Debian 8 to Debian 9 upgrade, causes non functional Confluence

[Graham van der Wielen]

Last weekend I upgraded my Debian 8 (jessie) OS, upon which Confluence (6.1.1 I believe) runs, to Debian 9 (stretch). 

During the upgrade I was prompted that postgresql 9.4 would be considered obsolete and 9.6 installed:

The PostgreSQL version 9.4 is obsolete, but the server or client packages are still installed. Please install the latest packages (postgresql-9.6 and postgresql-client-9.6) and upgrade the existing  clusters with pg_upgradecluster (see manpage).  

Please be aware that the installation of postgresql-9.6 will automatically create a default cluster 9.6/main. If you want to upgrade the 9.4/main cluster, you need to remove the already existing 9.6 cluster (pg_dropcluster --stop 9.6 main, see manpage for details).                                                                                                                              

The old server and client packages are no longer supported. After the existing clusters are upgraded, the postgresql-9.4 and postgresql-client-9.4 packages should be removed.                                                                                  

Please see /usr/share/doc/postgresql-common/README.Debian.gz for details.

After completing the installation I upgraded my 9.4 cluster to 9.6 (but did not delete it) and competed the postgresql upgrade procedure. Made sure that postgresql was running on 5432 and started Confluence. However I couldn't reach it via HTTP. 

I figured this might be caused by https://jira.atlassian.com/browse/CONFSERVER-44216

I performed some action to put postgresql 9.4 back online and set 9.6 offline. Changed the ports and finished with restarting postgresql

sudo pg_lsclusters
Ver Cluster Port Status Owner Data directory Log file
9.4 main 5432 online postgres /var/lib/postgresql/9.4/main /var/log/postgresql/postgresql-9.4-main.log
9.6 main 5433 down postgres /var/lib/postgresql/9.6/main /var/log/postgresql/postgresql-9.6-main.log

Then restarted confluence.

However I still get a gateway timeout via Nginx (used as reversed proxy) and directly via 8090 I get a 404. 

Even though I see confluences is running (see systemctl) and also using the ports I expect:

$ sudo netstat -tulpn | grep java
tcp 0 0 0.0.0.0:8090 0.0.0.0:* LISTEN 26905/java
tcp 0 0 0.0.0.0:8091 0.0.0.0:* LISTEN 27205/java
tcp 0 0 127.0.0.1:8000 0.0.0.0:* LISTEN 26905/java

Any help would be appreciated

[AnnWorley · Accepted solution]

Thanks for the detailed description. Tomcat can start and listen on port 8090 without Confluence starting properly. Usually, the catalina.out log (<confluence_install>/logs/) will have an entry like "server startup in so-many ms" and the subsequent logging goes to the  <confluence_home>/logs/atlassian-confluence.log.
(The <confluence_home> directory is the path defined in the following file: <confluence_install>/confluence/WEB-INF/classes/confluence-init.properties) That's where you can see the progression of the Confluence application startup and identify errors that are causing Confluence not to serve content.

If you post the last 100 lines or so of the atlassian-confluence.log in a code block (from the Formats pulldown menu) I wll be happy to take a look for relevant errors.

[Graham van der Wielen]

Thanks for the reply!

Didn't know about the second log but should have. However I did look at the cataline.out again and saw some new errors, however at INFO level. So probably not so interesting as the atlassian-confluence.log (see second code entry). 

Note: further occurrences of HTTP header parsing errors will be logged at DEBUG level.
 java.lang.IllegalArgumentException: Invalid character found in method name. HTTP method names must be tokens
 at org.apache.coyote.http11.AbstractNioInputBuffer.parseRequestLine(AbstractNioInputBuffer.java:233)
 at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1017)
 at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
 at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1524)
 at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1480)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
 at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
 at java.lang.Thread.run(Thread.java:745)

atlassaian-confluence.log:

