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chapmanb/hs_err-bqsr_deflater.log

Created September 24, 2017 09:45
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Java error log from BQSR core dump on GATK4 beta5
Raw
hs_err-bqsr_deflater.log
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f9400380c30, pid=45651, tid=0x00007f93fdbde700
#
# JRE version: OpenJDK Runtime Environment (8.0_144-b01) (build 1.8.0_144-b01)
# Java VM: OpenJDK 64-Bit Server VM (25.144-b01 mixed mode linux-amd64 )
# Problematic frame:
# V [libjvm.so+0x617c30] InstanceKlass::oop_oop_iterate_nv(oopDesc*, FastScanClosure*)+0x1a0
#
# 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 visit:
# http://www.azulsystems.com/support/
#
--------------- T H R E A D ---------------
Current thread (0x00007f93f8095000): VMThread [stack: 0x00007f93fdade000,0x00007f93fdbdf000] [id=45653]
siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x00007f0000000000
Registers:
RAX=0x0000000000000001, RBX=0x00007f8a52101880, RCX=0x0000000000000008, RDX=0x0000000000000000
RSP=0x00007f93fdbdd090, RBP=0x00007f93fdbdd0e0, RSI=0x00007f0000000000, RDI=0x00007f8a521e4390
R8 =0x00007f8a521e3c90, R9 =0x00007f93fdbdd540, R10=0x00007f8a521e3c90, R11=0x0000000000000010
R12=0x00007f93fdbdd4a0, R13=0x00007f8a52101888, R14=0x0000000000000240, R15=0x00007f8821790968
RIP=0x00007f9400380c30, EFLAGS=0x0000000000010206, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
TRAPNO=0x000000000000000e
Top of Stack: (sp=0x00007f93fdbdd090)
0x00007f93fdbdd090: 00007f8c44152200 00007f88217906c0
0x00007f93fdbdd0a0: 00007f8a52101820 00007f8821790970
0x00007f93fdbdd0b0: 00007f8c44152200 00007f8a52101820
0x00007f93fdbdd0c0: 00007f8a521bb5c0 00007f9400c839e9
0x00007f93fdbdd0d0: 0000000000000240 00007f93fdbdd4a0
0x00007f93fdbdd0e0: 00007f93fdbdd130 00007f94006c8922
0x00007f93fdbdd0f0: 00007f93f8092760 00007f93f801bf30
0x00007f93fdbdd100: 00007f93fdbdd440 00007f93fdbdd4a0
0x00007f93fdbdd110: 00007f93f8018210 00007f93fdbdd440
0x00007f93fdbdd120: 00007f8a453dfaa0 00007f93f8094a50
0x00007f93fdbdd130: 00007f93fdbdd150 00007f9400248d90
0x00007f93fdbdd140: 00007f93f8017cf0 0000000000000001
0x00007f93fdbdd150: 00007f93fdbdd180 00007f940031f691
0x00007f93fdbdd160: 00007f8a453dfa88 00007f93fdbdd540
0x00007f93fdbdd170: 0000000000000000 00007f9400c839e8
0x00007f93fdbdd180: 00007f93fdbdd1a0 00007f9400249314
0x00007f93fdbdd190: 00007f93fdbdd570 00007f93fdbdd570
0x00007f93fdbdd1a0: 00007f93fdbdd210 00007f940067a73e
0x00007f93fdbdd1b0: 00007f93f8094a50 00000000000083b0
0x00007f93fdbdd1c0: 00007f8834256a40 00007f883425b6b8
0x00007f93fdbdd1d0: 00007f93fdbdd540 00007f88342536d0
0x00007f93fdbdd1e0: 0000000000000001 00007f93f8092760
0x00007f93fdbdd1f0: 00007f93f8092800 0000000000000001
0x00007f93fdbdd200: 00007f93fdbdd540 00007f93fdbdd570
0x00007f93fdbdd210: 00007f93fdbdd2b0 00007f940067b9c4
0x00007f93fdbdd220: 00007f93fdbdd250 00007f9400dd4836
0x00007f93fdbdd230: 000000000000efcd 0000000000002ecd
0x00007f93fdbdd240: 00000000fdbdd260 00007f93fdbdd650
0x00007f93fdbdd250: 000000000000efcd 00007f9400826552
0x00007f93fdbdd260: 00007f93fdbdd310 000000000000013b
0x00007f93fdbdd270: 00007f93fdbdd328 00007f93fdbdd5d0
0x00007f93fdbdd280: 00007f93fdbdd2b0 00007f93f8092760
Instructions: (pc=0x00007f9400380c30)
0x00007f9400380c10: 42 c6 82 b4 00 00 00 01 48 83 c3 08 49 39 dd 76
0x00007f9400380c20: 97 48 8b 33 48 85 f6 74 ef 49 39 74 24 48 76 e8
0x00007f9400380c30: 48 8b 06 83 e0 03 48 83 f8 03 74 a4 49 8b 7c 24
0x00007f9400380c40: 40 e8 7a 97 ec ff 48 89 03 49 8b 54 24 38 48 85
Register to memory mapping:
RAX=0x0000000000000001 is an unknown value
RBX=0x00007f8a52101880 is pointing into object: 0x00007f8a52101820
com.intel.gkl.compression.IntelDeflater
- klass: 'com/intel/gkl/compression/IntelDeflater'
RCX=0x0000000000000008 is an unknown value
RDX=0x0000000000000000 is an unknown value
RSP=0x00007f93fdbdd090 is an unknown value
RBP=0x00007f93fdbdd0e0 is an unknown value
RSI=0x00007f0000000000 is an unknown value
RDI=0x00007f8a521e4390 is an oop
[B
- klass: {type array byte}
- length: 0
R8 =0x00007f8a521e3c90 is an oop
[B
- klass: {type array byte}
- length: 512
R9 =0x00007f93fdbdd540 is an unknown value
R10=0x00007f8a521e3c90 is an oop
[B
- klass: {type array byte}
- length: 512
R11=0x0000000000000010 is an unknown value
R12=0x00007f93fdbdd4a0 is an unknown value
R13=0x00007f8a52101888 is an oop
java.io.FileOutputStream
- klass: 'java/io/FileOutputStream'
R14=0x0000000000000240 is an unknown value
R15=0x00007f8821790968 is pointing into metadata
Stack: [0x00007f93fdade000,0x00007f93fdbdf000], sp=0x00007f93fdbdd090, free space=1020k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V [libjvm.so+0x617c30] InstanceKlass::oop_oop_iterate_nv(oopDesc*, FastScanClosure*)+0x1a0
V [libjvm.so+0x95f922] ContiguousSpace::oop_since_save_marks_iterate_nv(FastScanClosure*)+0x72
V [libjvm.so+0x4dfd90] DefNewGeneration::oop_since_save_marks_iterate_nv(FastScanClosure*)+0x40
V [libjvm.so+0x5b6691] GenCollectedHeap::oop_since_save_marks_iterate(int, FastScanClosure*, FastScanClosure*)+0x31
V [libjvm.so+0x4e0314] DefNewGeneration::FastEvacuateFollowersClosure::do_void()+0x24
V [libjvm.so+0x91173e] ReferenceProcessor::process_phase3(DiscoveredList&, bool, BoolObjectClosure*, OopClosure*, VoidClosure*)+0x15e
V [libjvm.so+0x9129c4] ReferenceProcessor::process_discovered_reflist(DiscoveredList*, ReferencePolicy*, bool, BoolObjectClosure*, OopClosure*, VoidClosure*, AbstractRefProcTaskExecutor*)+0x184
V [libjvm.so+0x9130ce] ReferenceProcessor::process_discovered_references(BoolObjectClosure*, OopClosure*, VoidClosure*, AbstractRefProcTaskExecutor*, GCTimer*, GCId)+0x17e
V [libjvm.so+0x4e248a] DefNewGeneration::collect(bool, bool, unsigned long, bool)+0x5ca
V [libjvm.so+0x5b9375] GenCollectedHeap::do_collection(bool, bool, unsigned long, bool, int)+0x535
V [libjvm.so+0x46cee7] GenCollectorPolicy::satisfy_failed_allocation(unsigned long, bool)+0x137
V [libjvm.so+0xa38fc4] VM_GenCollectForAllocation::doit()+0x94
V [libjvm.so+0xa401c2] VM_Operation::evaluate()+0x52
V [libjvm.so+0xa3e6f1] VMThread::evaluate_operation(VM_Operation*)+0xb1
V [libjvm.so+0xa3eb43] VMThread::loop()+0x1c3
V [libjvm.so+0xa3f012] VMThread::run()+0x72
V [libjvm.so+0x8aa202] java_start(Thread*)+0x122
VM_Operation (0x00007f87ec7dd0e0): GenCollectForAllocation, mode: safepoint, requested by thread 0x00007f87d8018000
--------------- P R O C E S S ---------------
Java Threads: ( => current thread )
0x00007f8718059800 JavaThread "process reaper" daemon [_thread_blocked, id=45836, stack(0x00007f874a67b000,0x00007f874a6b4000)]
