Hi,
The JVM crash with SIGBUS looks like:
https://bugs.openjdk.java.net/browse/JDK-8168628
and see the comment 22-05-2018
"This change has been backed out of JDK 11 as it break sparse files."
which refers to:
https://bugs.openjdk.java.net/browse/JDK-8191278
fixed in version 14. Looks like a backport as well to java8 but that
might be OpenJDK8 only. Mikael is running java-8-oracle - not clear if
that has a backport.
I can't connect that to why the Fuseki nodetable becomes broken because
the transaction shouldn't happen. Even a partial commit should be
recovered (the journal is replayed on start-up if it has entries).
Andy
On 21/05/2021 09:14, Harri Kiiskinen wrote:
I seem to have similar problems as M. Pesonen in the other chain.
Summary:
Fuseki server encountered a "disk full" situation (see log and error
report below) during update leading to crash. After restart, some parts
of the database are corrupted: dump and compact fail with
NodeTableTRDF/Read exceptions (see third error log below), as well as
some queries, but not all.
The corruption has taken place in another dataset than the one that was
being update when the disk full occurred.
Logs below,
best
Harri Kiiskinen
Fuseki log for "disk full" crash:
--------------------------------------------------------------------
fuseki-server[216149]: [2021-05-20 21:37:07] Fuseki INFO [182050]
Update
fuseki-server[216149]: #
fuseki-server[216149]: # A fatal error has been detected by the Java
Runtime Environment:
fuseki-server[216149]: #
fuseki-server[216149]: # SIGBUS (0x7) at pc=0x00007f2b608b7e15,
pid=216149, tid=768713
...
--------------------------------------------------------------------
The error report /tmp/hs_err_pid216149.log:
----------------------------------------------------------------------
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGBUS (0x7) at pc=0x00007f2b608b7e15, pid=216149, tid=768713
#
# JRE version: OpenJDK Runtime Environment (11.0.11+9) (build
11.0.11+9-Ubuntu-0ubuntu2.20.04)
# Java VM: OpenJDK 64-Bit Server VM (11.0.11+9-Ubuntu-0ubuntu2.20.04,
mixed mode, sharing, tiered, compressed oops, g1 gc, linux-amd64)
# Problematic frame:
# v ~StubRoutines::jint_disjoint_arraycopy
#
# Core dump will be written. Default location: Core dumps may be
processed with "/usr/share/apport/apport %p %s %c %d %P %E" (or dumping
to //core.216149)
#
# If you would like to submit a bug report, please visit:
# https://bugs.launchpad.net/ubuntu/+source/openjdk-lts
#
--------------- S U M M A R Y ------------
Command Line: -Xmx2G org.apache.jena.fuseki.cmd.FusekiCmd
--jetty-config=/etc/fuseki/fuseki-jetty-https.xml
Host: Intel(R) Xeon(R) Gold 6254 CPU @ 3.10GHz, 2 cores, 15G, Ubuntu
20.04.2 LTS
Time: Thu May 20 21:37:07 2021 EEST elapsed time: 1517007.667502 seconds
(17d 13h 23m 27s)
...
Error message when running tdb2.tdbcompact
-----------------------------------------------------------------
org.apache.jena.tdb2.TDBException: NodeTableTRDF/Read
at
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87)
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:52)
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:206)
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:131)
...
at tdb2.tdbcompact.main(tdbcompact.java:28)
Caused by: org.apache.thrift.protocol.TProtocolException: Unrecognized
type 0
at
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:144)
at
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:60)
at
org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:433)
at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224)
at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213)
at org.apache.thrift.TUnion.read(TUnion.java:138)
at
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:82)
... 27 more
-----------------------------------------------------------------------
