diff --git a/content/posts/2018-12.md b/content/posts/2018-12.md index f47bbcd02..92b18a812 100644 --- a/content/posts/2018-12.md +++ b/content/posts/2018-12.md @@ -485,4 +485,41 @@ UPDATE 1 - After all that I started a full Discovery reindex to get the index name changes and rights updates +## 2018-12-29 + +- CGSpace went down today for a few minutes while I was at dinner and I quickly restarted Tomcat +- The top IP addresses as of this evening are: + +``` +# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "29/Dec/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 + 963 40.77.167.152 + 987 35.237.175.180 + 1062 40.77.167.55 + 1464 66.249.66.223 + 1660 34.218.226.147 + 1801 70.32.83.92 + 2005 50.116.102.77 + 3218 66.249.66.219 + 4608 205.186.128.185 + 5585 54.70.40.11 +``` + +- And just around the time of the alert: + +``` +# zcat --force /var/log/nginx/*.log.1 /var/log/nginx/*.log.2.gz | grep -E "29/Dec/2018:1(6|7|8)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 + 115 66.249.66.223 + 118 207.46.13.14 + 123 34.218.226.147 + 133 95.108.181.88 + 137 35.237.175.180 + 164 66.249.66.219 + 260 157.55.39.59 + 291 40.77.167.55 + 312 207.46.13.129 + 1253 54.70.40.11 +``` + +- All these look ok (`54.70.40.11` is known to us from earlier this month and should be reusing its Tomcat sessions) + diff --git a/docs/2015-11/index.html b/docs/2015-11/index.html index 5dad8eb9c..c92dc5c89 100644 --- a/docs/2015-11/index.html +++ b/docs/2015-11/index.html @@ -34,7 +34,7 @@ Last week I had increased the limit from 30 to 60, which seemed to help, but now $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace 78 "/> - + diff --git a/docs/2015-12/index.html b/docs/2015-12/index.html index 9a6294b02..90b4f0238 100644 --- a/docs/2015-12/index.html +++ b/docs/2015-12/index.html @@ -36,7 +36,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less -rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo -rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz "/> - + diff --git a/docs/2016-01/index.html b/docs/2016-01/index.html index 25afa6f0e..50728d415 100644 --- a/docs/2016-01/index.html +++ b/docs/2016-01/index.html @@ -26,7 +26,7 @@ Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_ I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated. Update GitHub wiki for documentation of maintenance tasks. "/> - + diff --git a/docs/2016-02/index.html b/docs/2016-02/index.html index fa2e6921a..f0ab02f85 100644 --- a/docs/2016-02/index.html +++ b/docs/2016-02/index.html @@ -40,7 +40,7 @@ I noticed we have a very interesting list of countries on CGSpace: Not only are there 49,000 countries, we have some blanks (25)… Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE” "/> - + diff --git a/docs/2016-03/index.html b/docs/2016-03/index.html index da7731ee3..769a54322 100644 --- a/docs/2016-03/index.html +++ b/docs/2016-03/index.html @@ -26,7 +26,7 @@ Looking at issues with author authorities on CGSpace For some reason we still have the index-lucene-update cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server "/> - + diff --git a/docs/2016-04/index.html b/docs/2016-04/index.html index 0641f2fa0..d8448c00b 100644 --- a/docs/2016-04/index.html +++ b/docs/2016-04/index.html @@ -30,7 +30,7 @@ After running DSpace for over five years I’ve never needed to look in any This will save us a few gigs of backup space we’re paying for on S3 Also, I noticed the checker log has some errors we should pay attention to: "/> - + diff --git a/docs/2016-05/index.html b/docs/2016-05/index.html index 49f5fa922..c87598e9c 100644 --- a/docs/2016-05/index.html +++ b/docs/2016-05/index.html @@ -34,7 +34,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period! # awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l 3168 "/> - + diff --git a/docs/2016-06/index.html b/docs/2016-06/index.html index 4cf53a8a9..c48fa4a2d 100644 --- a/docs/2016-06/index.html +++ b/docs/2016-06/index.html @@ -32,7 +32,7 @@ This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRec You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship "/> - + diff --git a/docs/2016-07/index.html b/docs/2016-07/index.html index 98c5e16c0..3635b2c23 100644 --- a/docs/2016-07/index.html +++ b/docs/2016-07/index.html @@ -48,7 +48,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and In this case the select query was showing 95 results before the update "/> - + diff --git a/docs/2016-08/index.html b/docs/2016-08/index.html index 05a1276fe..3a7b008c6 100644 --- a/docs/2016-08/index.html +++ b/docs/2016-08/index.html @@ -42,7 +42,7 @@ $ git checkout -b 55new 5_x-prod $ git reset --hard ilri/5_x-prod $ git rebase -i dspace-5.5 "/> - + diff --git a/docs/2016-09/index.html b/docs/2016-09/index.html index 627bc4e68..57b1cb479 100644 --- a/docs/2016-09/index.html +++ b/docs/2016-09/index.html @@ -34,7 +34,7 @@ It looks like we might be able to use OUs now, instead of DCs: $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)" "/> - + diff --git a/docs/2016-10/index.html b/docs/2016-10/index.html index d4f83d661..96fcb1a9a 100644 --- a/docs/2016-10/index.html +++ b/docs/2016-10/index.html @@ -42,7 +42,7 @@ I exported a random item’s metadata as CSV, deleted all columns except id 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X "/> - + diff --git a/docs/2016-11/index.html b/docs/2016-11/index.html index f8755880b..47492bf8d 100644 --- a/docs/2016-11/index.html +++ b/docs/2016-11/index.html @@ -26,7 +26,7 @@ Add dc.type to the output options for Atmire’s Listings and Reports module "/> - + diff --git a/docs/2016-12/index.html b/docs/2016-12/index.html index bf95aee83..94c4888f3 100644 --- a/docs/2016-12/index.html +++ b/docs/2016-12/index.html @@ -50,7 +50,7 @@ I see thousands of them in the logs for the last few months, so it’s not r I’ve raised a ticket with Atmire to ask Another worrying error from dspace.log is: "/> - + diff --git a/docs/2017-01/index.html b/docs/2017-01/index.html index 76553d3e3..37783083a 100644 --- a/docs/2017-01/index.html +++ b/docs/2017-01/index.html @@ -26,7 +26,7 @@ I checked to see if the Solr sharding task that is supposed to run on January 1s I tested on DSpace Test as well and it doesn’t work there either I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’ve ever had the sharding task run successfully over all these years "/> - + diff --git a/docs/2017-02/index.html b/docs/2017-02/index.html index e107c8ee7..a1fe1db66 100644 --- a/docs/2017-02/index.html +++ b/docs/2017-02/index.html @@ -54,7 +54,7 @@ DELETE 1 Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301) Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name "/> - + diff --git a/docs/2017-03/index.html b/docs/2017-03/index.html index dfe75d64f..d188c056a 100644 --- a/docs/2017-03/index.html +++ b/docs/2017-03/index.html @@ -58,7 +58,7 @@ Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing reg $ identify ~/Desktop/alc_contrastes_desafios.jpg /Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000 "/> - + diff --git a/docs/2017-04/index.html b/docs/2017-04/index.html index 99a9f5f0a..e0d4b871d 100644 --- a/docs/2017-04/index.html +++ b/docs/2017-04/index.html @@ -44,7 +44,7 @@ Testing the CMYK patch on a collection with 650 items: $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media-cmyk.txt "/> - + diff --git a/docs/2017-05/index.html b/docs/2017-05/index.html index 9b2fb8fa5..58823ae87 100644 --- a/docs/2017-05/index.html +++ b/docs/2017-05/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/2017-06/index.html b/docs/2017-06/index.html index 1389ecab3..45fc9b427 100644 --- a/docs/2017-06/index.html +++ b/docs/2017-06/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/2017-07/index.html b/docs/2017-07/index.html index 38ec13399..fd6ecb78c 100644 --- a/docs/2017-07/index.html +++ b/docs/2017-07/index.html @@ -38,7 +38,7 @@ Merge changes for WLE Phase II theme rename (#329) Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML: "/> - + diff --git a/docs/2017-08/index.html b/docs/2017-08/index.html index c7ec22605..7a0f91d3f 100644 --- a/docs/2017-08/index.html +++ b/docs/2017-08/index.html @@ -58,7 +58,7 @@ This was due to newline characters in the dc.description.abstract column, which I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet "/> - + diff --git a/docs/2017-09/index.html b/docs/2017-09/index.html index 4fa931aa7..8007e6c5d 100644 --- a/docs/2017-09/index.html +++ b/docs/2017-09/index.html @@ -34,7 +34,7 @@ Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account is both in the approvers step as well as the group "/> - + diff --git a/docs/2017-10/index.html b/docs/2017-10/index.html index 683ed3953..d41e47cf1 100644 --- a/docs/2017-10/index.html +++ b/docs/2017-10/index.html @@ -38,7 +38,7 @@ http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336 There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections "/> - + diff --git a/docs/2017-11/index.html b/docs/2017-11/index.html index 05b4c716a..541a0b236 100644 --- a/docs/2017-11/index.html +++ b/docs/2017-11/index.html @@ -58,7 +58,7 @@ Generate list of authors on CGSpace for Peter to go through and correct: dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv; COPY 54701 "/> - + diff --git a/docs/2017-12/index.html b/docs/2017-12/index.html index ea3601b43..5b3e7eeb4 100644 --- a/docs/2017-12/index.html +++ b/docs/2017-12/index.html @@ -28,7 +28,7 @@ The logs say “Timeout waiting for idle object” PostgreSQL activity says there are 115 connections currently The list of connections to XMLUI and REST API for today: "/> - + diff --git a/docs/2018-01/index.html b/docs/2018-01/index.html index 247ebf1f1..8ea6712ab 100644 --- a/docs/2018-01/index.html +++ b/docs/2018-01/index.html @@ -166,7 +166,7 @@ dspace.log.2018-01-02:34 Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains "/> - + diff --git a/docs/2018-02/index.html b/docs/2018-02/index.html index d13a7af0f..42bd45067 100644 --- a/docs/2018-02/index.html +++ b/docs/2018-02/index.html @@ -28,7 +28,7 @@ We don’t need to distinguish between internal and external works, so that Yesterday I figured out how to monitor DSpace sessions using JMX I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01 "/> - + diff --git a/docs/2018-03/index.html b/docs/2018-03/index.html index 45a7394a9..aaf03a04a 100644 --- a/docs/2018-03/index.html +++ b/docs/2018-03/index.html @@ -22,7 +22,7 @@ Export a CSV of the IITA community metadata for Martin Mueller Export a CSV of the IITA community metadata for Martin Mueller "/> - + diff --git a/docs/2018-04/index.html b/docs/2018-04/index.html index e9959712b..6c1acd04b 100644 --- a/docs/2018-04/index.html +++ b/docs/2018-04/index.html @@ -24,7 +24,7 @@ Catalina logs at least show some memory errors yesterday: I tried to test something on DSpace Test but noticed that it’s down since god knows when Catalina logs at least show some memory errors yesterday: "/> - + diff --git a/docs/2018-05/index.html b/docs/2018-05/index.html index 9397635a5..3eb1fc319 100644 --- a/docs/2018-05/index.html +++ b/docs/2018-05/index.html @@ -36,7 +36,7 @@ http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E Then I reduced the JVM heap size from 6144 back to 5120m Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use "/> - + diff --git a/docs/2018-06/index.html b/docs/2018-06/index.html index 637e0c972..e0b2d0b30 100644 --- a/docs/2018-06/index.html +++ b/docs/2018-06/index.html @@ -64,7 +64,7 @@ real 74m42.646s user 8m5.056s sys 2m7.289s "/> - + diff --git a/docs/2018-07/index.html b/docs/2018-07/index.html index 6df174cf0..40c2cf6a1 100644 --- a/docs/2018-07/index.html +++ b/docs/2018-07/index.html @@ -42,7 +42,7 @@ During the mvn package stage on the 5.8 branch I kept getting issues with java r There is insufficient memory for the Java Runtime Environment to continue. "/> - + diff --git a/docs/2018-08/index.html b/docs/2018-08/index.html index b08a149aa..79caa20d5 100644 --- a/docs/2018-08/index.html +++ b/docs/2018-08/index.html @@ -50,7 +50,7 @@ Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did The server only has 8GB of RAM so we’ll eventually need to upgrade to a larger one because we’ll start starving the OS, PostgreSQL, and command line batch processes I ran all system updates on DSpace Test and rebooted it "/> - + diff --git a/docs/2018-09/index.html b/docs/2018-09/index.html index 406448068..c3237864c 100644 --- a/docs/2018-09/index.html +++ b/docs/2018-09/index.html @@ -28,7 +28,7 @@ I’ll update the DSpace role in our Ansible infrastructure playbooks and ru Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again: "/> - + diff --git a/docs/2018-10/index.html b/docs/2018-10/index.html index 8b8a8c658..eb6d1d038 100644 --- a/docs/2018-10/index.html +++ b/docs/2018-10/index.html @@ -24,7 +24,7 @@ I created a GitHub issue to track this #389, because I’m super busy in Nai Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items I created a GitHub issue to track this #389, because I’m super busy in Nairobi right now "/> - + diff --git a/docs/2018-11/index.html b/docs/2018-11/index.html index 70a5d473f..4f82588c7 100644 --- a/docs/2018-11/index.html +++ b/docs/2018-11/index.html @@ -38,7 +38,7 @@ Send a note about my dspace-statistics-api to the dspace-tech mailing list Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage Today these are the top 10 IPs: "/> - + diff --git a/docs/2018-12/index.html b/docs/2018-12/index.html index d022bee2e..a1e11d6e3 100644 --- a/docs/2018-12/index.html +++ b/docs/2018-12/index.html @@ -21,7 +21,7 @@ I noticed that there is another issue with PDF thumbnails on CGSpace, and I see " /> - + @@ -38,7 +38,7 @@ Then I ran all system updates and restarted the server I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week "/> - + @@ -48,9 +48,9 @@ I noticed that there is another issue with PDF thumbnails on CGSpace, and I see "@type": "BlogPosting", "headline": "December, 2018", "url": "https://alanorth.github.io/cgspace-notes/2018-12/", - "wordCount": "2940", + "wordCount": "3086", "datePublished": "2018-12-02T02:09:30+02:00", - "dateModified": "2018-12-20T12:56:16+02:00", + "dateModified": "2018-12-20T17:41:09+02:00", "author": { "@type": "Person", "name": "Alan Orth" @@ -670,6 +670,47 @@ UPDATE 1
