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  1. JDK
  2. JDK-8199012

SEGV in jni_DetachCurrentThread during VM shutdown

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    Details

    • Subcomponent:
    • Resolved In Build:
      b07
    • CPU:
      x86_64
    • OS:
      linux_ubuntu

      Description

      FULL PRODUCT VERSION :
      java version "1.8.0_161"
      Java(TM) SE Runtime Environment (build 1.8.0_161-b12)
      Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)


      FULL OS VERSION :
      Linux storage 4.4.0-43-generic #63-Ubuntu SMP Wed Oct 12 13:48:03 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux


      A DESCRIPTION OF THE PROBLEM :
      Use LevelDB JNI library use.


      THE PROBLEM WAS REPRODUCIBLE WITH -Xint FLAG: Yes

      THE PROBLEM WAS REPRODUCIBLE WITH -server FLAG: Yes

      REGRESSION. Last worked in version 8u161

      STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
      When finish all java code...

      ERROR MESSAGES/STACK TRACES THAT OCCUR :
      #
      # A fatal error has been detected by the Java Runtime Environment:
      #
      # SIGSEGV (0xb) at pc=0x00007f7ae5a2d436, pid=18113, tid=0x00007f7ae6d56700
      #
      # JRE version: Java(TM) SE Runtime Environment (8.0_161-b12) (build 1.8.0_161-b12)
      # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.161-b12 mixed mode linux-amd64 compressed oops)
      # Problematic frame:
      # V [libjvm.so+0x8e6436] Monitor::ILock(Thread*)+0xb6
      #
      # Core dump written. Default location: /home/users/tag/uniprot/core or core.18113
      #
      # If you would like to submit a bug report, please visit:
      # http://bugreport.java.com/bugreport/crash.jsp
      #

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

      Current thread is native thread

      siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0000000000000188

      Registers:
      RAX=0x00007f7ae035bd01, RBX=0x00007f7ae0006970, RCX=0x0000000000000001, RDX=0x00007f7ae035bd01
      RSP=0x00007f7ae6d55e90, RBP=0x00007f7ae6d55eb0, RSI=0x0000000000000000, RDI=0x00007f7ae0006970
      R8 =0x00007f7ae0000940, R9 =0x0000000000000000, R10=0x0000000000000008, R11=0x0000000000000206
      R12=0x0000000000000000, R13=0x00007f7ae61128c0, R14=0x0000000000000000, R15=0x00007f7ae6d56c18
      RIP=0x00007f7ae5a2d436, EFLAGS=0x0000000000010202, CSGSFS=0x3ff3000000000033, ERR=0x0000000000000004
        TRAPNO=0x000000000000000e

      Top of Stack: (sp=0x00007f7ae6d55e90)
      0x00007f7ae6d55e90: 00007f7ae0006970 0000000000000000
      0x00007f7ae6d55ea0: 00007f7ae6b402c8 0000000000000004
      0x00007f7ae6d55eb0: 00007f7ae6d55ed0 00007f7ae5a2d79f
      0x00007f7ae6d55ec0: 00007f7ae6d56a48 0000000000000000
      0x00007f7ae6d55ed0: 00007f7ae6d55ee0 00007f7ae5c1f689
      0x00007f7ae6d55ee0: 00007f7ae6d55f00 00007f7ae581a73d
      0x00007f7ae6d55ef0: 0000000500010002 00007f7ae6d56a48
      0x00007f7ae6d55f00: 00007f7ae6b402f8 00007f7a8a02a639
      0x00007f7ae6d55f10: 00007f7ae6d56a28 00007f7ae692e439
      0x00007f7ae6d55f20: 00007f7ae6d55f70 0000000000000000
      0x00007f7ae6d55f30: 0000000000000000 0000000000000000
      0x00007f7ae6d55f40: 00007ffd3778ecef 00007f7ae6d569c0
      0x00007f7ae6d55f50: 0000000000000002 00007f7ae692f870
      0x00007f7ae6d55f60: 0000000000000000 00007f7ae6d56700
      0x00007f7ae6d55f70: 00007f7ae6d56700 9cc7aa1684e9a956
      0x00007f7ae6d55f80: 0000000000000000 00007ffd3778ecef
      0x00007f7ae6d55f90: 00007f7ae6d569c0 0000000000000002
      0x00007f7ae6d55fa0: 623267bc3a29a956 623267336813a956
      0x00007f7ae6d55fb0: 0000000000000000 0000000000000000
      0x00007f7ae6d55fc0: 0000000000000000 0000000000000000
      0x00007f7ae6d55fd0: 0000000000000000 0000000000000000
      0x00007f7ae6d55fe0: 0000000000000000 0000000000000000
      0x00007f7ae6d55ff0: 00007f7ae6d56700 00007f7ae624b41d
      0x00007f7ae6d56000: 0000000000000000 0000000000000000
      0x00007f7ae6d56010: 0000000000000000 0000000000000000
      0x00007f7ae6d56020: 0000000000000000 0000000000000000
      0x00007f7ae6d56030: 0000000000000000 0000000000000000
      0x00007f7ae6d56040: 0000000000000000 0000000000000000
      0x00007f7ae6d56050: 0000000000000000 0000000000000000
      0x00007f7ae6d56060: 0000000000000000 0000000000000000
      0x00007f7ae6d56070: 0000000000000000 0000000000000000
      0x00007f7ae6d56080: 0000000000000000 0000000000000000