0x00007f872402f800 JavaThread "process reaper" daemon [_thread_blocked, id=45833, stack(0x00007f874a6b4000,0x00007f874a6ed000)]
0x00007f87540f2000 JavaThread "process reaper" daemon [_thread_blocked, id=45827, stack(0x00007f87ec02e000,0x00007f87ec067000)]
0x00007f87240c5800 JavaThread "process reaper" daemon [_thread_blocked, id=45825, stack(0x00007f87ec067000,0x00007f87ec0a0000)]
0x00007f871802e800 JavaThread "process reaper" daemon [_thread_blocked, id=45823, stack(0x00007f87ec0a0000,0x00007f87ec0d9000)]
0x00007f87400ff800 JavaThread "process reaper" daemon [_thread_blocked, id=45822, stack(0x00007f882001a000,0x00007f8820053000)]
0x00007f875c071800 JavaThread "process reaper" daemon [_thread_blocked, id=45821, stack(0x00007f8820053000,0x00007f882008c000)]
0x00007f873006c000 JavaThread "process reaper" daemon [_thread_blocked, id=45820, stack(0x00007f93fc025000,0x00007f93fc05e000)]
0x00007f87e8002800 JavaThread "Executor task launch worker-17" daemon [_thread_blocked, id=45810, stack(0x00007f874a8ef000,0x00007f874a9f0000)]
0x00007f87f8008000 JavaThread "Executor task launch worker-16" daemon [_thread_blocked, id=45738, stack(0x00007f874b0f3000,0x00007f874b1f4000)]
0x00007f87e0001000 JavaThread "task-result-getter-3" daemon [_thread_blocked, id=45737, stack(0x00007f874b1f4000,0x00007f874b2f5000)]
0x00007f87e4001000 JavaThread "task-result-getter-2" daemon [_thread_blocked, id=45736, stack(0x00007f874b2f5000,0x00007f874b3f6000)]
0x00007f87f0003000 JavaThread "task-result-getter-1" daemon [_thread_blocked, id=45735, stack(0x00007f874b3f6000,0x00007f874b4f7000)]
0x00007f87f0002000 JavaThread "task-result-getter-0" daemon [_thread_blocked, id=45734, stack(0x00007f874b4f7000,0x00007f874b5f8000)]
0x00007f87d8030800 JavaThread "Executor task launch worker-15" daemon [_thread_blocked, id=45733, stack(0x00007f874b7f8000,0x00007f874b8f9000)]
0x00007f87d802e800 JavaThread "Executor task launch worker-14" daemon [_thread_blocked, id=45732, stack(0x00007f874b8f9000,0x00007f874b9fa000)]
0x00007f87d802d000 JavaThread "Executor task launch worker-13" daemon [_thread_blocked, id=45731, stack(0x00007f874b9fa000,0x00007f874bafb000)]
0x00007f87d802b000 JavaThread "Executor task launch worker-12" daemon [_thread_blocked, id=45730, stack(0x00007f874bafb000,0x00007f874bbfc000)]
0x00007f87d8029800 JavaThread "Executor task launch worker-11" daemon [_thread_blocked, id=45729, stack(0x00007f874bbfc000,0x00007f874bcfd000)]
0x00007f87d8027800 JavaThread "Executor task launch worker-10" daemon [_thread_blocked, id=45728, stack(0x00007f874bcfd000,0x00007f874bdfe000)]
0x00007f87d8026000 JavaThread "Executor task launch worker-9" daemon [_thread_blocked, id=45727, stack(0x00007f874bdfe000,0x00007f874beff000)]
0x00007f87d8024800 JavaThread "Executor task launch worker-8" daemon [_thread_blocked, id=45726, stack(0x00007f874beff000,0x00007f874c000000)]
0x00007f87d8021000 JavaThread "Executor task launch worker-6" daemon [_thread_blocked, id=45724, stack(0x00007f87ec1da000,0x00007f87ec2db000)]
0x00007f87d801f800 JavaThread "Executor task launch worker-5" daemon [_thread_blocked, id=45723, stack(0x00007f87ec2db000,0x00007f87ec3dc000)]
0x00007f87d801d800 JavaThread "Executor task launch worker-4" daemon [_thread_blocked, id=45722, stack(0x00007f87ec3dc000,0x00007f87ec4dd000)]
0x00007f87d801c000 JavaThread "Executor task launch worker-3" daemon [_thread_blocked, id=45721, stack(0x00007f87ec4dd000,0x00007f87ec5de000)]
0x00007f87d801a800 JavaThread "Executor task launch worker-2" daemon [_thread_blocked, id=45720, stack(0x00007f87ec5de000,0x00007f87ec6df000)]
0x00007f87d8018000 JavaThread "Executor task launch worker-1" daemon [_thread_blocked, id=45719, stack(0x00007f87ec6df000,0x00007f87ec7e0000)]
0x00007f87d8016000 JavaThread "Executor task launch worker-0" daemon [_thread_blocked, id=45718, stack(0x00007f87ec7e0000,0x00007f87ec8e1000)]
0x00007f93fa457000 JavaThread "SparkListenerBus" daemon [_thread_blocked, id=45717, stack(0x00007f87ed6e1000,0x00007f87ed7e2000)]
0x00007f93fa453000 JavaThread "context-cleaner-periodic-gc" daemon [_thread_blocked, id=45716, stack(0x00007f87ed7e2000,0x00007f87ed8e3000)]
0x00007f93fa451800 JavaThread "Spark Context Cleaner" daemon [_thread_blocked, id=45715, stack(0x00007f87ed8e3000,0x00007f87ed9e4000)]
0x00007f93fa15b800 JavaThread "shuffle-server-0" daemon [_thread_blocked, id=45714, stack(0x00007f87edbe4000,0x00007f87edce5000)]
0x00007f93fa202800 JavaThread "driver-heartbeater" daemon [_thread_blocked, id=45713, stack(0x00007f87edce5000,0x00007f87edde6000)]
0x00007f93fa1ee000 JavaThread "dag-scheduler-event-loop" daemon [_thread_blocked, id=45712, stack(0x00007f87edde6000,0x00007f87edee7000)]
0x00007f879000c800 JavaThread "netty-rpc-env-timeout" daemon [_thread_blocked, id=45711, stack(0x00007f87ee0e7000,0x00007f87ee1e8000)]
0x00007f93fa1ca800 JavaThread "Timer-0" daemon [_thread_blocked, id=45710, stack(0x00007f87ee1e8000,0x00007f87ee2e9000)]
0x00007f8804003800 JavaThread "heartbeat-receiver-event-loop-thread" daemon [_thread_blocked, id=45709, stack(0x00007f87ee2e9000,0x00007f87ee3ea000)]
0x00007f93fa157000 JavaThread "SparkUI-73" daemon [_thread_blocked, id=45708, stack(0x00007f87ee3ea000,0x00007f87ee4eb000)]
0x00007f93fa155000 JavaThread "SparkUI-72" daemon [_thread_blocked, id=45707, stack(0x00007f87ee4eb000,0x00007f87ee5ec000)]
0x00007f93fa153800 JavaThread "SparkUI-71-acceptor-1@662984d6-ServerConnector@17591c{HTTP/1.1}{0.0.0.0:4040}" daemon [_thread_blocked, id=45706, stack(0x00007f87ee5ec000,0x00007f87ee6ed000)]
0x00007f93fa152000 JavaThread "SparkUI-70-acceptor-0@ed0a6b6-ServerConnector@17591c{HTTP/1.1}{0.0.0.0:4040}" daemon [_thread_in_native, id=45705, stack(0x00007f87ee6ed000,0x00007f87ee7ee000)]
0x00007f93fa150000 JavaThread "SparkUI-69-selector-ServerConnectorManager@38498b7d/3" daemon [_thread_in_native, id=45704, stack(0x00007f87ee7ee000,0x00007f87ee8ef000)]
0x00007f93fa14e800 JavaThread "SparkUI-68-selector-ServerConnectorManager@38498b7d/2" daemon [_thread_in_native, id=45703, stack(0x00007f87ee8ef000,0x00007f87ee9f0000)]
0x00007f93fa14d800 JavaThread "SparkUI-67-selector-ServerConnectorManager@38498b7d/1" daemon [_thread_in_native, id=45702, stack(0x00007f87ee9f0000,0x00007f87eeaf1000)]
0x00007f93fa145800 JavaThread "SparkUI-66-selector-ServerConnectorManager@38498b7d/0" daemon [_thread_in_native, id=45701, stack(0x00007f87eeaf1000,0x00007f87eebf2000)]
0x00007f93fa061800 JavaThread "map-output-dispatcher-7" daemon [_thread_blocked, id=45699, stack(0x00007f87eedf2000,0x00007f87eeef3000)]
0x00007f93fa05f800 JavaThread "map-output-dispatcher-6" daemon [_thread_blocked, id=45698, stack(0x00007f87eeef3000,0x00007f87eeff4000)]
