Latest revision as of 06:26, 11 September 2020

see also Get_your_own_copy_of_WikiData - this was the seventh attempt after five failures and one success with a truthy datset. The main success factor was to use a 4 TB SSD disk which was kindly supplied by the ConfIDent project

Environment

Mac Pro Mid 2010
12 core 3.46 GHz
64 GB RAM
macOS High Sierra 10.13.6
Source Disk: 4 TB 7200 rpm hard disk WD Gold WDC WD4002FYYZ Blackmagic speed rating: 175 MB/s write 175 MB/s read
Target Disk: 4 TB SSD Samsung 860 EVO Blackmagic speed rating: 257 MB/s write 270 MB/s read

java -version
openjdk version "11.0.5" 2019-10-15
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.5+10)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.5+10, mixed mode)

Summary

trying to replicate success story of https://issues.apache.org/jira/projects/JENA/issues/JENA-1909
download of 111 GB took some 7 h
unzipping to some 2030 GB took some 12 h 30
counting 13.9 billion lines took some 3 h 20
phased import of some 13.9 billion lines is in loading phase 2 (index) at some 13.6 billion lines after some 10 days phase 1 loading took 4.5 days phase 2 indexing is at day 5.5

Download and unpack

Downloading took some 7 h unpacking took some 12h 30

date;wget https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.nt.bz2;date
Sat Aug 15 17:47:23 CEST 2020
--2020-08-15 17:47:24--  https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.nt.bz2
Resolving dumps.wikimedia.org (dumps.wikimedia.org)... 2620::861:1:208:80:154:7, 208.80.154.7
Connecting to dumps.wikimedia.org (dumps.wikimedia.org)|2620::861:1:208:80:154:7|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 119725690213 (112G) [application/octet-stream]
Saving to: ‘latest-all.nt.bz2’
latest-all.nt.bz2           0%[                                    ]  34.15M  4.61MB/s    eta 6h 58m 
...
latest-all.nt.bz2         100%[===================================>] 111.50G  4.88MB/s    in  6h 49m  
2020-08-16 00:37:06 (4.64 MB/s) - ‘latest-all.nt.bz2’ saved [119725690213/119725690213]
Sun Aug 16 00:37:06 CEST 2020
date;bzip2 -dk latest-all.nt.bz2;date
Sun Aug 16 07:02:30 CEST 2020
Sun Aug 16 19:37:34 CEST 2020
ls -l latest-all.nt
-rw-r--r--  1 wf  admin  2180458524345 Aug 13 20:22 latest-all.nt

Count lines

date;wc -l latest-all.nt;date
Mon Aug 17 07:49:38 CEST 2020
 13854100336 latest-all.nt
Mon Aug 17 11:07:07 CEST 2020