      Instructions: (pc=0x00007f7ae5a2d436)
      0x00007f7ae5a2d416: 5e c9 c3 0f 1f 80 00 00 00 00 48 8b 05 69 a1 69
      0x00007f7ae5a2d426: 00 0f b6 08 e9 75 ff ff ff 90 4c 89 f6 48 89 df
      0x00007f7ae5a2d436: 4d 8b a6 88 01 00 00 e8 ae fb ff ff 85 c0 75 ca
      0x00007f7ae5a2d446: 41 c7 44 24 20 00 00 00 00 41 83 7d 00 01 0f 84

      Register to memory mapping:

      RAX=0x00007f7ae035bd01 is an unknown value
      RBX=0x00007f7ae0006970 is an unknown value
      RCX=0x0000000000000001 is an unknown value
      RDX=0x00007f7ae035bd01 is an unknown value
      RSP=0x00007f7ae6d55e90 is an unknown value
      RBP=0x00007f7ae6d55eb0 is an unknown value
      RSI=0x0000000000000000 is an unknown value
      RDI=0x00007f7ae0006970 is an unknown value
      R8 =0x00007f7ae0000940 is an unknown value
      R9 =0x0000000000000000 is an unknown value
      R10=0x0000000000000008 is an unknown value
      R11=0x0000000000000206 is an unknown value
      R12=0x0000000000000000 is an unknown value
      R13=0x00007f7ae61128c0: <offset 0xfcb8c0> in /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so at 0x00007f7ae5147000
      R14=0x0000000000000000 is an unknown value
      R15=0x00007f7ae6d56c18 is an unknown value


      Stack: [0x00007f7ae6c56000,0x00007f7ae6d57000], sp=0x00007f7ae6d55e90, free space=1023k
      Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
      V [libjvm.so+0x8e6436] Monitor::ILock(Thread*)+0xb6
      V [libjvm.so+0x8e679f] Monitor::lock_without_safepoint_check()+0x2f
      V [libjvm.so+0xad8689] VM_Exit::wait_if_vm_exited()+0x39
      V [libjvm.so+0x6d373d] jni_DetachCurrentThread+0x3d


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

      VM state:at safepoint (shutting down)

      VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
      [0x00007f7ae0006970] Threads_lock - owner thread: 0x00007f7ae031c000

      Heap:
       PSYoungGen total 225792K, used 116130K [0x00000006c4780000, 0x00000006d4380000, 0x00000007c0000000)
        eden space 193536K, 60% used [0x00000006c4780000,0x00000006cb8e8840,0x00000006d0480000)
        from space 32256K, 0% used [0x00000006d2400000,0x00000006d2400000,0x00000006d4380000)
        to space 32256K, 0% used [0x00000006d0480000,0x00000006d0480000,0x00000006d2400000)
       ParOldGen total 516096K, used 0K [0x00000004cd600000, 0x00000004ece00000, 0x00000006c4780000)
        object space 516096K, 0% used [0x00000004cd600000,0x00000004cd600000,0x00000004ece00000)
       Metaspace used 8441K, capacity 8618K, committed 8832K, reserved 1056768K
        class space used 982K, capacity 1059K, committed 1152K, reserved 1048576K

