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- #
- # A fatal error has been detected by the Java Runtime Environment:
- #
- # SIGSEGV (0xb) at pc=0x00002b13187338c1, pid=23413, tid=23414
- #
- # JRE version: OpenJDK Runtime Environment (11.0.19+7) (build 11.0.19+7-post-Ubuntu-0ubuntu118.04.1)
- # Java VM: OpenJDK 64-Bit Server VM (11.0.19+7-post-Ubuntu-0ubuntu118.04.1, mixed mode, sharing, tiered, compressed oops, serial gc, linux-amd64)
- # Problematic frame:
- # C [libgurobi100.so+0x7338c1] PRIVATE000000000089e67f+0x411
- #
- # Core dump will be written. Default location: /scicore/home/nimwegen/micuby52/core.23413
- #
- # If you would like to submit a bug report, please visit:
- # https://bugs.launchpad.net/ubuntu/+source/openjdk-lts
- # The crash happened outside the Java Virtual Machine in native code.
- # See problematic frame for where to report the bug.
- #
- --------------- S U M M A R Y ------------
- Command Line: -Xmx24g -Djava.io.tmpdir=/tmp/moma.20230922-123241.0JWui/java.io.tmpdir -Djava.library.path=/opt/gurobi/linux64/lib/:/moma/tensorflow -Dimagej.tensorflow.models.dir=/tmp/moma.20230922-123241.0JWui/tensorflow -Djava.util.prefs.systemRoot=/tmp/moma.20230922-123241.0JWui -Djava.util.prefs.userRoot=/tmp/moma.20230922-123241.0JWui /build_dir/target//MotherMachine-v0.10.2.20230911-100708.03a6665.jar -headless -reload /scicore/home/nimwegen/GROUP/MM_Data/Bor/20230831_25/preprocessing/20230831_preprocess_positions__output__20230915-121216/1-Pos000/1-Pos000_GL58 -analysis 20230831_25_batch_short_slurm_zlad__replicate_2_michael -i /scicore/home/nimwegen/GROUP/MM_Data/Bor/20230831_25/preprocessing/20230831_preprocess_positions__output__20230915-121216/1-Pos000/1-Pos000_GL58/oxi_stress_0_15_0_2_rep1_1_MMStack__1-Pos000_GL58.tif
- Host: AMD EPYC 7742 64-Core Processor, 128 cores, 503G, Ubuntu 18.04.6 LTS
- Time: Fri Sep 22 12:32:50 2023 CEST elapsed time: 8.981452 seconds (0d 0h 0m 8s)
- --------------- T H R E A D ---------------
- Current thread (0x00002b12cc017000): JavaThread "main" [_thread_in_native, id=23414, stack(0x00002b12c7f1b000,0x00002b12c801c000)]
- Stack: [0x00002b12c7f1b000,0x00002b12c801c000], sp=0x00002b12c8019df0, free space=1019k
- Native frames: (J=compiled Java code, A=aot compiled Java code, j=interpreted, Vv=VM code, C=native code)
- C [libgurobi100.so+0x7338c1] PRIVATE000000000089e67f+0x411
- Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
- j gurobi.GurobiJni.readmodel(JLjava/lang/String;)J+0
- j gurobi.GRBModel.<init>(Lgurobi/GRBEnv;Ljava/lang/String;)V+103
- j com.jug.Growthlane.generateILP(Lcom/jug/gui/progress/DialogProgress;)V+72
- j com.jug.datahandling.GlDataLoader.generateILPs()V+31
- j com.jug.MoMA.main([Ljava/lang/String;)V+1439
- v ~StubRoutines::call_stub
- siginfo: si_signo: 11 (SIGSEGV), si_code: 128 (SI_KERNEL), si_addr: 0x0000000000000000
- Register to memory mapping:
- RAX=0x0 is NULL
- RBX=0x0 is NULL
- RCX=0x0 is NULL
- RDX=0x000000000000007a is an unknown value
- RSP=0x00002b12c8019df0 is pointing into the stack for thread: 0x00002b12cc017000
- RBP=0x0 is NULL
- RSI=0x00002b12c801a538 is pointing into the stack for thread: 0x00002b12cc017000
- RDI=0x65646f6d5f69626f is an unknown value
- R8 =0x000000000000c000 is an unknown value
- R9 =0x0 is NULL
- R10=0x0 is NULL
- R11=0x00002b131a7f1830: <offset 0x00000000027f1830> in /opt/gurobi/linux64/lib/libgurobi100.so at 0x00002b1318000000
- R12=0x0 is NULL
- R13=0x0 is NULL
- R14=0x65646f6d5f69626f is an unknown value
- R15=0x0 is NULL
- Registers:
- RAX=0x0000000000000000, RBX=0x0000000000000000, RCX=0x0000000000000000, RDX=0x000000000000007a
- RSP=0x00002b12c8019df0, RBP=0x0000000000000000, RSI=0x00002b12c801a538, RDI=0x65646f6d5f69626f
- R8 =0x000000000000c000, R9 =0x0000000000000000, R10=0x0000000000000000, R11=0x00002b131a7f1830
- R12=0x0000000000000000, R13=0x0000000000000000, R14=0x65646f6d5f69626f, R15=0x0000000000000000
- RIP=0x00002b13187338c1, EFLAGS=0x0000000000010207, CSGSFS=0x0000000000000033, ERR=0x0000000000000000
- TRAPNO=0x000000000000000d
- Top of Stack: (sp=0x00002b12c8019df0)
- 0x00002b12c8019df0: 00002b13180014e8 00002b12c8325a6c
- 0x00002b12c8019e00: 00002b1200000002 0000000000000000
- 0x00002b12c8019e10: 00002b12c8019f10 00002b1300000003
- 0x00002b12c8019e20: 00002b12c8019f00 0000000000000000
- Instructions: (pc=0x00002b13187338c1)
- 0x00002b13187337c1: 24 20 02 00 00 48 89 84 24 28 02 00 00 48 89 84
- 0x00002b13187337d1: 24 30 02 00 00 48 89 84 24 38 02 00 00 48 89 84
- 0x00002b13187337e1: 24 40 02 00 00 48 89 84 24 48 02 00 00 48 89 84
- 0x00002b13187337f1: 24 50 02 00 00 48 89 84 24 58 02 00 00 48 89 84
- 0x00002b1318733801: 24 60 02 00 00 48 89 84 24 68 02 00 00 48 89 84
- 0x00002b1318733811: 24 70 02 00 00 48 89 84 24 78 02 00 00 c7 84 24
- 0x00002b1318733821: 44 04 00 00 01 00 00 00 89 9c 24 20 04 00 00 89
- 0x00002b1318733831: 9c 24 5c 04 00 00 48 89 84 24 18 04 00 00 89 9c
- 0x00002b1318733841: 24 10 04 00 00 89 9c 24 60 04 00 00 89 9c 24 64
- 0x00002b1318733851: 04 00 00 89 9c 24 70 04 00 00 48 89 84 24 80 02
- 0x00002b1318733861: 00 00 48 89 84 24 88 02 00 00 48 89 84 24 90 02
- 0x00002b1318733871: 00 00 48 89 84 24 98 02 00 00 48 89 84 24 a0 02
- 0x00002b1318733881: 00 00 48 89 84 24 a8 02 00 00 48 89 84 24 b0 02
- 0x00002b1318733891: 00 00 48 89 84 24 b8 02 00 00 f2 0f 11 8c 24 28
- 0x00002b13187338a1: 04 00 00 88 8c 24 08 04 00 00 88 8c 24 00 04 00
- 0x00002b13187338b1: 00 c6 84 24 c0 02 00 00 01 48 81 c4 a0 fd ff ff
- 0x00002b13187338c1: f2 41 0f 10 86 88 3d 00 00 4c 8d 84 24 b0 06 00
- 0x00002b13187338d1: 00 4c 8d 8c 24 b4 06 00 00 48 8d 8c 24 b8 06 00
- 0x00002b13187338e1: 00 4c 89 04 24 48 8d 94 24 a4 06 00 00 4c 89 4c
- 0x00002b13187338f1: 24 08 4c 8d 84 24 90 06 00 00 48 89 4c 24 10 48
