java.lang.OutOfMemoryError when 'java -jar gatk-package-4.1.2.0-local.jar' sometimes, but there is a lot of memory yet

wangyugui commented 5 years ago

Bug Report

java.lang.OutOfMemoryError when 'java -jar /usr/hpc-bio/gatk/gatk-package-4.1.2.0-local.jar' sometimes, but there is a lot of memeory yet.

And then all features can not be used.

This is the call stack.

java  -jar gatk/gatk-package-4.1.2.0-local.jar
Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit
        at java.util.Properties$LineReader.readLine(Properties.java:485)
        at java.util.Properties.load0(Properties.java:353)
        at java.util.Properties.load(Properties.java:317)
        at org.aeonbits.owner.loaders.PropertiesLoader.load(PropertiesLoader.java:50)
        at org.aeonbits.owner.loaders.PropertiesLoader.load(PropertiesLoader.java:43)
        at org.aeonbits.owner.LoadersManager.load(LoadersManager.java:46)
        at org.aeonbits.owner.Config$LoadType$2.load(Config.java:129)
        at org.aeonbits.owner.PropertiesManager.doLoad(PropertiesManager.java:290)
        at org.aeonbits.owner.PropertiesManager.load(PropertiesManager.java:163)
        at org.aeonbits.owner.PropertiesManager.load(PropertiesManager.java:153)
        at org.aeonbits.owner.PropertiesInvocationHandler.<init>(PropertiesInvocationHandler.java:54)
        at org.aeonbits.owner.DefaultFactory.create(DefaultFactory.java:46)
        at org.aeonbits.owner.ConfigCache.getOrCreate(ConfigCache.java:87)
        at org.aeonbits.owner.ConfigCache.getOrCreate(ConfigCache.java:40)
        at org.broadinstitute.hellbender.utils.config.ConfigFactory.getOrCreate(ConfigFactory.java:268)
        at org.broadinstitute.hellbender.utils.config.ConfigFactory.getOrCreateConfigFromFile(ConfigFactory.java:454)
        at org.broadinstitute.hellbender.utils.config.ConfigFactory.initializeConfigurationsFromCommandLineArgs(ConfigFactory.java:439)
        at org.broadinstitute.hellbender.utils.config.ConfigFactory.initializeConfigurationsFromCommandLineArgs(ConfigFactory.java:414)
        at org.broadinstitute.hellbender.Main.parseArgsForConfigSetup(Main.java:121)
        at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(Main.java:179)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:204)
        at org.broadinstitute.hellbender.Main.main(Main.java:291)

Affected version(s)

[x] Latest public release version [version?] Yes. 4.1.2.0
[ ] Latest master branch as of [date of test?] Not tested.

Steps to reproduce

Yet not clear. maybe the call stack above will help.

wangyugui commented 5 years ago

Maybe some relationship to multiple GATK4 process and the same time.

This problem happen on both java 8 and java 11.

# java -version
openjdk version "1.8.0_212"
OpenJDK Runtime Environment (build 1.8.0_212-b04)
OpenJDK 64-Bit Server VM (build 25.212-b04, mixed mode)
# java11 -version
openjdk version "11.0.3" 2019-04-16 LTS
OpenJDK Runtime Environment 18.9 (build 11.0.3+7-LTS)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.3+7-LTS, mixed mode, sharing)

davidbenjamin commented 4 years ago

@wangyugui What tool are you running? What is the maximum depth of your sample? How much RAM does your machine have? How much RAM did you request in your Java command?

wangyugui commented 4 years ago

The command was 'java -jar gatk/gatk-package-4.1.2.0-local.jar'. It should output the help message. The server has 256G memory.

there should be a bug of linux kernel or java jvm or gatk of some version.

Let's close it before I can reproduce it.

broadinstitute / gatk