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Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Loading Native Libraries causes segfault #4158

Open apeltzer opened 6 years ago

apeltzer commented 6 years ago

Hi!

I've created a container using Singularity and Alpine Linux 3.7, including all the mentioned dependencies for GATK 4.0.0.0 (JDK8, GCC, R, R-Dev, Python, libgomp) and tried running HaplotypeCaller on a sample of mine to test everything.

Unfortunately, it always breaks when running the steps with the JNI libraries. If I start running things on native Java (without the C++ libraries), things work well.

I copied my log file and the command + hs_err file in here.

Anything I missed here?

Using GATK jar /usr/bin/gatk-package-4.0.0.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -Xmx16g -jar /usr/bin/gatk-package-4.0.0.0-local.jar HaplotypeCaller -I file.bam -R human_g1k_v37.fasta -O test.vcf -ERC GVCF --create-output-variant-index --annotation MappingQualityRankSumTest --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation FisherStrand --annotation Coverage --dbsnp dbsnp_138.b37.vcf --verbosity INFO
12:18:41.830 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/bin/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:18:42.092 INFO  HaplotypeCaller - ------------------------------------------------------------
12:18:42.092 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.0.0
12:18:42.092 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
12:18:42.092 INFO  HaplotypeCaller - Executing as iiipe01@node050 on Linux v3.10.0-693.2.2.el7.x86_64 amd64
12:18:42.092 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_151-b12
12:18:42.092 INFO  HaplotypeCaller - Start Date/Time: January 15, 2018 12:18:41 PM GMT
12:18:42.092 INFO  HaplotypeCaller - ------------------------------------------------------------
12:18:42.092 INFO  HaplotypeCaller - ------------------------------------------------------------
12:18:42.093 INFO  HaplotypeCaller - HTSJDK Version: 2.13.2
12:18:42.093 INFO  HaplotypeCaller - Picard Version: 2.17.2
12:18:42.093 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 1
12:18:42.093 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:18:42.093 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:18:42.093 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:18:42.093 INFO  HaplotypeCaller - Deflater: IntelDeflater
12:18:42.093 INFO  HaplotypeCaller - Inflater: IntelInflater
12:18:42.093 INFO  HaplotypeCaller - GCS max retries/reopens: 20
12:18:42.093 INFO  HaplotypeCaller - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
12:18:42.093 INFO  HaplotypeCaller - Initializing engine
12:18:42.597 INFO  FeatureManager - Using codec VCFCodec to read file file:///beegfs/work/zxmai83/Reference/dbs/b37/dbsnp_138.b37.vcf
12:18:42.723 INFO  HaplotypeCaller - Done initializing engine
12:18:42.732 INFO  HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
12:18:42.732 INFO  HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
12:18:43.546 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/usr/bin/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
12:18:43.549 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/usr/bin/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
12:18:43.599 WARN  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00002b5f92e39fab, pid=85482, tid=0x00002b5f56e60ae8
#
# JRE version: OpenJDK Runtime Environment (8.0_151-b12) (build 1.8.0_151-b12)
# Java VM: OpenJDK 64-Bit Server VM (25.151-b12 mixed mode linux-amd64 compressed oops)
# Derivative: IcedTea 3.6.0
# Distribution: Custom build (Tue Nov 21 11:22:36 GMT 2017)
# Problematic frame:
# C  [libgomp.so.1+0x7fab]  omp_get_max_threads+0xb
#
# 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:
# /beegfs/work/iiipe01/Exome-Test/work/1e/fc972c6b14c8006857230849630a49/hs_err_pid85482.log
#
# If you would like to submit a bug report, please include
# instructions on how to reproduce the bug and visit:
#   http://icedtea.classpath.org/bugzilla
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

Here's the hs_err file:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00002b5f92e39fab, pid=85482, tid=0x00002b5f56e60ae8
#
# JRE version: OpenJDK Runtime Environment (8.0_151-b12) (build 1.8.0_151-b12)
# Java VM: OpenJDK 64-Bit Server VM (25.151-b12 mixed mode linux-amd64 compressed oops)
# Derivative: IcedTea 3.6.0
# Distribution: Custom build (Tue Nov 21 11:22:36 GMT 2017)
# Problematic frame:
# C  [libgomp.so.1+0x7fab]  omp_get_max_threads+0xb
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please include
# instructions on how to reproduce the bug and visit:
#   http://icedtea.classpath.org/bugzilla
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  T H R E A D  ---------------

Current thread (0x00005648765c2000):  JavaThread "main" [_thread_in_native, id=85483, stack(0x00002b5f56d60000,0x00002b5f56e60aa8)]

siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0000000000000091

Registers:
RAX=0x0000000000000091, RBX=0x00005648765c21e0, RCX=0x0000000000000020, RDX=0x0000000000000000
RSP=0x00002b5f56e5fb80, RBP=0x0000000000000032, RSI=0x0000000000000004, RDI=0x0000000000000000
R8 =0x00002b5f56e5fb10, R9 =0x00000000009d258d, R10=0x00000000000000b1, R11=0x0000000000001008
R12=0x0000000000000004, R13=0x0000000000000062, R14=0x0000000000000000, R15=0x0000000000000000
RIP=0x00002b5f92e39fab, EFLAGS=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00002b5f56e5fb80)
0x00002b5f56e5fb80:   0000000000000000 00002b5f930b9554
0x00002b5f56e5fb90:   00002b5f56e5fd38 00002b5f930b9350
0x00002b5f56e5fba0:   0000000000000000 0000000000000000
0x00002b5f56e5fbb0:   00002b5f92b76500 0000000000000000
0x00002b5f56e5fbc0:   0000000000000000 0000000000000000
0x00002b5f56e5fbd0:   0000000000000000 0000000000000000
0x00002b5f56e5fbe0:   0000000000000000 0000000000000000
0x00002b5f56e5fbf0:   0000000000000000 0000000000000000
0x00002b5f56e5fc00:   0000000000000000 0000000000000000
0x00002b5f56e5fc10:   0000000000000000 0000000000000000
0x00002b5f56e5fc20:   0000000000000000 0000000000000000
0x00002b5f56e5fc30:   0000000000000000 0000000000000000
0x00002b5f56e5fc40:   00005648765c2000 4a69b553d0bbd568
0x00002b5f56e5fc50:   00002b5f92b76578 00002b5f92b76578
0x00002b5f56e5fc60:   00002b5f56e5fd00 0000000000000000
0x00002b5f56e5fc70:   00002b5f92b76570 00002b5f56e5fd40
0x00002b5f56e5fc80:   00005648765c2000 00002b5f58a50774
0x00002b5f56e5fc90:   00002b5f00000000 00002b5f92b76578
0x00002b5f56e5fca0:   00002b5f56e5fd00 00002b5f58a504f9
0x00002b5f56e5fcb0:   fffffffe00000000 00002b5f58a504c2
0x00002b5f56e5fcc0:   00002b5f56e5fcc0 00002b5f92b76570
0x00002b5f56e5fcd0:   00002b5f56e5fd40 00002b5f92b767d8
0x00002b5f56e5fce0:   0000000000000000 00002b5f92b76578
0x00002b5f56e5fcf0:   0000000000000000 00002b5f56e5fd20
0x00002b5f56e5fd00:   00002b5f56e5fd88 00002b5f58a40ffd
0x00002b5f56e5fd10:   00000006704971f0 00002b5f58a4a278
0x00002b5f56e5fd20:   0000000000000000 0000000000000004
0x00002b5f56e5fd30:   0000000000000000 00000006704b9438
0x00002b5f56e5fd40:   00000006704b74f8 00002b5f56e5fd48
0x00002b5f56e5fd50:   00002b5f92b76255 00002b5f56e5fdb8
0x00002b5f56e5fd60:   00002b5f92b767d8 0000000000000000
0x00002b5f56e5fd70:   00002b5f92b76360 00002b5f56e5fd20 

