generating ,hic for big files: java heap space error

[Zhang Cheng]

Hi, 

I was trying to generate a few big .hic files, but encounter the `java.lang.OutOfMemoryError: Java heap space` error .

1. I was using pbs and requested 128gb mem 

2. I exported java options as suggested by the previous conversations in the group 

The full log is here: 

+Mon Aug 31+13:58:38 export 'IBM_JAVA_OPTIONS=-Xmx49152m -Xgcthreads1'

+Mon Aug 31+13:58:38 IBM_JAVA_OPTIONS='-Xmx49152m -Xgcthreads1'

+Mon Aug 31+13:58:38 export '_JAVA_OPTIONS=-Xmx49152m -Xms49152m'

+Mon Aug 31+13:58:38 _JAVA_OPTIONS='-Xmx49152m -Xms49152m'

+Mon Aug 31+13:58:38 juiceDir=/home/zhc268/scratch/juicer/scripts/common

+Mon Aug 31+13:58:38 /home/zhc268/scratch/juicer/scripts/common/juicer_tools pre -s /home/zhc268/scratch/juicer/work/RMM_307_1_2_3_RMM_308_1_2_3/mega/aligned//inter.txt -g /home/zhc268/scratch/juicer/work/RMM_307_1_2_3_RMM_308_1_2_3/mega/aligned//inter_hists.m -q 1 /home/zhc268/scratch/juicer/work/RMM_307_1_2_3_RMM_308_1_2_3/mega/aligned//merged_nodups.txt /home/zhc268/scratch/juicer/work/RMM_307_1_2_3_RMM_308_1_2_3/mega/aligned//inter.hic hg19

Picked up _JAVA_OPTIONS: -Xmx49152m -Xms49152m

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

        at java.base/java.util.Arrays.copyOf(Arrays.java:3689)

        at java.base/java.util.ArrayList.grow(ArrayList.java:237)

        at java.base/java.util.ArrayList.grow(ArrayList.java:242)

        at java.base/java.util.ArrayList.add(ArrayList.java:485)

        at java.base/java.util.ArrayList.add(ArrayList.java:498)

        at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.createWholeGenomeRecords(GenomeWideNormalizationVectorUpdater.java:207)

        at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.getWGVectors(GenomeWideNormalizationVectorUpdater.java:134)

        at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.updateHicFileForGWfromPreOnly(GenomeWideNormalizationVectorUpdater.java:226)

        at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:76)

        at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:126)

        at juicebox.tools.HiCTools.main(HiCTools.java:96)

The size of input `merged_nodups.txt` is 

822G Aug 26 18:30 /home/zhc268/scratch/juicer/work/RMM_307_1_2_3_RMM_308_1_2_3/mega/aligned//merged_nodups.txt

Do you have any suggestions? 

Best 

Frank

[Zhang Cheng]

The output logs are: 

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

WARN [2020-08-31T13:58:39,546]  [Globals.java:138] [main]  Development mode is enabled

Not including fragment map

Start preprocess

Writing header

Writing body

......................................................................................................................................................................................................................................................................................................................................

Writing footer

Finished preprocess

Calculating norms for zoom BP_2500000

Calculating norms for zoom BP_1000000

Calculating norms for zoom BP_500000

Calculating norms for zoom BP_250000

Calculating norms for zoom BP_100000

Calculating norms for zoom BP_50000

Calculating norms for zoom BP_25000

Calculating norms for zoom BP_10000

-------------

9.2G Sep  1 02:30 /home/zhc268/scratch/juicer/work/RMM_307_1_2_3_RMM_308_1_2_3/mega/aligned/inter.hic 

inter.hic was generated but without KR normalization info. When dump KR norm, it shows `Norm KR missing`

[Muhammad Saad Shamim]

Hey Frank,

It seems as though the java lines weren't updated to use 128GB, so the JVM was still 50GB or so.

You'll need to update the JAVA_OPTIONS and juicertools script to use -Xmx128g etc.

Best,

- Muhammad Saad Shamim

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[Zhang Cheng]

Hi Muhammad, 

Thanks for your reply. 

Are you suggesting to increase JVM from 50gb to 128gb etc? I can try that. 

Do you have any idea what's the minimal JVM mem  given a 822G merge_nodup.txt? I've try 16gb, 64gb but all failed in KR norm. 

Sorry for the confusion, 128gb was what I requested from pbs clusters and not the JVM mem. I am going to try a bigger JVM mem as you suggested. 

Best 

Frank

Zhang (Frank) Cheng

[Tom]

Hi Frank,

Have you solved this problem? I was stuck with the same problem and still don't know the proper way to fix it.

Thanks,

T