- 0x00002b1318733901: 8d 8c 24 bc 06 00 00 48 89 4c 24 18 48 8d 8c 24
- 0x00002b1318733911: 30 03 00 00 48 89 4c 24 20 48 8d 8c 24 38 03 00
- 0x00002b1318733921: 00 48 89 4c 24 28 48 8d 8c 24 40 03 00 00 48 89
- 0x00002b1318733931: 4c 24 30 48 8d 8c 24 48 03 00 00 48 89 4c 24 38
- 0x00002b1318733941: 48 8d 8c 24 50 03 00 00 48 89 4c 24 40 48 8d 8c
- 0x00002b1318733951: 24 58 03 00 00 48 89 4c 24 48 48 8d 8c 24 60 03
- 0x00002b1318733961: 00 00 48 89 4c 24 50 48 8d 8c 24 68 03 00 00 48
- 0x00002b1318733971: 89 4c 24 58 48 8d 8c 24 70 03 00 00 48 89 4c 24
- 0x00002b1318733981: 60 48 8d 8c 24 78 03 00 00 48 89 4c 24 68 48 8d
- 0x00002b1318733991: 8c 24 80 03 00 00 48 89 4c 24 70 48 8d 8c 24 28
- 0x00002b13187339a1: 03 00 00 48 89 4c 24 78 48 8d 8c 24 88 03 00 00
- 0x00002b13187339b1: 48 89 8c 24 80 00 00 00 48 8d 8c 24 90 03 00 00
- Stack slot to memory mapping:
- stack at sp + 0 slots: 0x00002b13180014e8: <offset 0x00000000000014e8> in /opt/gurobi/linux64/lib/libgurobi100.so at 0x00002b1318000000
- stack at sp + 1 slots: 0x00002b12c8325a6c: <offset 0x0000000000001a6c> in /lib/x86_64-linux-gnu/libc.so.6 at 0x00002b12c8324000
- stack at sp + 2 slots: 0x00002b1200000002 is an unknown value
- stack at sp + 3 slots: 0x0 is NULL
- stack at sp + 4 slots: 0x00002b12c8019f10 is pointing into the stack for thread: 0x00002b12cc017000
- stack at sp + 5 slots: 0x00002b1300000003 points into unknown readable memory: 00 13 2b 00 00
- stack at sp + 6 slots: 0x00002b12c8019f00 is pointing into the stack for thread: 0x00002b12cc017000
- stack at sp + 7 slots: 0x0 is NULL
- --------------- P R O C E S S ---------------
- Threads class SMR info:
- _java_thread_list=0x00002b12cc709ef0, length=16, elements={
- 0x00002b12cc017000, 0x00002b12cc0b8800, 0x00002b12cc0bb000, 0x00002b12cc0c4800,
- 0x00002b12cc0c6800, 0x00002b12cc0c8800, 0x00002b12cc0ca800, 0x00002b12cc0cc800,
- 0x00002b12cc10c000, 0x00002b12cc4c7000, 0x00002b12cc4e8800, 0x00002b12cc55b800,
- 0x00002b12cc55d000, 0x00002b132c05e800, 0x00002b12cc76c800, 0x00002b12cc709000
- }
- Java Threads: ( => current thread )
- =>0x00002b12cc017000 JavaThread "main" [_thread_in_native, id=23414, stack(0x00002b12c7f1b000,0x00002b12c801c000)]
- 0x00002b12cc0b8800 JavaThread "Reference Handler" daemon [_thread_blocked, id=23416, stack(0x00002b12ed10f000,0x00002b12ed210000)]
- 0x00002b12cc0bb000 JavaThread "Finalizer" daemon [_thread_blocked, id=23417, stack(0x00002b12ed210000,0x00002b12ed311000)]
- 0x00002b12cc0c4800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=23418, stack(0x00002b12ed311000,0x00002b12ed412000)]
- 0x00002b12cc0c6800 JavaThread "Service Thread" daemon [_thread_blocked, id=23419, stack(0x00002b12ed412000,0x00002b12ed513000)]
- 0x00002b12cc0c8800 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=23420, stack(0x00002b12ed513000,0x00002b12ed614000)]
- 0x00002b12cc0ca800 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=23421, stack(0x00002b12ed614000,0x00002b12ed715000)]
- 0x00002b12cc0cc800 JavaThread "Sweeper thread" daemon [_thread_blocked, id=23422, stack(0x00002b12ed715000,0x00002b12ed816000)]
- 0x00002b12cc10c000 JavaThread "Common-Cleaner" daemon [_thread_blocked, id=23424, stack(0x00002b12ed918000,0x00002b12eda19000)]
- 0x00002b12cc4c7000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=23434, stack(0x00002b131d4f8000,0x00002b131d5f9000)]
- 0x00002b12cc4e8800 JavaThread "AWT-XAWT" daemon [_thread_in_native, id=23435, stack(0x00002b131da09000,0x00002b131db0a000)]
- 0x00002b12cc55b800 JavaThread "AWT-Shutdown" [_thread_blocked, id=23436, stack(0x00002b131dd0a000,0x00002b131de0b000)]
- 0x00002b12cc55d000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=23437, stack(0x00002b131de0b000,0x00002b131df0c000)]
- 0x00002b132c05e800 JavaThread "TimerQueue" daemon [_thread_blocked, id=23438, stack(0x00002b131e313000,0x00002b131e414000)]
- 0x00002b12cc76c800 JavaThread "Timer-0" daemon [_thread_blocked, id=23445, stack(0x00002b131ec17000,0x00002b131ed18000)]
- 0x00002b12cc709000 JavaThread "SciJava-247950c3-Thread-0" [_thread_blocked, id=23447, stack(0x00002b12ee05a000,0x00002b12ee25a000)]
- Other Threads:
- 0x00002b12cc0b6000 VMThread "VM Thread" [stack: 0x00002b12ed00f000,0x00002b12ed10f000] [id=23415]
- 0x00002b12cc109800 WatcherThread [stack: 0x00002b12ed818000,0x00002b12ed918000] [id=23423]
- Threads with active compile tasks:
- VM state:not at safepoint (normal execution)
- VM Mutex/Monitor currently owned by a thread: None
- Heap address: 0x0000000200000000, size: 24576 MB, Compressed Oops mode: Zero based, Oop shift amount: 3
- Narrow klass base: 0x0000000800000000, Narrow klass shift: 3
- Compressed class space size: 1073741824 Address: 0x0000000840000000
- Heap:
- def new generation total 629248K, used 46588K [0x0000000200000000, 0x000000022aac0000, 0x0000000400000000)
- eden space 559360K, 8% used [0x0000000200000000, 0x0000000202d7f140, 0x0000000222240000)
- from space 69888K, 0% used [0x0000000222240000, 0x0000000222240000, 0x0000000226680000)
- to space 69888K, 0% used [0x0000000226680000, 0x0000000226680000, 0x000000022aac0000)
- tenured generation total 1398144K, used 37192K [0x0000000400000000, 0x0000000455560000, 0x0000000800000000)
- the space 1398144K, 2% used [0x0000000400000000, 0x00000004024523a8, 0x0000000402452400, 0x0000000455560000)
- Metaspace used 35592K, capacity 36263K, committed 36824K, reserved 1081344K
- class space used 4729K, capacity 5036K, committed 5080K, reserved 1048576K
- Card table byte_map: [0x00002b12e780b000,0x00002b12ea80c000] _byte_map_base: 0x00002b12e680b000
- Polling page: 0x00002b12c7f13000
- Metaspace:
- Usage:
- Non-class: 30.50 MB capacity, 30.14 MB ( 99%) used, 276.76 KB ( <1%) free+waste, 87.19 KB ( <1%) overhead.