Instructions: (pc=0x00002b5f92e39fab)
0x00002b5f92e39f8b:   08 e8 0f ff ff ff 8b 50 08 8b 40 0c 89 55 00 89
0x00002b5f92e39f9b:   03 58 5b 5d c3 48 83 ec 08 31 ff e8 f5 fe ff ff
0x00002b5f92e39fab:   48 8b 00 5a c3 48 83 ec 08 31 ff e8 e5 fe ff ff
0x00002b5f92e39fbb:   8b 40 14 ba ff ff ff 7f 85 c0 0f 48 c2 5a c3 85 

Register to memory mapping:

RAX=0x0000000000000091 is an unknown value
RBX=0x00005648765c21e0 is an unknown value
RCX=0x0000000000000020 is an unknown value
RDX=0x0000000000000000 is an unknown value
RSP=0x00002b5f56e5fb80 is pointing into the stack for thread: 0x00005648765c2000
RBP=0x0000000000000032 is an unknown value
RSI=0x0000000000000004 is an unknown value
RDI=0x0000000000000000 is an unknown value
R8 =0x00002b5f56e5fb10 is pointing into the stack for thread: 0x00005648765c2000
R9 =0x00000000009d258d is an unknown value
R10=0x00000000000000b1 is an unknown value
R11=0x0000000000001008 is an unknown value
R12=0x0000000000000004 is an unknown value
R13=0x0000000000000062 is an unknown value
R14=0x0000000000000000 is an unknown value
R15=0x0000000000000000 is an unknown value

Stack: [0x00002b5f56d60000,0x00002b5f56e60aa8],  sp=0x00002b5f56e5fb80,  free space=1022k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [libgomp.so.1+0x7fab]  omp_get_max_threads+0xb

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  com.intel.gkl.pairhmm.IntelPairHmm.initNative(Ljava/lang/Class;Ljava/lang/Class;ZIZ)V+0
j  com.intel.gkl.pairhmm.IntelPairHmm.initialize(Lorg/broadinstitute/gatk/nativebindings/pairhmm/PairHMMNativeArguments;)V+109
j  org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM.<init>(Lorg/broadinstitute/hellbender/utils/pairhmm/VectorLoglessPairHMM$Implementation;Lorg/broadinstitute/gatk/nativebindings/pairhmm/PairHMMNativeArguments;)V+183
j  org.broadinstitute.hellbender.utils.pairhmm.PairHMM$Implementation.lambda$static$6(Lorg/broadinstitute/gatk/nativebindings/pairhmm/PairHMMNativeArguments;)Lorg/broadinstitute/hellbender/utils/pairhmm/PairHMM;+8
j  org.broadinstitute.hellbender.utils.pairhmm.PairHMM$Implementation$$Lambda$13.apply(Ljava/lang/Object;)Ljava/lang/Object;+4
j  org.broadinstitute.hellbender.utils.pairhmm.PairHMM$Implementation.makeNewHMM(Lorg/broadinstitute/gatk/nativebindings/pairhmm/PairHMMNativeArguments;)Lorg/broadinstitute/hellbender/utils/pairhmm/PairHMM;+5
j  org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.<init>(BLorg/broadinstitute/gatk/nativebindings/pairhmm/PairHMMNativeArguments;Lorg/broadinstitute/hellbender/utils/pairhmm/PairHMM$Implementation;DLorg/broadinstitute/hellbender/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine$PCRErrorModel;B)V+70
j  org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils.createLikelihoodCalculationEngine(Lorg/broadinstitute/hellbender/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection;)Lorg/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine;+89
j  org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initialize(ZZ)V+207
j  org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.<init>(Lorg/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection;ZZLhtsjdk/samtools/SAMFileHeader;Lhtsjdk/samtools/reference/ReferenceSequenceFile;Lorg/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine;)V+100
j  org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.<init>(Lorg/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection;ZZLhtsjdk/samtools/SAMFileHeader;Lhtsjdk/samtools/reference/ReferenceSequenceFile;)V+9
j  org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.onTraversalStart()V+30
j  org.broadinstitute.hellbender.engine.GATKTool.doWork()Ljava/lang/Object;+1
j  org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool()Ljava/lang/Object;+27
j  org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs()Ljava/lang/Object;+239
j  org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain([Ljava/lang/String;)Ljava/lang/Object;+14
j  org.broadinstitute.hellbender.Main.runCommandLineProgram(Lorg/broadinstitute/hellbender/cmdline/CommandLineProgram;[Ljava/lang/String;)Ljava/lang/Object;+20
j  org.broadinstitute.hellbender.Main.mainEntry([Ljava/lang/String;)V+20
j  org.broadinstitute.hellbender.Main.main([Ljava/lang/String;)V+8
v  ~StubRoutines::call_stub

---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x000056487678c000 JavaThread "Service Thread" daemon [_thread_blocked, id=85493, stack(0x00002b5f8f3c8000,0x00002b5f8f4c8aa8)]
  0x000056487672d800 JavaThread "C1 CompilerThread1" daemon [_thread_blocked, id=85492, stack(0x00002b5f8f2c7000,0x00002b5f8f3c7aa8)]
  0x000056487672a000 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=85491, stack(0x00002b5f8f1c5000,0x00002b5f8f2c5aa8)]
  0x0000564876728000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=85490, stack(0x00002b5f8f0c3000,0x00002b5f8f1c3aa8)]
  0x00005648766f3800 JavaThread "Finalizer" daemon [_thread_blocked, id=85489, stack(0x00002b5f8efc2000,0x00002b5f8f0c2aa8)]
  0x00005648766f0800 JavaThread "Reference Handler" daemon [_thread_blocked, id=85488, stack(0x00002b5f8eec1000,0x00002b5f8efc1aa8)]
=>0x00005648765c2000 JavaThread "main" [_thread_in_native, id=85483, stack(0x00002b5f56d60000,0x00002b5f56e60aa8)]