Start and progress

egrep "000\.000\.000" -A1  tdb2-err.log

nohup ./wikidata2jena&
tail -f tdb2-err.log 
19:54:45 INFO  loader          :: Loader = LoaderPhased
19:54:45 INFO  loader          :: Start: latest-all.nt
19:54:50 INFO  loader          :: Add: 500.000 latest-all.nt (Batch: 95.474 / Avg: 95.474)
19:54:53 INFO  loader          :: Add: 1.000.000 latest-all.nt (Batch: 186.846 / Avg: 126.374)
19:54:55 INFO  loader          :: Add: 1.500.000 latest-all.nt (Batch: 207.986 / Avg: 145.391)
19:54:58 INFO  loader          :: Add: 2.000.000 latest-all.nt (Batch: 166.500 / Avg: 150.150)
19:55:03 INFO  loader          :: Add: 2.500.000 latest-all.nt (Batch: 100.603 / Avg: 136.686)
19:55:08 INFO  loader          :: Add: 3.000.000 latest-all.nt (Batch: 100.745 / Avg: 129.015)
19:55:13 INFO  loader          :: Add: 3.500.000 latest-all.nt (Batch: 99.226 / Avg: 123.709)
19:55:18 INFO  loader          :: Add: 4.000.000 latest-all.nt (Batch: 99.383 / Avg: 120.037)
19:55:24 INFO  loader          :: Add: 4.500.000 latest-all.nt (Batch: 94.589 / Avg: 116.553)
19:55:29 INFO  loader          :: Add: 5.000.000 latest-all.nt (Batch: 89.269 / Avg: 113.096)
19:55:29 INFO  loader          ::   Elapsed: 44,21 seconds [2020/08/16 19:55:29 MESZ]
19:55:35 INFO  loader          :: Add: 5.500.000 latest-all.nt (Batch: 93.861 / Avg: 111.028)
...
22:02:30 INFO  loader          :: Add: 1.000.000.000 latest-all.nt (Batch: 103.199 / Avg: 130.468)
22:02:30 INFO  loader          ::   Elapsed: 7.664,71 seconds [2020/08/16 22:02:30 MESZ]
...
00:30:49 INFO  loader          :: Add: 2.000.000.000 latest-all.nt (Batch: 117.647 / Avg: 120.741)
00:30:49 INFO  loader          ::   Elapsed: 16.564,27 seconds [2020/08/17 00:30:49 MESZ]
--
03:00:51 INFO  loader          :: Add: 3.000.000.000 latest-all.nt (Batch: 112.688 / Avg: 117.341)
03:00:51 INFO  loader          ::   Elapsed: 25.566,39 seconds [2020/08/17 03:00:51 MESZ]
--
06:33:58 INFO  loader          :: Add: 4.000.000.000 latest-all.nt (Batch: 41.569 / Avg: 104.293)
06:33:58 INFO  loader          ::   Elapsed: 38.353,15 seconds [2020/08/17 06:33:58 MESZ]
...
18:15:56 INFO  loader          :: Add: 5.000.000.000 latest-all.nt (Batch: 26.435 / Avg: 62.134)
18:15:56 INFO  loader          ::   Elapsed: 80.471,07 seconds [2020/08/17 18:15:56 MESZ]
...
01:36:06 INFO  loader          :: Add: 6.000.000.000 latest-all.nt (Batch: 46.027 / Avg: 56.136)
01:36:06 INFO  loader          ::   Elapsed: 106.881,45 seconds [2020/08/18 01:36:06 MESZ]
...
07:45:01 INFO  loader          :: Add: 7.000.000.000 latest-all.nt (Batch: 40.769 / Avg: 54.257)
07:45:01 INFO  loader          ::   Elapsed: 129.015,49 seconds [2020/08/18 07:45:01 MESZ]
...
14:49:08 INFO  loader          :: Add: 8.000.000.000 latest-all.nt (Batch: 39.607 / Avg: 51.792)
14:49:08 INFO  loader          ::   Elapsed: 154.462,80 seconds [2020/08/18 14:49:08 MESZ]
...
23:42:25 INFO  loader          :: Add: 9.000.000.000 latest-all.nt (Batch: 30.543 / Avg: 48.267)
23:42:25 INFO  loader          ::   Elapsed: 186.460,13 seconds [2020/08/18 23:42:25 MESZ]
...
09:28:31 INFO  loader          :: Add: 10.000.000.000 latest-all.nt (Batch: 33.464 / Avg: 45.121)
09:28:31 INFO  loader          ::   Elapsed: 221.625,86 seconds [2020/08/19 09:28:31 MESZ]
...
20:20:57 INFO  loader          :: Add: 11.000.000.000 latest-all.nt (Batch: 26.867 / Avg: 42.182)
20:20:57 INFO  loader          ::   Elapsed: 260.772,17 seconds [2020/08/19 20:20:57 MESZ]
...
08:01:14 INFO  loader          :: Add: 12.000.000.000 latest-all.nt (Batch: 25.588 / Avg: 39.631)
