Java VM 因堆大小增加而失败
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Java VM fails with heap size increase
提问by Tom
S0 the command I am trying to run is;
S0 我试图运行的命令是；
java -jar -Xmx290G /ibers/ernie/home/thh32/rumenISPG/GenomeAnalysisTK.jar -T VariantFiltration -R Contigs_1.fa -V Rank10_clean.fasta.gz.Contig_1-sort.bam.vcf1.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQuality RankSum < -12.5 " --filterName "testing_filter" -o filtered_snps.vcf
The machine I am running it on has access to 500G RAM so shouldnt be an issue, however I keep getting this error message;
我正在运行它的机器可以访问 500G RAM，所以应该不是问题，但是我不断收到此错误消息；
Error occurred during initialization of VM
Unable to allocate 9502720KB bitmaps for parallel garbage collection for the requested 304087040KB heap.
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Has anyone else experienced this issue and if so did you resolve it?
有没有其他人遇到过这个问题，如果有，你解决了吗？
Oh also just incase people wonder why I am giving this program so much memory, when I didnt I got this message which indicates that it needs more RAM. This was with 100G heaps size.
哦也只是为了防止人们想知道为什么我给这个程序这么多内存，当我没有收到这条消息时，表明它需要更多的内存。这是 100G 的堆大小。
INFO 09:55:57,953 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:55:57,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
INFO 09:55:57,956 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 09:55:57,956 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 09:55:57,961 HelpFormatter - Program Args: -T VariantFiltration -R Contigs_1.fa -V Rank10_clean.fasta.gz.Contig_1-sort.bam.vcf1.vcf --filterExpression QD < 2.0 || FS > 60.0 ||
MQ < 40.0 || HaplotypeScore > 13.0 || MappingQuality RankSum < -12.5 --filterName testing_filter -o filtered_snps.vcf
INFO 09:55:57,967 HelpFormatter - Executing as thh32@node011 on Linux 2.6.32-504.30.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_40-b26.
INFO 09:55:57,968 HelpFormatter - Date/Time: 2015/10/27 09:55:57
INFO 09:55:57,968 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:55:57,969 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:55:58,474 GenomeAnalysisEngine - Strictness is SILENT
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.4-46-gbc02625):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java
##### ERROR ------------------------------------------------------------------------------------------
Thanks, Tom
谢谢，汤姆
回答by Bhushan Karmarkar
Reduce the values in Xms and Xmx parameters in JAVA_OPTS. Set the values based on how much is required for your application and considering available RAM space.
减少 JAVA_OPTS 中 Xms 和 Xmx 参数中的值。根据您的应用程序需要多少并考虑可用 RAM 空间来设置值。