Other Threads:
  0x00005648766e6800 VMThread [stack: 0x00002b5f8edc0000,0x00002b5f8eec0aa8] [id=85487]
  0x00005648767b7000 WatcherThread [stack: 0x00002b5f8f4ca000,0x00002b5f8f5caaa8] [id=85494]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap:
 PSYoungGen      total 1003520K, used 156121K [0x000000066ab00000, 0x00000006aef00000, 0x00000007c0000000)
  eden space 946688K, 10% used [0x000000066ab00000,0x0000000670bff978,0x00000006a4780000)
  from space 56832K, 99% used [0x00000006a5900000,0x00000006a9076d70,0x00000006a9080000)
  to   space 85504K, 0% used [0x00000006a9b80000,0x00000006a9b80000,0x00000006aef00000)
 ParOldGen       total 1497088K, used 20019K [0x00000003c0000000, 0x000000041b600000, 0x000000066ab00000)
  object space 1497088K, 1% used [0x00000003c0000000,0x00000003c138ceb0,0x000000041b600000)
 Metaspace       used 36791K, capacity 37258K, committed 37504K, reserved 1081344K
  class space    used 5023K, capacity 5176K, committed 5248K, reserved 1048576K

Card table byte_map: [0x00002b5f67df9000,0x00002b5f69dfa000] byte_map_base: 0x00002b5f65ff9000

Marking Bits: (ParMarkBitMap*) 0x00002b5f57e71fa0
 Begin Bits: [0x00002b5f6b656000, 0x00002b5f7b656000)
 End Bits:   [0x00002b5f7b656000, 0x00002b5f8b656000)

Polling page: 0x00002b5f56e61000

CodeCache: size=245760Kb used=5233Kb max_used=5233Kb free=240526Kb
 bounds [0x00002b5f58a39000, 0x00002b5f58f59000, 0x00002b5f67a39000]
 total_blobs=2060 nmethods=1583 adapters=391
 compilation: enabled

Compilation events (10 events):
Event: 4.330 Thread 0x000056487672d800 1579       1       java.lang.ThreadLocal::getMap (5 bytes)
Event: 4.330 Thread 0x000056487672d800 nmethod 1579 0x00002b5f58f55ed0 code [0x00002b5f58f56020, 0x00002b5f58f56130]
Event: 4.333 Thread 0x000056487672d800 1580       3       java.io.FileOutputStream::write (12 bytes)
Event: 4.333 Thread 0x000056487672d800 nmethod 1580 0x00002b5f58f56550 code [0x00002b5f58f566c0, 0x00002b5f58f56848]
Event: 4.333 Thread 0x000056487672d800 1582       3       java.io.FilterInputStream::read (9 bytes)
Event: 4.333 Thread 0x000056487672d800 nmethod 1582 0x00002b5f58f56910 code [0x00002b5f58f56a80, 0x00002b5f58f56ca8]
Event: 4.344 Thread 0x000056487672d800 1583       3       java.util.Formatter$Flags::<init> (10 bytes)
Event: 4.344 Thread 0x000056487672d800 nmethod 1583 0x00002b5f58f56d50 code [0x00002b5f58f56ec0, 0x00002b5f58f57070]
Event: 4.344 Thread 0x000056487672d800 1584       3       java.lang.String::getBytes (27 bytes)
Event: 4.344 Thread 0x000056487672d800 nmethod 1584 0x00002b5f58f57110 code [0x00002b5f58f572a0, 0x00002b5f58f57538]

