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I tried to test something on DSpace Test but noticed that it’ s down since god knows when
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Catalina logs at least show some memory errors yesterday:
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I tried to test something on DSpace Test but noticed that it’ s down since god knows when
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Catalina logs at least show some memory errors yesterday:
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< h1 class = "blog-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/" rel = "home" > CGSpace Notes< / a > < / h1 >
< p class = "lead blog-description" dir = "auto" > Documenting day-to-day work on the < a href = "https://cgspace.cgiar.org" > CGSpace< / a > repository.< / p >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-04/" > April, 2018< / a > < / h2 >
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< time datetime = "2018-04-01T16:13:54+02:00" > Sun Apr 01, 2018< / time >
in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/categories/notes/" rel = "category tag" > Notes< / a >
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< / header >
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< h2 id = "2018-04-01" > 2018-04-01< / h2 >
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< ul >
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< li > I tried to test something on DSpace Test but noticed that it’ s down since god knows when< / li >
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< li > Catalina logs at least show some memory errors yesterday:< / li >
< / ul >
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< pre tabindex = "0" > < code > Mar 31, 2018 10:26:42 PM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
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SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]]
java.lang.OutOfMemoryError: Java heap space
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Exception in thread " ContainerBackgroundProcessor[StandardEngine[Catalina]]" java.lang.OutOfMemoryError: Java heap space
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< / code > < / pre > < ul >
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< li > So this is getting super annoying< / li >
< li > I ran all system updates on DSpace Test and rebooted it< / li >
< li > For some reason Listings and Reports is not giving any results for any queries now… < / li >
< li > I posted a message on Yammer to ask if people are using the Duplicate Check step from the Metadata Quality Module< / li >
< li > Help Lili Szilagyi with a question about statistics on some CCAFS items< / li >
< / ul >
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< h2 id = "2018-04-04" > 2018-04-04< / h2 >
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< ul >
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< li > Peter noticed that there were still some old CRP names on CGSpace, because I hadn’ t forced the Discovery index to be updated after I fixed the others last week< / li >
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< li > For completeness I re-ran the CRP corrections on CGSpace:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p ' fuuu'
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Fixed 1 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH
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< / code > < / pre > < ul >
< li > Then started a full Discovery index:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ export JAVA_OPTS=' -Dfile.encoding=UTF-8 -Xmx1024m'
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$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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real 76m13.841s
user 8m22.960s
sys 2m2.498s
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< / code > < / pre > < ul >
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< li > Elizabeth from CIAT emailed to ask if I could help her by adding ORCID identifiers to all of Joseph Tohme’ s items< / li >
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< li > I used my < a href = "https://gist.githubusercontent.com/alanorth/a49d85cd9c5dea89cddbe809813a7050/raw/f67b6e45a9a940732882ae4bb26897a9b245ef31/add-orcid-identifiers-csv.py" > add-orcid-identifiers-csv.py< / a > script:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ ./add-orcid-identifiers-csv.py -i /tmp/jtohme-2018-04-04.csv -db dspace -u dspace -p ' fuuu'
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< / code > < / pre > < ul >
< li > The CSV format of < code > jtohme-2018-04-04.csv< / code > was:< / li >
< / ul >
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< pre tabindex = "0" > < code class = "language-csv" data-lang = "csv" > dc.contributor.author,cg.creator.id
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" Tohme, Joseph M." ,Joe Tohme: 0000-0003-2765-7101
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< / code > < / pre > < ul >
< li > There was a quoting error in my CRP CSV and the replacements for < code > Forests, Trees and Agroforestry< / code > got messed up< / li >