      Card table byte_map: [0x00007f7acf07c000,0x00007f7ad0812000] byte_map_base: 0x00007f7acca11000

      Marking Bits: (ParMarkBitMap*) 0x00007f7ae6116920
       Begin Bits: [0x00007f7aa86b0000, 0x00007f7ab4358000)
       End Bits: [0x00007f7ab4358000, 0x00007f7ac0000000)

      Polling page: 0x00007f7ae6d69000

      CodeCache: size=245760Kb used=4543Kb max_used=4543Kb free=241216Kb
       bounds [0x00007f7ad0bd2000, 0x00007f7ad1052000, 0x00007f7adfbd2000]
       total_blobs=1013 nmethods=679 adapters=246
       compilation: enabled

      Compilation events (10 events):
      Event: 0.541 Thread 0x00007f7ae0365800 nmethod 674 0x00007f7ad103dc10 code [0x00007f7ad103dd80, 0x00007f7ad103dfd8]
      Event: 0.545 Thread 0x00007f7ae0372000 nmethod 672 0x00007f7ad103cad0 code [0x00007f7ad103cca0, 0x00007f7ad103d2b0]
      Event: 1.147 Thread 0x00007f7ae035f800 676 4 java.lang.String::indexOf (166 bytes)
      Event: 1.152 Thread 0x00007f7ae037c800 677 3 java.lang.ClassLoader::compareCerts (149 bytes)
      Event: 1.153 Thread 0x00007f7ae037c800 nmethod 677 0x00007f7ad1039b10 code [0x00007f7ad1039ce0, 0x00007f7ad103a598]
      Event: 1.156 Thread 0x00007f7ae035f800 nmethod 676 0x00007f7ad1041dd0 code [0x00007f7ad1041f40, 0x00007f7ad1042458]
      Event: 1.173 Thread 0x00007f7ae0376000 678 ! 3 java.lang.StringCoding::encode (120 bytes)
      Event: 1.175 Thread 0x00007f7ae0376000 nmethod 678 0x00007f7ad103f050 code [0x00007f7ad103f3a0, 0x00007f7ad1040e58]
      Event: 1.186 Thread 0x00007f7ae037a000 680 3 java.util.zip.InflaterInputStream::<init> (79 bytes)
      Event: 1.186 Thread 0x00007f7ae037a000 nmethod 680 0x00007f7ad103e450 code [0x00007f7ad103e600, 0x00007f7ad103ecf8]

      GC Heap History (0 events):
      No events

      Deoptimization events (3 events):
      Event: 0.375 Thread 0x00007f7ae000a800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f7ad0f393e8 method=java.lang.String.replace(CC)Ljava/lang/String; @ 26
      Event: 0.405 Thread 0x00007f7ae000a800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f7ad0f03e54 method=java.lang.String.indexOf([CII[CIII)I @ 3
      Event: 1.179 Thread 0x00007f7ae000a800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007f7ad103d218 method=java.lang.Float.compare(FF)I @ 11

      Classes redefined (0 events):
      No events

      Internal exceptions (10 events):
      Event: 0.133 Thread 0x00007f7ae000a800 Exception <a 'java/security/PrivilegedActionException'> (0x00000006c48581e8) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/prims/jvm.cpp, line 1390]
      Event: 0.133 Thread 0x00007f7ae000a800 Exception <a 'java/security/PrivilegedActionException'> (0x00000006c48583f8) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/prims/jvm.cpp, line 1390]
      Event: 0.155 Thread 0x00007f7ae000a800 Exception <a 'java/security/PrivilegedActionException'> (0x00000006c48eee98) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/prims/jvm.cpp, line 1390]
      Event: 0.155 Thread 0x00007f7ae000a800 Exception <a 'java/security/PrivilegedActionException'> (0x00000006c48ef0a8) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/prims/jvm.cpp, line 1390]
      Event: 0.156 Thread 0x00007f7ae000a800 Exception <a 'java/security/PrivilegedActionException'> (0x00000006c48f1510) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/prims/jvm.cpp, line 1390]
      Event: 0.156 Thread 0x00007f7ae000a800 Exception <a 'java/security/PrivilegedActionException'> (0x00000006c48f1720) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/prims/jvm.cpp, line 1390]
      Event: 0.209 Thread 0x00007f7ae000a800 Exception <a 'java/io/FileNotFoundException'> (0x00000006c582a1f0) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/prims/jni.cpp, line 709]
      Event: 0.466 Thread 0x00007f7ae000a800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x00000006c66e8178) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/prims/methodHandles.cpp, line 1167]
      Event: 0.468 Thread 0x00007f7ae000a800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x00000006c66f5838) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/prims/methodHandles.cpp, line 1167]
      Event: 1.156 Thread 0x00007f7ae000a800 Exception <a 'java/lang/NoSuchMethodError': org.slf4j.impl.StaticMDCBinder.getSingleton()Lorg/slf4j/impl/StaticMDCBinder;> (0x00000006cb2c1ed0) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u161/10277/hotspot/src/share/vm/interpreter/linkResolver