08:01:14 INFO  loader          ::   Elapsed: 302.788,94 seconds [2020/08/20 08:01:14 MESZ]
...
20:38:09 INFO  loader          :: Add: 13.000.000.000 latest-all.nt (Batch: 24.601 / Avg: 37.334)
20:38:09 INFO  loader          ::   Elapsed: 348.203,59 seconds [2020/08/20 20:38:09 MESZ]
...
07:58:23 INFO  loader          :: Add: 13.850.000.000 latest-all.nt (Batch: 18.268 / Avg: 35.602)
07:58:23 INFO  loader          ::   Elapsed: 389.017,56 seconds [2020/08/21 07:58:23 MESZ]
--
08:12:49 INFO  loader          :: Add: 10.000.000 Index (Batch: 175.284 / Avg: 199.668)
08:12:49 INFO  loader          ::   Elapsed: 50,08 seconds [2020/08/21 08:12:49 MESZ]
--
08:22:19 INFO  loader          :: Add: 110.000.000 Index (Batch: 190.114 / Avg: 177.441)
08:22:19 INFO  loader          ::   Elapsed: 619,92 seconds [2020/08/21 08:22:19 MESZ]
...
11:32:39 INFO  loader          :: Add: 1.000.000.000 Index (Batch: 45.949 / Avg: 83.060)
11:32:39 INFO  loader          ::   Elapsed: 12.039,42 seconds [2020/08/21 11:32:39 MESZ]
...
06:36:51 INFO  loader          :: Add: 2.000.000.000 Index (Batch: 11.018 / Avg: 24.785)
06:36:51 INFO  loader          ::   Elapsed: 80.691,88 seconds [2020/08/22 06:36:51 MESZ]
...
19:31:22 INFO  loader          :: Add: 3.000.000.000 Index (Batch: 47.892 / Avg: 23.591)
19:31:22 INFO  loader          ::   Elapsed: 127.162,89 seconds [2020/08/22 19:31:22 MESZ]
...
06:57:00 INFO  loader          :: Add: 4.000.000.000 Index (Batch: 22.606 / Avg: 23.767)
06:57:00 INFO  loader          ::   Elapsed: 168.300,31 seconds [2020/08/23 06:57:00 MESZ]
...
15:02:37 INFO  loader          :: Add: 5.000.000.000 Index (Batch: 35.418 / Avg: 25.324)
15:02:37 INFO  loader          ::   Elapsed: 197.437,88 seconds [2020/08/23 15:02:37 MESZ]
...
23:55:44 INFO  loader          :: Add: 6.000.000.000 Index (Batch: 62.790 / Avg: 26.152)
23:55:44 INFO  loader          ::   Elapsed: 229.424,58 seconds [2020/08/23 23:55:44 MESZ]
...
07:56:25 INFO  loader          :: Add: 7.000.000.000 Index (Batch: 36.004 / Avg: 27.103)
07:56:25 INFO  loader          ::   Elapsed: 258.265,50 seconds [2020/08/24 07:56:25 MESZ]
...
15:16:24 INFO  loader          :: Add: 8.000.000.000 Index (Batch: 33.847 / Avg: 28.103)
15:16:24 INFO  loader          ::   Elapsed: 284.664,53 seconds [2020/08/24 15:16:24 MESZ]
...
23:47:53 INFO  loader          :: Add: 9.000.000.000 Index (Batch: 56.129 / Avg: 28.539)
23:47:53 INFO  loader          ::   Elapsed: 315.353,50 seconds [2020/08/24 23:47:53 MESZ]
...
07:46:36 INFO  loader          :: Add: 10.000.000.000 Index (Batch: 30.033 / Avg: 29.063)
07:46:36 INFO  loader          ::   Elapsed: 344.076,53 seconds [2020/08/25 07:46:36 MESZ]
...
16:00:04 INFO  loader          :: Add: 11.000.000.000 Index (Batch: 55.282 / Avg: 29.436)
16:00:04 INFO  loader          ::   Elapsed: 373.684,63 seconds [2020/08/25 16:00:04 MESZ]
...
01:35:49 INFO  loader          :: Add: 12.000.000.000 Index (Batch: 36.424 / Avg: 29.395)
01:35:50 INFO  loader          ::   Elapsed: 408.230,25 seconds [2020/08/26 01:35:49 MESZ]
...
11:17:08 INFO  loader          :: Add: 13.000.000.000 Index (Batch: 26.727 / Avg: 29.338)
11:17:08 INFO  loader          ::   Elapsed: 443.108,84 seconds [2020/08/26 11:17:08 MESZ]
...
16:55:00 INFO  loader          :: Add: 13.620.000.000 Index (Batch: 37.603 / Avg: 29.392)
16:55:00 INFO  loader          ::   Elapsed: 463.380,28 seconds [2020/08/26 16:55:00 MESZ]
...
17:25:28 INFO  loader          :: Time = 855.042,638 seconds : Triples = 13.854.100.336 : Rate = 16.203 /s