< li > So I fixed them and had to re-index again!< / li >
< li > I started preparing the git branch for the the DSpace 5.5→5.8 upgrade:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ git checkout -b 5_x-dspace-5.8 5_x-prod
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$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.8
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< / code > < / pre > < ul >
< li > I was prepared to skip some commits that I had cherry picked from the upstream < code > dspace-5_x< / code > branch when we did the DSpace 5.5 upgrade (see notes on 2016-10-19 and 2017-12-17):
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< ul >
< li > [DS-3246] Improve cleanup in recyclable components (upstream commit on dspace-5_x: 9f0f5940e7921765c6a22e85337331656b18a403)< / li >
< li > [DS-3250] applying patch provided by Atmire (upstream commit on dspace-5_x: c6fda557f731dbc200d7d58b8b61563f86fe6d06)< / li >
< li > bump up to latest minor pdfbox version (upstream commit on dspace-5_x: b5330b78153b2052ed3dc2fd65917ccdbfcc0439)< / li >
< li > DS-3583 Usage of correct Collection Array (#1731) (upstream commit on dspace-5_x: c8f62e6f496fa86846bfa6bcf2d16811087d9761)< / li >
< / ul >
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< / li >
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< li > … but somehow git knew, and didn’ t include them in my interactive rebase!< / li >
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< li > I need to send this branch to Atmire and also arrange payment (see < a href = "https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560" > ticket #560< / a > in their tracker)< / li >
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< li > Fix Sisay’ s SSH access to the new DSpace Test server (linode19)< / li >
2019-11-28 16:30:45 +01:00
< / ul >
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< h2 id = "2018-04-05" > 2018-04-05< / h2 >
2018-04-10 07:27:55 +02:00
< ul >
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< li > Fix Sisay’ s sudo access on the new DSpace Test server (linode19)< / li >
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< li > The reindexing process on DSpace Test took < em > forever< / em > yesterday:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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real 599m32.961s
user 9m3.947s
sys 2m52.585s
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< / code > < / pre > < ul >
< li > So we really should not use this Linode block storage for Solr< / li >
< li > Assetstore might be fine but would complicate things with configuration and deployment (ughhh)< / li >
< li > Better to use Linode block storage only for backup< / li >
< li > Help Peter with the GDPR compliance / reporting form for CGSpace< / li >
< li > DSpace Test crashed due to memory issues again:< / li >
< / ul >
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< pre tabindex = "0" > < code > # grep -c ' java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
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16
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< / code > < / pre > < ul >
< li > I ran all system updates on DSpace Test and rebooted it< / li >
< li > Proof some records on DSpace Test for Udana from IWMI< / li >
< li > He has done better with the small syntax and consistency issues but then there are larger concerns with not linking to DOIs, copying titles incorrectly, etc< / li >
2018-04-10 07:27:55 +02:00
< / ul >
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< h2 id = "2018-04-10" > 2018-04-10< / h2 >
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< ul >
< li > I got a notice that CGSpace CPU usage was very high this morning< / li >
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< li > Looking at the nginx logs, here are the top users today so far:< / li >
< / ul >
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< pre tabindex = "0" > < code > # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 10/Apr/2018" | awk ' {print $1}' | sort | uniq -c | sort -n | tail -n 10
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282 207.46.13.112
286 54.175.208.220
287 207.46.13.113
298 66.249.66.153
322 207.46.13.114
780 104.196.152.243
3994 178.154.200.38
4295 70.32.83.92
4388 95.108.181.88
7653 45.5.186.2
< / code > < / pre > < ul >
< li > 45.5.186.2 is of course CIAT< / li >
< li > 95.108.181.88 appears to be Yandex:< / li >
< / ul >
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< pre tabindex = "0" > < code > 95.108.181.88 - - [09/Apr/2018:06:34:16 +0000] " GET /bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg HTTP/1.1" 200 2638 " -" " Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)"
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< / code > < / pre > < ul >
< li > And for some reason Yandex created a lot of Tomcat sessions today:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ grep -c -E ' session_id=[A-Z0-9]{32}:ip_addr=95.108.181.88' dspace.log.2018-04-10
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4363
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< / code > < / pre > < ul >