      Events (10 events):
      Event: 1.188 loading class java/util/concurrent/ScheduledFuture
      Event: 1.188 loading class java/util/concurrent/Delayed
      Event: 1.188 loading class java/util/concurrent/Delayed done
      Event: 1.188 loading class java/util/concurrent/ScheduledFuture done
      Event: 1.188 loading class java/util/concurrent/RunnableScheduledFuture done
      Event: 1.188 loading class java/util/concurrent/Executors$DefaultThreadFactory
      Event: 1.188 loading class java/util/concurrent/Executors$DefaultThreadFactory done
      Event: 1.189 Thread 0x00007f7ae000a800 Thread exited: 0x00007f7ae000a800
      Event: 1.189 Thread 0x00007f7ae000a800 Thread added: 0x00007f7ae000a800
      Event: 1.189 Thread 0x00007f7ae000a800 Thread exited: 0x00007f7ae000a800


      Dynamic libraries:
      00400000-00401000 r-xp 00000000 fc:00 6427238 /usr/lib/jvm/java-8-oracle/jre/bin/java
      00600000-00601000 rw-p 00000000 fc:00 6427238 /usr/lib/jvm/java-8-oracle/jre/bin/java
      018e4000-01905000 rw-p 00000000 00:00 0 [heap]
      4cd600000-4ece00000 rw-p 00000000 00:00 0
      4ece00000-6c4780000 ---p 00000000 00:00 0
      6c4780000-6d4380000 rw-p 00000000 00:00 0
      6d4380000-7c0000000 ---p 00000000 00:00 0
      7c0000000-7c0120000 rw-p 00000000 00:00 0
      7c0120000-800000000 ---p 00000000 00:00 0
      7f79fc000000-7f79fc021000 rw-p 00000000 00:00 0
      7f79fc021000-7f7a00000000 ---p 00000000 00:00 0
      7f7a00000000-7f7a00021000 rw-p 00000000 00:00 0
      7f7a00021000-7f7a04000000 ---p 00000000 00:00 0
      7f7a04000000-7f7a040c9000 rw-p 00000000 00:00 0
      7f7a040c9000-7f7a08000000 ---p 00000000 00:00 0
      7f7a08000000-7f7a08021000 rw-p 00000000 00:00 0
      7f7a08021000-7f7a0c000000 ---p 00000000 00:00 0
      7f7a0c000000-7f7a0c0b8000 rw-p 00000000 00:00 0
      7f7a0c0b8000-7f7a10000000 ---p 00000000 00:00 0
      7f7a10000000-7f7a100ae000 rw-p 00000000 00:00 0
      7f7a100ae000-7f7a14000000 ---p 00000000 00:00 0
      7f7a14000000-7f7a140f6000 rw-p 00000000 00:00 0
      7f7a140f6000-7f7a18000000 ---p 00000000 00:00 0
      7f7a18000000-7f7a180d9000 rw-p 00000000 00:00 0
      7f7a180d9000-7f7a1c000000 ---p 00000000 00:00 0
      7f7a1c000000-7f7a1c047000 rw-p 00000000 00:00 0
      7f7a1c047000-7f7a20000000 ---p 00000000 00:00 0
      7f7a20000000-7f7a20085000 rw-p 00000000 00:00 0
      7f7a20085000-7f7a24000000 ---p 00000000 00:00 0
      7f7a24000000-7f7a24152000 rw-p 00000000 00:00 0
      7f7a24152000-7f7a28000000 ---p 00000000 00:00 0
      7f7a28000000-7f7a28114000 rw-p 00000000 00:00 0
      7f7a28114000-7f7a2c000000 ---p 00000000 00:00 0
