratch}$case.mme$updn
> if (-e ${scratch}$case.symmat$updn) rm ${scratch}$case.symmat$updn
> if (-e ${scratch}$case.mommat2$updn) rm ${scratch}$case.mommat2$updn
> if (-e ${scratch}$case.mat_diag$updn) rm ${scratch}$case.mat_diag$updn
> touch ${scratch}$case.symmat$updn
> touch ${scratch}$case.mommat2$updn
> touch ${scratch}$case.mat_diag$updn
> touch ${scratch}$case.mme$updn
>
> mv $case.symop_1 $case.symop
> rm $case.symop_*
> if( "$hf" != "hf" ) then
> opticcopy_lapw
> endif
>
> set i = 1
> while ($i <= $maxproc)
> if ( $i == 1 ) then
> # testinput $case.symmat_$i$updn scratchwarning
> cat ${scratch}$case.symmat_$i$updn > ${scratch}$case.symmat$updn
> cat ${scratch}$case.symma1_${i}$updn > ${scratch}$case.symma1$updn
> cat ${scratch}$case.symma2_${i}$updn > ${scratch}$case.symma2$updn
> if (-e ${scratch}$case.mommat2_$i$updn) then
> cat ${scratch}$case.mommat2_$i$updn > ${scratch}$case.mommat2$updn
> endif
> cat ${scratch}$case.mat_diag_$i$updn > ${scratch}$case.mat_diag$updn
> cat ${scratch}$case.mme_$i$updn > ${scratch}$case.mme$updn
> else
> tail -n +2 ${scratch}$case.symmat_$i$updn >>
> ${scratch}$case.symmat$updn
> tail -n +2 ${scratch}$case.symma1_${i}$updn >>
> ${scratch}$case.symma1$updn
> tail -n +2 ${scratch}$case.symma2_${i}$updn >>
> ${scratch}$case.symma2$updn
> if (-e ${scratch}$case.mommat2_$i$updn) then
> tail -n +2 ${scratch}$case.mommat2_$i$updn >>
> ${scratch}$case.mommat2$updn
> endif
> tail -n +2 ${scratch}$case.mat_diag_$i$updn >>
> ${scratch}$case.mat_diag$updn
> tail -n +2 ${scratch}$case.mme_$i$updn >> ${scratch}$case.mme$updn
> endif
> rm ${scratch}$case.symmat_$i$updn
> rm -f ${scratch}$case.mommat2_$i$updn
> rm ${scratch}$case.mat_diag_$i$updn
> rm ${scratch}$case.mme_$i$updn
> @ i ++
> end
>
> echo "<- "done at `date` >>$log
> echo
> "-----------------------------------------------------------------">>$log
> rm $def.error
> #rm .in.tmp .in.tmp1
> touch $def.error
> rm $tmp* >&/dev/null
> rm .optic${cmplx}para.$$.`hostname` >&/dev/null
> echo "DONE" >.opticpara
> exit 0
>
> single:
> echo "running in single mode"
> $exe $def.def
> rm $tmp* >&/dev/null
> rm .optic${cmplx}para.$$.`hostname` >&/dev/null
> exit 0
>
> scratchwarning:
> echo "Could not find $case.symmat_$i$updn , which is probably because you
> used a scratch directory $SCRATCH"
> echo "Copy these files from the remote machines and concatenate them
> yourself"
> echo "with commands like (for all your parallel calculations i):"
> echo " cat $case.symmat_"'$i'"$updn >> $case.symmat$updn when $i
> =1a "
> echo " tail -n +2 $case.symmat_"'$i'"$updn >> $case.symmat$updn else"
> exit 1
>
> error:
> echo "** " OPTIC crashed!
> echo "** " OPTIC crashed at `date`>>$log
> echo "** " check ERROR FILES! >>$log
> echo
> "-----------------------------------------------------------------">>$log
> echo "** " Error in Parallel OPTIC >>$def.error
> rm $tmp* >&/dev/null
> rm .optic${cmplx}para.$$.`hostname` >&/dev/null
> echo "ERROR" >.opticpara
> exit 1
>
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