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< li > 70.32.83.92 appears to be some harvester we’ ve seen before, but on a new IP< / li >
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< li > They are not creating new Tomcat sessions so there is no problem there< / li >
< li > 178.154.200.38 also appears to be Yandex, and is also creating many Tomcat sessions:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ grep -c -E ' session_id=[A-Z0-9]{32}:ip_addr=178.154.200.38' dspace.log.2018-04-10
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3982
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< / code > < / pre > < ul >
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< li > I’ m not sure why Yandex creates so many Tomcat sessions, as its user agent should match the Crawler Session Manager valve< / li >
< li > Let’ s try a manual request with and without their user agent:< / li >
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< / ul >
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< pre tabindex = "0" > < code > $ http --print Hh https://cgspace.cgiar.org/bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg ' User-Agent:Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)'
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GET /bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg HTTP/1.1
Accept: */*
Accept-Encoding: gzip, deflate
Connection: keep-alive
Host: cgspace.cgiar.org
User-Agent: Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)
HTTP/1.1 200 OK
Connection: keep-alive
Content-Language: en-US
Content-Length: 2638
Content-Type: image/jpeg;charset=ISO-8859-1
Date: Tue, 10 Apr 2018 05:18:37 GMT
Expires: Tue, 10 Apr 2018 06:18:37 GMT
Last-Modified: Tue, 25 Apr 2017 07:05:54 GMT
Server: nginx
Strict-Transport-Security: max-age=15768000
Vary: User-Agent
X-Cocoon-Version: 2.2.0
X-Content-Type-Options: nosniff
X-Frame-Options: SAMEORIGIN
X-XSS-Protection: 1; mode=block
$ http --print Hh https://cgspace.cgiar.org/bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg
GET /bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg HTTP/1.1
Accept: */*
Accept-Encoding: gzip, deflate
Connection: keep-alive
Host: cgspace.cgiar.org
User-Agent: HTTPie/0.9.9
HTTP/1.1 200 OK
Connection: keep-alive
Content-Language: en-US
Content-Length: 2638
Content-Type: image/jpeg;charset=ISO-8859-1
Date: Tue, 10 Apr 2018 05:20:08 GMT
Expires: Tue, 10 Apr 2018 06:20:08 GMT
Last-Modified: Tue, 25 Apr 2017 07:05:54 GMT
Server: nginx
Set-Cookie: JSESSIONID=31635DB42B66D6A4208CFCC96DD96875; Path=/; Secure; HttpOnly
Strict-Transport-Security: max-age=15768000
Vary: User-Agent
X-Cocoon-Version: 2.2.0
X-Content-Type-Options: nosniff
X-Frame-Options: SAMEORIGIN
X-XSS-Protection: 1; mode=block
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< / code > < / pre > < ul >
< li > So it definitely looks like Yandex requests are getting assigned a session from the Crawler Session Manager valve< / li >
< li > And if I look at the DSpace log I see its IP sharing a session with other crawlers like Google (66.249.66.153)< / li >
< li > Indeed the number of Tomcat sessions appears to be normal:< / li >
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< / ul >
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< p > < img src = "/cgspace-notes/2018/04/jmx_dspace_sessions-week.png" alt = "Tomcat sessions week" > < / p >
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< ul >
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< li > In other news, it looks like the number of total requests processed by nginx in March went down from the previous months:< / li >
< / ul >
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< pre tabindex = "0" > < code > # time zcat --force /var/log/nginx/* | grep -cE " [0-9]{1,2}/Mar/2018"
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2266594
real 0m13.658s
user 0m16.533s
sys 0m1.087s
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< / code > < / pre > < ul >
< li > In other other news, the database cleanup script has an issue again:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ dspace cleanup -v
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...
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Error: ERROR: update or delete on table " bitstream" violates foreign key constraint " bundle_primary_bitstream_id_fkey" on table " bundle"
Detail: Key (bitstream_id)=(151626) is still referenced from table " bundle" .
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< / code > < / pre > < ul >
< li > The solution is, as always:< / li >
< / ul >
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< pre tabindex = "0" > < code > $ psql dspace -c ' update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (151626);'
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UPDATE 1
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< / code > < / pre > < ul >
< li > Looking at abandoned connections in Tomcat:< / li >
< / ul >
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< pre tabindex = "0" > < code > # zcat /var/log/tomcat7/catalina.out.[1-9].gz | grep -c ' org.apache.tomcat.jdbc.pool.ConnectionPool abandon'
