DynComp: a fatal error has been detected by the Java Runtime Environment (ClassNotFoundException)

[boyang9602]

Hi,

I met another JVM fatal error, different from #340. It only happens to Chart-19. Below is the output

$ java -Xmx43G -cp /home/ubuntu/daikon-5.8.8/daikon.jar:build/:build-tests/:/home/ubuntu/APR_Projects/Chart/19/Chart19f/lib/itext-2.0.2.jar:/home/ubuntu/APR_Projects/Chart/19/Chart19f/lib/itext-2.0.6.jar:/home/ubuntu/APR_Projects/Chart/19/Chart19f/lib/junit.jar:/home/ubuntu/APR_Projects/Chart/19/Chart19f/lib/servlet.jar:/home/ubuntu/launcher/ daikon.DynComp '--ppt-select-pattern=^org\.jfree\.chart\.plot\.CategoryPlot' --output-dir=ft_invariants_files0 TestRunner org.jfree.chart.plot.junit.CategoryPlotTests::testGetRangeAxisIndex org.jfree.chart.plot.junit.CategoryPlotTests::testGetDomainAxisIndex |& tee ft_invariants_files0/dyncomp-output.txt
java.lang.ClassNotFoundException
 - klass: 'java/lang/ClassNotFoundException'
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  Internal Error (exceptions.cpp:460), pid=28779, tid=0x00007f2e6605b700
#  fatal error: ExceptionMark constructor expects no pending exceptions
#
# JRE version: OpenJDK Runtime Environment (8.0_292-b10) (build 1.8.0_292-8u292-b10-0ubuntu1~18.04-b10)
# Java VM: OpenJDK 64-Bit Server VM (25.292-b10 mixed mode linux-amd64 )
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/ubuntu/APR_Projects/Chart/19/Chart19f/hs_err_pid28779.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
#

If I run the tests directly, it works fine,

$ java -Xmx43G -cp /home/ubuntu/daikon-5.8.8/daikon.jar:build/:build-tests/:/home/ubuntu/APR_Projects/Chart/19/Chart19f/lib/itext-2.0.2.jar:/home/ubuntu/APR_Projects/Chart/19/Chart19f/lib/itext-2.0.6.jar:/home/ubuntu/APR_Projects/Chart/19/Chart19f/lib/junit.jar:/home/ubuntu/APR_Projects/Chart/19/Chart19f/lib/servlet.jar:/home/ubuntu/launcher/  TestRun
ner org.jfree.chart.plot.junit.CategoryPlotTests::testGetRangeAxisIndex org.jfree.chart.plot.junit.CategoryPlotTests::testGetDomainAxisIndex
SUCCESS
SUCCESS

ubuntu@repair:~$ java -version
openjdk version "1.8.0_292"
OpenJDK Runtime Environment (build 1.8.0_292-8u292-b10-0ubuntu1~18.04-b10)
OpenJDK 64-Bit Server VM (build 25.292-b10, mixed mode)

The steps to reproduce the issue:

1. install defects4j, https://github.com/rjust/defects4j
2. checkout the Chart-19f using defects4j checkout -p Chart -v 19f -w Chart19f
3. go to Chart19f and compile the project using defects4j compile
4. compile the TestRunner
5. go to Chart19f and run CLASSPATH=$(find "$PWD" -name '*.jar' -type f -printf ':%p\n' | sort -u | tr -d '\n'); java -Xmx43G -cp $DAIKONDIR/daikon.jar:build/:build-tests/$CLASSPATH:<TestRunner path> TestRunner org.jfree.chart.plot.junit.CategoryPlotTests::testGetRangeAxisIndex org.jfree.chart.plot.junit.CategoryPlotTests::testGetDomainAxisIndex

[markro49]