0x00007f93fa05e000 JavaThread "map-output-dispatcher-5" daemon [_thread_blocked, id=45697, stack(0x00007f87eeff4000,0x00007f87ef0f5000)]
0x00007f93fa05c000 JavaThread "map-output-dispatcher-4" daemon [_thread_blocked, id=45696, stack(0x00007f87ef0f5000,0x00007f87ef1f6000)]
0x00007f93fa05a800 JavaThread "map-output-dispatcher-3" daemon [_thread_blocked, id=45695, stack(0x00007f87ef1f6000,0x00007f87ef2f7000)]
0x00007f93fa058800 JavaThread "map-output-dispatcher-2" daemon [_thread_blocked, id=45694, stack(0x00007f87ef2f7000,0x00007f87ef3f8000)]
0x00007f93fa057000 JavaThread "map-output-dispatcher-1" daemon [_thread_blocked, id=45693, stack(0x00007f87ef3f8000,0x00007f87ef4f9000)]
0x00007f93fa056000 JavaThread "map-output-dispatcher-0" daemon [_thread_blocked, id=45692, stack(0x00007f87ef4f9000,0x00007f87ef5fa000)]
0x00007f93fa03b000 JavaThread "shuffle-server-0" daemon [_thread_blocked, id=45691, stack(0x00007f87ef5fa000,0x00007f87ef6fb000)]
0x00007f93f9e0c000 JavaThread "dispatcher-event-loop-15" daemon [_thread_blocked, id=45689, stack(0x00007f87efafb000,0x00007f87efbfc000)]
0x00007f93f9e0a800 JavaThread "dispatcher-event-loop-14" daemon [_thread_blocked, id=45688, stack(0x00007f87efbfc000,0x00007f87efcfd000)]
0x00007f93f9e08800 JavaThread "dispatcher-event-loop-13" daemon [_thread_blocked, id=45687, stack(0x00007f87efcfd000,0x00007f87efdfe000)]
0x00007f93f9e07000 JavaThread "dispatcher-event-loop-12" daemon [_thread_blocked, id=45686, stack(0x00007f87efdfe000,0x00007f87efeff000)]
0x00007f93f9e05000 JavaThread "dispatcher-event-loop-11" daemon [_thread_blocked, id=45685, stack(0x00007f87efeff000,0x00007f87f0000000)]
0x00007f93f9e03800 JavaThread "dispatcher-event-loop-10" daemon [_thread_blocked, id=45684, stack(0x00007f882008c000,0x00007f882018d000)]
0x00007f93f9e02000 JavaThread "dispatcher-event-loop-9" daemon [_thread_blocked, id=45683, stack(0x00007f882018d000,0x00007f882028e000)]
0x00007f93f9e00000 JavaThread "dispatcher-event-loop-8" daemon [_thread_blocked, id=45682, stack(0x00007f882028e000,0x00007f882038f000)]
0x00007f93f9dfe800 JavaThread "dispatcher-event-loop-7" daemon [_thread_blocked, id=45681, stack(0x00007f882038f000,0x00007f8820490000)]
0x00007f93f9dfc800 JavaThread "dispatcher-event-loop-6" daemon [_thread_blocked, id=45680, stack(0x00007f8820490000,0x00007f8820591000)]
0x00007f93f9dfb000 JavaThread "dispatcher-event-loop-5" daemon [_thread_blocked, id=45679, stack(0x00007f8820591000,0x00007f8820692000)]
0x00007f93f9df9000 JavaThread "dispatcher-event-loop-4" daemon [_thread_blocked, id=45678, stack(0x00007f8820692000,0x00007f8820793000)]
0x00007f93f9df7800 JavaThread "dispatcher-event-loop-3" daemon [_thread_blocked, id=45677, stack(0x00007f8820793000,0x00007f8820894000)]
0x00007f93f9df6000 JavaThread "dispatcher-event-loop-2" daemon [_thread_blocked, id=45676, stack(0x00007f8820894000,0x00007f8820995000)]
0x00007f93f9df4800 JavaThread "dispatcher-event-loop-1" daemon [_thread_blocked, id=45675, stack(0x00007f8820995000,0x00007f8820a96000)]
0x00007f93f9df3800 JavaThread "dispatcher-event-loop-0" daemon [_thread_blocked, id=45674, stack(0x00007f886801b000,0x00007f886811c000)]
0x00007f93f80ee000 JavaThread "Service Thread" daemon [_thread_blocked, id=45669, stack(0x00007f93fcace000,0x00007f93fcbcf000)]
0x00007f93f80eb000 JavaThread "C1 CompilerThread11" daemon [_thread_blocked, id=45668, stack(0x00007f93fcbcf000,0x00007f93fccd0000)]
0x00007f93f80e9000 JavaThread "C1 CompilerThread10" daemon [_thread_blocked, id=45667, stack(0x00007f93fccd0000,0x00007f93fcdd1000)]
0x00007f93f80e6000 JavaThread "C1 CompilerThread9" daemon [_thread_blocked, id=45666, stack(0x00007f93fcdd1000,0x00007f93fced2000)]
0x00007f93f80e4000 JavaThread "C1 CompilerThread8" daemon [_thread_blocked, id=45665, stack(0x00007f93fced2000,0x00007f93fcfd3000)]
0x00007f93f80e2800 JavaThread "C2 CompilerThread7" daemon [_thread_blocked, id=45664, stack(0x00007f93fcfd3000,0x00007f93fd0d4000)]
0x00007f93f80e0800 JavaThread "C2 CompilerThread6" daemon [_thread_blocked, id=45663, stack(0x00007f93fd0d4000,0x00007f93fd1d5000)]
0x00007f93f80de800 JavaThread "C2 CompilerThread5" daemon [_thread_blocked, id=45662, stack(0x00007f93fd1d5000,0x00007f93fd2d6000)]
0x00007f93f80dc800 JavaThread "C2 CompilerThread4" daemon [_thread_blocked, id=45661, stack(0x00007f93fd2d6000,0x00007f93fd3d7000)]
0x00007f93f80da800 JavaThread "C2 CompilerThread3" daemon [_thread_blocked, id=45660, stack(0x00007f93fd3d7000,0x00007f93fd4d8000)]
0x00007f93f80d9000 JavaThread "C2 CompilerThread2" daemon [_thread_blocked, id=45659, stack(0x00007f93fd4d8000,0x00007f93fd5d9000)]
0x00007f93f80d6800 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=45658, stack(0x00007f93fd5d9000,0x00007f93fd6da000)]
0x00007f93f80d4800 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=45657, stack(0x00007f93fd6da000,0x00007f93fd7db000)]
0x00007f93f80d3000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=45656, stack(0x00007f93fd7db000,0x00007f93fd8dc000)]
0x00007f93f80a1800 JavaThread "Finalizer" daemon [_thread_blocked, id=45655, stack(0x00007f93fd8dc000,0x00007f93fd9dd000)]
0x00007f93f809d000 JavaThread "Reference Handler" daemon [_thread_blocked, id=45654, stack(0x00007f93fd9dd000,0x00007f93fdade000)]
0x00007f93f800a800 JavaThread "main" [_thread_blocked, id=45652, stack(0x00007f94017d9000,0x00007f94018da000)]
Other Threads:
=>0x00007f93f8095000 VMThread [stack: 0x00007f93fdade000,0x00007f93fdbdf000] [id=45653]
0x00007f93f80f0800 WatcherThread [stack: 0x00007f93fc9cd000,0x00007f93fcace000] [id=45670]
VM state:at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
[0x00007f93f8006bf0] Threads_lock - owner thread: 0x00007f93f8095000
[0x00007f93f80070f0] Heap_lock - owner thread: 0x00007f87d8018000
Heap:
def new generation total 8614912K, used 8514548K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 100% used [0x00007f8871a00000, 0x00007f8a45040000, 0x00007f8a45040000)
from space 957184K, 89% used [0x00007f8a7f700000, 0x00007f8ab3bbd158, 0x00007f8ab9dc0000)
to space 957184K, 22% used [0x00007f8a45040000, 0x00007f8a521e43a8, 0x00007f8a7f700000)
tenured generation total 19144156K, used 11358947K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 59% used [0x00007f8c44150000, 0x00007f8ef9608c28, 0x00007f8ef9608e00, 0x00007f90d48c7000)
Metaspace used 68797K, capacity 70009K, committed 70144K, reserved 71680K
Card table byte_map: [0x00007f886be44000,0x00007f8871a00000] byte_map_base: 0x00007f48a7ab7000
Polling page: 0x00007f94018e3000
CodeCache: size=245760Kb used=30094Kb max_used=30241Kb free=215665Kb
bounds [0x00007f93e9000000, 0x00007f93eadd0000, 0x00007f93f8000000]
total_blobs=9423 nmethods=8811 adapters=522
compilation: enabled
Compilation events (10 events):