      7f7a2c000000-7f7a2c02b000 rw-p 00000000 00:00 0
      7f7a2c02b000-7f7a30000000 ---p 00000000 00:00 0
      7f7a30000000-7f7a30022000 rw-p 00000000 00:00 0
      7f7a30022000-7f7a34000000 ---p 00000000 00:00 0
      7f7a34000000-7f7a34021000 rw-p 00000000 00:00 0
      7f7a34021000-7f7a38000000 ---p 00000000 00:00 0
      7f7a38000000-7f7a380ba000 rw-p 00000000 00:00 0
      7f7a380ba000-7f7a3c000000 ---p 00000000 00:00 0
      7f7a3c000000-7f7a3c021000 rw-p 00000000 00:00 0
      7f7a3c021000-7f7a40000000 ---p 00000000 00:00 0
      7f7a40000000-7f7a40021000 rw-p 00000000 00:00 0
      7f7a40021000-7f7a44000000 ---p 00000000 00:00 0
      7f7a44000000-7f7a44021000 rw-p 00000000 00:00 0
      7f7a44021000-7f7a48000000 ---p 00000000 00:00 0
      7f7a48000000-7f7a48021000 rw-p 00000000 00:00 0
      7f7a48021000-7f7a4c000000 ---p 00000000 00:00 0
      7f7a4c000000-7f7a4c021000 rw-p 00000000 00:00 0
      7f7a4c021000-7f7a50000000 ---p 00000000 00:00 0
      7f7a54000000-7f7a54021000 rw-p 00000000 00:00 0
      7f7a54021000-7f7a58000000 ---p 00000000 00:00 0
      7f7a5c000000-7f7a5c021000 rw-p 00000000 00:00 0
      7f7a5c021000-7f7a60000000 ---p 00000000 00:00 0
      7f7a64000000-7f7a64021000 rw-p 00000000 00:00 0
      7f7a64021000-7f7a68000000 ---p 00000000 00:00 0
      7f7a6c000000-7f7a6c021000 rw-p 00000000 00:00 0
      7f7a6c021000-7f7a70000000 ---p 00000000 00:00 0
      7f7a74000000-7f7a74021000 rw-p 00000000 00:00 0
      7f7a74021000-7f7a78000000 ---p 00000000 00:00 0
      7f7a7c000000-7f7a7c021000 rw-p 00000000 00:00 0
      7f7a7c021000-7f7a80000000 ---p 00000000 00:00 0
      7f7a84000000-7f7a84021000 rw-p 00000000 00:00 0
      7f7a84021000-7f7a88000000 ---p 00000000 00:00 0
      7f7a89a76000-7f7a89a8c000 r-xp 00000000 fc:00 1180047 /lib/x86_64-linux-gnu/libgcc_s.so.1
      7f7a89a8c000-7f7a89c8b000 ---p 00016000 fc:00 1180047 /lib/x86_64-linux-gnu/libgcc_s.so.1
      7f7a89c8b000-7f7a89c8c000 rw-p 00015000 fc:00 1180047 /lib/x86_64-linux-gnu/libgcc_s.so.1
      7f7a89c8c000-7f7a89dfe000 r-xp 00000000 fc:00 4722349 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
      7f7a89dfe000-7f7a89ffe000 ---p 00172000 fc:00 4722349 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
      7f7a89ffe000-7f7a8a008000 r--p 00172000 fc:00 4722349 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
      7f7a8a008000-7f7a8a00a000 rw-p 0017c000 fc:00 4722349 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
      7f7a8a00a000-7f7a8a00e000 rw-p 00000000 00:00 0
      7f7a8a00e000-7f7a8a068000 r-xp 00000000 fc:00 6553618 /tmp/libleveldbjni-64-1-7477885568638760905.8 (deleted)