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2115
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< / code > < / pre > < ul >
< li > Apparently from these stacktraces we should be able to see which code is not closing connections properly< / li >
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< li > Here’ s a pretty good overview of days where we had database issues recently:< / li >
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< / ul >
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< pre tabindex = "0" > < code > # zcat /var/log/tomcat7/catalina.out.[1-9].gz | grep ' org.apache.tomcat.jdbc.pool.ConnectionPool abandon' | awk ' {print $1,$2, $3}' | sort | uniq -c | sort -n
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1 Feb 18, 2018
1 Feb 19, 2018
1 Feb 20, 2018
1 Feb 24, 2018
2 Feb 13, 2018
3 Feb 17, 2018
5 Feb 16, 2018
5 Feb 23, 2018
5 Feb 27, 2018
6 Feb 25, 2018
40 Feb 14, 2018
63 Feb 28, 2018
154 Mar 19, 2018
202 Feb 21, 2018
264 Feb 26, 2018
268 Mar 21, 2018
524 Feb 22, 2018
570 Feb 15, 2018
< / code > < / pre > < ul >
< li > In Tomcat 8.5 the < code > removeAbandoned< / code > property has been split into two: < code > removeAbandonedOnBorrow< / code > and < code > removeAbandonedOnMaintenance< / code > < / li >
< li > See: < a href = "https://tomcat.apache.org/tomcat-8.5-doc/jndi-datasource-examples-howto.html#Database_Connection_Pool_(DBCP_2)_Configurations" > https://tomcat.apache.org/tomcat-8.5-doc/jndi-datasource-examples-howto.html#Database_Connection_Pool_(DBCP_2)_Configurations< / a > < / li >
< li > I assume we want < code > removeAbandonedOnBorrow< / code > and make updates to the Tomcat 8 templates in Ansible< / li >
2020-01-27 15:20:44 +01:00
< li > After reading more documentation I see that Tomcat 8.5’ s default DBCP seems to now be Commons DBCP2 instead of Tomcat DBCP< / li >
< li > It can be overridden in Tomcat’ s < em > server.xml< / em > by setting < code > factory=" org.apache.tomcat.jdbc.pool.DataSourceFactory" < / code > in the < code > < Resource> < / code > < / li >
< li > I think we should use this default, so we’ ll need to remove some other settings that are specific to Tomcat’ s DBCP like < code > jdbcInterceptors< / code > and < code > abandonWhenPercentageFull< / code > < / li >
2019-11-28 16:30:45 +01:00
< li > Merge the changes adding ORCID identifier to advanced search and Atmire Listings and Reports (< a href = "https://github.com/ilri/DSpace/pull/371" > #371< / a > )< / li >
< li > Fix one more issue of missing XMLUI strings (for CRP subject when clicking “ view more” in the Discovery sidebar)< / li >
< li > I told Udana to fix the citation and abstract of the one item, and to correct the < code > dc.language.iso< / code > for the five Spanish items in his Book Chapters collection< / li >
< li > Then we can import the records to CGSpace< / li >
2018-04-12 10:43:49 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-11" > 2018-04-11< / h2 >
2018-04-12 10:43:49 +02:00
< ul >
2019-11-28 16:30:45 +01:00
< li > DSpace Test (linode19) crashed again some time since yesterday:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # grep -c ' java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
2018-04-12 10:43:49 +02:00
168
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > I ran all system updates and rebooted the server< / li >
2018-04-12 10:43:49 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-12" > 2018-04-12< / h2 >
2018-04-12 10:43:49 +02:00
< ul >
< li > I caught wind of an interesting XMLUI performance optimization coming in DSpace 6.3: < a href = "https://jira.duraspace.org/browse/DS-3883" > https://jira.duraspace.org/browse/DS-3883< / a > < / li >
< li > I asked for it to be ported to DSpace 5.x< / li >
2018-04-10 10:33:36 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-13" > 2018-04-13< / h2 >
2018-04-13 19:24:30 +02:00
< ul >
< li > Add < code > PII-LAM_CSAGender< / code > to CCAFS Phase II project tags in < code > input-forms.xml< / code > < / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-15" > 2018-04-15< / h2 >
2018-04-15 09:20:44 +02:00
< ul >
2019-11-28 16:30:45 +01:00
< li > While testing an XMLUI patch for < a href = "https://jira.duraspace.org/browse/DS-3883" > DS-3883< / a > I noticed that there is still some remaining Authority / Solr configuration left that we need to remove:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > 2018-04-14 18:55:25,841 ERROR org.dspace.authority.AuthoritySolrServiceImpl @ Authority solr is not correctly configured, check " solr.authority.server" property in the dspace.cfg
2018-04-15 09:20:44 +02:00
java.lang.NullPointerException
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > I assume we need to remove < code > authority< / code > from the consumers in < code > dspace/config/dspace.cfg< / code > :< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > event.dispatcher.default.consumers = authority, versioning, discovery, eperson, harvester, statistics,batchedit, versioningmqm
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > I see the same error on DSpace Test so this is definitely a problem< / li >
< li > After disabling the authority consumer I no longer see the error< / li >