GC Heap History (10 events):
Event: 1.261 GC heap before
{Heap before GC invocations=1 (full 0):
 PSYoungGen      total 601600K, used 92898K [0x000000066ab00000, 0x0000000694a00000, 0x00000007c0000000)
  eden space 516096K, 18% used [0x000000066ab00000,0x00000006705b8b90,0x000000068a300000)
  from space 85504K, 0% used [0x000000068f680000,0x000000068f680000,0x0000000694a00000)
  to   space 85504K, 0% used [0x000000068a300000,0x000000068a300000,0x000000068f680000)
 ParOldGen       total 1375232K, used 0K [0x00000003c0000000, 0x0000000413f00000, 0x000000066ab00000)
  object space 1375232K, 0% used [0x00000003c0000000,0x00000003c0000000,0x0000000413f00000)
 Metaspace       used 20965K, capacity 21134K, committed 21296K, reserved 1069056K
  class space    used 2601K, capacity 2668K, committed 2688K, reserved 1048576K
Event: 1.276 GC heap after
Heap after GC invocations=1 (full 0):
 PSYoungGen      total 601600K, used 17406K [0x000000066ab00000, 0x00000006b4200000, 0x00000007c0000000)
  eden space 516096K, 0% used [0x000000066ab00000,0x000000066ab00000,0x000000068a300000)
  from space 85504K, 20% used [0x000000068a300000,0x000000068b3ff9a0,0x000000068f680000)
  to   space 85504K, 0% used [0x00000006aee80000,0x00000006aee80000,0x00000006b4200000)
 ParOldGen       total 1375232K, used 16K [0x00000003c0000000, 0x0000000413f00000, 0x000000066ab00000)
  object space 1375232K, 0% used [0x00000003c0000000,0x00000003c0004000,0x0000000413f00000)
 Metaspace       used 20965K, capacity 21134K, committed 21296K, reserved 1069056K
  class space    used 2601K, capacity 2668K, committed 2688K, reserved 1048576K
}
Event: 1.276 GC heap before
{Heap before GC invocations=2 (full 1):
 PSYoungGen      total 601600K, used 17406K [0x000000066ab00000, 0x00000006b4200000, 0x00000007c0000000)
  eden space 516096K, 0% used [0x000000066ab00000,0x000000066ab00000,0x000000068a300000)
  from space 85504K, 20% used [0x000000068a300000,0x000000068b3ff9a0,0x000000068f680000)
  to   space 85504K, 0% used [0x00000006aee80000,0x00000006aee80000,0x00000006b4200000)
 ParOldGen       total 1375232K, used 16K [0x00000003c0000000, 0x0000000413f00000, 0x000000066ab00000)
  object space 1375232K, 0% used [0x00000003c0000000,0x00000003c0004000,0x0000000413f00000)
 Metaspace       used 20965K, capacity 21134K, committed 21296K, reserved 1069056K
  class space    used 2601K, capacity 2668K, committed 2688K, reserved 1048576K
Event: 1.308 GC heap after
Heap after GC invocations=2 (full 1):
 PSYoungGen      total 601600K, used 0K [0x000000066ab00000, 0x00000006b4200000, 0x00000007c0000000)
  eden space 516096K, 0% used [0x000000066ab00000,0x000000066ab00000,0x000000068a300000)
  from space 85504K, 0% used [0x000000068a300000,0x000000068a300000,0x000000068f680000)
  to   space 85504K, 0% used [0x00000006aee80000,0x00000006aee80000,0x00000006b4200000)
 ParOldGen       total 882176K, used 16449K [0x00000003c0000000, 0x00000003f5d80000, 0x000000066ab00000)
  object space 882176K, 1% used [0x00000003c0000000,0x00000003c10107d8,0x00000003f5d80000)
 Metaspace       used 20965K, capacity 21134K, committed 21296K, reserved 1069056K
  class space    used 2601K, capacity 2668K, committed 2688K, reserved 1048576K
}
Event: 2.927 GC heap before
{Heap before GC invocations=3 (full 1):
 PSYoungGen      total 601600K, used 412879K [0x000000066ab00000, 0x00000006b4200000, 0x00000007c0000000)
  eden space 516096K, 80% used [0x000000066ab00000,0x0000000683e33dd8,0x000000068a300000)
  from space 85504K, 0% used [0x000000068a300000,0x000000068a300000,0x000000068f680000)
  to   space 85504K, 0% used [0x00000006aee80000,0x00000006aee80000,0x00000006b4200000)
 ParOldGen       total 882176K, used 16449K [0x00000003c0000000, 0x00000003f5d80000, 0x000000066ab00000)
  object space 882176K, 1% used [0x00000003c0000000,0x00000003c10107d8,0x00000003f5d80000)
 Metaspace       used 34958K, capacity 35252K, committed 35456K, reserved 1079296K
  class space    used 4777K, capacity 4915K, committed 4992K, reserved 1048576K
Event: 2.941 GC heap after
Heap after GC invocations=3 (full 1):
 PSYoungGen      total 684544K, used 17783K [0x000000066ab00000, 0x00000006b0000000, 0x00000007c0000000)
  eden space 666624K, 0% used [0x000000066ab00000,0x000000066ab00000,0x0000000693600000)
  from space 17920K, 99% used [0x00000006aee80000,0x00000006affdde10,0x00000006b0000000)
  to   space 85504K, 0% used [0x00000006a5900000,0x00000006a5900000,0x00000006aac80000)
 ParOldGen       total 882176K, used 16457K [0x00000003c0000000, 0x00000003f5d80000, 0x000000066ab00000)
  object space 882176K, 1% used [0x00000003c0000000,0x00000003c10127d8,0x00000003f5d80000)
 Metaspace       used 34958K, capacity 35252K, committed 35456K, reserved 1079296K
  class space    used 4777K, capacity 4915K, committed 4992K, reserved 1048576K
}
Event: 2.941 GC heap before
{Heap before GC invocations=4 (full 2):
 PSYoungGen      total 684544K, used 17783K [0x000000066ab00000, 0x00000006b0000000, 0x00000007c0000000)
  eden space 666624K, 0% used [0x000000066ab00000,0x000000066ab00000,0x0000000693600000)
  from space 17920K, 99% used [0x00000006aee80000,0x00000006affdde10,0x00000006b0000000)
  to   space 85504K, 0% used [0x00000006a5900000,0x00000006a5900000,0x00000006aac80000)
 ParOldGen       total 882176K, used 16457K [0x00000003c0000000, 0x00000003f5d80000, 0x000000066ab00000)
  object space 882176K, 1% used [0x00000003c0000000,0x00000003c10127d8,0x00000003f5d80000)
 Metaspace       used 34958K, capacity 35252K, committed 35456K, reserved 1079296K
  class space    used 4777K, capacity 4915K, committed 4992K, reserved 1048576K
Event: 2.982 GC heap after
Heap after GC invocations=4 (full 2):
 PSYoungGen      total 684544K, used 0K [0x000000066ab00000, 0x00000006b0000000, 0x00000007c0000000)
  eden space 666624K, 0% used [0x000000066ab00000,0x000000066ab00000,0x0000000693600000)
  from space 17920K, 0% used [0x00000006aee80000,0x00000006aee80000,0x00000006b0000000)
  to   space 85504K, 0% used [0x00000006a5900000,0x00000006a5900000,0x00000006aac80000)
 ParOldGen       total 1497088K, used 20011K [0x00000003c0000000, 0x000000041b600000, 0x000000066ab00000)
  object space 1497088K, 1% used [0x00000003c0000000,0x00000003c138aeb0,0x000000041b600000)
 Metaspace       used 34958K, capacity 35252K, committed 35456K, reserved 1079296K
  class space    used 4777K, capacity 4915K, committed 4992K, reserved 1048576K
}
Event: 4.177 GC heap before
{Heap before GC invocations=5 (full 2):
 PSYoungGen      total 684544K, used 666624K [0x000000066ab00000, 0x00000006b0000000, 0x00000007c0000000)
  eden space 666624K, 100% used [0x000000066ab00000,0x0000000693600000,0x0000000693600000)
  from space 17920K, 0% used [0x00000006aee80000,0x00000006aee80000,0x00000006b0000000)
  to   space 85504K, 0% used [0x00000006a5900000,0x00000006a5900000,0x00000006aac80000)
 ParOldGen       total 1497088K, used 20011K [0x00000003c0000000, 0x000000041b600000, 0x000000066ab00000)
  object space 1497088K, 1% used [0x00000003c0000000,0x00000003c138aeb0,0x000000041b600000)
 Metaspace       used 36690K, capacity 37148K, committed 37248K, reserved 1081344K
  class space    used 5012K, capacity 5167K, committed 5248K, reserved 1048576K
Event: 4.218 GC heap after
Heap after GC invocations=5 (full 2):
 PSYoungGen      total 1003520K, used 56795K [0x000000066ab00000, 0x00000006aef00000, 0x00000007c0000000)
  eden space 946688K, 0% used [0x000000066ab00000,0x000000066ab00000,0x00000006a4780000)
  from space 56832K, 99% used [0x00000006a5900000,0x00000006a9076d70,0x00000006a9080000)
  to   space 85504K, 0% used [0x00000006a9b80000,0x00000006a9b80000,0x00000006aef00000)
 ParOldGen       total 1497088K, used 20019K [0x00000003c0000000, 0x000000041b600000, 0x000000066ab00000)
  object space 1497088K, 1% used [0x00000003c0000000,0x00000003c138ceb0,0x000000041b600000)
 Metaspace       used 36690K, capacity 37148K, committed 37248K, reserved 1081344K
  class space    used 5012K, capacity 5167K, committed 5248K, reserved 1048576K
}