      7f7a8a068000-7f7a8a268000 ---p 0005a000 fc:00 6553618 /tmp/libleveldbjni-64-1-7477885568638760905.8 (deleted)
      7f7a8a268000-7f7a8a26b000 rw-p 0005a000 fc:00 6553618 /tmp/libleveldbjni-64-1-7477885568638760905.8 (deleted)
      7f7a8a26b000-7f7a8a2e9000 r--s 00891000 fc:01 30412538955 /home/users/tag/uniprot/createnr_lib/eclipse-collections-8.2.0.jar
      7f7a8a2e9000-7f7a8a40f000 r--s 010b2000 fc:01 30412538958 /home/users/tag/uniprot/createnr_lib/fastutil-8.1.0.jar
      7f7a8a40f000-7f7a8a410000 ---p 00000000 00:00 0
      7f7a8a410000-7f7a8a510000 rw-p 00000000 00:00 0
      7f7a8a510000-7f7a8a513000 ---p 00000000 00:00 0
      7f7a8a513000-7f7a8a611000 rw-p 00000000 00:00 0
      7f7a8a611000-7f7a8a614000 ---p 00000000 00:00 0
      7f7a8a614000-7f7a8a712000 rw-p 00000000 00:00 0
      7f7a8a712000-7f7a8a715000 ---p 00000000 00:00 0
      7f7a8a715000-7f7a8a813000 rw-p 00000000 00:00 0
      7f7a8a813000-7f7a8a816000 ---p 00000000 00:00 0
      7f7a8a816000-7f7a8a914000 rw-p 00000000 00:00 0
      7f7a8a914000-7f7a8a917000 ---p 00000000 00:00 0
      7f7a8a917000-7f7a8aa15000 rw-p 00000000 00:00 0
      7f7a8aa15000-7f7a8aa18000 ---p 00000000 00:00 0
      7f7a8aa18000-7f7a8ab16000 rw-p 00000000 00:00 0
      7f7a8ab16000-7f7a8ab19000 ---p 00000000 00:00 0
      7f7a8ab19000-7f7a8ac17000 rw-p 00000000 00:00 0
      7f7a8ac17000-7f7a8ac1a000 ---p 00000000 00:00 0
      7f7a8ac1a000-7f7a8ad18000 rw-p 00000000 00:00 0
      7f7a8ad18000-7f7a8ad1b000 ---p 00000000 00:00 0
      7f7a8ad1b000-7f7a8ae19000 rw-p 00000000 00:00 0
      7f7a8ae19000-7f7a8ae1c000 ---p 00000000 00:00 0
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      7f7ae6d5c000-7f7ae6d5e000 r--s 001eb000 fc:01 30412538988 /home/users/tag/uniprot/createnr_lib/snappy-java-1.1.7.1.jar
      7f7ae6d5e000-7f7ae6d60000 r--s 00012000 fc:01 30425276952 /home/users/tag/uniprot/createnr_lib/compress-lzf-1.0.4.jar
      7f7ae6d60000-7f7ae6d68000 rw-s 00000000 fc:00 6553603 /tmp/hsperfdata_tag/18113 (deleted)
      7f7ae6d68000-7f7ae6d69000 rw-p 00000000 00:00 0
      7f7ae6d69000-7f7ae6d6a000 ---p 00000000 00:00 0
      7f7ae6d6a000-7f7ae6d6b000 r--p 00025000 fc:00 1180069 /lib/x86_64-linux-gnu/ld-2.23.so
      7f7ae6d6b000-7f7ae6d6c000 rw-p 00026000 fc:00 1180069 /lib/x86_64-linux-gnu/ld-2.23.so
      7f7ae6d6c000-7f7ae6d6d000 rw-p 00000000 00:00 0
      7ffd37775000-7ffd37796000 rw-p 00000000 00:00 0 [stack]
      7ffd3779f000-7ffd377a1000 r--p 00000000 00:00 0 [vvar]
      7ffd377a1000-7ffd377a3000 r-xp 00000000 00:00 0 [vdso]
      ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