< li > I merged a pull request to the < code > 5_x-prod< / code > branch to clean that up (< a href = "https://github.com/ilri/DSpace/pull/372" > #372< / a > )< / li >
2020-01-27 15:20:44 +01:00
< li > File a ticket on DSpace’ s Jira for the < code > target=" _blank" < / code > security and performance issue (< a href = "https://jira.duraspace.org/browse/DS-3891" > DS-3891< / a > )< / li >
2019-11-28 16:30:45 +01:00
< li > I re-deployed DSpace Test (linode19) and was surprised by how long it took the ant update to complete:< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > BUILD SUCCESSFUL
2018-04-15 10:18:17 +02:00
Total time: 4 minutes 12 seconds
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > The Linode block storage is much slower than the instance storage< / li >
< li > I ran all system updates and rebooted DSpace Test (linode19)< / li >
2018-04-15 09:20:44 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-16" > 2018-04-16< / h2 >
2018-04-16 11:10:44 +02:00
< ul >
< li > Communicate with Bioversity about their project to migrate their e-Library (Typo3) and Sci-lit databases to CGSpace< / li >
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-18" > 2018-04-18< / h2 >
2018-04-18 11:38:12 +02:00
< ul >
< li > IWMI people are asking about building a search query that outputs RSS for their reports< / li >
< li > They want the same results as this Discovery query: < a href = "https://cgspace.cgiar.org/discover?filtertype_1=dateAccessioned&filter_relational_operator_1=contains&filter_1=2018&submit_apply_filter=&query=&scope=10568%2F16814&rpp=100&sort_by=dc.date.issued_dt&order=desc" > https://cgspace.cgiar.org/discover?filtertype_1=dateAccessioned& filter_relational_operator_1=contains& filter_1=2018& submit_apply_filter=& query=& scope=10568%2F16814& rpp=100& sort_by=dc.date.issued_dt& order=desc< / a > < / li >
2020-01-27 15:20:44 +01:00
< li > They will need to use OpenSearch, but I can’ t remember all the parameters< / li >
2019-11-28 16:30:45 +01:00
< li > Apparently search sort options for OpenSearch are in < code > dspace.cfg< / code > :< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > webui.itemlist.sort-option.1 = title:dc.title:title
2018-04-18 11:38:12 +02:00
webui.itemlist.sort-option.2 = dateissued:dc.date.issued:date
webui.itemlist.sort-option.3 = dateaccessioned:dc.date.accessioned:date
webui.itemlist.sort-option.4 = type:dc.type:text
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > They want items by issue date, so we need to use sort option 2< / li >
< li > According to the DSpace Manual there are only the following parameters to OpenSearch: format, scope, rpp, start, and sort_by< / li >
< li > The OpenSearch < code > query< / code > parameter expects a Discovery search filter that is defined in < code > dspace/config/spring/api/discovery.xml< / code > < / li >
< li > So for IWMI they should be able to use something like this: < a href = "https://cgspace.cgiar.org/open-search/discover?query=dateIssued:2018&scope=10568/16814&sort_by=2&order=DESC&format=rss" > https://cgspace.cgiar.org/open-search/discover?query=dateIssued:2018& scope=10568/16814& sort_by=2& order=DESC& format=rss< / a > < / li >
< li > There are also < code > rpp< / code > (results per page) and < code > start< / code > parameters but in my testing now on DSpace 5.5 they behave very strangely< / li >
< li > For example, set < code > rpp=1< / code > and then check the results for < code > start< / code > values of 0, 1, and 2 and they are all the same!< / li >
< li > If I have time I will check if this behavior persists on DSpace 6.x on the official DSpace demo and file a bug< / li >
< li > Also, the DSpace Manual as of 5.x has very poor documentation for OpenSearch< / li >
2020-01-27 15:20:44 +01:00
< li > They don’ t tell you to use Discovery search filters in the < code > query< / code > (with format < code > query=dateIssued:2018< / code > )< / li >
< li > They don’ t tell you that the sort options are actually defined in < code > dspace.cfg< / code > (ie, you need to use < code > 2< / code > instead of < code > dc.date.issued_dt< / code > )< / li >
2019-11-28 16:30:45 +01:00
< li > They are missing the < code > order< / code > parameter (ASC vs DESC)< / li >
< li > I notice that DSpace Test has crashed again, due to memory:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # grep -c ' java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
2018-04-18 11:38:12 +02:00
178
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
2020-01-27 15:20:44 +01:00
< li > I will increase the JVM heap size from 5120M to 6144M, though we don’ t have much room left to grow as DSpace Test (linode19) is using a smaller instance size than CGSpace< / li >
2019-11-28 16:30:45 +01:00
< li > Gabriela from CIP asked if I could send her a list of all CIP authors so she can do some replacements on the name formats< / li >
< li > I got a list of all the CIP collections manually and use the same query that I used in < a href = "/cgspace-notes/2017-08" > August, 2017< / a > :< / li >
2019-05-05 15:45:12 +02:00
