mirror of
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598 lines
19 KiB
HTML
598 lines
19 KiB
HTML
<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta property="og:title" content="January, 2018" />
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<meta property="og:description" content="2018-01-02
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Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time
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I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary
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The nginx logs show HTTP 200s until 02/Jan/2018:11:27:17 +0000 when Uptime Robot got an HTTP 500
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In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”
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And just before that I see this:
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Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
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Ah hah! So the pool was actually empty!
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I need to increase that, let’s try to bump it up from 50 to 75
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After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw
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I notice this error quite a few times in dspace.log:
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2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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And there are many of these errors every day for the past month:
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$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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dspace.log.2017-11-22:1
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dspace.log.2017-11-23:4
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dspace.log.2017-11-24:11
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dspace.log.2017-11-25:0
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dspace.log.2017-11-26:1
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dspace.log.2017-11-27:7
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dspace.log.2017-11-28:21
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dspace.log.2017-11-29:31
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dspace.log.2017-11-30:15
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dspace.log.2017-12-01:15
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dspace.log.2017-12-02:20
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dspace.log.2017-12-03:38
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dspace.log.2017-12-04:65
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dspace.log.2017-12-05:43
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dspace.log.2017-12-06:72
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dspace.log.2017-12-07:27
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dspace.log.2017-12-08:15
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dspace.log.2017-12-09:29
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dspace.log.2017-12-10:35
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dspace.log.2017-12-11:20
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dspace.log.2017-12-12:44
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dspace.log.2017-12-13:36
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dspace.log.2017-12-14:59
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dspace.log.2017-12-15:104
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dspace.log.2017-12-16:53
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dspace.log.2017-12-17:66
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dspace.log.2017-12-18:83
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dspace.log.2017-12-19:101
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dspace.log.2017-12-20:74
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dspace.log.2017-12-21:55
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dspace.log.2017-12-22:66
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dspace.log.2017-12-23:50
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dspace.log.2017-12-24:85
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dspace.log.2017-12-25:62
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dspace.log.2017-12-26:49
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dspace.log.2017-12-27:30
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dspace.log.2017-12-28:54
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dspace.log.2017-12-29:68
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dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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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
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-01/" />
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<meta property="article:published_time" content="2018-01-02T08:35:54-08:00"/>
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<meta property="article:modified_time" content="2018-01-05T07:05:14-08:00"/>
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<meta name="twitter:card" content="summary"/><meta name="twitter:title" content="January, 2018"/>
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<meta name="twitter:description" content="2018-01-02
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Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time
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|
I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary
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|
The nginx logs show HTTP 200s until 02/Jan/2018:11:27:17 +0000 when Uptime Robot got an HTTP 500
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In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”
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And just before that I see this:
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Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
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Ah hah! So the pool was actually empty!