- Class: 4.92 MB capacity, 4.62 MB ( 94%) used, 262.64 KB ( 5%) free+waste, 44.00 KB ( <1%) overhead.
- Both: 35.41 MB capacity, 34.76 MB ( 98%) used, 539.40 KB ( 1%) free+waste, 131.19 KB ( <1%) overhead.
- Virtual space:
- Non-class space: 32.00 MB reserved, 31.00 MB ( 97%) committed
- Class space: 1.00 GB reserved, 4.96 MB ( <1%) committed
- Both: 1.03 GB reserved, 35.96 MB ( 3%) committed
- Chunk freelists:
- Non-Class: 357.00 KB
- Class: 20.00 KB
- Both: 377.00 KB
- MaxMetaspaceSize: unlimited
- CompressedClassSpaceSize: 1.00 GB
- Initial GC threshold: 20.80 MB
- Current GC threshold: 57.64 MB
- CDS: on
- CodeHeap 'non-profiled nmethods': size=120036Kb used=1882Kb max_used=1882Kb free=118154Kb
- bounds [0x00002b12e02d2000, 0x00002b12e0542000, 0x00002b12e780b000]
- CodeHeap 'profiled nmethods': size=120032Kb used=7463Kb max_used=7463Kb free=112568Kb
- bounds [0x00002b12d8d9a000, 0x00002b12d94ea000, 0x00002b12e02d2000]
- CodeHeap 'non-nmethods': size=5692Kb used=1430Kb max_used=1448Kb free=4261Kb
- bounds [0x00002b12d880b000, 0x00002b12d8a7b000, 0x00002b12d8d9a000]
- total_blobs=4528 nmethods=3753 adapters=690
- compilation: enabled
- stopped_count=0, restarted_count=0
- full_count=0
- Compilation events (20 events):
- Event: 8.880 Thread 0x00002b12cc0c8800 3748 ! 4 net.imglib2.roi.labeling.LabelingMapping::addLabelToSetAtIndex (141 bytes)
- Event: 8.892 Thread 0x00002b12cc0c8800 nmethod 3748 0x00002b12e04a3310 code [0x00002b12e04a35e0, 0x00002b12e04a4690]
- Event: 8.892 Thread 0x00002b12cc0c8800 3715 4 java.util.AbstractCollection::<init> (5 bytes)
- Event: 8.892 Thread 0x00002b12cc0c8800 nmethod 3715 0x00002b12e04a5490 code [0x00002b12e04a5620, 0x00002b12e04a5698]
- Event: 8.892 Thread 0x00002b12cc0c8800 3701 4 net.imglib2.img.array.AbstractArrayLocalizingCursor::fwd (84 bytes)
- Event: 8.894 Thread 0x00002b12cc0c8800 nmethod 3701 0x00002b12e04a5790 code [0x00002b12e04a5940, 0x00002b12e04a5ab8]
- Event: 8.894 Thread 0x00002b12cc0c8800 3709 4 net.imglib2.Localizable::getIntPosition (9 bytes)
- Event: 8.894 Thread 0x00002b12cc0c8800 nmethod 3709 0x00002b12e04a5c90 code [0x00002b12e04a5e20, 0x00002b12e04a5ef8]
- Event: 8.894 Thread 0x00002b12cc0c8800 3710 4 com.jug.util.componenttree.LocalizableImpl::getLongPosition (23 bytes)
- Event: 8.895 Thread 0x00002b12cc0c8800 nmethod 3710 0x00002b12e04a6010 code [0x00002b12e04a61a0, 0x00002b12e04a6258]
- Event: 8.895 Thread 0x00002b12cc0c8800 3714 4 net.imglib2.converter.AbstractConvertedCursor::getLongPosition (11 bytes)
- Event: 8.895 Thread 0x00002b12cc0c8800 nmethod 3714 0x00002b12e04a6310 code [0x00002b12e04a64a0, 0x00002b12e04a6578]
- Event: 8.895 Thread 0x00002b12cc0c8800 3739 4 net.imglib2.roi.labeling.ImgLabeling$LabelingConvertedRandomAccess::get (5 bytes)
- Event: 8.895 Thread 0x00002b12cc0c8800 nmethod 3739 0x00002b12e04a6690 code [0x00002b12e04a6820, 0x00002b12e04a6898]
- Event: 8.895 Thread 0x00002b12cc0c8800 3751 4 net.imglib2.converter.AbstractConvertedRandomAccess::setPosition (11 bytes)
- Event: 8.913 Thread 0x00002b12cc0c8800 nmethod 3751 0x00002b12e04a6990 code [0x00002b12e04a6b80, 0x00002b12e04a76f8]
- Event: 8.913 Thread 0x00002b12cc0c8800 3752 4 net.imglib2.roi.labeling.LabelingType::add (50 bytes)
- Event: 8.915 Thread 0x00002b12cc0c8800 nmethod 3752 0x00002b12e04a7b90 code [0x00002b12e04a7d60, 0x00002b12e04a7fe8]
- Event: 8.915 Thread 0x00002b12cc0c8800 3758 4 net.imglib2.type.numeric.integer.IntType::setInteger (6 bytes)
- Event: 8.915 Thread 0x00002b12cc0c8800 nmethod 3758 0x00002b12e04a8410 code [0x00002b12e04a85a0, 0x00002b12e04a8698]
- GC Heap History (6 events):
- Event: 4.821 GC heap before
- {Heap before GC invocations=0 (full 0):
- def new generation total 629120K, used 559232K [0x0000000200000000, 0x000000022aaa0000, 0x0000000400000000)
- eden space 559232K, 100% used [0x0000000200000000, 0x0000000222220000, 0x0000000222220000)
- from space 69888K, 0% used [0x0000000222220000, 0x0000000222220000, 0x0000000226660000)
- to space 69888K, 0% used [0x0000000226660000, 0x0000000226660000, 0x000000022aaa0000)
- tenured generation total 1398144K, used 0K [0x0000000400000000, 0x0000000455560000, 0x0000000800000000)
- the space 1398144K, 0% used [0x0000000400000000, 0x0000000400000000, 0x0000000400000200, 0x0000000455560000)
- Metaspace used 17523K, capacity 18063K, committed 18304K, reserved 1064960K
- class space used 1778K, capacity 2060K, committed 2176K, reserved 1048576K
- }
- Event: 4.933 GC heap after
- {Heap after GC invocations=1 (full 0):
- def new generation total 629120K, used 69888K [0x0000000200000000, 0x000000022aaa0000, 0x0000000400000000)
- eden space 559232K, 0% used [0x0000000200000000, 0x0000000200000000, 0x0000000222220000)
- from space 69888K, 100% used [0x0000000226660000, 0x000000022aaa0000, 0x000000022aaa0000)
- to space 69888K, 0% used [0x0000000222220000, 0x0000000222220000, 0x0000000226660000)
- tenured generation total 1398144K, used 167409K [0x0000000400000000, 0x0000000455560000, 0x0000000800000000)
- the space 1398144K, 11% used [0x0000000400000000, 0x000000040a37c458, 0x000000040a37c600, 0x0000000455560000)
- Metaspace used 17523K, capacity 18063K, committed 18304K, reserved 1064960K
- class space used 1778K, capacity 2060K, committed 2176K, reserved 1048576K
- }
- Event: 5.883 GC heap before
- {Heap before GC invocations=1 (full 0):
- def new generation total 629120K, used 598486K [0x0000000200000000, 0x000000022aaa0000, 0x0000000400000000)
- eden space 559232K, 94% used [0x0000000200000000, 0x0000000220435908, 0x0000000222220000)
- from space 69888K, 100% used [0x0000000226660000, 0x000000022aaa0000, 0x000000022aaa0000)
- to space 69888K, 0% used [0x0000000222220000, 0x0000000222220000, 0x0000000226660000)
- tenured generation total 1398144K, used 167409K [0x0000000400000000, 0x0000000455560000, 0x0000000800000000)