Deoptimization events (10 events):
Event: 1.099 Thread 0x00005648765c2000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00002b5f58d4d8e0 method=sun.net.www.ParseUtil.encodePath(Ljava/lang/String;Z)Ljava/lang/String; @ 109
Event: 1.099 Thread 0x00005648765c2000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00002b5f58d12bf4 method=sun.net.www.ParseUtil.encodePath(Ljava/lang/String;Z)Ljava/lang/String; @ 109
Event: 1.755 Thread 0x00005648765c2000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00002b5f58d13c48 method=sun.nio.cs.UTF_8$Decoder.decode([BII[C)I @ 30
Event: 2.301 Thread 0x00005648765c2000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00002b5f58d8b648 method=java.lang.String.lastIndexOf([CII[CIII)I @ 75
Event: 2.593 Thread 0x00005648765c2000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x00002b5f58e51be0 method=java.lang.Throwable.<init>(Ljava/lang/String;Ljava/lang/Throwable;)V @ 24
Event: 2.709 Thread 0x00005648765c2000 Uncommon trap: reason=predicate action=maybe_recompile pc=0x00002b5f58d7b4ac method=sun.net.www.ParseUtil.encodePath(Ljava/lang/String;Z)Ljava/lang/String; @ 36
Event: 2.986 Thread 0x00005648765c2000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x00002b5f58d5eed4 method=java.util.concurrent.ConcurrentHashMap.putVal(Ljava/lang/Object;Ljava/lang/Object;Z)Ljava/lang/Object; @ 192
Event: 3.375 Thread 0x00005648765c2000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00002b5f58c42f0c method=java.lang.AbstractStringBuilder.append(Ljava/lang/String;)Ljava/lang/AbstractStringBuilder; @ 1
Event: 3.378 Thread 0x00005648765c2000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x00002b5f58eb80a0 method=java.util.regex.Matcher.search(I)Z @ 86
Event: 3.378 Thread 0x00005648765c2000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00002b5f58eb80f8 method=java.util.regex.Matcher.search(I)Z @ 30

Internal exceptions (10 events):
Event: 3.005 Thread 0x00005648765c2000 Exception <a 'java/lang/ClassNotFoundException': java/lang/StringEditor> (0x000000066aceafb0) thrown at [/home/buildozer/aports/community/openjdk8/src/icedtea-3.6.0/openjdk/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
Event: 3.005 Thread 0x00005648765c2000 Exception <a 'java/lang/ClassNotFoundException': java/lang/StringEditor> (0x000000066acebcd0) thrown at [/home/buildozer/aports/community/openjdk8/src/icedtea-3.6.0/openjdk/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
Event: 3.005 Thread 0x00005648765c2000 Exception <a 'java/lang/ClassNotFoundException': java/lang/StringEditor> (0x000000066acec9b8) thrown at [/home/buildozer/aports/community/openjdk8/src/icedtea-3.6.0/openjdk/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
Event: 3.006 Thread 0x00005648765c2000 Exception <a 'java/lang/ClassNotFoundException': java/lang/StringEditor> (0x000000066aced6a0) thrown at [/home/buildozer/aports/community/openjdk8/src/icedtea-3.6.0/openjdk/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
Event: 3.375 Thread 0x00005648765c2000 Implicit null exception at 0x00002b5f58c42b36 to 0x00002b5f58c42ef5
Event: 3.376 Thread 0x00005648765c2000 Exception <a 'sun/nio/fs/UnixException'> (0x0000000677b47a30) thrown at [/home/buildozer/aports/community/openjdk8/src/icedtea-3.6.0/openjdk/hotspot/src/share/vm/prims/jni.cpp, line 709]
Event: 3.485 Thread 0x00005648765c2000 Exception <a 'java/lang/NoSuchMethodError': java.lang.Object.lambda$comparing$77a9974f$1(Ljava/util/function/Function;Ljava/lang/Object;Ljava/lang/Object;)I> (0x000000067b1efd78) thrown at [/home/buildozer/aports/community/openjdk8/src/icedtea-3.6.0/openj
Event: 3.490 Thread 0x00005648765c2000 Exception <a 'java/lang/NoSuchMethodError': java.lang.Object.lambda$comparing$ea9a8b3a$1(Ljava/util/Comparator;Ljava/util/function/Function;Ljava/lang/Object;Ljava/lang/Object;)I> (0x000000067b20f3e0) thrown at [/home/buildozer/aports/community/openjdk8/s
Event: 3.490 Thread 0x00005648765c2000 Exception <a 'java/lang/NoSuchMethodError': java.lang.Object.lambda$comparingInt$7b0bb60$1(Ljava/util/function/ToIntFunction;Ljava/lang/Object;Ljava/lang/Object;)I> (0x000000067b219168) thrown at [/home/buildozer/aports/community/openjdk8/src/icedtea-3.6.
Event: 3.491 Thread 0x00005648765c2000 Exception <a 'java/lang/NoSuchMethodError': java.lang.Object.lambda$thenComparing$36697e65$1(Ljava/util/Comparator;Ljava/lang/Object;Ljava/lang/Object;)I> (0x000000067b220588) thrown at [/home/buildozer/aports/community/openjdk8/src/icedtea-3.6.0/openjdk/

Events (10 events):
Event: 4.325 loading class com/intel/gkl/pairhmm/IntelPairHmmOMP
Event: 4.325 loading class com/intel/gkl/pairhmm/IntelPairHmmOMP done
Event: 4.325 loading class com/intel/gkl/pairhmm/IntelPairHmm
Event: 4.325 loading class com/intel/gkl/pairhmm/IntelPairHmm done
Event: 4.326 loading class com/intel/gkl/IntelGKLUtils
Event: 4.326 loading class com/intel/gkl/IntelGKLUtils done
Event: 4.379 loading class org/broadinstitute/gatk/nativebindings/pairhmm/ReadDataHolder
Event: 4.379 loading class org/broadinstitute/gatk/nativebindings/pairhmm/ReadDataHolder done
Event: 4.379 loading class org/broadinstitute/gatk/nativebindings/pairhmm/HaplotypeDataHolder
Event: 4.379 loading class org/broadinstitute/gatk/nativebindings/pairhmm/HaplotypeDataHolder done