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I need to increase that, let’s try to bump it up from 50 to 75
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|
After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw
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|
I notice this error quite a few times in dspace.log:
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2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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And there are many of these errors every day for the past month:
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$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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dspace.log.2017-11-22:1
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dspace.log.2017-11-23:4
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dspace.log.2017-11-24:11
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dspace.log.2017-11-25:0
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dspace.log.2017-11-26:1
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dspace.log.2017-11-27:7
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dspace.log.2017-11-28:21
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dspace.log.2017-11-29:31
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dspace.log.2017-11-30:15
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dspace.log.2017-12-01:15
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dspace.log.2017-12-02:20
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dspace.log.2017-12-03:38
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dspace.log.2017-12-04:65
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dspace.log.2017-12-05:43
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dspace.log.2017-12-06:72
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dspace.log.2017-12-07:27
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dspace.log.2017-12-08:15
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dspace.log.2017-12-09:29
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dspace.log.2017-12-10:35
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dspace.log.2017-12-11:20
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dspace.log.2017-12-12:44
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dspace.log.2017-12-13:36
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dspace.log.2017-12-14:59
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dspace.log.2017-12-15:104
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dspace.log.2017-12-16:53
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dspace.log.2017-12-17:66
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dspace.log.2017-12-18:83
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dspace.log.2017-12-19:101
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dspace.log.2017-12-20:74
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dspace.log.2017-12-21:55
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dspace.log.2017-12-22:66
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dspace.log.2017-12-23:50
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dspace.log.2017-12-24:85
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dspace.log.2017-12-25:62
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dspace.log.2017-12-26:49
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dspace.log.2017-12-27:30
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dspace.log.2017-12-28:54
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dspace.log.2017-12-29:68
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dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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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
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"/>
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<meta name="generator" content="Hugo 0.32.2" />
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<script type="application/ld+json">
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{
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"headline": "January, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-01/",
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"wordCount": "1046",
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"datePublished": "2018-01-02T08:35:54-08:00",
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"dateModified": "2018-01-05T07:05:14-08:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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},
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"keywords": "Notes"
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}
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</script>
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2018-01/">
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<title>January, 2018 | CGSpace Notes</title>
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<!-- combined, minified CSS -->
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<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-O8wjsnz02XiyrPxnhfF6AVOv6YLBaEGRCnVF+DL3gCPBy9cieyHcpixIrVyD2JS5" crossorigin="anonymous">
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</head>
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<body>
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<div class="blog-masthead">
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<div class="container">
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<nav class="nav blog-nav">
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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</nav>
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</div>
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</div>
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<header class="blog-header">
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<div class="container">
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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</div>
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</header>
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<div class="container">
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<div class="row">
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<div class="col-sm-8 blog-main">
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-01-02">2018-01-02</h2>
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<ul>
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<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
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<li>I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary</li>
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<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
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<li>In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”</li>
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<li>And just before that I see this:</li>
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</ul>
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<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
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</code></pre>
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<ul>
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<li>Ah hah! So the pool was actually empty!</li>
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<li>I need to increase that, let’s try to bump it up from 50 to 75</li>
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<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw</li>
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<li>I notice this error quite a few times in dspace.log:</li>
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</ul>
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<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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</code></pre>
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<ul>
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<li>And there are many of these errors every day for the past month:</li>
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</ul>
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<pre><code>$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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dspace.log.2017-11-22:1
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dspace.log.2017-11-23:4
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dspace.log.2017-11-24:11
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dspace.log.2017-11-25:0
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dspace.log.2017-11-26:1
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dspace.log.2017-11-27:7
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dspace.log.2017-11-28:21
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dspace.log.2017-11-29:31
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dspace.log.2017-11-30:15
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dspace.log.2017-12-01:15
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dspace.log.2017-12-02:20
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dspace.log.2017-12-03:38
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dspace.log.2017-12-04:65
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dspace.log.2017-12-05:43
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dspace.log.2017-12-06:72
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dspace.log.2017-12-07:27
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dspace.log.2017-12-08:15
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dspace.log.2017-12-09:29
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dspace.log.2017-12-10:35
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dspace.log.2017-12-11:20
