WikiData Import 2022-06-25
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retry with more disk space
| Import | |
|---|---|
| state | ✅ |
| url | https://wiki.bitplan.com/index.php/WikiData_Import_2022-06-25 |
| target | QLever |
| start | 2022-06-25 |
| end | 2022-06-27 |
| days | 1.1 |
| os | |
| cpu | Intel(R) Xeon(R) CPU E5-2670 v2 @ 2.50GHz |
| ram | 128 |
| triples | |
| comment | |
Context
see QLever/script as discussed in QLever Issue #562 for the script which makes reproducing this attempt easier.
see QLever Discussions for more details on this attempt series.
since the https://github.com/ad-freiburg/qlever-control now has an official "qlever" script we have rename the script that has the purpose to make the import attempts reproducible to qleverauto.
Beware of https://github.com/ad-freiburg/qlever-control/issues/4 - make sure ulimit -n is set!. This attempt had to be restarted since setting the value within a script did not work.
Preparations
see WikiData_Import_2022-06-24#Preparations
Wikidata data download
df
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sda1 3844660232 97397140 3551895876 3% /hd/seel
./qleverauto -wd
downloading wikidata lexemes:latest-lexemes.ttl.bz2 ... please wait typically 3min ...
wikidata lexemes download started at Sa 25. Jun 19:44:32 CEST 2022
--2022-06-25 19:44:32-- https://dumps.wikimedia.org/wikidatawiki/entities//latest-lexemes.ttl.bz2
Resolving dumps.wikimedia.org (dumps.wikimedia.org)... 2620:0:861:1:208:80:154:7, 208.80.154.7
Connecting to dumps.wikimedia.org (dumps.wikimedia.org)|2620:0:861:1:208:80:154:7|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 329141448 (314M) [application/octet-stream]
Saving to: ‘latest-lexemes.ttl.bz2’
latest-lexemes.ttl.bz2 10%[===> ] 34,29M 4,60MB/s eta 64s
...
latest-lexemes.ttl.bz2 100%[===========================================>] 313,89M 4,56MB/s in 70s
2022-06-25 19:45:43 (4,49 MB/s) - ‘latest-lexemes.ttl.bz2’ saved [329141448/329141448]
wikidata lexemes download finished at Sa 25. Jun 19:45:43 CEST 2022 after 71 seconds
downloading wikidata dump:latest-all.ttl.bz2 ... please wait typically 6hours ...
wikidata dump download started at Sa 25. Jun 19:45:43 CEST 2022
--2022-06-25 19:45:43-- https://dumps.wikimedia.org/wikidatawiki/entities//latest-all.ttl.bz2
Resolving dumps.wikimedia.org (dumps.wikimedia.org)... 2620:0:861:1:208:80:154:7, 208.80.154.7
Connecting to dumps.wikimedia.org (dumps.wikimedia.org)|2620:0:861:1:208:80:154:7|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 95427655992 (89G) [application/octet-stream]
Saving to: ‘latest-all.ttl.bz2’
latest-all.ttl.bz2 0%[ ] 50,66M 4,42MB/s eta 5h 38m
...
latest-all.ttl.bz2 100%[===========================================>] 88,87G 5,01MB/s in 5h 38m
2022-06-26 01:24:35 (4,48 MB/s) - ‘latest-all.ttl.bz2’ saved [95427655992/95427655992]
wikidata dump download finished at So 26. Jun 01:24:35 CEST 2022 after 20332 seconds