Dynamic libraries:
3c0000000-41b600000 rw-p 00000000 00:00 0 
41b600000-66ab00000 ---p 00000000 00:00 0 
66ab00000-6aef00000 rw-p 00000000 00:00 0 
6aef00000-7c0000000 ---p 00000000 00:00 0 
7c0000000-7c0520000 rw-p 00000000 00:00 0 
7c0520000-800000000 ---p 00000000 00:00 0 
2b5f56cd5000-2b5f56d5e000 r-xp 00000000 07:00 565                        /lib/ld-musl-x86_64.so.1
2b5f56d5e000-2b5f56d60000 ---p 00000000 00:00 0 
2b5f56d60000-2b5f56d63000 ---p 00000000 00:00 0 
2b5f56d63000-2b5f56e61000 rw-p 00000000 00:00 0                          [stack:85483]
2b5f56e61000-2b5f56e62000 r--p 00000000 00:00 0 
2b5f56e62000-2b5f56e63000 rw-p 00000000 00:00 0 
2b5f56e63000-2b5f56e6b000 rw-s 00000000 08:01 69704933                   /tmp/hsperfdata_iiipe01/85482
2b5f56e6b000-2b5f56f3c000 rw-p 00000000 00:00 0 
2b5f56f3c000-2b5f56f3d000 r--s 00000000 08:01 67151449                   /etc/localtime
2b5f56f3d000-2b5f56f58000 r--s 001d6000 07:00 6686                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/ext/nashorn.jar
2b5f56f58000-2b5f56f5d000 r--s 00055000 07:00 6705                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/jsse.jar
2b5f56f5d000-2b5f56f5e000 r--p 00088000 07:00 565                        /lib/ld-musl-x86_64.so.1
2b5f56f5e000-2b5f56f5f000 rw-p 00089000 07:00 565                        /lib/ld-musl-x86_64.so.1
2b5f56f5f000-2b5f56f62000 rw-p 00000000 00:00 0 
2b5f56f62000-2b5f5716e000 r-xp 00000000 07:00 6628                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/jli/libjli.so
2b5f5716e000-2b5f5716f000 r--p 0000c000 07:00 6628                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/jli/libjli.so
2b5f5716f000-2b5f57170000 rw-p 0000d000 07:00 6628                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/jli/libjli.so
2b5f57170000-2b5f57385000 r-xp 00000000 07:00 582                        /lib/libz.so.1.2.11
2b5f57385000-2b5f57386000 r--p 00015000 07:00 582                        /lib/libz.so.1.2.11
2b5f57386000-2b5f57387000 rw-p 00016000 07:00 582                        /lib/libz.so.1.2.11
2b5f57387000-2b5f57da1000 r-xp 00000000 07:00 6667                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/server/libjvm.so
2b5f57da1000-2b5f57e36000 r--p 0081a000 07:00 6667                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/server/libjvm.so
2b5f57e36000-2b5f57e5e000 rw-p 008af000 07:00 6667                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/server/libjvm.so
2b5f57e5e000-2b5f57e8e000 rw-p 00000000 00:00 0 
2b5f57e8e000-2b5f581ce000 r-xp 00000000 07:00 6940                       /usr/lib/libstdc++.so.6.0.22
2b5f581ce000-2b5f581dc000 r--p 00140000 07:00 6940                       /usr/lib/libstdc++.so.6.0.22
2b5f581dc000-2b5f581dd000 rw-p 0014e000 07:00 6940                       /usr/lib/libstdc++.so.6.0.22
2b5f581dd000-2b5f581e0000 rw-p 00000000 00:00 0 
2b5f581e0000-2b5f583f0000 r-xp 00000000 07:00 6826                       /usr/lib/libgcc_s.so.1
2b5f583f0000-2b5f583f1000 r--p 00010000 07:00 6826                       /usr/lib/libgcc_s.so.1
2b5f583f1000-2b5f583f2000 rw-p 00011000 07:00 6826                       /usr/lib/libgcc_s.so.1
2b5f583f2000-2b5f585fe000 r-xp 00000000 07:00 6662                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libverify.so
2b5f585fe000-2b5f58600000 r--p 0000c000 07:00 6662                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libverify.so
2b5f58600000-2b5f58601000 rw-p 0000e000 07:00 6662                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libverify.so
2b5f58601000-2b5f5882d000 r-xp 00000000 07:00 6644                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libjava.so
2b5f5882d000-2b5f5882e000 r--p 0002c000 07:00 6644                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libjava.so
2b5f5882e000-2b5f5882f000 rw-p 0002d000 07:00 6644                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libjava.so
2b5f5882f000-2b5f58830000 rw-p 00000000 00:00 0 
2b5f58830000-2b5f58a37000 r-xp 00000000 07:00 6663                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libzip.so
2b5f58a37000-2b5f58a38000 r--p 00007000 07:00 6663                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libzip.so
2b5f58a38000-2b5f58a39000 rw-p 00008000 07:00 6663                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libzip.so
2b5f58a39000-2b5f58f59000 rwxp 00000000 00:00 0 
2b5f58f59000-2b5f67a39000 ---p 00000000 00:00 0 
2b5f67a39000-2b5f67a4e000 rw-p 00000000 00:00 0 
2b5f67a4e000-2b5f67df9000 ---p 00000000 00:00 0 
2b5f67df9000-2b5f680d4000 rw-p 00000000 00:00 0 
2b5f680d4000-2b5f6934e000 ---p 00000000 00:00 0 
2b5f6934e000-2b5f69571000 rw-p 00000000 00:00 0 
2b5f69571000-2b5f69df9000 ---p 00000000 00:00 0 
2b5f69df9000-2b5f6a0d5000 rw-p 00000000 00:00 0 
2b5f6a0d5000-2b5f6b350000 ---p 00000000 00:00 0 
2b5f6b350000-2b5f6b351000 ---p 00000000 00:00 0 
2b5f6b351000-2b5f6b452000 rw-p 00000000 00:00 0                          [stack:85484]
2b5f6b452000-2b5f6b453000 ---p 00000000 00:00 0 
2b5f6b453000-2b5f6b554000 rw-p 00000000 00:00 0                          [stack:85485]
2b5f6b554000-2b5f6b555000 ---p 00000000 00:00 0 