Event: 2416.030 Thread 0x00007f93f80d4800 14321 ! 4 sun.reflect.GeneratedSerializationConstructorAccessor4089::newInstance (49 bytes)
Event: 2416.032 Thread 0x00007f93f80d4800 nmethod 14321 0x00007f93e9949590 code [0x00007f93e9949700, 0x00007f93e9949848]
Event: 2416.034 Thread 0x00007f93f80d4800 14322 % 4 org.apache.spark.util.collection.ExternalSorter::insertAll @ 147 (212 bytes)
Event: 2416.054 Thread 0x00007f93f80dc800 14323 ! 4 sun.reflect.GeneratedSerializationConstructorAccessor4080::newInstance (49 bytes)
Event: 2416.054 Thread 0x00007f93f80d4800 nmethod 14322% 0x00007f93e99581d0 code [0x00007f93e9958400, 0x00007f93e9958d50]
Event: 2416.055 Thread 0x00007f93f80dc800 nmethod 14323 0x00007f93e9957e10 code [0x00007f93e9957f80, 0x00007f93e99580c8]
Event: 2416.067 Thread 0x00007f93f80d9000 14324 4 org.apache.spark.util.collection.ExternalSorter::insertAll (212 bytes)
Event: 2416.082 Thread 0x00007f93f80e2800 14325 ! 4 sun.reflect.GeneratedSerializationConstructorAccessor4104::newInstance (49 bytes)
Event: 2416.084 Thread 0x00007f93f80e2800 nmethod 14325 0x00007f93e9cea850 code [0x00007f93e9cea9c0, 0x00007f93e9ceaae8]
Event: 2416.084 Thread 0x00007f93f80e2800 14326 ! 4 sun.reflect.GeneratedSerializationConstructorAccessor4111::newInstance (49 bytes)
GC Heap History (10 events):
Event: 2367.417 GC heap after
Heap after GC invocations=255 (full 59):
def new generation total 8614912K, used 957183K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 0% used [0x00007f8871a00000, 0x00007f8871a00000, 0x00007f8a45040000)
from space 957184K, 99% used [0x00007f8a7f700000, 0x00007f8ab9dbfff8, 0x00007f8ab9dc0000)
to space 957184K, 0% used [0x00007f8a45040000, 0x00007f8a45040000, 0x00007f8a7f700000)
tenured generation total 19144156K, used 15439901K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 80% used [0x00007f8c44150000, 0x00007f8ff2757580, 0x00007f8ff2757600, 0x00007f90d48c7000)
Metaspace used 67184K, capacity 68233K, committed 68608K, reserved 69632K
}
Event: 2367.417 GC heap before
{Heap before GC invocations=255 (full 59):
def new generation total 8614912K, used 976518K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 0% used [0x00007f8871a00000, 0x00007f8872ce1980, 0x00007f8a45040000)
from space 957184K, 99% used [0x00007f8a7f700000, 0x00007f8ab9dbfff8, 0x00007f8ab9dc0000)
to space 957184K, 0% used [0x00007f8a45040000, 0x00007f8a45040000, 0x00007f8a7f700000)
tenured generation total 19144156K, used 15439901K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 80% used [0x00007f8c44150000, 0x00007f8ff2757580, 0x00007f8ff2757600, 0x00007f90d48c7000)
Metaspace used 67184K, capacity 68233K, committed 68608K, reserved 69632K
Event: 2367.818 GC heap after
Heap after GC invocations=256 (full 59):
def new generation total 8614912K, used 4K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 0% used [0x00007f8871a00000, 0x00007f8871a00000, 0x00007f8a45040000)
from space 957184K, 0% used [0x00007f8a45040000, 0x00007f8a45041210, 0x00007f8a7f700000)
to space 957184K, 0% used [0x00007f8a7f700000, 0x00007f8a7f700000, 0x00007f8ab9dc0000)
tenured generation total 19144156K, used 16397085K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 85% used [0x00007f8c44150000, 0x00007f902ce174f8, 0x00007f902ce17600, 0x00007f90d48c7000)
Metaspace used 67184K, capacity 68233K, committed 68608K, reserved 69632K
}
Event: 2372.067 GC heap before
{Heap before GC invocations=256 (full 59):
def new generation total 8614912K, used 7657732K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 100% used [0x00007f8871a00000, 0x00007f8a45040000, 0x00007f8a45040000)
from space 957184K, 0% used [0x00007f8a45040000, 0x00007f8a45041210, 0x00007f8a7f700000)
to space 957184K, 0% used [0x00007f8a7f700000, 0x00007f8a7f700000, 0x00007f8ab9dc0000)
tenured generation total 19144156K, used 16397085K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 85% used [0x00007f8c44150000, 0x00007f902ce174f8, 0x00007f902ce17600, 0x00007f90d48c7000)
Metaspace used 67232K, capacity 68293K, committed 68608K, reserved 69632K
Event: 2387.122 GC heap after
Heap after GC invocations=257 (full 60):
def new generation total 8614912K, used 0K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 0% used [0x00007f8871a00000, 0x00007f8871a00000, 0x00007f8a45040000)
from space 957184K, 0% used [0x00007f8a7f700000, 0x00007f8a7f700000, 0x00007f8ab9dc0000)
to space 957184K, 0% used [0x00007f8a45040000, 0x00007f8a45040000, 0x00007f8a7f700000)
tenured generation total 19144156K, used 6580328K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 34% used [0x00007f8c44150000, 0x00007f8dd5b6a080, 0x00007f8dd5b6a200, 0x00007f90d48c7000)
Metaspace used 66895K, capacity 67873K, committed 68608K, reserved 69632K
}
Event: 2391.374 GC heap before
{Heap before GC invocations=257 (full 60):
def new generation total 8614912K, used 7639089K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 99% used [0x00007f8871a00000, 0x00007f8a43e0c6c8, 0x00007f8a45040000)
from space 957184K, 0% used [0x00007f8a7f700000, 0x00007f8a7f700000, 0x00007f8ab9dc0000)
to space 957184K, 0% used [0x00007f8a45040000, 0x00007f8a45040000, 0x00007f8a7f700000)
tenured generation total 19144156K, used 6580328K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 34% used [0x00007f8c44150000, 0x00007f8dd5b6a080, 0x00007f8dd5b6a200, 0x00007f90d48c7000)
Metaspace used 66896K, capacity 67873K, committed 68608K, reserved 69632K
Event: 2396.729 GC heap after
Heap after GC invocations=258 (full 60):
def new generation total 8614912K, used 957184K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 0% used [0x00007f8871a00000, 0x00007f8871a00000, 0x00007f8a45040000)
from space 957184K, 100% used [0x00007f8a45040000, 0x00007f8a7f700000, 0x00007f8a7f700000)
to space 957184K, 0% used [0x00007f8a7f700000, 0x00007f8a7f700000, 0x00007f8ab9dc0000)
tenured generation total 19144156K, used 10407604K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 54% used [0x00007f8c44150000, 0x00007f8ebf4fd2e8, 0x00007f8ebf4fd400, 0x00007f90d48c7000)
Metaspace used 66896K, capacity 67873K, committed 68608K, reserved 69632K
}
Event: 2411.210 GC heap before
{Heap before GC invocations=258 (full 60):
def new generation total 8614912K, used 8614912K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 100% used [0x00007f8871a00000, 0x00007f8a45040000, 0x00007f8a45040000)
from space 957184K, 100% used [0x00007f8a45040000, 0x00007f8a7f700000, 0x00007f8a7f700000)
to space 957184K, 0% used [0x00007f8a7f700000, 0x00007f8a7f700000, 0x00007f8ab9dc0000)
tenured generation total 19144156K, used 10407604K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 54% used [0x00007f8c44150000, 0x00007f8ebf4fd2e8, 0x00007f8ebf4fd400, 0x00007f90d48c7000)