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dspace.log.2017-12-12:44
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dspace.log.2017-12-13:36
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dspace.log.2017-12-14:59
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dspace.log.2017-12-15:104
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dspace.log.2017-12-16:53
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dspace.log.2017-12-17:66
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dspace.log.2017-12-18:83
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dspace.log.2017-12-19:101
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dspace.log.2017-12-20:74
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dspace.log.2017-12-21:55
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dspace.log.2017-12-22:66
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dspace.log.2017-12-23:50
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dspace.log.2017-12-24:85
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dspace.log.2017-12-25:62
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dspace.log.2017-12-26:49
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dspace.log.2017-12-27:30
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dspace.log.2017-12-28:54
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dspace.log.2017-12-29:68
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dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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</code></pre>
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<ul>
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<li>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</li>
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</ul>
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<p></p>
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<h2 id="2018-01-03">2018-01-03</h2>
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<ul>
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<li>I woke up to more up and down of CGSpace, this time UptimeRobot noticed a few rounds of up and down of a few minutes each and Linode also notified of high CPU load from 12 to 2 PM</li>
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<li>Looks like I need to increase the database pool size again:</li>
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</ul>
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<pre><code>$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
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dspace.log.2018-01-01:0
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dspace.log.2018-01-02:1972
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dspace.log.2018-01-03:1909
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</code></pre>
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<ul>
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<li>For some reason there were a lot of “active” connections last night:</li>
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</ul>
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<p><img src="/cgspace-notes/2018/01/postgres_connections-day.png" alt="CGSpace PostgreSQL connections" /></p>
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<ul>
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<li>The active IPs in XMLUI are:</li>
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</ul>
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<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E "3/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
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607 40.77.167.141
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611 2a00:23c3:8c94:7800:392c:a491:e796:9c50
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663 188.226.169.37
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759 157.55.39.245
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887 68.180.229.254
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1037 157.55.39.175
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1068 216.244.66.245
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1495 66.249.64.91
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1934 104.196.152.243
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2219 134.155.96.78
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</code></pre>
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<ul>
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<li>134.155.96.78 appears to be at the University of Mannheim in Germany</li>
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<li>They identify as: Mozilla/5.0 (compatible; heritrix/3.2.0 +<a href="http://ifm.uni-mannheim.de">http://ifm.uni-mannheim.de</a>)</li>
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<li>This appears to be the <a href="https://github.com/internetarchive/heritrix3">Internet Archive’s open source bot</a></li>
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<li>They seem to be re-using their Tomcat session so I don’t need to do anything to them just yet:</li>
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</ul>
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<pre><code>$ grep 134.155.96.78 dspace.log.2018-01-03 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
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2
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</code></pre>
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<ul>
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<li>The API logs show the normal users:</li>
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</ul>
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<pre><code># cat /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E "3/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
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32 207.46.13.182
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38 40.77.167.132
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38 68.180.229.254
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43 66.249.64.91
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46 40.77.167.141
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49 157.55.39.245
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79 157.55.39.175
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1533 50.116.102.77
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4069 70.32.83.92
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9355 45.5.184.196
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</code></pre>
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<ul>
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<li>In other related news I see a sizeable amount of requests coming from python-requests</li>
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<li>For example, just in the last day there were 1700!</li>
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</ul>
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<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -c python-requests
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1773
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</code></pre>
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<ul>
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<li>But they come from hundreds of IPs, many of which are 54.x.x.x:</li>
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</ul>
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<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep python-requests | awk '{print $1}' | sort -n | uniq -c | sort -h | tail -n 30
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9 54.144.87.92
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9 54.146.222.143
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9 54.146.249.249
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9 54.158.139.206
|
|
9 54.161.235.224
|
|
9 54.163.41.19
|
|
9 54.163.4.51
|
|
9 54.196.195.107
|
|
9 54.198.89.134
|
|
9 54.80.158.113
|
|
10 54.198.171.98
|
|
10 54.224.53.185
|
|
10 54.226.55.207
|
|
10 54.227.8.195
|
|
10 54.242.234.189
|
|
10 54.242.238.209
|
|
10 54.80.100.66
|
|
11 54.161.243.121
|
|
11 54.205.154.178
|
|
11 54.234.225.84
|
|
11 54.87.23.173
|
|
11 54.90.206.30
|
|
12 54.196.127.62
|
|
12 54.224.242.208
|
|
12 54.226.199.163
|
|
13 54.162.149.249
|
|
13 54.211.182.255
|
|
19 50.17.61.150
|
|
21 54.211.119.107
|
|
139 164.39.7.62
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I have no idea what these are but they seem to be coming from Amazon…</li>
|
|
<li>I guess for now I just have to increase the database connection pool’s max active</li>
|
|
<li>It’s currently 75 and normally I’d just bump it by 25 but let me be a bit daring and push it by 50 to 125, because I used to see at least 121 connections in pg_stat_activity before when we were using the shitty default pooling</li>
|
|
</ul>
|
|
|
|
<h2 id="2018-01-04">2018-01-04</h2>
|
|
|
|
<ul>
|
|
<li>CGSpace went down and up a bunch of times last night and ILRI staff were complaining a lot last night</li>
|
|
<li>The XMLUI logs show this activity:</li>
|
|
</ul>
|
|
|
|
<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E "4/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
|
|
968 197.211.63.81
|
|
981 213.55.99.121
|
|
1039 66.249.64.93
|
|
1258 157.55.39.175
|
|
1273 207.46.13.182
|
|
1311 157.55.39.191
|
|
1319 157.55.39.197
|
|
1775 66.249.64.78
|
|
2216 104.196.152.243
|
|
3366 66.249.64.91
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Again we ran out of PostgreSQL database connections, even after bumping the pool max active limit from 50 to 75 to 125 yesterday!</li>
|
|
</ul>
|
|
|
|
<pre><code>2018-01-04 07:36:08,089 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
|
|
org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-256] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:125; busy:125; idle:0; lastwait:5000].