      VM Arguments:
      java_command: createnr.jar uniprot-search 1455.1:1455.3
      java_class_path (initial): createnr.jar
      Launcher Type: SUN_STANDARD

      Environment Variables:
      JAVA_HOME=/home/users/tag/jdk1.7.0_21
      PATH=/home/users/tag/.sdkman/candidates/groovy/current/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin
      SHELL=/bin/bash

      Signal Handlers:
      SIGSEGV: [libjvm.so+0xad01e0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
      SIGBUS: [libjvm.so+0xad01e0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
      SIGFPE: [libjvm.so+0x927fb0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
      SIGPIPE: [libjvm.so+0x927fb0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
      SIGXFSZ: [libjvm.so+0x927fb0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
      SIGILL: [libjvm.so+0x927fb0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
      SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
      SIGUSR2: [libjvm.so+0x9297f0], sa_mask[0]=00000000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
      SIGHUP: [libjvm.so+0x92abf0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
      SIGINT: [libjvm.so+0x92abf0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
      SIGTERM: [libjvm.so+0x92abf0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
      SIGQUIT: [libjvm.so+0x92abf0], 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 16.04.4 LTS"

      uname:Linux 4.4.0-43-generic #63-Ubuntu SMP Wed Oct 12 13:48:03 UTC 2016 x86_64
      libc:glibc 2.23 NPTL 2.23
      rlimit: STACK 8192k, CORE infinity, NPROC 193021, NOFILE 1048576, AS infinity
      load average:0.00 0.86 0.90

      /proc/meminfo:
      MemTotal: 49451300 kB
      MemFree: 1997292 kB
      MemAvailable: 47398980 kB
      Buffers: 126520 kB
      Cached: 44501492 kB
      SwapCached: 18536 kB
      Active: 5358076 kB
      Inactive: 40509464 kB
      Active(anon): 173592 kB
      Inactive(anon): 1100592 kB
      Active(file): 5184484 kB
      Inactive(file): 39408872 kB
      Unevictable: 0 kB
      Mlocked: 0 kB
      SwapTotal: 1048572 kB
      SwapFree: 729704 kB
      Dirty: 520 kB
      Writeback: 0 kB
      AnonPages: 1224796 kB
      Mapped: 79752 kB
      Shmem: 34656 kB
      Slab: 1362320 kB
      SReclaimable: 1269080 kB
      SUnreclaim: 93240 kB
      KernelStack: 6672 kB
      PageTables: 11188 kB
      NFS_Unstable: 0 kB
      Bounce: 0 kB
      WritebackTmp: 0 kB
      CommitLimit: 25774220 kB
      Committed_AS: 35748364 kB
      VmallocTotal: 34359738367 kB
      VmallocUsed: 0 kB
      VmallocChunk: 0 kB
      HardwareCorrupted: 0 kB
      AnonHugePages: 1044480 kB
      CmaTotal: 0 kB
      CmaFree: 0 kB
      HugePages_Total: 0
      HugePages_Free: 0
      HugePages_Rsvd: 0
      HugePages_Surp: 0
      Hugepagesize: 2048 kB
      DirectMap4k: 345472 kB
      DirectMap2M: 32151552 kB
      DirectMap1G: 19922944 kB


      CPU:total 24 (initial active 24) (6 cores per cpu, 2 threads per core) family 6 model 44 stepping 2, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, aes, clmul, ht, tsc, tscinvbit, tscinv

      /proc/cpuinfo:
      processor : 0
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 0
      cpu cores : 6
      apicid : 0
      initial apicid : 0
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 1
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 1
      cpu cores : 6
      apicid : 2
      initial apicid : 2
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 2
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 2
      cpu cores : 6
      apicid : 4
      initial apicid : 4
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 3
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 8
      cpu cores : 6
      apicid : 16
      initial apicid : 16
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 4
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 9
      cpu cores : 6
      apicid : 18
      initial apicid : 18
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 5
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 10
      cpu cores : 6
      apicid : 20
      initial apicid : 20
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 6
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 0
      cpu cores : 6
      apicid : 32
      initial apicid : 32
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 7
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 1
      cpu cores : 6
      apicid : 34
      initial apicid : 34
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 8
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 2
      cpu cores : 6
      apicid : 36
      initial apicid : 36
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 9
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 8
      cpu cores : 6
      apicid : 48
      initial apicid : 48
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 10
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 2000.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 9
      cpu cores : 6
      apicid : 50
      initial apicid : 50
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 11
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 10
      cpu cores : 6
      apicid : 52
      initial apicid : 52
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 12
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 2401.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 0
      cpu cores : 6
      apicid : 1
      initial apicid : 1
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 13
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 1
      cpu cores : 6
      apicid : 3
      initial apicid : 3
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 14
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 2
      cpu cores : 6
      apicid : 5
      initial apicid : 5
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 15
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1867.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 8
      cpu cores : 6
      apicid : 17
      initial apicid : 17
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 16
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 2133.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 9
      cpu cores : 6
      apicid : 19
      initial apicid : 19
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 17
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 2401.000
      cache size : 12288 KB
      physical id : 0
      siblings : 12
      core id : 10
      cpu cores : 6
      apicid : 21
      initial apicid : 21
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.67
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 18
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 0
      cpu cores : 6
      apicid : 33
      initial apicid : 33
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 19
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 2000.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 1
      cpu cores : 6
      apicid : 35
      initial apicid : 35
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 20
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 2
      cpu cores : 6
      apicid : 37
      initial apicid : 37
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 21
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 8
      cpu cores : 6
      apicid : 49
      initial apicid : 49
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 22
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 1600.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 9
      cpu cores : 6
      apicid : 51
      initial apicid : 51
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:

