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annotate bin/_s2t.sh @ 2:b4801f5696b2

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compute node workers, see cirrus_home/bin repo for login node masters
author Henry S. Thompson <ht@inf.ed.ac.uk>
date Mon, 18 Jul 2022 19:22:42 +0100
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children f035d36cec45
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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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1 #!/bin/bash
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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2 # run cdx2tsv.py in parallel, taking input directly from cdx-00{000..299}.gz
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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4 N=$SLURM_JOB_NUM_NODES
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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5 n=$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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6 c=$SLURM_CPUS_PER_TASK
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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7 nodename=$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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8 local=$SLURM_LOCALID
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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9 node=$SLURM_NODEID
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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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11 tPerN=$((n / N))
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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13 task=$((local + (node * tPerN)))
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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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15 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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16 pjobs=$((c / $threadsPerTask))
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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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19 cc=$1
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
Henry S. Thompson <ht@inf.ed.ac.uk>
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20 resdir=$W/hst/results/$1/$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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21 s1=$3
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 sn=$4
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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 echo $(date) task $n.$task on $nodename:$N.$node start
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b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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26 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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27 mkdir -p /dev/shm/hst
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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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29 doit () { echo $(date) start $1 $task $PARALLEL_SEQ; uz /beegfs/common_crawl/$cc/cdx/warc/cdx-00$1.gz | python3 $WSHARED/bin/cdx2tsv.py '(filename,f.split("/",maxsplit=5)[3].split(".")[1])' '(filename,f.split("/",maxsplit=5)[4][0])' '(url,("1" if (f.split(":",maxsplit=1)[0]=="https") else "0"))' languages > /dev/shm/hst/$1.tsv; echo $(date) moving $1 $task $PARALLEL_SEQ ; mv /dev/shm/hst/$1.tsv $resdir; echo $(date) end $1 $task $PARALLEL_SEQ ;}
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
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31 export -f doit
b4801f5696b2 compute node workers, see cirrus_home/bin repo for login node masters
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32 export cc resdir n task
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
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34 seq $s1 $sn | while read i; do if [ $((i % $n)) -eq $task ]; then printf '%03g\n' $i; fi; done | \
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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35 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>
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37 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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