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annotate bin/_ex1.sh @ 231:c48f859889da

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author Henry S. Thompson <ht@inf.ed.ac.uk>
date Thu, 29 Feb 2024 15:01:10 +0000
parents 668579197bec
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
parents:
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1 #!/bin/bash
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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2 # This runs on the compute nodes...
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668579197bec oops, 1.1 was half-modified, bogus
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3 # count http vs. https vs. english, chinese in parallel, taking input directly from /work/dc007/dc007/hst/results/$1/cdx_counts/xxx.tsv
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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5 N=$SLURM_JOB_NUM_NODES
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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6 n=$SLURM_NTASKS
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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7 c=$SLURM_CPUS_PER_TASK
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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8 nodename=$SLURMD_NODENAME
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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9 local=$SLURM_LOCALID
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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10 node=$SLURM_NODEID
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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11 task=$SLURM_PROCID
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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13 threadsPerTask=2
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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14 pjobs=$((c / $threadsPerTask))
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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16 cc=$1
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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17 resdir=$W/$USER/results/$cc/$2
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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18 srcdir=$W/hst/results/$cc/cdx_counts
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19 s1=$3
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20 sn=$4
2
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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22 echo $(date) task $n.$task on $nodename:$N.$node start
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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24 mkdir -p $resdir
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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25
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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26 doit () {
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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27 echo $(date) start $1 $task $PARALLEL_SEQ
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668579197bec oops, 1.1 was half-modified, bogus
Henry S. Thompson <ht@inf.ed.ac.uk>
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28 fgrep ' w ' $srcdir/$1.tsv | cut -f 3,4 | uniq -c | \
668579197bec oops, 1.1 was half-modified, bogus
Henry S. Thompson <ht@inf.ed.ac.uk>
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29 $W/shared/bin/uniq_merge.py > $resdir/ex1_$1.tsv
2
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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30 echo $(date) end $1 $task $PARALLEL_SEQ
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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31 }
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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33 export -f doit
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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34 export srcdir resdir task
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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36 seq $s1 $sn | while read i
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
parents:
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37 do if [ $((i % $n)) -eq $task ]
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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38 then printf '%03g\n' $i
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
parents:
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39 fi
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
parents:
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40 done | \
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
parents:
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41 parallel -j $pjobs doit '{}'
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
parents:
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43 echo $(date) task $n.$task on $nodename:$N.$node end
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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parents:
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