2b5f6b555000-2b5f8df96000 rw-p 00000000 00:00 0                          [stack:85486]
2b5f8df96000-2b5f8e165000 r--s 01f49000 07:00 6719                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/rt.jar
2b5f8e165000-2b5f8edbf000 rw-p 00000000 00:00 0 
2b5f8edbf000-2b5f8edc0000 ---p 00000000 00:00 0 
2b5f8edc0000-2b5f8eec1000 rw-p 00000000 00:00 0                          [stack:85487]
2b5f8eec1000-2b5f8eec4000 ---p 00000000 00:00 0 
2b5f8eec4000-2b5f8efc2000 rw-p 00000000 00:00 0                          [stack:85488]
2b5f8efc2000-2b5f8efc5000 ---p 00000000 00:00 0 
2b5f8efc5000-2b5f8f0c3000 rw-p 00000000 00:00 0                          [stack:85489]
2b5f8f0c3000-2b5f8f0c6000 ---p 00000000 00:00 0 
2b5f8f0c6000-2b5f8f1c4000 rw-p 00000000 00:00 0                          [stack:85490]
2b5f8f1c4000-2b5f8f1c5000 ---p 00000000 00:00 0 
2b5f8f1c5000-2b5f8f1c8000 ---p 00000000 00:00 0 
2b5f8f1c8000-2b5f8f2c6000 rw-p 00000000 00:00 0                          [stack:85491]
2b5f8f2c6000-2b5f8f2c7000 ---p 00000000 00:00 0 
2b5f8f2c7000-2b5f8f2ca000 ---p 00000000 00:00 0 
2b5f8f2ca000-2b5f8f3c8000 rw-p 00000000 00:00 0                          [stack:85492]
2b5f8f3c8000-2b5f8f3cb000 ---p 00000000 00:00 0 
2b5f8f3cb000-2b5f8f4c9000 rw-p 00000000 00:00 0                          [stack:85493]
2b5f8f4c9000-2b5f8f4ca000 ---p 00000000 00:00 0 
2b5f8f4ca000-2b5f8f5cb000 rw-p 00000000 00:00 0                          [stack:85494]
2b5f8f5cb000-2b5f904b9000 r--s 0f987000 07:00 728                        /usr/bin/gatk-package-4.0.0.0-local.jar
2b5f904b9000-2b5f90738000 rw-p 00000000 00:00 0 
2b5f90738000-2b5f90940000 r-xp 00000000 07:00 6654                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libmanagement.so
2b5f90940000-2b5f90941000 r--p 00008000 07:00 6654                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libmanagement.so
2b5f90941000-2b5f90942000 rw-p 00009000 07:00 6654                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libmanagement.so
2b5f90942000-2b5f9095d000 r--s 003b7000 07:00 6681                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/ext/cldrdata.jar
2b5f9095d000-2b5f90968000 r--s 0011c000 07:00 6684                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/ext/localedata.jar
2b5f90968000-2b5f9097b000 r--s 00102000 07:00 6718                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/resources.jar
2b5f9097b000-2b5f90b7b000 rw-p 00000000 00:00 0 
2b5f90b7b000-2b5f90d91000 r-xp 00000000 07:00 6656                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libnet.so
2b5f90d91000-2b5f90d92000 r--p 00016000 07:00 6656                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libnet.so
2b5f90d92000-2b5f90d93000 rw-p 00017000 07:00 6656                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libnet.so
2b5f90d93000-2b5f91114000 rw-p 00000000 00:00 0 
2b5f91114000-2b5f91325000 r-xp 00000000 07:00 6657                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libnio.so
2b5f91325000-2b5f91326000 r--p 00011000 07:00 6657                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libnio.so
2b5f91326000-2b5f91327000 rw-p 00012000 07:00 6657                       /usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/libnio.so
2b5f91327000-2b5f919a5000 rw-p 00000000 00:00 0 
2b5f919ce000-2b5f91dce000 rw-p 00000000 00:00 0 
2b5f91e22000-2b5f92022000 rw-p 00000000 00:00 0 
2b5f92208000-2b5f92608000 rw-p 00000000 00:00 0 
2b5f92608000-2b5f9282e000 r-xp 00000000 08:01 101239188                  /tmp/iiipe01/libgkl_compression869223110120306175.so
2b5f9282e000-2b5f92831000 rw-p 00026000 08:01 101239188                  /tmp/iiipe01/libgkl_compression869223110120306175.so
2b5f92831000-2b5f92bb1000 rw-p 00000000 00:00 0 
2b5f92bb1000-2b5f92c31000 ---p 00000000 00:00 0 
2b5f92c31000-2b5f92e31000 r-xp 00000000 08:01 101239189                  /tmp/iiipe01/libgkl_utils5286078004483445841.so
2b5f92e31000-2b5f92e32000 rw-p 00000000 08:01 101239189                  /tmp/iiipe01/libgkl_utils5286078004483445841.so
2b5f92e32000-2b5f93052000 r-xp 00000000 07:00 6838                       /usr/lib/libgomp.so.1.0.0
2b5f93052000-2b5f93053000 r--p 00020000 07:00 6838                       /usr/lib/libgomp.so.1.0.0
2b5f93053000-2b5f93054000 rw-p 00021000 07:00 6838                       /usr/lib/libgomp.so.1.0.0
2b5f93054000-2b5f93374000 r-xp 00000000 08:01 101239190                  /tmp/iiipe01/libgkl_pairhmm_omp6754956421048173304.so
2b5f93374000-2b5f9337d000 rw-p 00120000 08:01 101239190                  /tmp/iiipe01/libgkl_pairhmm_omp6754956421048173304.so
2b5f9337d000-2b5f934c9000 rw-p 00000000 00:00 0 
5648750a4000-5648750a5000 r-xp 00000000 07:00 6614                       /usr/lib/jvm/java-1.8-openjdk/jre/bin/java
5648752a4000-5648752a5000 r--p 00000000 07:00 6614                       /usr/lib/jvm/java-1.8-openjdk/jre/bin/java
5648752a5000-5648752a6000 rw-p 00001000 07:00 6614                       /usr/lib/jvm/java-1.8-openjdk/jre/bin/java
5648765ab000-56487910f000 rw-p 00000000 00:00 0                          [heap]
7ffdbd7c6000-7ffdbd7e7000 rw-p 00000000 00:00 0                          [stack]
7ffdbd7fc000-7ffdbd7fe000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