Confluence Remote Page View - Plugin (com.atlassian.confluence.plugins.confluence-remote-page-view-plugin, Version: 1.12, Installed: bundled)
Confluence Request Access Plugin (com.atlassian.confluence.plugins.confluence-request-access-plugin, Version: 2.4.0, Installed: bundled)
Confluence Required Health Checks Plugin (com.atlassian.confluence.plugins.confluence-required-health-checks, Version: 6.1.1, Installed: bundled)
Confluence Restrictions Dialog (com.atlassian.confluence.plugins.confluence-page-restrictions-dialog, Version: 6.1.1, Installed: bundled)
Confluence Roadmap Planner (com.atlassian.confluence.plugins.confluence-roadmap-plugin, Version: 14.0.0, Installed: bundled)
Confluence Russian (Russia) Language Pack (tac.confluence.languages.ru_RU, Version: 6.1.0.rc1-v2r87448-2017-03-13, Installed: bundled)
Confluence SAL Plugin (com.atlassian.confluence.plugins.confluence-sal-plugin, Version: 6.1.1, Installed: bundled)
Confluence Scheduled Job Administration UI (com.atlassian.confluence.plugins.confluence-schedule-admin, Version: 6.1.1, Installed: bundled)
Confluence Scheduler SPI (com.atlassian.confluence.plugins.confluence-scheduler-spi, Version: 6.1.1, Installed: bundled)
Confluence Search Plugin (com.atlassian.confluence.plugins.search.confluence-search, Version: 2.3.14, Installed: bundled)
Confluence Software Project Blueprint (com.atlassian.confluence.plugins.confluence-software-project, Version: 1.0.8, Installed: bundled)
Confluence Sortable Tables (com.atlassian.confluence.plugins.confluence-sortable-tables, Version: 6.1.1, Installed: bundled)
Confluence Soy Template Support (com.atlassian.confluence.plugins.soy, Version: 6.1.1, Installed: bundled)
Confluence Space Blueprints Plugin (com.atlassian.confluence.plugins.confluence-space-blueprints, Version: 1.5.8, Installed: bundled)
Confluence Space Directory (com.atlassian.confluence.plugins.confluence-space-directory, Version: 6.1.1, Installed: bundled)
Confluence Space IA Plugin (com.atlassian.confluence.plugins.confluence-space-ia, Version: 13.1.2, Installed: bundled)
Confluence Spaces (com.atlassian.confluence.plugins.confluence-spaces, Version: 6.1.1, Installed: bundled)
Confluence Spanish (Spain) Language Pack (tac.confluence.languages.es_ES, Version: 6.1.0.rc1-v2r17910-2017-03-13, Installed: bundled)
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Confluence UI REST (com.atlassian.confluence.plugins.confluence-ui-rest, Version: 6.1.1, Installed: bundled)
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Confluence User Rest (com.atlassian.confluence.plugins.confluence-user-rest, Version: 6.1.1, Installed: bundled)
Confluence View File Macro (com.atlassian.confluence.plugins.confluence-view-file-macro, Version: 2.0.3, Installed: bundled)
Confluence View Source (com.atlassian.confluence.plugins.view-source, Version: 6.1.1, Installed: bundled)
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Crowd System Password Encoders (crowd.system.passwordencoders, Version: 1.0, Installed: bundled)
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Default Macro Metadata Provider (confluence.macro.metadata.provider, Version: 1.0, Installed: bundled)
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Did You Mean Index Building Interface (confluence.sections.admin.indexing, Version: 1.0, Installed: bundled)
Document Conversion Library (com.atlassian.plugins.document-conversion-library, Version: 1.2.22, Installed: bundled)
Dynamic Task List 2 Plugin (confluence.extra.dynamictasklist2, Version: 4.3.1, Installed: bundled)
Edit Settings Sections (confluence.sections.settings.edit, Version: 1.0, Installed: bundled)
Editor Actions (confluence.editor.actions, Version: 1.0, Installed: bundled)
Embedded Gadgets Plugin (com.atlassian.gadgets.embedded, Version: 4.2.14, Installed: bundled)
Follow list resources (confluence.sections.user.follow.list, Version: 1.0, Installed: bundled)
Gadget Directory Plugin (com.atlassian.gadgets.directory, Version: 4.2.14, Installed: bundled)
Gadget Spec Publisher Plugin (com.atlassian.gadgets.publisher, Version: 4.2.14, Installed: bundled)
Gadgets Plugin (com.atlassian.confluence.plugins.gadgets, Version: 8.0.1, Installed: bundled)
Gadgets Plugin SPI (com.atlassian.confluence.plugins.gadgets.spi, Version: 8.0.1, Installed: bundled)
Global Header Image Links (confluence.header.imagelinks, Version: 1.0, Installed: bundled)
Google Calendar (net.customware.confluence.plugin.google.calendar, Version: 4.2.0, Installed: Mar 14, 2017)
Help Menu Items (confluence.sections.help, Version: 1.0, Installed: bundled)
ICU4J (com.atlassian.bundles.icu4j-3.8.0.1, Version: 3.8.0.1, Installed: bundled)
IM Presence NG Plugin (confluence.extra.impresence2, Version: 3.0.0, Installed: bundled)
ImageEffectsPlugin (com.atlassian.confluence.image.effects.ImageEffectsPlugin, Version: 1.5.1, Installed: bundled)
ImageIO enabler (com.atlassian.plugins.imageio-enabler-0.0.0, Version: 0.0.0, Installed: bundled)
Information Macros (confluence.extra.information, Version: 4.0.0, Installed: bundled)
Issue Status Plugin (com.atlassian.plugins.issue-status-plugin, Version: 1.1.7, Installed: bundled)
JIRA Integration :: Plugin (com.atlassian.integration.jira.jira-integration-plugin, Version: 3.0.2, Installed: bundled)
JSON Library (com.atlassian.bundles.json-20070829.0.0.1, Version: 20070829.0.0.1, Installed: bundled)
Java Concurrency in Practice Annotations (com.springsource.net.jcip.annotations-1.0.0, Version: 1.0.0, Installed: bundled)
Layout Macros (confluence.extra.layout, Version: 2.2.3, Installed: bundled)
License REST plugin for Confluence (com.atlassian.confluence.plugins.confluence-license-rest, Version: 6.1.1, Installed: bundled)
Lucene Boosting Strategies (confluence.search.lucene.boosting, Version: 1.0, Installed: bundled)
Lucene Compatibility Plugin (com.atlassian.labs.lucene-compat-plugin, Version: 1.1.1, Installed: bundled)
Lucene Searcher Initializers (confluence.search.lucene.initialisation, Version: 1.0, Installed: bundled)
Macro Usage Admin Plugin (com.atlassian.confluence.plugins.confluence-macro-usage-admin-plugin, Version: 1.0.9, Installed: bundled)
News Tabs (confluence.sections.news, Version: 1.0, Installed: bundled)