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > dspace#= \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = ' contributor' and qualifier = ' author' ) AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in (' 10568/89347' , ' 10568/88229' , ' 10568/53086' , ' 10568/53085' , ' 10568/69069' , ' 10568/53087' , ' 10568/53088' , ' 10568/53089' , ' 10568/53090' , ' 10568/53091' , ' 10568/53092' , ' 10568/70150' , ' 10568/53093' , ' 10568/64874' , ' 10568/53094' ))) group by text_value order by count desc) to /tmp/cip-authors.csv with csv;
2019-12-17 13:49:24 +01:00
< / code > < / pre > < h2 id = "2018-04-19" > 2018-04-19< / h2 >
2018-04-19 10:04:36 +02:00
< ul >
< li > Run updates on DSpace Test (linode19) and reboot the server< / li >
2019-11-28 16:30:45 +01:00
< li > Also try deploying updated GeoLite database during ant update while re-deploying code:< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > $ ant update update_geolite clean_backups
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > I also re-deployed CGSpace (linode18) to make the ORCID search, authority cleanup, CCAFS project tag < code > PII-LAM_CSAGender< / code > live< / li >
< li > When re-deploying I also updated the GeoLite databases so I hope the country stats become more accurate… < / li >
< li > After re-deployment I ran all system updates on the server and rebooted it< / li >
< li > After the reboot I forced a reïndexing of the Discovery to populate the new ORCID index:< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > $ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
2018-04-19 13:28:16 +02:00
real 73m42.635s
user 8m15.885s
sys 2m2.687s
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > This time is with about 70,000 items in the repository< / li >
2018-04-19 11:40:52 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-20" > 2018-04-20< / h2 >
2018-04-20 21:24:48 +02:00
< ul >
2020-01-27 15:20:44 +01:00
< li > Gabriela from CIP emailed to say that CGSpace was returning a white page, but I haven’ t seen any emails from UptimeRobot< / li >
< li > I confirm that it’ s just giving a white page around 4:16< / li >
2019-11-28 16:30:45 +01:00
< li > The DSpace logs show that there are no database connections:< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-715] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:250; busy:18; idle:0; lastwait:5000].
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > And there have been shit tons of errors in the last (starting only 20 minutes ago luckily):< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # grep -c ' org.apache.tomcat.jdbc.pool.PoolExhaustedException' /home/cgspace.cgiar.org/log/dspace.log.2018-04-20
2018-04-20 21:24:48 +02:00
32147
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
2020-01-27 15:20:44 +01:00
< li > I can’ t even log into PostgreSQL as the < code > postgres< / code > user, WTF?< / li >
2019-11-28 16:30:45 +01:00
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > $ psql -c ' select * from pg_stat_activity' | grep -o -E ' (dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
2018-04-20 21:24:48 +02:00
^C
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Here are the most active IPs today:< / li >
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 20/Apr/2018" | awk ' {print $1}' | sort | uniq -c | sort -n | tail -n 10
2019-11-28 16:30:45 +01:00
917 207.46.13.182
935 213.55.99.121
970 40.77.167.134
978 207.46.13.80
1422 66.249.64.155
1577 50.116.102.77
2456 95.108.181.88
3216 104.196.152.243
4325 70.32.83.92
10718 45.5.184.2
< / code > < / pre > < ul >
2020-01-27 15:20:44 +01:00
< li > It doesn’ t even seem like there is a lot of traffic compared to the previous days:< / li >
2019-11-28 16:30:45 +01:00
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 20/Apr/2018" | wc -l
2018-04-20 21:24:48 +02:00
74931
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/*.log.1 /var/log/nginx/*.log.2.gz| grep -E " 19/Apr/2018" | wc -l
2018-04-20 21:24:48 +02:00
91073
2022-03-04 13:30:06 +01:00
# zcat --force /var/log/nginx/*.log.2.gz /var/log/nginx/*.log.3.gz| grep -E " 18/Apr/2018" | wc -l
2018-04-20 21:24:48 +02:00
93459
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > I tried to restart Tomcat but < code > systemctl< / code > hangs< / li >
2020-01-27 15:20:44 +01:00
< li > I tried to reboot the server from the command line but after a few minutes it didn’ t come back up< / li >
2019-11-28 16:30:45 +01:00
< li > Looking at the Linode console I see that it is stuck trying to shut down< / li >
2020-01-27 15:20:44 +01:00
< li > Even “ Reboot” via Linode console doesn’ t work!< / li >
2019-11-28 16:30:45 +01:00
< li > After shutting it down a few times via the Linode console it finally rebooted< / li >
< li > Everything is back but I have no idea what caused this—I suspect something with the hosting provider< / li >
< li > Also super weird, the last entry in the DSpace log file is from < code > 2018-04-20 16:35:09< / code > , and then immediately it goes to < code > 2018-04-20 19:15:04< / code > (three hours later!):< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > 2018-04-20 16:35:09,144 ERROR org.dspace.app.util.AbstractDSpaceWebapp @ Failed to record shutdown in Webapp table.