VM Arguments:
jvm_args: -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -Xmx16g 
java_command: /usr/bin/gatk-package-4.0.0.0-local.jar HaplotypeCaller -I CMT_Project04172015_20150062801_S_2.bam -R /beegfs/work/zxmai83/Reference/genome/b37/human_g1k_v37.fasta -O CMT_Project04172015_20150062801_S_2_variants.vcf -ERC GVCF --create-output-variant-index --annotation MappingQualityRankSumTest --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation FisherStrand --annotation Coverage --dbsnp /beegfs/work/zxmai83/Reference/dbs/b37/dbsnp_138.b37.vcf --verbosity INFO
java_class_path (initial): /usr/bin/gatk-package-4.0.0.0-local.jar
Launcher Type: SUN_STANDARD

Environment Variables:
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
LD_LIBRARY_PATH=/usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-1.8-openjdk/jre/lib/amd64:/usr/lib/jvm/java-1.8-openjdk/jre/../lib/amd64:/.singularity.d/libs

Signal Handlers:
SIGSEGV: [libjvm.so+0x632f3c], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGBUS: [libjvm.so+0x632f3c], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGFPE: [libjvm.so+0x5622fa], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGPIPE: [libjvm.so+0x5622fa], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGXFSZ: [libjvm.so+0x5622fa], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGILL: [libjvm.so+0x5622fa], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
SIGUSR2: [libjvm.so+0x562499], sa_mask[0]=00000000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
SIGHUP: [libjvm.so+0x56457d], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGINT: [libjvm.so+0x56457d], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGTERM: [libjvm.so+0x56457d], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGQUIT: [libjvm.so+0x56457d], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO

---------------  S Y S T E M  ---------------

OS:NAME="Alpine Linux"
ID=alpine
VERSION_ID=3.7.0
PRETTY_NAME="Alpine Linux v3.7"
HOME_URL="http://alpinelinux.org"
BUG_REPORT_URL="http://bugs.alpinelinux.org"

uname:Linux 3.10.0-693.2.2.el7.x86_64 #1 SMP Sat Sep 9 03:55:24 EDT 2017 x86_64
libc:glibc 2.9 NPTL 
rlimit: STACK infinity, CORE 0k, NPROC 515180, NOFILE 32768, AS infinity
load average:15.97 16.04 16.37

/proc/meminfo:
MemTotal:       131915956 kB
MemFree:        125850452 kB
MemAvailable:   128351176 kB
Buffers:           49496 kB
Cached:          2830848 kB
SwapCached:        12880 kB
Active:          2140832 kB
Inactive:        1911172 kB
Active(anon):    1244276 kB
Inactive(anon):   117404 kB
Active(file):     896556 kB
Inactive(file):  1793768 kB
Unevictable:       79828 kB
Mlocked:           79828 kB
SwapTotal:       8388604 kB
SwapFree:        8322480 kB
Dirty:              2812 kB
Writeback:             0 kB
AnonPages:       1100336 kB
Mapped:           115412 kB
Shmem:            155280 kB
Slab:             724052 kB
SReclaimable:     487676 kB
SUnreclaim:       236376 kB
KernelStack:        9680 kB
PageTables:         8072 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:    74346580 kB
Committed_AS:    4020976 kB
VmallocTotal:   34359738367 kB
VmallocUsed:      670716 kB
VmallocChunk:   34258282492 kB
HardwareCorrupted:     0 kB
AnonHugePages:    872448 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB
DirectMap4k:      333160 kB
DirectMap2M:    14249984 kB
DirectMap1G:    121634816 kB

CPU:total 10 (initial active 3) (14 cores per cpu, 2 threads per core) family 6 model 79 stepping 1, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, rtm, 3dnowpref, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2, adx

/proc/cpuinfo:
processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 0
cpu cores   : 14
apicid      : 0
initial apicid  : 0
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 1
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 1
cpu cores   : 14
apicid      : 2
initial apicid  : 2
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 2
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 2
cpu cores   : 14
apicid      : 4
initial apicid  : 4
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 3
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 3
cpu cores   : 14
apicid      : 6
initial apicid  : 6
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 4
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 4
cpu cores   : 14
apicid      : 8
initial apicid  : 8
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 5
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 5
cpu cores   : 14
apicid      : 10
initial apicid  : 10
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 6
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 6
cpu cores   : 14
apicid      : 12
initial apicid  : 12
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 7
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2900.062
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 8
cpu cores   : 14
apicid      : 16
initial apicid  : 16
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 8
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.968
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 9
cpu cores   : 14
apicid      : 18
initial apicid  : 18
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 9
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.968
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 10
cpu cores   : 14
apicid      : 20
initial apicid  : 20
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 10
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.968
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 11
cpu cores   : 14
apicid      : 22
initial apicid  : 22
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 11
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 12
cpu cores   : 14
apicid      : 24
initial apicid  : 24
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 12
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 13
cpu cores   : 14
apicid      : 26
initial apicid  : 26
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 13
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 0
siblings    : 14
core id     : 14
cpu cores   : 14
apicid      : 28
initial apicid  : 28
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4788.74
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 14
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 0
cpu cores   : 14
apicid      : 32
initial apicid  : 32
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 15
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 1
cpu cores   : 14
apicid      : 34
initial apicid  : 34
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 16
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 2
cpu cores   : 14
apicid      : 36
initial apicid  : 36
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 17
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 3
cpu cores   : 14
apicid      : 38
initial apicid  : 38
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 18
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 4
cpu cores   : 14
apicid      : 40
initial apicid  : 40
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 19
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2799.937
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 5
cpu cores   : 14
apicid      : 42
initial apicid  : 42
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 20
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.875
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 6
cpu cores   : 14
apicid      : 44
initial apicid  : 44
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 21
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.968
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 8
cpu cores   : 14
apicid      : 48
initial apicid  : 48
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 22
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.968
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 9
cpu cores   : 14
apicid      : 50
initial apicid  : 50
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 23
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.968
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 10
cpu cores   : 14
apicid      : 52
initial apicid  : 52
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 24
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.968
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 11
cpu cores   : 14
apicid      : 54
initial apicid  : 54
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 25
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.968
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 12
cpu cores   : 14
apicid      : 56
initial apicid  : 56
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 26
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.875
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 13
cpu cores   : 14
apicid      : 58
initial apicid  : 58
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

processor   : 27
vendor_id   : GenuineIntel
cpu family  : 6
model       : 79
model name  : Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
stepping    : 1
microcode   : 0xb000021
cpu MHz     : 2899.687
cache size  : 17920 KB
physical id : 1
siblings    : 14
core id     : 14
cpu cores   : 14
apicid      : 60
initial apicid  : 60
fpu     : yes
fpu_exception   : yes
cpuid level : 20
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips    : 4803.25
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

Memory: 4k page, physical 131915956k(125850452k free), swap 8388604k(8322480k free)

vm_info: OpenJDK 64-Bit Server VM (25.151-b12) for linux-amd64 JRE (1.8.0_151-b12), built on Nov 21 2017 11:32:26 by "buildozer" with gcc 6.4.0

time: Mon Jan 15 13:18:43 2018
elapsed time: 4 seconds (0d 0h 0m 4s)
droazen commented 6 years ago

@gspowley Could you and your team please have a look a this one?

gspowley commented 6 years ago

The segfault happens in libgomp:

# Problematic frame:
# C  [libgomp.so.1+0x7fab]  omp_get_max_threads+0xb

Here's similar issue, which also used Alpine Linux: https://github.com/bytedeco/javacv/issues/716. The resolution was to move to a different Linux distro.

@apeltzer, assuming you want to use Alpine, please try running without libgomp installed. This will provide single-threaded AVX PairHMM, which will be faster than the Java PairHMM.

apeltzer commented 6 years ago

I'll test and let you know asap. Thanks for the hint!

apeltzer commented 6 years ago

Unfortunately, that doesn't resolve the issue. I'll see whether I can put some logs together to get you a better overview.