Office Connector plugin (com.atlassian.confluence.extra.officeconnector, Version: 5.0.7, Installed: bundled)
Opensocial Plugin (com.atlassian.gadgets.opensocial, Version: 4.2.14, Installed: bundled)
Page Highlight Actions - Plugin (com.atlassian.confluence.plugins.confluence-highlight-actions, Version: 1.6.16, Installed: bundled)
Page Operations (confluence.sections.page.operations, Version: 1.0, Installed: bundled)
Page Properties Macros - Plugin (confluence.extra.masterdetail, Version: 5.0.13, Installed: bundled)
Page Tabs (confluence.search.mappers.lucene, Version: 1.0, Installed: bundled)
Page Tabs (confluence.sections.page, Version: 1.0, Installed: bundled)
Page Tree Plugin (com.atlassian.confluence.plugins.pagetree, Version: 2.4.6, Installed: bundled)
Profile Macros (confluence.macros.profile, Version: 1.0, Installed: bundled)
Profile Picture (com.atlassian.confluence.plugins.profile-picture, Version: 2.0.3, Installed: bundled)
Profile Tabs (confluence.sections.profile, Version: 1.0, Installed: bundled)
Project Creation Capability Product REST Plugin (com.atlassian.plugins.atlassian-project-creation-plugin, Version: 2.0.9, Installed: bundled)
Project Creation Plugin SPI for Confluence (com.atlassian.plugins.confluence-project-creation, Version: 2.0.9, Installed: bundled)
Recently Viewed Plugin (com.atlassian.confluence.plugins.recently-viewed-plugin, Version: 5.1.1, Installed: bundled)
SAML for Atlassian Data Center (com.atlassian.plugins.authentication.atlassian-authentication-plugin, Version: 2.0.4, Installed: bundled)
Search Web Interface (confluence.sections.search.view, Version: 1.0, Installed: bundled)
Search Web Interface (confluence.sections.admin.generalconfig, Version: 1.0, Installed: bundled)
Share Page (com.atlassian.confluence.plugins.share-page, Version: 5.2, Installed: bundled)
Space Admin Sections (confluence.sections.space.admin, Version: 1.0, Installed: bundled)
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Space Browse Sections (confluence.sections.space.browse, Version: 1.0, Installed: bundled)
Space Export Web Interface (confluence.sections.space.export.view, Version: 1.0, Installed: bundled)
Space Item Tabs (confluence.sections.space, Version: 1.0, Installed: bundled)
Space Pages Sections (confluence.sections.space.pages, Version: 1.0, Installed: bundled)
Space Tools Sections (confluence.sections.space.tools, Version: 1.0, Installed: bundled)
Spring Interceptor Adapter Plugin (com.atlassian.plugins.atlassian-spring-interceptor-adapter-plugin-1.1, Version: 1.1, Installed: bundled)
Status Macro (com.atlassian.confluence.plugins.status-macro, Version: 2.18, Installed: bundled)
Sticky Table Headers (com.atlassian.confluence.plugins.sticky-table-headers, Version: 1.17, Installed: bundled)
Streams API (com.atlassian.streams.streams-api, Version: 6.0.15, Installed: bundled)
Streams Core Plugin (com.atlassian.streams.core, Version: 6.0.15, Installed: bundled)
Streams Inline Actions Plugin (com.atlassian.streams.actions, Version: 6.0.15, Installed: bundled)
Streams Plugin (com.atlassian.streams, Version: 6.0.15, Installed: bundled)
Streams SPI (com.atlassian.streams.streams-spi, Version: 6.0.15, Installed: bundled)
Streams Third Party Provider Plugin (com.atlassian.streams.streams-thirdparty-plugin, Version: 6.0.15, Installed: bundled)
Support Healthcheck Plugin (com.atlassian.support.healthcheck.support-healthcheck-plugin, Version: 2.2.3, Installed: Mar 14, 2017)
Support Tools Plugin (com.atlassian.support.stp, Version: 3.10.1, Installed: Mar 14, 2017)
Synchrony Interop Bootstrap Plugin (com.atlassian.confluence.plugins.synchrony-interop, Version: 6.1.1, Installed: bundled)
System Templates (com.atlassian.confluence.plugins.system-templates, Version: 6.1.1, Installed: bundled)
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System Web Panels (confluence.web.panels, Version: 1.0, Installed: bundled)
System Web Panels (confluence.web.panel.renderers, Version: 1.0, Installed: bundled)
System Web Resources (confluence.web.resources, Version: 1.0, Installed: bundled)
TDM Merger (com.atlassian.plugins.confluence-tdm-merger, Version: 6.1.1, Installed: bundled)
Table of Contents Plugin (org.randombits.confluence.toc, Version: 3.1.1, Installed: bundled)
Upgrade Administration Interface (confluence.sections.admin.upgrade, Version: 1.0, Installed: bundled)
User Administration (confluence.admin.user, Version: 1.0, Installed: bundled)
User Hover Menu Sections (confluence.user.hover.menu, Version: 1.0, Installed: bundled)
User Lister (confluence.extra.userlister, Version: 2.7.4, Installed: bundled)
User Menu Sections (confluence.user.menu, Version: 1.0, Installed: bundled)
User Menu Sections (confluence.user.menu.concise, Version: 1.0, Installed: bundled)
View Profile Web Interface (confluence.sections.profile.view, Version: 1.0, Installed: bundled)
View follow resources (confluence.sections.user.view.follow, Version: 1.0, Installed: bundled)
WebDAV Plugin (confluence.extra.webdav, Version: 4.3.4, Installed: bundled)
Widget Connector (com.atlassian.confluence.extra.widgetconnector, Version: 3.0.3, Installed: bundled)
Wiki Markup Plugin (confluence.xhtml.wikimarkup, Version: 1.0, Installed: bundled)
Wiki Renderer Components (confluence.renderer.components, Version: 1.0, Installed: bundled)
Workbox - Common Plugin (com.atlassian.mywork.mywork-common-plugin, Version: 5.0.4, Installed: bundled)
Workbox - Confluence Provider Plugin (com.atlassian.mywork.mywork-confluence-provider-plugin, Version: 5.0.4, Installed: bundled)
Workbox - Host Plugin (com.atlassian.mywork.mywork-confluence-host-plugin, Version: 5.0.4, Installed: bundled)
atlassian-failure-cache-plugin (com.atlassian.atlassian-failure-cache-plugin, Version: 0.15, Installed: bundled)
atlassian-help-tips (com.atlassian.plugins.atlassian-help-tips, Version: 2.0.1, Installed: bundled)
confluence-browser-metrics (com.atlassian.confluence.plugins.confluence-browser-metrics, Version: 2.0.13, Installed: bundled)
confluence-software-blueprints (com.atlassian.confluence.plugins.confluence-software-blueprints, Version: 3.1.7, Installed: bundled)
jquery (com.atlassian.plugins.jquery, Version: 1.7.2.1-confluence-custom-m03, Installed: bundled)

