2024-09-09 09:20:09 +02:00
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Upgrade CGSpace to DSpace 7.6.2
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2024-09-30 06:56:53 +02:00
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Upgrade CGSpace to DSpace 7.6.2
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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/2024-09/" > September, 2024< / a > < / h2 >
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< time datetime = "2024-09-01T21:16:00-07:00" > Sun Sep 01, 2024< / time >
in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2024-09-01" > 2024-09-01< / h2 >
< ul >
< li > Upgrade CGSpace to DSpace 7.6.2< / li >
< / ul >
< h2 id = "2024-09-05" > 2024-09-05< / h2 >
< ul >
< li > Finalize work on migrating DSpace Angular from Yarn to NPM< / li >
< / ul >
< h2 id = "2024-09-06" > 2024-09-06< / h2 >
< ul >
< li > This morning Tomcat crashed due to an OOM kill:< / li >
< / ul >
< pre tabindex = "0" > < code > Sep 06 00:00:24 server systemd[1]: tomcat9.service: A process of this unit has been killed by the OOM killer.
Sep 06 00:00:25 server systemd[1]: tomcat9.service: Main process exited, code=killed, status=9/KILL
Sep 06 00:00:25 server systemd[1]: tomcat9.service: Failed with result ' oom-kill' .
< / code > < / pre > < ul >
< li > According to the system journal, it was a Node.js dspace-angular process that tried to allocate memory and failed, thus invoking the OOM killer< / li >
< li > Currently I see high memory usage in those processes:< / li >
< / ul >
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > $ pm2 status
< / span > < / span > < span style = "display:flex;" > < span > ┌────┬──────────────┬─────────────┬─────────┬─────────┬──────────┬────────┬──────┬───────────┬──────────┬──────────┬──────────┬──────────┐
< / span > < / span > < span style = "display:flex;" > < span > │ id │ name │ namespace │ version │ mode │ pid │ uptime │ ↺ │ status │ cpu │ mem │ user │ watching │
< / span > < / span > < span style = "display:flex;" > < span > ├────┼──────────────┼─────────────┼─────────┼─────────┼──────────┼────────┼──────┼───────────┼──────────┼──────────┼──────────┼──────────┤
< / span > < / span > < span style = "display:flex;" > < span > │ 0 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 994 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
< / span > < / span > < span style = "display:flex;" > < span > │ 1 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 1015 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
< / span > < / span > < span style = "display:flex;" > < span > │ 2 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 1029 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
< / span > < / span > < span style = "display:flex;" > < span > │ 3 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 1042 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
< / span > < / span > < span style = "display:flex;" > < span > └────┴──────────────┴─────────────┴─────────┴─────────┴──────────┴────────┴──────┴───────────┴──────────┴──────────┴──────────┴──────────┘
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > I bet if I look in the logs I’ d find some kind of heavy traffic on the frontend, causing high caching for Angular SSR< / li >
< / ul >
< h2 id = "2024-09-08" > 2024-09-08< / h2 >
< ul >
< li > Analyzing memory use in our DSpace hosts, which have 32GB of memory
< ul >
< li > Effective cache of PostgreSQL is estimated at 11GB, which seems way high since the database is only 2GB< / li >
< li > Realistically this should be how we adjust, with PostgreSQL using ~8GB (or less) and each dspace-angular process pinned at 2GB… < / li >
< / ul >
< / li >
< / ul >
< blockquote >
< p > Total - Solr - Tomcat Postgres - Nginx - Angular
31366 − × − − × − … < / p >
< / blockquote >
< ul >
< li > I put some of these changes in on DSpace Test and will monitor this week< / li >
< / ul >
2024-09-14 22:02:16 +02:00
< h2 id = "2024-09-10" > 2024-09-10< / h2 >
< ul >
< li > Some bot in South Africa made a ton of requests on the API and made the load hit the roof:< / li >
< / ul >
< pre tabindex = "0" > < code > # grep -E ' 10/Sep/2024:[10-11]' /var/log/nginx/api-access.log | awk ' {print $1}' | sort | uniq -c | sort -h
...