disk usage

At 13.6 billion indexed triples:

du -sm *
2002139	data
0	tmp

When finished:

du -sm data/
2003251	data/

Scripts

wikidata2jena

#!/bin/bash
# WF 2020-05-10

# global settings
jena=apache-jena-3.16.0
tgz=$jena.tar.gz
jenaurl=http://mirror.easyname.ch/apache/jena/binaries/$tgz
base=/Volumes/Torterra/wikidata2020-08-15
data=$base/data
tdbloader=$jena/bin/tdb2.tdbloader

getjena() {
# download
if [ ! -f $tgz ]
then
  echo "downloading $tgz from $jenaurl"
	wget $jenaurl
else
  echo "$tgz already downloaded"
fi
# unpack
if [ ! -d $jena ]
then
  echo "unpacking $jena from $tgz"
	tar xvzf $tgz
else
  echo "$jena already unpacked"
fi
# create data directory
if [ ! -d $data ]
then
  echo "creating $data directory"
  mkdir -p $data
else
  echo "$data directory already created"
fi
}

#
# show the given timestamp
#
timestamp() {
 local msg="$1"
 local ts=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
 echo "$msg at $ts"
}

#
# load data for the given data dir and input
#
loaddata() {
	local data="$1"
	local input="$2"
  timestamp "start loading $input to $data"
  $tdbloader --loc "$data" "$input" > tdb2-out.log 2> tdb2-err.log
	timestamp "finished loading $input to $data"
}

getjena
export TMPDIR=$base/tmp
if [ ! -d $TMPDIR ]
then
  echo "creating temporary directory $TMPDIR"
  mkdir $TMPDIR
else
  echo "using temporary directory $TMPDIR"
fi
loaddata $data latest-all.nt

check extract speed

./speed 
149 MB in 3 s =  49 MB/s = 172 GB/h
315/2014 GB (15 %) todo: 1699 GB
ETA 9.9 h

speed

#!/bin/bash
# WF 2020-08-16
# check extract speed

#
# check the speed of extraction
#
checkSpeed() {
  local l_secs="$1"
	local l_total="$2"
	totalgb=$(expr $l_total / 1024 / 1024 / 1024)
  first=$(du -sm latest-all.nt | cut -f1)
  sleep $l_secs 
  second=$(du -sm latest-all.nt | cut -f1)
  mbytes=$(expr $second - $first)
	mpersec=$(expr $mbytes / $l_secs)
	gperh=$(expr $mpersec \* 3600 / 1024)
	echo "$mbytes MB in $l_secs s =  $mpersec MB/s = $gperh GB/h"
	donegb=$(expr $second / 1024)
	todogb=$(expr $totalgb - $donegb)
	percent=$(expr $donegb \* 100 / $totalgb)
	eta=$(expr $todogb / $gperh)
	echo "$donegb/$totalgb GB ($percent %) todo: $todogb GB"
	awk -v todo=$todogb -v gperh=$gperh 'BEGIN { printf("ETA %.1f h\n",todo/gperh) }'
}

checkSpeed 3 2162713035569

Difference between revisions of "WikiData Import 2020-08-15"