  • After all that I started a full Discovery reindex to get the index name changes and rights updates
    • +

    2018-12-29

    + + + +
    # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "29/Dec/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
+    963 40.77.167.152
+    987 35.237.175.180
+   1062 40.77.167.55
+   1464 66.249.66.223
+   1660 34.218.226.147
+   1801 70.32.83.92
+   2005 50.116.102.77
+   3218 66.249.66.219
+   4608 205.186.128.185
+   5585 54.70.40.11
+
    + + + +
    # zcat --force /var/log/nginx/*.log.1 /var/log/nginx/*.log.2.gz | grep -E "29/Dec/2018:1(6|7|8)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
+    115 66.249.66.223
+    118 207.46.13.14
+    123 34.218.226.147
+    133 95.108.181.88
+    137 35.237.175.180
+    164 66.249.66.219
+    260 157.55.39.59
+    291 40.77.167.55
+    312 207.46.13.129
+   1253 54.70.40.11
+
    + + + diff --git a/docs/404.html b/docs/404.html index 9d40901dc..b9a617886 100644 --- a/docs/404.html +++ b/docs/404.html @@ -13,7 +13,7 @@ - + diff --git a/docs/categories/index.html b/docs/categories/index.html index 6b3f6282a..69ca72d26 100644 --- a/docs/categories/index.html +++ b/docs/categories/index.html @@ -13,7 +13,7 @@ - + diff --git a/docs/categories/notes/index.html b/docs/categories/notes/index.html index 64732a163..80b2cc91b 100644 --- a/docs/categories/notes/index.html +++ b/docs/categories/notes/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/2/index.html b/docs/categories/page/2/index.html index 4a784573f..210016516 100644 --- a/docs/categories/page/2/index.html +++ b/docs/categories/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/3/index.html b/docs/categories/page/3/index.html index bae16134e..38d39ea37 100644 --- a/docs/categories/page/3/index.html +++ b/docs/categories/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/4/index.html b/docs/categories/page/4/index.html index 9d2b3ac89..e9b11c870 100644 --- a/docs/categories/page/4/index.html +++ b/docs/categories/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/cgiar-library-migration/index.html b/docs/cgiar-library-migration/index.html index cb909aeba..85e1ef47e 100644 --- a/docs/cgiar-library-migration/index.html +++ b/docs/cgiar-library-migration/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/index.html b/docs/index.html index 460cd28a7..83c2b59b0 100644 --- a/docs/index.html +++ b/docs/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/2/index.html b/docs/page/2/index.html index e219c9822..5736c36db 100644 --- a/docs/page/2/index.html +++ b/docs/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/3/index.html b/docs/page/3/index.html index b007864a8..fedb32bf8 100644 --- a/docs/page/3/index.html +++ b/docs/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/4/index.html b/docs/page/4/index.html index a3d6b0387..711ce59f9 100644 --- a/docs/page/4/index.html +++ b/docs/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/index.html b/docs/posts/index.html index 961532633..b6d4c48ad 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/2/index.html b/docs/posts/page/2/index.html index 1ed99e02a..f456a0e6a 100644 --- a/docs/posts/page/2/index.html +++ b/docs/posts/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/3/index.html b/docs/posts/page/3/index.html index d5b2af316..56cb159b0 100644 --- a/docs/posts/page/3/index.html +++ b/docs/posts/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/4/index.html b/docs/posts/page/4/index.html index 156392835..82060f0da 100644 --- a/docs/posts/page/4/index.html +++ b/docs/posts/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 3ca8e603b..5a887615e 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -4,7 +4,7 @@ https://alanorth.github.io/cgspace-notes/2018-12/ - 2018-12-20T12:56:16+02:00 + 2018-12-20T17:41:09+02:00 @@ -199,7 +199,7 @@ https://alanorth.github.io/cgspace-notes/ - 2018-12-20T12:56:16+02:00 + 2018-12-20T17:41:09+02:00 0 @@ -210,7 +210,7 @@ https://alanorth.github.io/cgspace-notes/tags/notes/ - 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