2018-04-20 21:24:48 +02:00
org.apache.tomcat.jdbc.pool.PoolExhaustedException: [localhost-startStop-2] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:250; busy:18; idle
:0; lastwait:5000].
2019-11-28 16:30:45 +01:00
at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:685)
at org.apache.tomcat.jdbc.pool.ConnectionPool.getConnection(ConnectionPool.java:187)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.getConnection(DataSourceProxy.java:128)
at org.dspace.storage.rdbms.DatabaseManager.getConnection(DatabaseManager.java:632)
at org.dspace.core.Context.init(Context.java:121)
at org.dspace.core.Context.< init> (Context.java:95)
at org.dspace.app.util.AbstractDSpaceWebapp.deregister(AbstractDSpaceWebapp.java:97)
at org.dspace.app.util.DSpaceContextListener.contextDestroyed(DSpaceContextListener.java:146)
at org.apache.catalina.core.StandardContext.listenerStop(StandardContext.java:5115)
at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5779)
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:224)
at org.apache.catalina.core.ContainerBase$StopChild.call(ContainerBase.java:1588)
at org.apache.catalina.core.ContainerBase$StopChild.call(ContainerBase.java:1577)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
2018-04-20 21:24:48 +02:00
2018-04-20 19:15:04,006 INFO org.dspace.core.ConfigurationManager @ Loading from classloader: file:/home/cgspace.cgiar.org/config/dspace.cfg
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Very suspect!< / li >
2018-04-20 21:24:48 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-24" > 2018-04-24< / h2 >
2018-04-24 15:38:05 +02:00
< ul >
2020-01-27 15:20:44 +01:00
< li > Testing my Ansible playbooks with a clean and updated installation of Ubuntu 18.04 and I fixed some issues that I hadn’ t run into a few weeks ago< / li >
2018-04-24 15:38:05 +02:00
< li > There seems to be a new issue with Java dependencies, though< / li >
< li > The < code > default-jre< / code > package is going to be Java 10 on Ubuntu 18.04, but I want to use < code > openjdk-8-jre-headless< / code > (well, the JDK actually, but it uses this JRE)< / li >
< li > Tomcat and Ant are fine with Java 8, but the < code > maven< / code > package wants to pull in Java 10 for some reason< / li >
< li > Looking closer, I see that < code > maven< / code > depends on < code > java7-runtime-headless< / code > , which is indeed provided by < code > openjdk-8-jre-headless< / code > < / li >
2020-01-27 15:20:44 +01:00
< li > So it must be one of Maven’ s dependencies… < / li >
< li > I will watch it for a few days because it could be an issue that will be resolved before Ubuntu 18.04’ s release< / li >
2018-04-24 15:38:05 +02:00
< li > Otherwise I will post a bug to the ubuntu-release mailing list< / li >
2018-04-25 12:15:38 +02:00
< li > Looks like the only way to fix this is to install < code > openjdk-8-jdk-headless< / code > before (so it pulls in the JRE) in a separate transaction, or to manually install < code > openjdk-8-jre-headless< / code > in the same apt transaction as < code > maven< / code > < / li >
2018-04-24 15:53:28 +02:00
< li > Also, I started porting PostgreSQL 9.6 into the Ansible infrastructure scripts< / li >
< li > This should be a drop in I believe, though I will definitely test it more locally as well as on DSpace Test once we move to DSpace 5.8 and Ubuntu 18.04 in the coming months< / li >
2018-04-24 15:38:05 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-25" > 2018-04-25< / h2 >
2018-04-25 12:15:38 +02:00
< ul >
< li > Still testing the < a href = "https://github.com/ilri/rmg-ansible-public" > Ansible infrastructure playbooks< / a > for Ubuntu 18.04, Tomcat 8.5, and PostgreSQL 9.6< / li >
< li > One other new thing I notice is that PostgreSQL 9.6 no longer uses < code > createuser< / code > and < code > nocreateuser< / code > , as those have actually meant < code > superuser< / code > and < code > nosuperuser< / code > and have been deprecated for < em > ten years< / em > < / li >