Metaspace used 67959K, capacity 68981K, committed 69120K, reserved 69632K
Event: 2412.558 GC heap after
Heap after GC invocations=259 (full 60):
def new generation total 8614912K, used 856820K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 0% used [0x00007f8871a00000, 0x00007f8871a00000, 0x00007f8a45040000)
from space 957184K, 89% used [0x00007f8a7f700000, 0x00007f8ab3bbd158, 0x00007f8ab9dc0000)
to space 957184K, 0% used [0x00007f8a45040000, 0x00007f8a45040000, 0x00007f8a7f700000)
tenured generation total 19144156K, used 10594820K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 55% used [0x00007f8c44150000, 0x00007f8ecabd1060, 0x00007f8ecabd1200, 0x00007f90d48c7000)
Metaspace used 67959K, capacity 68981K, committed 69120K, reserved 69632K
}
Event: 2416.086 GC heap before
{Heap before GC invocations=259 (full 60):
def new generation total 8614912K, used 8514548K [0x00007f8871a00000, 0x00007f8ab9dc0000, 0x00007f8c44150000)
eden space 7657728K, 100% used [0x00007f8871a00000, 0x00007f8a45040000, 0x00007f8a45040000)
from space 957184K, 89% used [0x00007f8a7f700000, 0x00007f8ab3bbd158, 0x00007f8ab9dc0000)
to space 957184K, 0% used [0x00007f8a45040000, 0x00007f8a45040000, 0x00007f8a7f700000)
tenured generation total 19144156K, used 10594820K [0x00007f8c44150000, 0x00007f90d48c7000, 0x00007f93e9000000)
the space 19144156K, 55% used [0x00007f8c44150000, 0x00007f8ecabd1060, 0x00007f8ecabd1200, 0x00007f90d48c7000)
Metaspace used 68797K, capacity 70009K, committed 70144K, reserved 71680K
Deoptimization events (10 events):
Event: 2415.777 Thread 0x00007f87d801c000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93e9c10f44 method=org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp()V @ 9
Event: 2415.788 Thread 0x00007f87d8027800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93e9c10f44 method=org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp()V @ 9
Event: 2415.808 Thread 0x00007f87e8002800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93e9c10f44 method=org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp()V @ 9
Event: 2415.809 Thread 0x00007f87d8024800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93e9c10f44 method=org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp()V @ 9
Event: 2415.815 Thread 0x00007f87d8029800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93e9c10f44 method=org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp()V @ 9
Event: 2415.831 Thread 0x00007f87d8018000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93e9c10f44 method=org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp()V @ 9
Event: 2415.835 Thread 0x00007f87d801f800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93e9c10f44 method=org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp()V @ 9
Event: 2415.844 Thread 0x00007f87d8016000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93e9c10f44 method=org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp()V @ 9
Event: 2415.878 Thread 0x00007f87d802b000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93e9c10f44 method=org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp()V @ 9
Event: 2416.085 Thread 0x00007f87d801a800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f93eac87900 method=java.util.concurrent.locks.ReentrantLock$Sync.nonfairTryAcquire(I)Z @ 19
Internal exceptions (10 events):
Event: 2399.240 Thread 0x00007f87d8016000 Exception <a 'sun/nio/fs/UnixException'> (0x00007f891545f4e8) thrown at [/export/home/tester/jenkins/workspace/zulu8-silver-build-rhel64/zulu-src/hotspot/src/share/vm/prims/jni.cpp, line 709]
Event: 2399.977 Thread 0x00007f87d801a800 Exception <a 'sun/nio/fs/UnixException'> (0x00007f8933782a68) thrown at [/export/home/tester/jenkins/workspace/zulu8-silver-build-rhel64/zulu-src/hotspot/src/share/vm/prims/jni.cpp, line 709]
Event: 2399.978 Thread 0x00007f87d801a800 Exception <a 'sun/nio/fs/UnixException'> (0x00007f893393d8e0) thrown at [/export/home/tester/jenkins/workspace/zulu8-silver-build-rhel64/zulu-src/hotspot/src/share/vm/prims/jni.cpp, line 709]
Event: 2401.724 Thread 0x00007f87d801a800 Implicit null exception at 0x00007f93ea8a18cb to 0x00007f93ea8a1b81
Event: 2401.725 Thread 0x00007f87d801a800 Implicit null exception at 0x00007f93ea89efbe to 0x00007f93ea89f270
Event: 2401.725 Thread 0x00007f87d801a800 Implicit null exception at 0x00007f93ea89a0a9 to 0x00007f93ea89a357
Event: 2401.725 Thread 0x00007f87d801a800 Implicit null exception at 0x00007f93ea896083 to 0x00007f93ea8962e0
Event: 2401.725 Thread 0x00007f87d801a800 Implicit null exception at 0x00007f93ea83b255 to 0x00007f93ea83b409
Event: 2410.491 Thread 0x00007f93f9e0a800 Exception <a 'java/lang/NoSuchMethodError': <clinit>> (0x00007f8a1b17eab0) thrown at [/export/home/tester/jenkins/workspace/zulu8-silver-build-rhel64/zulu-src/hotspot/src/share/vm/prims/jni.cpp, line 1613]
Event: 2410.656 Thread 0x00007f87d8029800 Implicit null exception at 0x00007f93e9d2ce49 to 0x00007f93e9d2d149
Events (10 events):
Event: 2415.914 loading class htsjdk/samtools/SAMBinaryTagAndValueConstructorAccess
Event: 2415.914 loading class htsjdk/samtools/SAMBinaryTagAndValueConstructorAccess done
Event: 2415.915 loading class htsjdk/samtools/CigarElementConstructorAccess
Event: 2415.915 loading class htsjdk/samtools/CigarElementConstructorAccess done
Event: 2416.078 Thread 0x00007f87d8018000 DEOPT PACKING pc=0x00007f93ead27bbe sp=0x00007f87ec7dd420
Event: 2416.078 Thread 0x00007f87d8018000 DEOPT UNPACKING pc=0x00007f93e9047373 sp=0x00007f87ec7dd210 mode 0
Event: 2416.084 Thread 0x00007f87f8008000 DEOPT PACKING pc=0x00007f93ead27bbe sp=0x00007f874b1f11a0
Event: 2416.084 Thread 0x00007f87f8008000 DEOPT UNPACKING pc=0x00007f93e9047373 sp=0x00007f874b1f0f90 mode 0
Event: 2416.085 Executing VM operation: GenCollectForAllocation
Event: 2416.085 Thread 0x00007f87d801a800 Uncommon trap: trap_request=0xffffff65 fr.pc=0x00007f93eac87900
Dynamic libraries:
003ff000-00400000 rw-p 00000000 ca:50 18092476 /mnt/work/bcbio/anaconda/bin/java
00400000-00401000 r-xp 00001000 ca:50 18092476 /mnt/work/bcbio/anaconda/bin/java
00600000-00601000 rw-p 00001000 ca:50 18092476 /mnt/work/bcbio/anaconda/bin/java
00cc5000-00ce6000 rw-p 00000000 00:00 0 [heap]
7f86e4000000-7f86e4021000 rw-p 00000000 00:00 0
7f86e4021000-7f86e8000000 ---p 00000000 00:00 0
7f86e8000000-7f86e8021000 rw-p 00000000 00:00 0
7f86e8021000-7f86ec000000 ---p 00000000 00:00 0
7f86ec000000-7f86ec021000 rw-p 00000000 00:00 0
7f86ec021000-7f86f0000000 ---p 00000000 00:00 0
7f86f0000000-7f86f0021000 rw-p 00000000 00:00 0