      processor : 23
      vendor_id : GenuineIntel
      cpu family : 6
      model : 44
      model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
      stepping : 2
      microcode : 0x13
      cpu MHz : 2401.000
      cache size : 12288 KB
      physical id : 1
      siblings : 12
      core id : 10
      cpu cores : 6
      apicid : 53
      initial apicid : 53
      fpu : yes
      fpu_exception : yes
      cpuid level : 11
      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 pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
      bugs :
      bogomips : 4800.18
      clflush size : 64
      cache_alignment : 64
      address sizes : 40 bits physical, 48 bits virtual
      power management:



      Memory: 4k page, physical 49451300k(1997292k free), swap 1048572k(729704k free)

      vm_info: Java HotSpot(TM) 64-Bit Server VM (25.161-b12) for linux-amd64 JRE (1.8.0_161-b12), built on Dec 19 2017 16:12:43 by "java_re" with gcc 4.3.0 20080428 (Red Hat 4.3.0-8)

      time: Sat Mar 3 16:46:53 2018
      elapsed time: 1 seconds (0d 0h 0m 1s)



      REPRODUCIBILITY :
      This bug can be reproduced always.

      ---------- BEGIN SOURCE ----------
      if (SystemUtils.IS_OS_LINUX) {
      pathCsv = "/home/users/tag/uniprot/trembl.csv";
      pathDb = "/home/users/tag/uniprot/trembl.leveldb";

      }
      JniDBFactory.pushMemoryPool(1024 * 512);
      Options options = getLevelDBOptions();
      DB db = JniDBFactory.factory.open(new File(pathDb), options);

      DBIterator iterator = db.iterator();
      Range range = new Range(toBytes(from), toBytes(to));
      String stats = db.getProperty("leveldb.stats");
      log.debug("Status " + stats);
      long[] approximateSizes = db.getApproximateSizes(range);
      log.debug("Approximate Sizes " + FileUtils.byteCountToDisplaySize(approximateSizes[0]));
      log.debug("Search " + from + " " + to);

      // while (iterator.hasNext()) {
      // }

      iterator.seek(range.start());
      // maks 619.3581
      // iterator.seekToFirst();

      try {
      int c = 0;
      while (iterator.hasNext()) {
      Entry<byte[], byte[]> entry = iterator.next();
      byte[] k = entry.getKey(); // iterator.peekNext().getKey();

      byte[] v = entry.getValue(); // iterator.peekNext().getValue();
      float mass = BiteUtil.toFloat(k);
      if (mass > to) {
      log.debug("Finish on mass to: " + mass);
      break;
      }
      Map<String, List<AccTax>> res = UniprotFormat3.uncompressPeptidesJava(v);

      // log.debug(c + " : " + mass + " " + res.keySet() + " " + res.values());
      // log.debug("================" + mass + "");
      Set<Entry<String, List<AccTax>>> entrySet = res.entrySet();

      for (Entry<String, List<AccTax>> e : entrySet) {
      // log.debug(mass + " " + e.getKey() + " " + e.getValue());
      System.out.println(mass + " " + e.getKey() + " " + e.getValue());
      }
      c++;
      }
      log.debug("Found unique mass: " + c);
      } finally {
      // Make sure you close the iterator to avoid resource leaks.
      System.out.println("it close");
      iterator.close();
      System.out.println("db close");
      db.close();
      System.out.println("pop memory pool");
      JniDBFactory.popMemoryPool();
      }
      ---------- END SOURCE ----------

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            Assignee:
            dholmes David Holmes
            Reporter:
            webbuggrp Webbug Group
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              Created:
              Updated:
              Resolved: