SegmentNotFoundException in AEM logs and Instance not working

Download oak-run jar file from here http://repo1.maven.org/maven2/org/apache/jackrabbit/oak-run/

Stop AEM.

Run this command:

java -jar oak-run-*.jar check --bin=-1 crx-quickstart/repository/segmentstore/

This command searches backwards through the revisions until it finds a consistent one:

14:00:30.783 [main] INFO  o.a.j.o.p.s.f.t.ConsistencyChecker - Found latest good revision afdb922d-ba53-4a1b-aa1b-1cb044b535cf:234880

(In case the ConsistencyChecker fails, go to the next section)

Revert the repository to this revision by editing.

/crx-quickstart/repository/segmentstore/journal.log.

Delete all lines after the line containing the latest good revision. If you would like to find out what date and time you are reverting the repository to, run this command in the segmentstore folder (replace afdb922d-ba53-4a1b-aa1b-1cb044b535cf with the latest good revision in your journal.log):

find . -type f -name "data*.tar" -exec sh -c "tar -tvf {} |grep afdb922d-ba53-4a1b-aa1b-1cb044b535cf" \; -print

The output would show you an approximate date and time of that revision.

Remove all ./crx-quickstart/repository/segmentstore/*.bak files.

If using AEM6.0, then download the oak-run version matching what is installed in AEM for the remaining steps.  Download it from here http://repo1.maven.org/maven2/org/apache/jackrabbit/oak-run/.

Run checkpoint clean-up to remove orphaned checkpoints:

java -jar oak-run-*.jar checkpoints ./crx-quickstart/repository/segmentstore rm-unreferenced.

Finally compact the repository:

java -jar oak-run-*.jar compact ./crx-quickstart/repository/segmentstore/

Stop AEM.

Use the Oak run console and load the childCount groovy script to identify the corrupt nodes in the segment store:

Load the oak-run console shell:

java -jar oak-run-*.jar console crx-quickstart/repository/segmentstore

Run the two commands below in the shell to load the script and run it:

:load https://gist.githubusercontent.com/stillalex/e7067bcb86c89bef66c8/raw/d7a5a9b839c3bb0ae5840252022f871fd38374d3/childCount.groovy

countNodes(session.workingNode)

This results in the following output indicating the path to the corrupted node(s):

21:21:42.029 [main] ERROR o.a.j.o.p.segment.SegmentTracker - Segment not found: 63ae05a4-b506-445c-baa2-cfa1b13b6e2f. Creation date delta is 3 ms.
warning unable to read node /content/dam/test.txt/jcr:content/renditions/original/jcr:content

In some cases the issue is linked to binary properties and the childCount groovy script is unable to locate any corrupted nodes.  In these cases you can use the following command instead which will read the first 1024 bytes for every binary encountered during the traversal (Please note this command will be slower and should only be used when the one above doesn't return the expected results):

countNodes(session.workingNode,true)

Remove all the identified corrupted nodes listed in the output of the last command using rmNodes.groovy

Load the oak-run console shell:

java -jar oak-run-*.jar console crx-quickstart/repository/segmentstore

Load the groovy script:

:load https://gist.githubusercontent.com/stillalex/43c49af065e3dd1fd5bf/raw/9e726a59f75b46e7b474f7ac763b0888d5a3f0c3/rmNode.groovy

Run the rmNode command to remove the corrupt node, replace /path/to/corrupt/node with the path to the corrupt node you need to remove.

rmNode(session, "/path/to/corrupt/node")

Where the corrupt node path is the path obtained in step 2, for example: "/content/dam/test.txt/jcr:content/renditions/original/jcr:content/"

Repeat step 3 for all nodes found in step 2.

This above rmNode command should return true for the corrupt path, which means it deleted it. Make sure these found three corrupt paths get deleted by re-running the rmNode command on those paths. Next run it should return false.

If still you see that the same paths are there in repository, then use the patched version of oak-run jar i.e. oak-run-1.2.18-NPR-17596

What does patched version of Oak run Jar Do?

This version of jar skips unreadable binaries on compaction replacing them with 0-byte binaries and logging the exception and the path to syserr. The thus compacted repository should then pass oak-run check, the node count script and you should also be able to compact it again using a non- patched oak-run.

Perform a checkpoint cleanup by listing checkpoints using below. If there are more than one checkpoint, then clean them up:

nohup java -Xmx4096m -jar oak-run-1.2.18.jar checkpoints /app/AEM6/author/crx-quickstart/repository/segmentstore rm-all>>nohup.out &

Run an offline compaction.  If you do not know how to run offline compaction then see here.

Start the server wait for indexing completion.