7f86f0021000-7f86f4000000 ---p 00000000 00:00 0
7f86f4000000-7f86f4021000 rw-p 00000000 00:00 0
7f86f4021000-7f86f8000000 ---p 00000000 00:00 0
7f86f8000000-7f86f8021000 rw-p 00000000 00:00 0
7f86f8021000-7f86fc000000 ---p 00000000 00:00 0
7f86fc000000-7f86fc021000 rw-p 00000000 00:00 0
7f86fc021000-7f8700000000 ---p 00000000 00:00 0
7f8700000000-7f8700021000 rw-p 00000000 00:00 0
7f8700021000-7f8704000000 ---p 00000000 00:00 0
7f8704000000-7f870411b000 rw-p 00000000 00:00 0
7f870411b000-7f8708000000 ---p 00000000 00:00 0
7f8708000000-7f8708021000 rw-p 00000000 00:00 0
7f8708021000-7f870c000000 ---p 00000000 00:00 0
7f870c000000-7f870c021000 rw-p 00000000 00:00 0
7f870c021000-7f8710000000 ---p 00000000 00:00 0
7f8710000000-7f8710021000 rw-p 00000000 00:00 0
7f8710021000-7f8714000000 ---p 00000000 00:00 0
7f8714000000-7f8714021000 rw-p 00000000 00:00 0
7f8714021000-7f8718000000 ---p 00000000 00:00 0
7f8718000000-7f87181ab000 rw-p 00000000 00:00 0
7f87181ab000-7f871c000000 ---p 00000000 00:00 0
7f871c000000-7f871c161000 rw-p 00000000 00:00 0
7f871c161000-7f8720000000 ---p 00000000 00:00 0
7f8720000000-7f8720027000 rw-p 00000000 00:00 0
7f8720027000-7f8724000000 ---p 00000000 00:00 0
7f8724000000-7f87241d6000 rw-p 00000000 00:00 0
7f87241d6000-7f8728000000 ---p 00000000 00:00 0
7f8728000000-7f872802f000 rw-p 00000000 00:00 0
7f872802f000-7f872c000000 ---p 00000000 00:00 0
7f872c000000-7f872c1bd000 rw-p 00000000 00:00 0
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7f882467e000-7f8828000000 ---p 00000000 00:00 0
7f8828000000-7f8828021000 rw-p 00000000 00:00 0
7f8828021000-7f882c000000 ---p 00000000 00:00 0
7f882c000000-7f882c8ab000 rw-p 00000000 00:00 0
7f882c8ab000-7f8830000000 ---p 00000000 00:00 0
7f8830000000-7f88303a2000 rw-p 00000000 00:00 0
7f88303a2000-7f8834000000 ---p 00000000 00:00 0
7f8834000000-7f8835701000 rw-p 00000000 00:00 0
7f8835701000-7f8838000000 ---p 00000000 00:00 0
7f8838000000-7f88386fd000 rw-p 00000000 00:00 0
7f88386fd000-7f883c000000 ---p 00000000 00:00 0
7f883c000000-7f883cd07000 rw-p 00000000 00:00 0
7f883cd07000-7f8840000000 ---p 00000000 00:00 0
7f8840000000-7f8841848000 rw-p 00000000 00:00 0
7f8841848000-7f8844000000 ---p 00000000 00:00 0
7f8844000000-7f88453ed000 rw-p 00000000 00:00 0
7f88453ed000-7f8848000000 ---p 00000000 00:00 0
7f8848000000-7f884919b000 rw-p 00000000 00:00 0
7f884919b000-7f884c000000 ---p 00000000 00:00 0
7f884c000000-7f884d4ff000 rw-p 00000000 00:00 0
7f884d4ff000-7f8850000000 ---p 00000000 00:00 0
7f8850000000-7f88518f5000 rw-p 00000000 00:00 0
7f88518f5000-7f8854000000 ---p 00000000 00:00 0
7f8854000000-7f8854021000 rw-p 00000000 00:00 0
7f8854021000-7f8858000000 ---p 00000000 00:00 0
7f8858000000-7f8859340000 rw-p 00000000 00:00 0
7f8859340000-7f885c000000 ---p 00000000 00:00 0
7f885c000000-7f885c021000 rw-p 00000000 00:00 0
7f885c021000-7f8860000000 ---p 00000000 00:00 0
7f8860000000-7f8860021000 rw-p 00000000 00:00 0
7f8860021000-7f8864000000 ---p 00000000 00:00 0
7f8864000000-7f886446b000 rw-p 00000000 00:00 0
7f886446b000-7f8868000000 ---p 00000000 00:00 0
7f886801b000-7f886801e000 ---p 00000000 00:00 0
7f886801e000-7f886a5a0000 rw-p 00000000 00:00 0
7f886a5a0000-7f886be44000 ---p 00000000 00:00 0
7f886be44000-7f886d086000 rw-p 00000000 00:00 0
7f886d086000-7f886dcd7000 ---p 00000000 00:00 0
7f886dcd7000-7f887015c000 rw-p 00000000 00:00 0
7f887015c000-7f88719ff000 ---p 00000000 00:00 0
7f88719ff000-7f8ab9dc0000 rw-p 00000000 00:00 0
7f8ab9dc0000-7f8c44150000 ---p 00000000 00:00 0
7f8c44150000-7f90d48c7000 rw-p 00000000 00:00 0
7f90d48c7000-7f93e9000000 ---p 00000000 00:00 0
7f93e9000000-7f93eadd0000 rwxp 00000000 00:00 0
7f93eadd0000-7f93f8000000 ---p 00000000 00:00 0
7f93f8000000-7f93fb1d7000 rw-p 00000000 00:00 0
7f93fb1d7000-7f93fc000000 ---p 00000000 00:00 0
7f93fc025000-7f93fc028000 ---p 00000000 00:00 0
7f93fc028000-7f93fc05e000 rw-p 00000000 00:00 0
7f93fc05e000-7f93fc071000 r--s 00346000 ca:50 18092631 /mnt/work/bcbio/anaconda/jre/lib/resources.jar
7f93fc071000-7f93fc08d000 r--s 00393000 ca:50 18092632 /mnt/work/bcbio/anaconda/jre/lib/ext/cldrdata.jar
7f93fc08d000-7f93fc0a8000 r--s 001d6000 ca:50 18092628 /mnt/work/bcbio/anaconda/jre/lib/ext/nashorn.jar
7f93fc0a8000-7f93fc3a9000 rw-p 00000000 00:00 0
7f93fc3a9000-7f93fc3c0000 r-xp 00000000 ca:50 18092578 /mnt/work/bcbio/anaconda/jre/lib/amd64/libnet.so
7f93fc3c0000-7f93fc5bf000 ---p 00017000 ca:50 18092578 /mnt/work/bcbio/anaconda/jre/lib/amd64/libnet.so
7f93fc5bf000-7f93fc5c0000 rw-p 00016000 ca:50 18092578 /mnt/work/bcbio/anaconda/jre/lib/amd64/libnet.so
7f93fc5c0000-7f93fc5c2000 rw-p 0001d000 ca:50 18092578 /mnt/work/bcbio/anaconda/jre/lib/amd64/libnet.so
7f93fc5c2000-7f93fc7c2000 rw-p 00000000 00:00 0
7f93fc7c2000-7f93fc7ca000 r-xp 00000000 ca:50 18092564 /mnt/work/bcbio/anaconda/jre/lib/amd64/libmanagement.so
7f93fc7ca000-7f93fc9ca000 ---p 00008000 ca:50 18092564 /mnt/work/bcbio/anaconda/jre/lib/amd64/libmanagement.so
7f93fc9ca000-7f93fc9cb000 rw-p 00008000 ca:50 18092564 /mnt/work/bcbio/anaconda/jre/lib/amd64/libmanagement.so
7f93fc9cb000-7f93fc9cd000 rw-p 0000c000 ca:50 18092564 /mnt/work/bcbio/anaconda/jre/lib/amd64/libmanagement.so
7f93fc9cd000-7f93fc9ce000 ---p 00000000 00:00 0
7f93fc9ce000-7f93fcace000 rw-p 00000000 00:00 0
7f93fcace000-7f93fcad1000 ---p 00000000 00:00 0
7f93fcad1000-7f93fcbcf000 rw-p 00000000 00:00 0
7f93fcbcf000-7f93fcbd2000 ---p 00000000 00:00 0
7f93fcbd2000-7f93fccd0000 rw-p 00000000 00:00 0
7f93fccd0000-7f93fccd3000 ---p 00000000 00:00 0
7f93fccd3000-7f93fcdd1000 rw-p 00000000 00:00 0
7f93fcdd1000-7f93fcdd4000 ---p 00000000 00:00 0
7f93fcdd4000-7f93fced2000 rw-p 00000000 00:00 0
7f93fced2000-7f93fced5000 ---p 00000000 00:00 0
7f93fced5000-7f93fcfd3000 rw-p 00000000 00:00 0
7f93fcfd3000-7f93fcfd6000 ---p 00000000 00:00 0
7f93fcfd6000-7f93fd0d4000 rw-p 00000000 00:00 0
7f93fd0d4000-7f93fd0d7000 ---p 00000000 00:00 0
7f93fd0d7000-7f93fd1d5000 rw-p 00000000 00:00 0
7f93fd1d5000-7f93fd1d8000 ---p 00000000 00:00 0
7f93fd1d8000-7f93fd2d6000 rw-p 00000000 00:00 0
7f93fd2d6000-7f93fd2d9000 ---p 00000000 00:00 0
7f93fd2d9000-7f93fd3d7000 rw-p 00000000 00:00 0
7f93fd3d7000-7f93fd3da000 ---p 00000000 00:00 0
7f93fd3da000-7f93fd4d8000 rw-p 00000000 00:00 0
7f93fd4d8000-7f93fd4db000 ---p 00000000 00:00 0
7f93fd4db000-7f93fd5d9000 rw-p 00000000 00:00 0
7f93fd5d9000-7f93fd5dc000 ---p 00000000 00:00 0
7f93fd5dc000-7f93fd6da000 rw-p 00000000 00:00 0
7f93fd6da000-7f93fd6dd000 ---p 00000000 00:00 0
7f93fd6dd000-7f93fd7db000 rw-p 00000000 00:00 0
7f93fd7db000-7f93fd7de000 ---p 00000000 00:00 0
7f93fd7de000-7f93fd8dc000 rw-p 00000000 00:00 0
7f93fd8dc000-7f93fd8df000 ---p 00000000 00:00 0
7f93fd8df000-7f93fd9dd000 rw-p 00000000 00:00 0