2020-01-27 15:20:44 +01:00
< li > So for my notes, when I’ m importing a CGSpace database dump I need to amend my notes to give super user permission to a user, rather than create user:< / li >
2019-11-28 16:30:45 +01:00
< / ul >
2022-03-04 13:30:06 +01:00
< pre tabindex = "0" > < code > $ psql dspacetest -c ' alter user dspacetest superuser;'
2018-04-25 12:15:38 +02:00
$ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-18.backup
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
2020-01-27 15:20:44 +01:00
< li > There’ s another issue with Tomcat in Ubuntu 18.04:< / li >
2019-11-28 16:30:45 +01:00
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code > 25-Apr-2018 13:26:21.493 SEVERE [http-nio-127.0.0.1-8443-exec-1] org.apache.coyote.AbstractProtocol$ConnectionHandler.process Error reading request, ignored
2019-11-28 16:30:45 +01:00
java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer;
at org.apache.coyote.http11.Http11InputBuffer.init(Http11InputBuffer.java:688)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:672)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
< / code > < / pre > < ul >
2020-01-27 15:20:44 +01:00
< li > There’ s a < a href = "https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=895866" > Debian bug about this from a few weeks ago< / a > < / li >
< li > Apparently Tomcat was compiled with Java 9, so doesn’ t work with Java 8< / li >
2018-04-29 11:36:13 +02:00
< / ul >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-29" > 2018-04-29< / h2 >
2018-04-29 11:36:13 +02:00
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< li > DSpace Test crashed again, looks like memory issues again< / li >
2020-01-27 15:20:44 +01:00
< li > JVM heap size was last increased to 6144m but the system only has 8GB total so there’ s not much we can do here other than get a bigger Linode instance or remove the massive Solr Statistics data< / li >
2018-04-29 11:36:13 +02:00
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2019-12-17 13:49:24 +01:00
< h2 id = "2018-04-30" > 2018-04-30< / h2 >
2018-04-30 17:45:30 +02:00
< ul >
< li > DSpace Test crashed again< / li >
< li > I will email the CGSpace team to ask them whether or not we want to commit to having a public test server that accurately mirrors CGSpace (ie, to upgrade to the next largest Linode)< / li >
< / ul >
2018-04-01 16:21:58 +02:00
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< h4 > Recent Posts< / h4 >
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2022-08-01 15:36:13 +02:00
< li > < a href = "/cgspace-notes/2022-08/" > August, 2022< / a > < / li >
2022-07-04 08:25:14 +02:00
< li > < a href = "/cgspace-notes/2022-07/" > July, 2022< / a > < / li >
2022-06-06 08:45:43 +02:00
< li > < a href = "/cgspace-notes/2022-06/" > June, 2022< / a > < / li >
2022-05-04 10:09:45 +02:00
< li > < a href = "/cgspace-notes/2022-05/" > May, 2022< / a > < / li >
2022-04-27 08:58:45 +02:00
< li > < a href = "/cgspace-notes/2022-04/" > April, 2022< / a > < / li >
2022-03-01 15:48:40 +01:00
2018-04-01 16:21:58 +02:00
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< h4 > Links< / h4 >
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< li > < a href = "https://cgspace.cgiar.org" > CGSpace< / a > < / li >
< li > < a href = "https://dspacetest.cgiar.org" > DSpace Test< / a > < / li >
< li > < a href = "https://github.com/ilri/DSpace" > CGSpace @ GitHub< / a > < / li >
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2019-10-11 10:19:42 +02:00
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2018-04-01 16:21:58 +02:00
Blog template created by < a href = "https://twitter.com/mdo" > @mdo< / a > , ported to Hugo by < a href = 'https://twitter.com/mralanorth' > @mralanorth< / a > .
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