I am unable to reproduce this problem. I followed your steps and all looks ok:
[markro@buffalo Chart19f]$ java -cp /scratch/markro/clones/daikon/daikon.jar:build/:build-tests/:$CLASSPATH:. daikon.DynComp '--ppt-select-pattern=^org.jfree.chart.plot.CategoryPlot' --output-dir=ft_invariants_files0 TestRunner org.jfree.chart.plot.junit.CategoryPlotTests::testGetRangeAxisIndex org.jfree.chart.plot.junit.CategoryPlotTests::testGetDomainAxisIndex
SUCCESS
SUCCESS
[markro@buffalo Chart19f]$ l -rt ft_invariants_files0
total 4148
drwxr-xr-x 14 markro rtech_cs 4096 May 25 12:23 ..
drwxr-xr-x 2 markro rtech_cs 4096 May 25 12:23 .
-rw-r--r-- 1 markro rtech_cs 4237887 May 25 12:27 TestRunner.decls-DynComp
[markro@buffalo Chart19f]$
I am using Daikon #338.

[boyang9602]

Thank you for your reply. Here is my machine info:

Distributor ID: Ubuntu
Description:    Ubuntu 18.04.2 LTS
Release:        18.04
Codename:       bionic

I can always reproduce it on this machine. I'll try if the problem could be reproduced on other machines and update it here.

[markro49]

I was able to reproduce on Ubuntu 18.04. I haven't tried 20.04. Are you able to try 20.04?

[boyang9602]

Yes, my 20.04 is a windows subsystem, it is a little bit slow. It is compiling DynComp now, I will update it later.

[boyang9602]

I can reproduce it on Ubuntu 20.04.

bo@LAPTOP-E1MFF41S:/mnt/c/Users/boyan/projects/APR_Projects/Chart19f$ java -cp $DAIKONDIR/daikon.jar:build/:build-tests/:$CLASSPATH:. daikon.DynComp '--ppt-select-pattern=^org.jfree.chart.plot.CategoryPlot' --output-dir=ft_invariants_files0 TestRunner org.jfree.chart.plot.junit.CategoryPlotTests::testGetRangeAxisIndex org.jfree.chart.plot.junit.CategoryPlotTests::testGetDomainAxisIndex
java.lang.ClassNotFoundException
 - klass: 'java/lang/ClassNotFoundException'
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  Internal Error (exceptions.cpp:460), pid=8591, tid=0x00007fc1e8b6f700
#  fatal error: ExceptionMark constructor expects no pending exceptions
#
# JRE version: OpenJDK Runtime Environment (8.0_292-b10) (build 1.8.0_292-8u292-b10-0ubuntu1~20.04-b10)
# Java VM: OpenJDK 64-Bit Server VM (25.292-b10 mixed mode linux-amd64 compressed oops)
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /mnt/c/Users/boyan/projects/APR_Projects/Chart19f/hs_err_pid8591.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
#
bo@LAPTOP-E1MFF41S:/mnt/c/Users/boyan/projects/APR_Projects/Chart19f$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 20.04.1 LTS
Release:        20.04
Codename:       focal

[markro49]

I have found the problem and it appears to be a bug in the Ubuntu JVM. The root cause is that the build of Chart19f fails to build a valid version of lib/itext-2.0.6.jar:

markro ~/defects4j/Chart19f]$ jar -tf lib/itext-2.0.6.jar
java.util.zip.ZipException: error in opening zip file
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.(ZipFile.java:225)
at java.util.zip.ZipFile.(ZipFile.java:155)
at java.util.zip.ZipFile.(ZipFile.java:126)
at sun.tools.jar.Main.list(Main.java:1115)
at sun.tools.jar.Main.run(Main.java:293)
at sun.tools.jar.Main.main(Main.java:1288)
markro ~/defects4j/Chart19f]$

If you remove this jar from CLASSPATH all works fine. If you leave the bad jar in the classpath both CentOS and Fedora still work fine and output the message:
CLASSPATH component /home/markro/defects4j/Chart19f/lib/itext-2.0.6.jar: java.util.zip.ZipException: error in opening zip file

Ubuntu core dumps instead => I think its a bug in Ubuntu JVM.

Bottom line: remove itext-2.0.6.jar from classpath and/or run on Fedora instead.