7f93fd9dd000-7f93fd9e0000 ---p 00000000 00:00 0
7f93fd9e0000-7f93fdade000 rw-p 00000000 00:00 0
7f93fdade000-7f93fdadf000 ---p 00000000 00:00 0
7f93fdadf000-7f93fdc2d000 rw-p 00000000 00:00 0
7f93fdc2d000-7f93fddfd000 r--s 03c42000 ca:50 18092637 /mnt/work/bcbio/anaconda/jre/lib/rt.jar
7f93fddfd000-7f93fe5fd000 rw-p 00000000 00:00 0
7f93fe5fd000-7f93fe675000 rw-p 00000000 00:00 0
7f93fe675000-7f93fe9bd000 ---p 00000000 00:00 0
7f93fe9bd000-7f93fe9d7000 r-xp 00000000 ca:50 18092579 /mnt/work/bcbio/anaconda/jre/lib/amd64/libzip.so
7f93fe9d7000-7f93febd6000 ---p 0001a000 ca:50 18092579 /mnt/work/bcbio/anaconda/jre/lib/amd64/libzip.so
7f93febd6000-7f93febd7000 rw-p 00019000 ca:50 18092579 /mnt/work/bcbio/anaconda/jre/lib/amd64/libzip.so
7f93febd7000-7f93febd8000 rw-p 0001e000 ca:50 18092579 /mnt/work/bcbio/anaconda/jre/lib/amd64/libzip.so
7f93febd8000-7f93febe3000 r-xp 00000000 ca:01 401696 /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f93febe3000-7f93fede2000 ---p 0000b000 ca:01 401696 /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f93fede2000-7f93fede3000 r--p 0000a000 ca:01 401696 /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f93fede3000-7f93fede4000 rw-p 0000b000 ca:01 401696 /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f93fede4000-7f93fedea000 rw-p 00000000 00:00 0
7f93fedea000-7f93fedf5000 r-xp 00000000 ca:01 401699 /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f93fedf5000-7f93feff4000 ---p 0000b000 ca:01 401699 /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f93feff4000-7f93feff5000 r--p 0000a000 ca:01 401699 /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f93feff5000-7f93feff6000 rw-p 0000b000 ca:01 401699 /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f93feff6000-7f93ff00c000 r-xp 00000000 ca:01 401691 /lib/x86_64-linux-gnu/libnsl-2.23.so
7f93ff00c000-7f93ff20b000 ---p 00016000 ca:01 401691 /lib/x86_64-linux-gnu/libnsl-2.23.so
7f93ff20b000-7f93ff20c000 r--p 00015000 ca:01 401691 /lib/x86_64-linux-gnu/libnsl-2.23.so
7f93ff20c000-7f93ff20d000 rw-p 00016000 ca:01 401691 /lib/x86_64-linux-gnu/libnsl-2.23.so
7f93ff20d000-7f93ff20f000 rw-p 00000000 00:00 0
7f93ff20f000-7f93ff217000 r-xp 00000000 ca:01 401705 /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f93ff217000-7f93ff416000 ---p 00008000 ca:01 401705 /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f93ff416000-7f93ff417000 r--p 00007000 ca:01 401705 /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f93ff417000-7f93ff418000 rw-p 00008000 ca:01 401705 /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f93ff418000-7f93ff442000 r-xp 00000000 ca:50 18092588 /mnt/work/bcbio/anaconda/jre/lib/amd64/libjava.so
7f93ff442000-7f93ff642000 ---p 0002a000 ca:50 18092588 /mnt/work/bcbio/anaconda/jre/lib/amd64/libjava.so
7f93ff642000-7f93ff644000 rw-p 0002a000 ca:50 18092588 /mnt/work/bcbio/anaconda/jre/lib/amd64/libjava.so
7f93ff644000-7f93ff648000 rw-p 00036000 ca:50 18092588 /mnt/work/bcbio/anaconda/jre/lib/amd64/libjava.so
7f93ff648000-7f93ff655000 r-xp 00000000 ca:50 18092567 /mnt/work/bcbio/anaconda/jre/lib/amd64/libverify.so
7f93ff655000-7f93ff855000 ---p 0000d000 ca:50 18092567 /mnt/work/bcbio/anaconda/jre/lib/amd64/libverify.so
7f93ff855000-7f93ff857000 rw-p 0000d000 ca:50 18092567 /mnt/work/bcbio/anaconda/jre/lib/amd64/libverify.so
7f93ff857000-7f93ff858000 rw-p 00011000 ca:50 18092567 /mnt/work/bcbio/anaconda/jre/lib/amd64/libverify.so
7f93ff858000-7f93ff85f000 r-xp 00000000 ca:01 401701 /lib/x86_64-linux-gnu/librt-2.23.so
7f93ff85f000-7f93ffa5e000 ---p 00007000 ca:01 401701 /lib/x86_64-linux-gnu/librt-2.23.so
7f93ffa5e000-7f93ffa5f000 r--p 00006000 ca:01 401701 /lib/x86_64-linux-gnu/librt-2.23.so
7f93ffa5f000-7f93ffa60000 rw-p 00007000 ca:01 401701 /lib/x86_64-linux-gnu/librt-2.23.so
7f93ffa60000-7f93ffb68000 r-xp 00000000 ca:01 401710 /lib/x86_64-linux-gnu/libm-2.23.so
7f93ffb68000-7f93ffd67000 ---p 00108000 ca:01 401710 /lib/x86_64-linux-gnu/libm-2.23.so
7f93ffd67000-7f93ffd68000 r--p 00107000 ca:01 401710 /lib/x86_64-linux-gnu/libm-2.23.so
7f93ffd68000-7f93ffd69000 rw-p 00108000 ca:01 401710 /lib/x86_64-linux-gnu/libm-2.23.so
7f93ffd69000-7f94009ab000 r-xp 00000000 ca:50 18092633 /mnt/work/bcbio/anaconda/jre/lib/amd64/server/libjvm.so
7f94009ab000-7f9400baa000 ---p 00c42000 ca:50 18092633 /mnt/work/bcbio/anaconda/jre/lib/amd64/server/libjvm.so
7f9400baa000-7f9400c7a000 rw-p 00c41000 ca:50 18092633 /mnt/work/bcbio/anaconda/jre/lib/amd64/server/libjvm.so
7f9400c7a000-7f9400cbc000 rw-p 00000000 00:00 0
7f9400cbc000-7f9400cbf000 rw-p 00f88000 ca:50 18092633 /mnt/work/bcbio/anaconda/jre/lib/amd64/server/libjvm.so
7f9400cbf000-7f9400e7f000 r-xp 00000000 ca:01 401715 /lib/x86_64-linux-gnu/libc-2.23.so
7f9400e7f000-7f940107f000 ---p 001c0000 ca:01 401715 /lib/x86_64-linux-gnu/libc-2.23.so
7f940107f000-7f9401083000 r--p 001c0000 ca:01 401715 /lib/x86_64-linux-gnu/libc-2.23.so
7f9401083000-7f9401085000 rw-p 001c4000 ca:01 401715 /lib/x86_64-linux-gnu/libc-2.23.so
7f9401085000-7f9401089000 rw-p 00000000 00:00 0
7f9401089000-7f940108c000 r-xp 00000000 ca:01 401704 /lib/x86_64-linux-gnu/libdl-2.23.so
7f940108c000-7f940128b000 ---p 00003000 ca:01 401704 /lib/x86_64-linux-gnu/libdl-2.23.so
7f940128b000-7f940128c000 r--p 00002000 ca:01 401704 /lib/x86_64-linux-gnu/libdl-2.23.so
7f940128c000-7f940128d000 rw-p 00003000 ca:01 401704 /lib/x86_64-linux-gnu/libdl-2.23.so
7f940128d000-7f94012a2000 r-xp 00000000 ca:50 18092598 /mnt/work/bcbio/anaconda/lib/libjli.so
7f94012a2000-7f94014a2000 ---p 00015000 ca:50 18092598 /mnt/work/bcbio/anaconda/lib/libjli.so
7f94014a2000-7f94014a3000 rw-p 00015000 ca:50 18092598 /mnt/work/bcbio/anaconda/lib/libjli.so
7f94014a3000-7f94014a4000 rw-p 00052000 ca:50 18092598 /mnt/work/bcbio/anaconda/lib/libjli.so
7f94014a4000-7f94014bc000 r-xp 00000000 ca:01 401698 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f94014bc000-7f94016bb000 ---p 00018000 ca:01 401698 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f94016bb000-7f94016bc000 r--p 00017000 ca:01 401698 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f94016bc000-7f94016bd000 rw-p 00018000 ca:01 401698 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f94016bd000-7f94016c1000 rw-p 00000000 00:00 0
7f94016c1000-7f94016e7000 r-xp 00000000 ca:01 401692 /lib/x86_64-linux-gnu/ld-2.23.so
7f94016f1000-7f94016f6000 r--s 0009a000 ca:50 18092620 /mnt/work/bcbio/anaconda/jre/lib/jsse.jar
7f94016f6000-7f9401700000 r--s 00116000 ca:50 18092627 /mnt/work/bcbio/anaconda/jre/lib/ext/localedata.jar
7f9401700000-7f94017d1000 rw-p 00000000 00:00 0
7f94017d1000-7f94017d9000 rw-s 00000000 ca:01 330 /tmp/hsperfdata_ubuntu/45651
7f94017d9000-7f94017dc000 ---p 00000000 00:00 0
7f94017dc000-7f94018de000 rw-p 00000000 00:00 0
7f94018e2000-7f94018e3000 rw-p 00000000 00:00 0
7f94018e3000-7f94018e4000 ---p 00000000 00:00 0
7f94018e4000-7f94018e6000 rw-p 00000000 00:00 0
7f94018e6000-7f94018e7000 r--p 00025000 ca:01 401692 /lib/x86_64-linux-gnu/ld-2.23.so
7f94018e7000-7f94018e8000 rw-p 00026000 ca:01 401692 /lib/x86_64-linux-gnu/ld-2.23.so
7f94018e8000-7f94018e9000 rw-p 00000000 00:00 0
7ffd90304000-7ffd90326000 rw-p 00000000 00:00 0 [stack]
7ffd9032f000-7ffd90331000 r--p 00000000 00:00 0 [vvar]
7ffd90331000-7ffd90333000 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 -Dsnappy.disable=true -Xms1000m -Xmx46965m -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/work/cwl/bcbio_validation_workflows/somatic-giab-mix/bunny_work/main-somatic-giab-mix-2017-09-23-094842.494/root/postprocess_alignment/2/bcbiotx/tmpLCoup3
java_command: /mnt/work/bcbio/anaconda/share/gatk4-4.0b5-0/gatk-package-4.beta.5-local.jar ApplyBQSRSpark --sparkMaster local[16] --input /mnt/work/cwl/bcbio_validation_workflows/somatic-giab-mix/bunny_work/main-somatic-giab-mix-2017-09-22-201054.451/root/alignment/2/merge_split_alignments/align/giab-mix-tumor/giab-mix-tumor-sort.bam --output /mnt/work/cwl/bcbio_validation_workflows/somatic-giab-mix/bunny_work/main-somatic-giab-mix-2017-09-23-094842.494/root/postprocess_alignment/2/bcbiotx/tmpLCoup3/giab-mix-tumor-sort-recal.bam --bqsr_recal_file /mnt/work/cwl/bcbio_validation_workflows/somatic-giab-mix/bunny_work/main-somatic-giab-mix-2017-09-23-094842.494/root/postprocess_alignment/2/align/giab-mix-tumor/giab-mix-tumor-sort-recal.grp
java_class_path (initial): /mnt/work/bcbio/anaconda/share/gatk4-4.0b5-0/gatk-package-4.beta.5-local.jar
Launcher Type: SUN_STANDARD
Environment Variables:
PATH=/mnt/work/bcbio/anaconda/bin:/mnt/work/bcbio/bin:/home/ubuntu/bin:/home/ubuntu/.local/bin:/mnt/work/bcbio/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/mnt/work/bcbio/bcbio-vm/anaconda/bin
SHELL=/bin/bash
DISPLAY=localhost:11.0
Signal Handlers:
SIGSEGV: [libjvm.so+0xa38840], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGBUS: [libjvm.so+0xa38840], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGFPE: [libjvm.so+0x8a3870], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGPIPE: [libjvm.so+0x8a3870], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGXFSZ: [libjvm.so+0x8a3870], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGILL: [libjvm.so+0x8a3870], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
SIGUSR2: [libjvm.so+0x8a4f50], sa_mask[0]=00100000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
SIGHUP: [libjvm.so+0x8a6640], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGINT: [libjvm.so+0x8a6640], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGTERM: [libjvm.so+0x8a6640], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGQUIT: [libjvm.so+0x8a6640], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
--------------- S Y S T E M ---------------
OS:DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=16.04
DISTRIB_CODENAME=xenial
DISTRIB_DESCRIPTION="Ubuntu 16.04.1 LTS"
uname:Linux 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64
libc:glibc 2.23 NPTL 2.23
rlimit: STACK 8192k, CORE 0k, NPROC 257603, NOFILE 65536, AS infinity
load average:4.28 5.45 6.13
/proc/meminfo:
MemTotal: 65960476 kB
MemFree: 361136 kB
MemAvailable: 35259008 kB
Buffers: 43296 kB
Cached: 34502672 kB
SwapCached: 0 kB
Active: 46333932 kB
Inactive: 18076480 kB
Active(anon): 29867904 kB
Inactive(anon): 8424 kB
Active(file): 16466028 kB
Inactive(file): 18068056 kB
Unevictable: 3656 kB
Mlocked: 3656 kB
SwapTotal: 0 kB
SwapFree: 0 kB
Dirty: 2486508 kB
Writeback: 0 kB
AnonPages: 29868624 kB
Mapped: 68552 kB
Shmem: 8940 kB
Slab: 958860 kB
SReclaimable: 892592 kB
SUnreclaim: 66268 kB
KernelStack: 10160 kB
PageTables: 65368 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 32980236 kB
Committed_AS: 32027616 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 0 kB
VmallocChunk: 0 kB
HardwareCorrupted: 0 kB
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DirectMap1G: 47185920 kB
CPU:total 16 (initial active 16) (8 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, lzcnt, ht, tsc, bmi1, bmi2
/proc/cpuinfo:
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 79
model name : Intel(R) Xeon(R) CPU E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 0
cpu cores : 8
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 1
cpu cores : 8
apicid : 2
initial apicid : 2
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 2
cpu cores : 8
apicid : 4
initial apicid : 4
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 3
cpu cores : 8
apicid : 6
initial apicid : 6
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 4
cpu cores : 8
apicid : 8
initial apicid : 8
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 5
cpu cores : 8
apicid : 10
initial apicid : 10
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 6
cpu cores : 8
apicid : 12
initial apicid : 12
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 7
cpu cores : 8
apicid : 14
initial apicid : 14
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 0
cpu cores : 8
apicid : 1
initial apicid : 1
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 1
cpu cores : 8
apicid : 3
initial apicid : 3
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 2
cpu cores : 8
apicid : 5
initial apicid : 5
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 3
cpu cores : 8
apicid : 7
initial apicid : 7
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 4
cpu cores : 8
apicid : 9
initial apicid : 9
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 5
cpu cores : 8
apicid : 11
initial apicid : 11
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 6
cpu cores : 8
apicid : 13
initial apicid : 13
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
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 E5-2686 v4 @ 2.30GHz
stepping : 1
microcode : 0xb000021
cpu MHz : 2300.054
cache size : 46080 KB
physical id : 0
siblings : 16
core id : 7
cpu cores : 8
apicid : 15
initial apicid : 15
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt
bugs :
bogomips : 4600.10
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
Memory: 4k page, physical 65960476k(361136k free), swap 0k(0k free)
vm_info: OpenJDK 64-Bit Server VM (25.144-b01) for linux-amd64 JRE (1.8.0_144-b01), built on Jul 26 2017 07:17:16 by "zulu_re" with gcc 4.4.7 20120313 (Red Hat 4.4.7-3)
time: Sat Sep 23 12:59:11 2017
elapsed time: 2417 seconds (0d 0h 40m 17s)
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