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>So for this week that is the number one problem!</li>
|
|
</ul>
|
|
|
|
<pre><code>$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
|
|
dspace.log.2018-01-01:0
|
|
dspace.log.2018-01-02:1972
|
|
dspace.log.2018-01-03:1909
|
|
dspace.log.2018-01-04:1559
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I will just bump the connection limit to 300 because I’m fucking fed up with this shit</li>
|
|
<li>Once I get back to Amman I will have to try to create different database pools for different web applications, like recently discussed on the dspace-tech mailing list</li>
|
|
<li>Create accounts on CGSpace for two CTA staff km4ard@cta.int and bheenick@cta.int</li>
|
|
</ul>
|
|
|
|
<h2 id="2018-01-05">2018-01-05</h2>
|
|
|
|
<ul>
|
|
<li>Peter said that CGSpac was down last night and Tsega restarted Tomcat</li>
|
|
<li>I don’t see any alerts from Linode or UptimeRobot, and there are no PostgreSQL connection errors in the dspace logs for today:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
|
|
dspace.log.2018-01-01:0
|
|
dspace.log.2018-01-02:1972
|
|
dspace.log.2018-01-03:1909
|
|
dspace.log.2018-01-04:1559
|
|
dspace.log.2018-01-05:0
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Daniel asked for help with their DAGRIS server (linode2328112) that has no disk space</li>
|
|
<li>I had a look and there is one Apache 2 log file that is 73GB, with lots of this:</li>
|
|
</ul>
|
|
|
|
<pre><code>[Fri Jan 05 09:31:22.965398 2018] [:error] [pid 9340] [client 213.55.99.121:64476] WARNING: Unable to find a match for "9-16-1-RV.doc" in "/home/files/journals/6//articles/9/". Skipping this file., referer: http://dagris.info/reviewtool/index.php/index/install/upgrade
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I will delete the log file for now and tell Danny</li>
|
|
</ul>
|
|
|
|
|
|
|
|
|
|
|
|
</article>
|
|
|
|
|
|
|
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</div> <!-- /.blog-main -->
|
|
|
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<aside class="col-sm-3 ml-auto blog-sidebar">
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|
|
|
|
|
|
<section class="sidebar-module">
|
|
<h4>Recent Posts</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
|
|
<li><a href="/cgspace-notes/2018-01/">January, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2017-12/">December, 2017</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2017-11/">November, 2017</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
|
|
|
|
<li><a href="/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></li>
|
|
|
|
</ol>
|
|
</section>
|
|
|
|
|
|
|
|
|
|
<section class="sidebar-module">
|
|
<h4>Links</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
<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>
|
|
|
|
</ol>
|
|
</section>
|
|
|
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</aside>
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</div> <!-- /.row -->
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<p>
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