qleverauto environment checks
./qleverauto -v
qleverauto version : 1.29 $ : 2022/05/23 06:15:28 $
./qleverauto -e
needed software
docker → /usr/bin/docker ✅
top → /usr/bin/top ✅
df → /usr/bin/df ✅
jq → /usr/bin/jq ✅
lsb_release → /usr/bin/lsb_release ✅
free → /usr/bin/free ✅
operating system
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
docker version
Docker version 20.10.16, build aa7e414
memory
total used free shared buff/cache available
Mem: 125Gi 1,8Gi 30Gi 27Mi 93Gi 122Gi
Swap: 2,0Gi 57Mi 1,9Gi
diskspace
/dev/sdb5 116G 25G 86G 23% /
tmpfs 63G 16K 63G 1% /dev/shm
/dev/sda1 3,6T 183G 3,3T 6% /hd/seel
/dev/sdb1 511M 4,0K 511M 1% /boot/efi
soft ulimit for files
1048576
wikidata files and index settings
wikidata$ ls -l
total 93512520
-rw-rw-r-- 1 wf wf 95427655992 Jun 23 10:50 latest-all.ttl.bz2
-rw-rw-r-- 1 wf wf 329141448 Jun 25 01:28 latest-lexemes.ttl.bz2
-rw-rw-r-- 1 wf wf 1188 Jun 26 08:08 Qleverfile
drwxrwxr-x 2 wf wf 4096 Jun 24 10:09 RCS
wf@sun:/hd/seel/qlever/wikidata$ vi wikidata.settings.json
wf@sun:/hd/seel/qlever/wikidata$ rcsdiff ./Qleverfile
===================================================================
RCS file: ./RCS/Qleverfile,v
retrieving revision 1.3
diff -r1.3 ./Qleverfile
wf@sun:/hd/seel/qlever/wikidata$ rcsdiff ./wikidata.settings.json
===================================================================
RCS file: ./RCS/wikidata.settings.json,v
retrieving revision 1.2
diff -r1.2 ./wikidata.settings.json
Qleverfile
cat Qleverfile
# Qleverfile for folder /hd/seel/qlever
# Automatically created on Sa 21. Mai 09:09:41 CEST 2022.
# Modify or expand as you see fit.
# Indexer settings
DB = wikidata
RDF_FILES = "latest-all.ttl.bz2 latest-lexemes.ttl.bz2"
CAT_FILES = "bzcat ${RDF_FILES}"
WITH_TEXT = false
SETTINGS_JSON = '{ "languages-internal": ["en"], "prefixes-external": [ "<http://www.wikidata.org/entity/statement", "<http://www.wikidata.org/value", "<http://www.wikidata.org/reference" ], "locale": { "language": "en", "country": "US", "ignore-punctuation": true }, "ascii-prefixes-only": true, "num-triples-per-batch": 10000000 }'
# Server settings
HOSTNAME = sun.bitplan.com
SERVER_PORT = 7001
MEMORY_FOR_QUERIES = 10
CACHE_MAX_SIZE_GB = 5
CACHE_MAX_SIZE_GB_SINGLE_ENTRY = 1
CACHE_MAX_NUM_ENTRIES = 100
# QLever binaries
QLEVER_BIN_DIR = /hd/seel/qlever/qlever-code/build/
USE_DOCKER = false
QLEVER_DOCKER_IMAGE = adfreiburg/qlever
QLEVER_DOCKER_CONTAINER = qlever.must_specify
# QLever UI
QLEVERUI_PORT = 7000
QLEVERUI_DIR = qlever-ui
QLEVERUI_CONFIG = default
wikidata.settings.json
cat wikidata.settings.json
{
"languages-internal": ["en"],
"prefixes-external": [
"<http://www.wikidata.org/entity/statement",
"<http://www.wikidata.org/value",
"<http://www.wikidata.org/reference"
],
"locale": {
"language": "en",
"country": "US",
"ignore-punctuation": true
},
"ascii-prefixes-only": true,
"num-triples-per-batch" : 10000000
}
Indexer
Relevant part of qleverauto script
#
# build the wikidata index
#
wikidata_index() {
cd $QLEVER_HOME/wikidata
chmod o+w .
show_timing "creating wikidata index" "started"
# docker run -i --rm -v $QLEVER_HOME/qlever-indices/wikidata:/index --entrypoint bash $dockerimage -c "cd /index && bzcat latest-all.ttl.bz2 latest-lexemes.ttl.bz2 | IndexBuilderMain -F ttl -f - -l -i wikidata -s wikidata.settings.json | tee wikidata.index-log.txt"
. ../qlever-control/qlever
check_installed IndexBuilderMain
qlever index
show_timing "creating wikidata index" "finished"
}
Symbolic Link for IndexBuilder Main
~/bin$ ls -l IndexBuilderMain
lrwxrwxrwx 1 wf wf 50 Mai 22 17:47 IndexBuilderMain -> /hd/seel/qlever/qlever-code/build/IndexBuilderMain
which IndexBuilderMain
/home/wf/bin/IndexBuilderMain
start
ulimit -n 1000000
ulimit -a | grep '(-n)'
open files (-n) 1000000
nohup ./qleverauto -wi&
tail -f nohup.out
bzcat latest-all.ttl.bz2 latest-lexemes.ttl.bz2 | IndexBuilderMain -F ttl -K wikidata -f - -i wikidata -s wikidata.settings.json | tee wikidata.index-log.txt
2022-06-26 08:14:31.955 - INFO: QLever IndexBuilder, compiled on Jun 24 2022 09:48:21
2022-06-26 08:14:31.955 - INFO: You specified the input format: TTL
2022-06-26 08:14:31.956 - INFO: You specified "locale = en_US" and "ignore-punctuation = 1"
2022-06-26 08:14:31.956 - INFO: You specified "ascii-prefixes-only = true", which enables faster parsing for well-behaved TTL files
2022-06-26 08:14:31.956 - INFO: You specified "num-triples-per-batch = 10,000,000", choose a lower value if the index builder runs out of memory
2022-06-26 08:14:31.956 - INFO: Integers that cannot be represented by QLever will throw an exception (this is the default behavior)
2022-06-26 08:14:31.956 - INFO: Processing input triples from /dev/stdin ...
2022-06-26 08:16:54.205 - INFO: Input triples processed: 100,000,000
2022-06-26 08:19:03.563 - INFO: Input triples processed: 200,000,000
...
2022-06-27 04:05:48.950 - INFO: Creating a pair of index permutations ...
2022-06-27 06:00:17.967 - INFO: Statistics for SPO: #relations = 2,808,258,381, #blocks = 30,045, #triples = 23,623,846,556
2022-06-27 06:00:17.967 - INFO: Exchanging multiplicities for SPO and SOP ...
2022-06-27 06:42:31.181 - INFO: Writing meta data for SPO and SOP ...
2022-06-27 06:42:47.139 - INFO: Number of distinct patterns: 7,168,422
2022-06-27 06:42:47.143 - INFO: Number of subjects with pattern: 2,808,258,381 [all]
2022-06-27 06:42:47.143 - INFO: Total number of distinct subject-predicate pairs: 11,082,607,100
2022-06-27 06:42:47.143 - INFO: Average number of predicates per subject: 3.9
2022-06-27 06:42:47.145 - INFO: Average number of subjects per predicate: 236,545
2022-06-27 08:07:24.260 - INFO: Creating a pair of index permutations ...
2022-06-27 09:52:23.085 - INFO: Statistics for OSP: #relations = 3,179,186,092, #blocks = 39,688, #triples = 23,623,846,556
2022-06-27 09:52:23.101 - INFO: Statistics for OPS: #relations = 3,179,186,092, #blocks = 39,688, #triples = 23,623,846,556
2022-06-27 09:52:23.101 - INFO: Exchanging multiplicities for OSP and OPS ...
2022-06-27 10:39:15.273 - INFO: Writing meta data for OSP and OPS ...
2022-06-27 10:39:20.510 - INFO: Index build completed
Progress