149720 102.182.38.90
< / code > < / pre > < ul >
< li > They are using several user agents so are obviously a bot:< / li >
< / ul >
< pre tabindex = "0" > < code > Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:130.0) Gecko/20100101 Firefox/130.0
Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:109.0) Gecko/20100101 Firefox/111.0
Mozilla/5.0 (Windows; U; Windows NT 6.1; rv:11.0) Gecko/20100101 Firefox/11.0
< / code > < / pre > < ul >
< li > I added them to the list of bot networks in nginx and the load went down< / li >
< / ul >
< h2 id = "2024-09-11" > 2024-09-11< / h2 >
< ul >
< li > Upgrade DSpace 7 Test to Ubuntu 24.04< / li >
< li > I did some minor maintenance to test dspace-statistics-api with Python 3.12
< ul >
< li > I tagged version 1.4.4 and released it on GitHub< / li >
< / ul >
< / li >
< / ul >
< h2 id = "2024-09-14" > 2024-09-14< / h2 >
< ul >
< li > Noticed a persistent higher than usual load on CGSpace and checked the server logs
< ul >
< li > Found some new data center subnets to block because they were making thousands of requests with normal user agents< / li >
< / ul >
< / li >
< li > I enabled HTTP/3 in nginx< / li >
< li > I enabled the SSR patch in Angular: < a href = "https://github.com/DSpace/dspace-angular/issues/3110" > https://github.com/DSpace/dspace-angular/issues/3110< / a > < / li >
< / ul >
2024-09-17 06:11:03 +02:00
< h2 id = "2024-09-16" > 2024-09-16< / h2 >
< ul >
< li > Experiment with the <!-- raw HTML omitted --> dspace-statistics-api-js<!-- raw HTML omitted --> on DSpace 7 Test
< ul >
< li > In the past it always caused Solr to run out of memory, but I increased Solr’ s heap from 2g to 3g and it runs without crashing< / li >
< li > I attached VisualVM to Solr with a 3g and 4g heap and iterated over 1260 pages of results in the dspace-statistics-api-js:< / li >
< / ul >
< / li >
< / ul >
< p > < img src = "/cgspace-notes/2024/09/2024-09-16-Solr-3g-heap.png" alt = "Solr with 3g heap" > < / p >
< p > < img src = "/cgspace-notes/2024/09/2024-09-16-Solr-4g-heap.png" alt = "Solr with 4g heap" > < / p >
2024-09-23 12:10:20 +02:00
< h2 id = "2024-09-23" > 2024-09-23< / h2 >
< ul >
< li > Upgrade PostgreSQL from version 14 to 15 on DSpace Test the same way I did last year:< / li >
< / ul >
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > # apt update
< / span > < / span > < span style = "display:flex;" > < span > # apt install postgresql-15
< / span > < / span > < span style = "display:flex;" > < span > # Update configs with Ansible
< / span > < / span > < span style = "display:flex;" > < span > # systemctl stop tomcat9
< / span > < / span > < span style = "display:flex;" > < span > # pg_ctlcluster < span style = "color:#ae81ff" > 14< / span > main stop
< / span > < / span > < span style = "display:flex;" > < span > # tar -cvzpf var-lib-postgresql-14.tar.gz /var/lib/postgresql/14
< / span > < / span > < span style = "display:flex;" > < span > # tar -cvzpf etc-postgresql-14.tar.gz /etc/postgresql/14
< / span > < / span > < span style = "display:flex;" > < span > # pg_ctlcluster < span style = "color:#ae81ff" > 15< / span > main stop
< / span > < / span > < span style = "display:flex;" > < span > # pg_dropcluster < span style = "color:#ae81ff" > 15< / span > main
< / span > < / span > < span style = "display:flex;" > < span > # pg_upgradecluster < span style = "color:#ae81ff" > 14< / span > main
< / span > < / span > < span style = "display:flex;" > < span > # pg_ctlcluster < span style = "color:#ae81ff" > 15< / span > main start
< / span > < / span > < span style = "display:flex;" > < span > ...
< / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" >
< / span > < / span > < / span > < span style = "display:flex;" > < span > < span style = "color:#960050;background-color:#1e0010" > < / span > ERROR: could not find function " xml_is_well_formed" in file " /usr/lib/postgresql/15/lib/pgxml.so"
< / span > < / span > < span style = "display:flex;" > < span > ERROR: function public.xml_is_well_formed(text) does not exist
< / span > < / span > < span style = "display:flex;" > < span > ERROR: could not find function " xml_is_well_formed" in file " /usr/lib/postgresql/15/lib/pgxml.so"
< / span > < / span > < span style = "display:flex;" > < span > ERROR: function public.xml_valid(text) does not exist
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > After that I < a href = "https://adamj.eu/tech/2021/04/13/reindexing-all-tables-after-upgrading-to-postgresql-13/" > re-indexed the database indexes< / a > using a query:< / li >
< / ul >
< div class = "highlight" > < pre tabindex = "0" style = "color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;" > < code class = "language-console" data-lang = "console" > < span style = "display:flex;" > < span > $ su - postgres
< / span > < / span > < span style = "display:flex;" > < span > $ cat /tmp/generate-reindex.sql
< / span > < / span > < span style = "display:flex;" > < span > SELECT ' REINDEX TABLE CONCURRENTLY ' || quote_ident(relname) || ' /*' || pg_size_pretty(pg_total_relation_size(C.oid)) || ' */;'
< / span > < / span > < span style = "display:flex;" > < span > FROM pg_class C
< / span > < / span > < span style = "display:flex;" > < span > LEFT JOIN pg_namespace N ON (N.oid = C.relnamespace)
< / span > < / span > < span style = "display:flex;" > < span > WHERE nspname = ' public'
< / span > < / span > < span style = "display:flex;" > < span > AND C.relkind = ' r'
< / span > < / span > < span style = "display:flex;" > < span > AND nspname !~ ' ^pg_toast'
< / span > < / span > < span style = "display:flex;" > < span > ORDER BY pg_total_relation_size(C.oid) ASC;
< / span > < / span > < span style = "display:flex;" > < span > $ psql dspace < /tmp/generate-reindex.sql > /tmp/reindex.sql
< / span > < / span > < span style = "display:flex;" > < span > $ < trim the extra stuff from /tmp/reindex.sql>
< / span > < / span > < span style = "display:flex;" > < span > $ psql dspace < /tmp/reindex.sql
< / span > < / span > < / code > < / pre > < / div > < ul >
< li > The database shrunk by 186MB!< / li >
< / ul >
2024-09-30 06:56:53 +02:00
< h2 id = "2024-09-29" > 2024-09-29< / h2 >
< ul >
< li > I upgraded the database on CGSpace to PostgreSQL 15< / li >
< / ul >
2024-09-09 09:20:09 +02:00
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< h4 > Recent Posts< / h4 >
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< li > < a href = "/cgspace-notes/2024-09/" > September, 2024< / a > < / li >
< li > < a href = "/cgspace-notes/2024-08/" > August, 2024< / a > < / li >
< li > < a href = "/cgspace-notes/2024-07/" > July, 2024< / a > < / li >
< li > < a href = "/cgspace-notes/2024-06/" > June, 2024< / a > < / li >
< li > < a href = "/cgspace-notes/2024-05/" > May, 2024< / a > < / li >
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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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