2017-07-11 17:51:11,979 INFO [localhost-startStop-1] [com.atlassian.confluence.lifecycle] init Confluence is ready to serve
2017-07-11 18:00:00,308 WARN [scheduler_Worker-4] [hql.internal.ast.HqlSqlWalker] generatePositionalParameter [DEPRECATION] Encountered positional parameter near line 1, column 110 in HQL: [SELECT usr.name, usr.lowerName FROM com.atlassian.crowd.model.user.InternalUser usr WHERE usr.directory.id = ? ORDER BY usr.lowerName]. Positional parameter are considered deprecated; use named parameters or JPA-style positional parameters instead.
2017-07-12 01:54:23,301 WARN [Caesium-1-1] [atlassian.upm.pac.PacClientImpl] getUpdates Update check request may take longer because of the number of add-ons
2017-07-12 13:00:03,820 WARN [scheduler_Worker-6] [hql.internal.ast.HqlSqlWalker] generatePositionalParameter [DEPRECATION] Encountered positional parameter near line 1, column 131 in HQL: [SELECT mem.parentGroup.name FROM com.atlassian.crowd.embedded.hibernate2.HibernateMembership mem WHERE mem.userMember.lowerName = ? and mem.parentGroup.directory.id = ? ORDER BY mem.parentGroup.lowerName]. Positional parameter are considered deprecated; use named parameters or JPA-style positional parameters instead.
2017-07-12 13:00:03,852 WARN [scheduler_Worker-6] [hql.internal.ast.HqlSqlWalker] generatePositionalParameter [DEPRECATION] Encountered positional parameter near line 1, column 168 in HQL: [SELECT mem.parentGroup.name FROM com.atlassian.crowd.embedded.hibernate2.HibernateMembership mem WHERE mem.userMember.lowerName = ? and mem.parentGroup.directory.id = ? ORDER BY mem.parentGroup.lowerName]. Positional parameter are considered deprecated; use named parameters or JPA-style positional parameters instead.
2017-07-13 01:54:23,385 WARN [Caesium-1-2] [atlassian.upm.pac.PacClientImpl] getUpdates Update check request may take longer because of the number of add-ons
2017-07-14 01:54:23,422 WARN [Caesium-1-1] [atlassian.upm.pac.PacClientImpl] getUpdates Update check request may take longer because of the number of add-ons

I currently have set my postgresql back to 9.4 btw.

[AnnWorley]

I am curious why the log is from the 11th - was that the last time it was started? 

This line is significant:

2017-07-11 17:51:11,979 INFO [localhost-startStop-1] [com.atlassian.confluence.lifecycle] init Confluence is ready to serve

 Since it's not followed by any report of Confluence shutting down again, I am hoping Confluence is serving but we are not accessing it on the right URL. Can you access the instance using the IP of the server and the port? This would bypass any issues with DNS or the proxy. If your network will allow it, please try http://<server_IP>:8090 and see if the login page comes up.

If there is an error message in the browser (besides the generic 404) please let me know what it says.

[Graham van der Wielen]

Indeed, last time I (re)started. I can of course do that again and get you a more current log.

I tried accessing it before on http://<server_IP>:8090 but got 404. Even now I get that. I even tried it from cli with lynx and curl. curl outputs a bit more than the rest:

$ curl -I http://<server_IP>:8090
HTTP/1.1 404 Not Found
Server: Apache-Coyote/1.1
Transfer-Encoding: chunked
Date: Fri, 14 Jul 2017 20:34:48 GMT

[Graham van der Wielen]

Might have posted to early...it seems that it does work on http://<Server_IP_or_DNS:8090/wiki/

Let me check somethings.

[AnnWorley]

That's good news, now we just have to get NGINX to act right. I should have checked your server.xml for a context path - the symptom of not putting the context path on the URL is usually a blank page and not a 404, so I was mistaken.

[Graham van der Wielen]

Seems the nginx reversed proxy is working now too. I'm rather confused. Maybe it just took a long time to load, more then usually, it isn't the fastest server. Still weird to get a 404 via the reversed proxy. And it certainly didn't work while using postgresql 9.6.

I guess I should at least upgrade my confluence to the lastest 6.2.4. 

[AnnWorley]

In case you want the very latest, Confluence 6.3.1 is out and supports PostgreSQL 9.6:

Supported Platforms

[Graham van der Wielen]

That's great. I shutdown my confluence, made some backups, upgraded postgresql from 9.4 to 9.6 (with some helpful tips from https://scottlinux.com/2015/11/14/upgrade-postgresql-on-debian-jessie-with-pg_upgradecluster/ but replaced version numbers where needed and didn't drop the old cluster yet). Then upgraded confluence to 6.3.1 and it all worked fine!

After that I did a dropcluster and removed the postgresql-9.4 packages.

Thanks again!

[AnnWorley]

Thanks for following up to let us know you did a sucessfull upgrade! Congratulations. :)

[Graham van der Wielen]

No problem. I was pleasantly surprised about the support via community (still via Atlassian Team) instead direct support. Wasn't sure what to expect when the direct support was dropped for starter licenses but I have to say I haven't noticed any difference worth mentioning.

Keep up the good work!