- the space 1398144K, 11% used [0x0000000400000000, 0x000000040a37c458, 0x000000040a37c600, 0x0000000455560000)
- Metaspace used 20413K, capacity 21023K, committed 21248K, reserved 1069056K
- class space used 2297K, capacity 2552K, committed 2560K, reserved 1048576K
- }
- Event: 5.913 GC heap after
- {Heap after GC invocations=2 (full 1):
- def new generation total 629248K, used 0K [0x0000000200000000, 0x000000022aac0000, 0x0000000400000000)
- eden space 559360K, 0% used [0x0000000200000000, 0x0000000200000000, 0x0000000222240000)
- from space 69888K, 0% used [0x0000000222240000, 0x0000000222240000, 0x0000000226680000)
- to space 69888K, 0% used [0x0000000226680000, 0x0000000226680000, 0x000000022aac0000)
- tenured generation total 1398144K, used 29880K [0x0000000400000000, 0x0000000455560000, 0x0000000800000000)
- the space 1398144K, 2% used [0x0000000400000000, 0x0000000401d2e368, 0x0000000401d2e400, 0x0000000455560000)
- Metaspace used 20413K, capacity 21023K, committed 21248K, reserved 1069056K
- class space used 2297K, capacity 2552K, committed 2560K, reserved 1048576K
- }
- Event: 8.096 GC heap before
- {Heap before GC invocations=2 (full 1):
- def new generation total 629248K, used 283353K [0x0000000200000000, 0x000000022aac0000, 0x0000000400000000)
- eden space 559360K, 50% used [0x0000000200000000, 0x00000002114b64c8, 0x0000000222240000)
- from space 69888K, 0% used [0x0000000222240000, 0x0000000222240000, 0x0000000226680000)
- to space 69888K, 0% used [0x0000000226680000, 0x0000000226680000, 0x000000022aac0000)
- tenured generation total 1398144K, used 29880K [0x0000000400000000, 0x0000000455560000, 0x0000000800000000)
- the space 1398144K, 2% used [0x0000000400000000, 0x0000000401d2e368, 0x0000000401d2e400, 0x0000000455560000)
- Metaspace used 34350K, capacity 34995K, committed 35416K, reserved 1079296K
- class space used 4579K, capacity 4871K, committed 4952K, reserved 1048576K
- }
- Event: 8.203 GC heap after
- {Heap after GC invocations=3 (full 2):
- def new generation total 629248K, used 0K [0x0000000200000000, 0x000000022aac0000, 0x0000000400000000)
- eden space 559360K, 0% used [0x0000000200000000, 0x0000000200000000, 0x0000000222240000)
- from space 69888K, 0% used [0x0000000222240000, 0x0000000222240000, 0x0000000226680000)
- to space 69888K, 0% used [0x0000000226680000, 0x0000000226680000, 0x000000022aac0000)
- tenured generation total 1398144K, used 37192K [0x0000000400000000, 0x0000000455560000, 0x0000000800000000)
- the space 1398144K, 2% used [0x0000000400000000, 0x00000004024523a8, 0x0000000402452400, 0x0000000455560000)
- Metaspace used 34350K, capacity 34995K, committed 35416K, reserved 1079296K
- class space used 4579K, capacity 4871K, committed 4952K, reserved 1048576K
- }
- Deoptimization events (20 events):
- Event: 8.599 Thread 0x00002b12cc017000 DEOPT PACKING pc=0x00002b12e048e588 sp=0x00002b12c801a0c0
- Event: 8.599 Thread 0x00002b12cc017000 DEOPT UNPACKING pc=0x00002b12d8854ea5 sp=0x00002b12c8019fc8 mode 2
- Event: 8.600 Thread 0x00002b12cc017000 Uncommon trap: trap_request=0xffffffbe fr.pc=0x00002b12e048e588 relative=0x00000000000020a8
- Event: 8.600 Thread 0x00002b12cc017000 Uncommon trap: reason=profile_predicate action=maybe_recompile pc=0x00002b12e048e588 method=net.imglib2.roi.util.iterationcode.IterationCodeBuilder.add(Lnet/imglib2/Localizable;)V @ 35 c2
- Event: 8.600 Thread 0x00002b12cc017000 DEOPT PACKING pc=0x00002b12e048e588 sp=0x00002b12c801a0c0
- Event: 8.600 Thread 0x00002b12cc017000 DEOPT UNPACKING pc=0x00002b12d8854ea5 sp=0x00002b12c8019fc8 mode 2
- Event: 8.600 Thread 0x00002b12cc017000 Uncommon trap: trap_request=0xffffffbe fr.pc=0x00002b12e048e588 relative=0x00000000000020a8
- Event: 8.600 Thread 0x00002b12cc017000 Uncommon trap: reason=profile_predicate action=maybe_recompile pc=0x00002b12e048e588 method=net.imglib2.roi.util.iterationcode.IterationCodeBuilder.add(Lnet/imglib2/Localizable;)V @ 35 c2
- Event: 8.600 Thread 0x00002b12cc017000 DEOPT PACKING pc=0x00002b12e048e588 sp=0x00002b12c801a0c0
- Event: 8.600 Thread 0x00002b12cc017000 DEOPT UNPACKING pc=0x00002b12d8854ea5 sp=0x00002b12c8019fc8 mode 2
- Event: 8.600 Thread 0x00002b12cc017000 Uncommon trap: trap_request=0xffffffbe fr.pc=0x00002b12e048e588 relative=0x00000000000020a8
- Event: 8.600 Thread 0x00002b12cc017000 Uncommon trap: reason=profile_predicate action=maybe_recompile pc=0x00002b12e048e588 method=net.imglib2.roi.util.iterationcode.IterationCodeBuilder.add(Lnet/imglib2/Localizable;)V @ 35 c2
- Event: 8.600 Thread 0x00002b12cc017000 DEOPT PACKING pc=0x00002b12e048e588 sp=0x00002b12c801a0c0
- Event: 8.600 Thread 0x00002b12cc017000 DEOPT UNPACKING pc=0x00002b12d8854ea5 sp=0x00002b12c8019fc8 mode 2
- Event: 8.658 Thread 0x00002b12cc017000 DEOPT PACKING pc=0x00002b12d94d08f6 sp=0x00002b12c8019f20
- Event: 8.658 Thread 0x00002b12cc017000 DEOPT UNPACKING pc=0x00002b12d885564a sp=0x00002b12c8019438 mode 0
- Event: 8.782 Thread 0x00002b12cc017000 DEOPT PACKING pc=0x00002b12d8e682c0 sp=0x00002b12c8019e10
- Event: 8.782 Thread 0x00002b12cc017000 DEOPT UNPACKING pc=0x00002b12d885564a sp=0x00002b12c8019348 mode 0
- Event: 8.813 Thread 0x00002b12cc017000 DEOPT PACKING pc=0x00002b12d8db6cd9 sp=0x00002b12c8019ef0
- Event: 8.813 Thread 0x00002b12cc017000 DEOPT UNPACKING pc=0x00002b12d885564a sp=0x00002b12c8019398 mode 0
- Classes redefined (0 events):
- No events
- Internal exceptions (20 events):
- Event: 6.261 Thread 0x00002b12cc017000 Exception <a 'java/lang/NoSuchMethodError'{0x000000020099e938}: 'int java.lang.invoke.DirectMethodHandle$Holder.invokeSpecialIFC(java.lang.Object, java.lang.Object, int)'> (0x000000020099e938) thrown at [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
- Event: 6.348 Thread 0x00002b12cc6ec000 Implicit null exception at 0x00002b12e0302a04 to 0x00002b12e0302edc
- Event: 6.360 Thread 0x00002b12cc017000 Exception <a 'java/lang/ClassNotFoundException'{0x00000002017dab38}: java/lang/ObjectCustomizer> (0x00000002017dab38) thrown at [src/hotspot/share/classfile/systemDictionary.cpp, line 230]
- Event: 6.371 Thread 0x00002b12cc017000 Exception <a 'java/lang/ClassNotFoundException'{0x00000002017ecd98}: net/miginfocom/layout/UnitValueCustomizer> (0x00000002017ecd98) thrown at [src/hotspot/share/classfile/systemDictionary.cpp, line 230]
- Event: 6.372 Thread 0x00002b12cc017000 Exception <a 'java/lang/ClassNotFoundException'{0x0000000201801650}: java/lang/ObjectCustomizer> (0x0000000201801650) thrown at [src/hotspot/share/classfile/systemDictionary.cpp, line 230]
- Event: 6.373 Thread 0x00002b12cc017000 Exception <a 'java/lang/ClassNotFoundException'{0x00000002018063c8}: net/miginfocom/layout/BoundSizeCustomizer> (0x00000002018063c8) thrown at [src/hotspot/share/classfile/systemDictionary.cpp, line 230]
- Event: 6.376 Thread 0x00002b12cc017000 Exception <a 'java/lang/NoSuchMethodError'{0x000000020183d600}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeVirtual(java.lang.Object, java.lang.Object, java.lang.Object)'> (0x000000020183d600) thrown at [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
- Event: 6.959 Thread 0x00002b12cc017000 Exception <a 'java/lang/NoSuchMethodError'{0x00000002079c5748}: 'int java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object)'> (0x00000002079c5748) thrown at [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
- Event: 6.976 Thread 0x00002b12cc017000 Exception <a 'java/lang/reflect/InvocationTargetException'{0x0000000207ca4300}> (0x0000000207ca4300) thrown at [src/hotspot/share/runtime/reflection.cpp, line 1247]
- Event: 6.976 Thread 0x00002b12cc017000 Exception <a 'java/lang/IllegalArgumentException'{0x0000000207ca3c90}> (0x0000000207ca3c90) thrown at [src/hotspot/share/prims/jni.cpp, line 617]
- Event: 6.994 Thread 0x00002b12cc017000 Exception <a 'java/lang/reflect/InvocationTargetException'{0x0000000207e19458}> (0x0000000207e19458) thrown at [src/hotspot/share/runtime/reflection.cpp, line 1247]
- Event: 6.994 Thread 0x00002b12cc017000 Exception <a 'java/lang/IllegalArgumentException'{0x0000000207e18e28}> (0x0000000207e18e28) thrown at [src/hotspot/share/prims/jni.cpp, line 617]
- Event: 6.999 Thread 0x00002b12cc017000 Exception <a 'java/lang/reflect/InvocationTargetException'{0x0000000207f8b9c0}> (0x0000000207f8b9c0) thrown at [src/hotspot/share/runtime/reflection.cpp, line 1247]
- Event: 6.999 Thread 0x00002b12cc017000 Exception <a 'java/lang/IllegalArgumentException'{0x0000000207f8b390}> (0x0000000207f8b390) thrown at [src/hotspot/share/prims/jni.cpp, line 617]
- Event: 7.005 Thread 0x00002b12cc017000 Exception <a 'java/lang/reflect/InvocationTargetException'{0x0000000208104938}> (0x0000000208104938) thrown at [src/hotspot/share/runtime/reflection.cpp, line 1247]
- Event: 7.005 Thread 0x00002b12cc017000 Exception <a 'java/lang/IllegalArgumentException'{0x0000000208104308}> (0x0000000208104308) thrown at [src/hotspot/share/prims/jni.cpp, line 617]
- Event: 7.180 Thread 0x00002b12cc017000 Implicit null exception at 0x00002b12e040b7cc to 0x00002b12e040b9c8
- Event: 7.545 Thread 0x00002b12cc017000 Exception <a 'java/lang/NoClassDefFoundError'{0x000000020f67ae08}: jupyter/Displayer> (0x000000020f67ae08) thrown at [src/hotspot/share/classfile/systemDictionary.cpp, line 219]
- Event: 7.682 Thread 0x00002b12cc017000 Implicit null exception at 0x00002b12e044f6e8 to 0x00002b12e04501fc
- Event: 8.242 Thread 0x00002b12cc017000 Exception <a 'java/lang/NoSuchMethodError'{0x00000002001c1918}: 'void java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, int, java.lang.Object)'> (0x00000002001c1918) thrown at [src/hotspot/share/interpreter/linkResolver.cpp, line 773]
- Events (20 events):
- Event: 8.477 loading class net/imglib2/roi/util/PositionableLocalizable
- Event: 8.477 loading class net/imglib2/roi/util/PositionableLocalizable done
- Event: 8.477 loading class net/imglib2/roi/util/PositionableInterval$Origin
- Event: 8.477 loading class net/imglib2/roi/util/PositionableInterval$Origin done
- Event: 8.477 loading class net/imglib2/RealPoint
- Event: 8.477 loading class net/imglib2/RealPoint done
- Event: 8.477 loading class net/imglib2/AbstractRealLocalizable
- Event: 8.477 loading class net/imglib2/AbstractRealLocalizable done
- Event: 8.563 loading class com/jug/util/componenttree/AdvancedComponentForest
- Event: 8.563 loading class com/jug/util/componenttree/AdvancedComponentForest done
- Event: 8.599 Executing VM operation: RevokeBias
- Event: 8.599 Executing VM operation: RevokeBias done
- Event: 8.952 loading class gurobi/GRBModel
- Event: 8.952 loading class gurobi/GRBModel done
- Event: 8.955 loading class gurobi/GRBExpr
- Event: 8.955 loading class gurobi/GRBExpr done
- Event: 8.955 loading class gurobi/GRBQuadExpr
- Event: 8.955 loading class gurobi/GRBQuadExpr done
- Event: 8.955 loading class gurobi/GRBLinExpr
- Event: 8.955 loading class gurobi/GRBLinExpr done
- Dynamic libraries:
- 200000000-22aac0000 rw-p 00000000 00:00 0
- 22aac0000-400000000 ---p 00000000 00:00 0
- 400000000-455560000 rw-p 00000000 00:00 0
- 455560000-800000000 ---p 00000000 00:00 0
- 800000000-800002000 rwxp 00001000 07:01 13741 /usr/lib/jvm/java-11-openjdk-amd64/lib/server/classes.jsa
- 800002000-8003cb000 rw-p 00003000 07:01 13741 /usr/lib/jvm/java-11-openjdk-amd64/lib/server/classes.jsa
- 8003cb000-800a9b000 r--p 003cc000 07:01 13741 /usr/lib/jvm/java-11-openjdk-amd64/lib/server/classes.jsa
- 800a9b000-800a9c000 rw-p 00a9c000 07:01 13741 /usr/lib/jvm/java-11-openjdk-amd64/lib/server/classes.jsa
- 840000000-8404f6000 rw-p 00000000 00:00 0
- 8404f6000-880000000 ---p 00000000 00:00 0
- 2b12c7ee8000-2b12c7f11000 r-xp 00000000 07:01 3474 /lib/x86_64-linux-gnu/ld-2.27.so
- 2b12c7f11000-2b12c7f13000 rw-p 00000000 00:00 0
- 2b12c7f13000-2b12c7f14000 ---p 00000000 00:00 0
- 2b12c7f14000-2b12c7f15000 r--p 00000000 00:00 0
- 2b12c7f19000-2b12c7f1b000 rw-p 00000000 00:00 0
- 2b12c7f1b000-2b12c7f1f000 ---p 00000000 00:00 0
- 2b12c7f1f000-2b12c801c000 rw-p 00000000 00:00 0
- 2b12c801c000-2b12c8024000 rw-s 00000000 08:02 529956 /tmp/hsperfdata_micuby52/23413
- 2b12c8024000-2b12c8029000 rw-p 00000000 00:00 0
- 2b12c8029000-2b12c8030000 ---p 00000000 00:00 0
- 2b12c8030000-2b12c810c000 rw-p 00000000 00:00 0
- 2b12c8111000-2b12c8112000 r--p 00029000 07:01 3474 /lib/x86_64-linux-gnu/ld-2.27.so
- 2b12c8112000-2b12c8113000 rw-p 0002a000 07:01 3474 /lib/x86_64-linux-gnu/ld-2.27.so
- 2b12c8113000-2b12c8114000 rw-p 00000000 00:00 0
- 2b12c8114000-2b12c8123000 r-xp 00000000 07:01 13689 /usr/lib/jvm/java-11-openjdk-amd64/lib/jli/libjli.so
- 2b12c8123000-2b12c8322000 ---p 0000f000 07:01 13689 /usr/lib/jvm/java-11-openjdk-amd64/lib/jli/libjli.so
- 2b12c8322000-2b12c8323000 r--p 0000e000 07:01 13689 /usr/lib/jvm/java-11-openjdk-amd64/lib/jli/libjli.so
- 2b12c8323000-2b12c8324000 rw-p 0000f000 07:01 13689 /usr/lib/jvm/java-11-openjdk-amd64/lib/jli/libjli.so
- 2b12c8324000-2b12c850b000 r-xp 00000000 07:01 3496 /lib/x86_64-linux-gnu/libc-2.27.so
- 2b12c850b000-2b12c870b000 ---p 001e7000 07:01 3496 /lib/x86_64-linux-gnu/libc-2.27.so
- 2b12c870b000-2b12c870f000 r--p 001e7000 07:01 3496 /lib/x86_64-linux-gnu/libc-2.27.so
- 2b12c870f000-2b12c8711000 rw-p 001eb000 07:01 3496 /lib/x86_64-linux-gnu/libc-2.27.so
- 2b12c8711000-2b12c8715000 rw-p 00000000 00:00 0
- 2b12c8715000-2b12c8731000 r-xp 00000000 07:01 3596 /lib/x86_64-linux-gnu/libz.so.1.2.11
- 2b12c8731000-2b12c8930000 ---p 0001c000 07:01 3596 /lib/x86_64-linux-gnu/libz.so.1.2.11
- 2b12c8930000-2b12c8931000 r--p 0001b000 07:01 3596 /lib/x86_64-linux-gnu/libz.so.1.2.11
- 2b12c8931000-2b12c8932000 rw-p 0001c000 07:01 3596 /lib/x86_64-linux-gnu/libz.so.1.2.11
- 2b12c8932000-2b12c8935000 r-xp 00000000 07:01 3508 /lib/x86_64-linux-gnu/libdl-2.27.so
- 2b12c8935000-2b12c8b34000 ---p 00003000 07:01 3508 /lib/x86_64-linux-gnu/libdl-2.27.so
- 2b12c8b34000-2b12c8b35000 r--p 00002000 07:01 3508 /lib/x86_64-linux-gnu/libdl-2.27.so
- 2b12c8b35000-2b12c8b36000 rw-p 00003000 07:01 3508 /lib/x86_64-linux-gnu/libdl-2.27.so
- 2b12c8b36000-2b12c8b50000 r-xp 00000000 07:01 3565 /lib/x86_64-linux-gnu/libpthread-2.27.so
- 2b12c8b50000-2b12c8d4f000 ---p 0001a000 07:01 3565 /lib/x86_64-linux-gnu/libpthread-2.27.so
- 2b12c8d4f000-2b12c8d50000 r--p 00019000 07:01 3565 /lib/x86_64-linux-gnu/libpthread-2.27.so
- 2b12c8d50000-2b12c8d51000 rw-p 0001a000 07:01 3565 /lib/x86_64-linux-gnu/libpthread-2.27.so
- 2b12c8d51000-2b12c8d55000 rw-p 00000000 00:00 0
- 2b12c8d55000-2b12c9e5c000 r-xp 00000000 07:01 13743 /usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjvm.so
- 2b12c9e5c000-2b12ca05c000 ---p 01107000 07:01 13743 /usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjvm.so
- 2b12ca05c000-2b12ca120000 r--p 01107000 07:01 13743 /usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjvm.so
- 2b12ca120000-2b12ca15b000 rw-p 011cb000 07:01 13743 /usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjvm.so
- 2b12ca15b000-2b12ca1b2000 rw-p 00000000 00:00 0
- 2b12ca1b2000-2b12ca32b000 r-xp 00000000 07:01 15214 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25
- 2b12ca32b000-2b12ca52b000 ---p 00179000 07:01 15214 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25
- 2b12ca52b000-2b12ca535000 r--p 00179000 07:01 15214 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25
- 2b12ca535000-2b12ca537000 rw-p 00183000 07:01 15214 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25
- 2b12ca537000-2b12ca53b000 rw-p 00000000 00:00 0
- 2b12ca53b000-2b12ca6d8000 r-xp 00000000 07:01 3529 /lib/x86_64-linux-gnu/libm-2.27.so
- 2b12ca6d8000-2b12ca8d7000 ---p 0019d000 07:01 3529 /lib/x86_64-linux-gnu/libm-2.27.so
- 2b12ca8d7000-2b12ca8d8000 r--p 0019c000 07:01 3529 /lib/x86_64-linux-gnu/libm-2.27.so
- 2b12ca8d8000-2b12ca8d9000 rw-p 0019d000 07:01 3529 /lib/x86_64-linux-gnu/libm-2.27.so
- 2b12ca8d9000-2b12ca8f0000 r-xp 00000000 07:01 3518 /lib/x86_64-linux-gnu/libgcc_s.so.1
- 2b12ca8f0000-2b12caaef000 ---p 00017000 07:01 3518 /lib/x86_64-linux-gnu/libgcc_s.so.1
- 2b12caaef000-2b12caaf0000 r--p 00016000 07:01 3518 /lib/x86_64-linux-gnu/libgcc_s.so.1
- 2b12caaf0000-2b12caaf1000 rw-p 00017000 07:01 3518 /lib/x86_64-linux-gnu/libgcc_s.so.1
- 2b12caaf1000-2b12caaf8000 r-xp 00000000 07:01 3571 /lib/x86_64-linux-gnu/librt-2.27.so
- 2b12caaf8000-2b12cacf7000 ---p 00007000 07:01 3571 /lib/x86_64-linux-gnu/librt-2.27.so
- 2b12cacf7000-2b12cacf8000 r--p 00006000 07:01 3571 /lib/x86_64-linux-gnu/librt-2.27.so
- 2b12cacf8000-2b12cacf9000 rw-p 00007000 07:01 3571 /lib/x86_64-linux-gnu/librt-2.27.so
- 2b12cacf9000-2b12cad06000 r-xp 00000000 07:01 13728 /usr/lib/jvm/java-11-openjdk-amd64/lib/libverify.so
- 2b12cad06000-2b12caf05000 ---p 0000d000 07:01 13728 /usr/lib/jvm/java-11-openjdk-amd64/lib/libverify.so
- 2b12caf05000-2b12caf07000 r--p 0000c000 07:01 13728 /usr/lib/jvm/java-11-openjdk-amd64/lib/libverify.so
- 2b12caf07000-2b12caf08000 rw-p 0000e000 07:01 13728 /usr/lib/jvm/java-11-openjdk-amd64/lib/libverify.so
- 2b12caf08000-2b12caf31000 r-xp 00000000 07:01 13707 /usr/lib/jvm/java-11-openjdk-amd64/lib/libjava.so
- 2b12caf31000-2b12cb130000 ---p 00029000 07:01 13707 /usr/lib/jvm/java-11-openjdk-amd64/lib/libjava.so
- 2b12cb130000-2b12cb131000 r--p 00028000 07:01 13707 /usr/lib/jvm/java-11-openjdk-amd64/lib/libjava.so
- 2b12cb131000-2b12cb132000 rw-p 00029000 07:01 13707 /usr/lib/jvm/java-11-openjdk-amd64/lib/libjava.so
- 2b12cb132000-2b12cb133000 rw-p 00000000 00:00 0
- 2b12cb133000-2b12cb138000 r-xp 00000000 07:01 13711 /usr/lib/jvm/java-11-openjdk-amd64/lib/libjimage.so
- 2b12cb138000-2b12cb337000 ---p 00005000 07:01 13711 /usr/lib/jvm/java-11-openjdk-amd64/lib/libjimage.so
- 2b12cb337000-2b12cb338000 r--p 00004000 07:01 13711 /usr/lib/jvm/java-11-openjdk-amd64/lib/libjimage.so
- 2b12cb338000-2b12cb339000 rw-p 00005000 07:01 13711 /usr/lib/jvm/java-11-openjdk-amd64/lib/libjimage.so
- 2b12cb339000-2b12cb341000 r-xp 00000000 07:01 3542 /lib/x86_64-linux-gnu/libnss_compat-2.27.so
- 2b12cb341000-2b12cb541000 ---p 00008000 07:01 3542 /lib/x86_64-linux-gnu/libnss_compat-2.27.so
- 2b12cb541000-2b12cb542000 r--p 00008000 07:01 3542 /lib/x86_64-linux-gnu/libnss_compat-2.27.so
- 2b12cb542000-2b12cb543000 rw-p 00009000 07:01 3542 /lib/x86_64-linux-gnu/libnss_compat-2.27.so
- 2b12cb543000-2b12cb54e000 r-xp 00000000 07:01 3550 /lib/x86_64-linux-gnu/libnss_nis-2.27.so
- 2b12cb54e000-2b12cb74d000 ---p 0000b000 07:01 3550 /lib/x86_64-linux-gnu/libnss_nis-2.27.so
- 2b12cb74d000-2b12cb74e000 r--p 0000a000 07:01 3550 /lib/x86_64-linux-gnu/libnss_nis-2.27.so
- 2b12cb74e000-2b12cb74f000 rw-p 0000b000 07:01 3550 /lib/x86_64-linux-gnu/libnss_nis-2.27.so
- 2b12cb74f000-2b12cb766000 r-xp 00000000 07:01 3540 /lib/x86_64-linux-gnu/libnsl-2.27.so
- 2b12cb766000-2b12cb965000 ---p 00017000 07:01 3540 /lib/x86_64-linux-gnu/libnsl-2.27.so
- 2b12cb965000-2b12cb966000 r--p 00016000 07:01 3540 /lib/x86_64-linux-gnu/libnsl-2.27.so
- 2b12cb966000-2b12cb967000 rw-p 00017000 07:01 3540 /lib/x86_64-linux-gnu/libnsl-2.27.so
- 2b12cb967000-2b12cb969000 rw-p 00000000 00:00 0
- 2b12cb969000-2b12cb974000 r-xp 00000000 07:01 3546 /lib/x86_64-linux-gnu/libnss_files-2.27.so
- 2b12cb974000-2b12cbb73000 ---p 0000b000 07:01 3546 /lib/x86_64-linux-gnu/libnss_files-2.27.so
- 2b12cbb73000-2b12cbb74000 r--p 0000a000 07:01 3546 /lib/x86_64-linux-gnu/libnss_files-2.27.so
- 2b12cbb74000-2b12cbb75000 rw-p 0000b000 07:01 3546 /lib/x86_64-linux-gnu/libnss_files-2.27.so
- 2b12cbb75000-2b12cbb7b000 rw-p 00000000 00:00 0
- 2b12cbb7b000-2b12cbb82000 r-xp 00000000 07:01 13729 /usr/lib/jvm/java-11-openjdk-amd64/lib/libzip.so
- 2b12cbb82000-2b12cbd82000 ---p 00007000 07:01 13729 /usr/lib/jvm/java-11-openjdk-amd64/lib/libzip.so
- 2b12cbd82000-2b12cbd83000 r--p 00007000 07:01 13729 /usr/lib/jvm/java-11-openjdk-amd64/lib/libzip.so
- 2b12cbd83000-2b12cbd84000 rw-p 00008000 07:01 13729 /usr/lib/jvm/java-11-openjdk-amd64/lib/libzip.so
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- 2b12cbd93000-2b12cbe6f000 ---p 00000000 00:00 0
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- 2b131ce9c000-2b131cea3000 r-xp 00000000 07:01 15074 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
- 2b131cea3000-2b131d0a2000 ---p 00007000 07:01 15074 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
- 2b131d0a2000-2b131d0a3000 r--p 00006000 07:01 15074 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
- 2b131d0a3000-2b131d0a4000 rw-p 00007000 07:01 15074 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
- 2b131d0a4000-2b131d0eb000 r-xp 00000000 07:01 3490 /lib/x86_64-linux-gnu/libblkid.so.1.1.0
- 2b131d0eb000-2b131d2eb000 ---p 00047000 07:01 3490 /lib/x86_64-linux-gnu/libblkid.so.1.1.0
- 2b131d2eb000-2b131d2ef000 r--p 00047000 07:01 3490 /lib/x86_64-linux-gnu/libblkid.so.1.1.0
- 2b131d2ef000-2b131d2f0000 rw-p 0004b000 07:01 3490 /lib/x86_64-linux-gnu/libblkid.so.1.1.0
- 2b131d2f0000-2b131d2f1000 rw-p 00000000 00:00 0
- 2b131d2f1000-2b131d2f7000 r-xp 00000000 07:01 3592 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
- 2b131d2f7000-2b131d4f6000 ---p 00006000 07:01 3592 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
- 2b131d4f6000-2b131d4f7000 r--p 00005000 07:01 3592 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
- 2b131d4f7000-2b131d4f8000 rw-p 00006000 07:01 3592 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
- 2b131d4f8000-2b131d4fc000 ---p 00000000 00:00 0
- 2b131d4fc000-2b131d5f9000 rw-p 00000000 00:00 0
- 2b131d5f9000-2b131d602000 r-xp 00000000 07:01 14985 /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
- 2b131d602000-2b131d801000 ---p 00009000 07:01 14985 /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
- 2b131d801000-2b131d802000 r--p 00008000 07:01 14985 /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
- 2b131d802000-2b131d803000 rw-p 00009000 07:01 14985 /usr/lib/x86_64-linux-gnu/libXcursor.so.1.0.2
- 2b131d803000-2b131d808000 r-xp 00000000 07:01 14995 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
- 2b131d808000-2b131da07000 ---p 00005000 07:01 14995 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
- 2b131da07000-2b131da08000 r--p 00004000 07:01 14995 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
- 2b131da08000-2b131da09000 rw-p 00005000 07:01 14995 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
- 2b131da09000-2b131da0d000 ---p 00000000 00:00 0
- 2b131da0d000-2b131dd0a000 rw-p 00000000 00:00 0
- 2b131dd0a000-2b131dd0e000 ---p 00000000 00:00 0
- 2b131dd0e000-2b131de0b000 rw-p 00000000 00:00 0
- 2b131de0b000-2b131de0f000 ---p 00000000 00:00 0
- 2b131de0f000-2b131e10c000 rw-p 00000000 00:00 0
- 2b131e10c000-2b131e111000 r-xp 00000000 07:01 3544 /lib/x86_64-linux-gnu/libnss_dns-2.27.so
- 2b131e111000-2b131e311000 ---p 00005000 07:01 3544 /lib/x86_64-linux-gnu/libnss_dns-2.27.so
- 2b131e311000-2b131e312000 r--p 00005000 07:01 3544 /lib/x86_64-linux-gnu/libnss_dns-2.27.so
- 2b131e312000-2b131e313000 rw-p 00006000 07:01 3544 /lib/x86_64-linux-gnu/libnss_dns-2.27.so
- 2b131e313000-2b131e317000 ---p 00000000 00:00 0
- 2b131e317000-2b131ea14000 rw-p 00000000 00:00 0
- 2b131ea14000-2b131ea15000 r-xp 00000000 07:01 13721 /usr/lib/jvm/java-11-openjdk-amd64/lib/libprefs.so
- 2b131ea15000-2b131ec15000 ---p 00001000 07:01 13721 /usr/lib/jvm/java-11-openjdk-amd64/lib/libprefs.so
- 2b131ec15000-2b131ec16000 r--p 00001000 07:01 13721 /usr/lib/jvm/java-11-openjdk-amd64/lib/libprefs.so
- 2b131ec16000-2b131ec17000 rw-p 00002000 07:01 13721 /usr/lib/jvm/java-11-openjdk-amd64/lib/libprefs.so
- 2b131ec17000-2b131ec1b000 ---p 00000000 00:00 0
- 2b131ec1b000-2b131f618000 rw-p 00000000 00:00 0
- 2b131f618000-2b131f718000 ---p 00000000 00:00 0
- 2b131f718000-2b131f719000 ---p 00000000 00:00 0
- 2b131f719000-2b131f919000 rw-p 00000000 00:00 0
- 2b1320000000-2b1320021000 rw-p 00000000 00:00 0
- 2b1320021000-2b1324000000 ---p 00000000 00:00 0
- 2b1324000000-2b1324021000 rw-p 00000000 00:00 0
- 2b1324021000-2b1328000000 ---p 00000000 00:00 0
- 2b1328000000-2b1328021000 rw-p 00000000 00:00 0
- 2b1328021000-2b132c000000 ---p 00000000 00:00 0
- 2b132c000000-2b132c066000 rw-p 00000000 00:00 0
- 2b132c066000-2b1330000000 ---p 00000000 00:00 0
- 2b1330000000-2b1330021000 rw-p 00000000 00:00 0
- 2b1330021000-2b1334000000 ---p 00000000 00:00 0
- 2b1334000000-2b13340be000 rw-p 00000000 00:00 0
- 2b13340be000-2b1338000000 ---p 00000000 00:00 0
- 2b1338000000-2b1338021000 rw-p 00000000 00:00 0
- 2b1338021000-2b133c000000 ---p 00000000 00:00 0
- 55b30d202000-55b30d203000 r-xp 00000000 07:01 13371 /usr/lib/jvm/java-11-openjdk-amd64/bin/java
- 55b30d403000-55b30d404000 r--p 00001000 07:01 13371 /usr/lib/jvm/java-11-openjdk-amd64/bin/java
- 55b30d404000-55b30d405000 rw-p 00002000 07:01 13371 /usr/lib/jvm/java-11-openjdk-amd64/bin/java
- 55b30f069000-55b30f08a000 rw-p 00000000 00:00 0 [heap]
- 7fff54d74000-7fff54d97000 rw-p 00000000 00:00 0 [stack]
- 7fff54db3000-7fff54db5000 r-xp 00000000 00:00 0 [vdso]
- ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
- VM Arguments:
- jvm_args: -Xmx24g -Djava.io.tmpdir=/tmp/moma.20230922-123241.0JWui/java.io.tmpdir -Djava.library.path=/opt/gurobi/linux64/lib/:/moma/tensorflow -Dimagej.tensorflow.models.dir=/tmp/moma.20230922-123241.0JWui/tensorflow -Djava.util.prefs.systemRoot=/tmp/moma.20230922-123241.0JWui -Djava.util.prefs.userRoot=/tmp/moma.20230922-123241.0JWui
- java_command: /build_dir/target//MotherMachine-v0.10.2.20230911-100708.03a6665.jar -headless -reload /scicore/home/nimwegen/GROUP/MM_Data/Bor/20230831_25/preprocessing/20230831_preprocess_positions__output__20230915-121216/1-Pos000/1-Pos000_GL58 -analysis 20230831_25_batch_short_slurm_zlad__replicate_2_michael -i /scicore/home/nimwegen/GROUP/MM_Data/Bor/20230831_25/preprocessing/20230831_preprocess_positions__output__20230915-121216/1-Pos000/1-Pos000_GL58/oxi_stress_0_15_0_2_rep1_1_MMStack__1-Pos000_GL58.tif
- java_class_path (initial): /build_dir/target//MotherMachine-v0.10.2.20230911-100708.03a6665.jar
- Launcher Type: SUN_STANDARD
- [Global flags]
- intx CICompilerCount = 2 {product} {ergonomic}
- size_t InitialHeapSize = 2147483648 {product} {ergonomic}
- size_t MaxHeapSize = 25769803776 {product} {command line}
- size_t MaxNewSize = 8589934592 {product} {ergonomic}
- size_t MinHeapDeltaBytes = 196608 {product} {ergonomic}
- size_t NewSize = 715784192 {product} {ergonomic}
- uintx NonNMethodCodeHeapSize = 5825164 {pd product} {ergonomic}
- uintx NonProfiledCodeHeapSize = 122916538 {pd product} {ergonomic}
- size_t OldSize = 1431699456 {product} {ergonomic}
- uintx ProfiledCodeHeapSize = 122916538 {pd product} {ergonomic}
- uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic}
- bool SegmentedCodeCache = true {product} {ergonomic}
- bool UseCompressedClassPointers = true {lp64_product} {ergonomic}
- bool UseCompressedOops = true {lp64_product} {ergonomic}
- bool UseSerialGC = true {product} {ergonomic}
- Logging:
- Log output configuration:
- #0: stdout all=warning uptime,level,tags
- #1: stderr all=off uptime,level,tags
- Environment Variables:
- PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/gurobi/linux64/bin
- LD_LIBRARY_PATH=/opt/gurobi/linux64:/opt/gurobi/linux64/lib:/.singularity.d/libs
- SHELL=/bin/bash
- DISPLAY=:0
- LANG=en_US.UTF-8
- LC_ALL=C
- TMPDIR=/tmp
- TMP=/scratch/micuby52/slurm-job.4586434
- TEMP=/scratch/micuby52/slurm-job.4586434
- Signal Handlers:
- SIGSEGV: [libjvm.so+0xe356a0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
- SIGBUS: [libjvm.so+0xe356a0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
- SIGFPE: [libjvm.so+0xe356a0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
- SIGPIPE: SIG_IGN, sa_mask[0]=00000000000010000000000000000000, sa_flags=SA_RESTART
- SIGXFSZ: [libjvm.so+0xb89cc0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
- SIGILL: [libjvm.so+0xe356a0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
- SIGUSR2: [libjvm.so+0xb89b50], sa_mask[0]=00000000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
- SIGHUP: [libjvm.so+0xb8a220], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
- SIGINT: [libjvm.so+0xb8a220], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
- SIGTERM: [libjvm.so+0xb8a220], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
- SIGQUIT: [libjvm.so+0xb8a220], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
- --------------- S Y S T E M ---------------
- OS:DISTRIB_ID=Ubuntu
- DISTRIB_RELEASE=18.04
- DISTRIB_CODENAME=bionic
- DISTRIB_DESCRIPTION="Ubuntu 18.04.6 LTS"
- uname:Linux 3.10.0-1160.66.1.el7.x86_64 #1 SMP Wed May 18 16:02:34 UTC 2022 x86_64
- OS uptime: 209 days 22:36 hours
- libc:glibc 2.27 NPTL 2.27
- rlimit (soft/hard): STACK infinity/infinity , CORE infinity/infinity , NPROC 2062567/2062567 , NOFILE 131072/131072 , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK infinity/infinity
- load average:24.76 29.43 27.47
- /proc/meminfo:
- MemTotal: 528038404 kB
- MemFree: 312735396 kB
- MemAvailable: 362764068 kB
- Buffers: 676000 kB
- Cached: 93388556 kB
- SwapCached: 133656 kB
- Active: 128015872 kB
- Inactive: 41926384 kB
- Active(anon): 91709076 kB
- Inactive(anon): 28391136 kB
- Active(file): 36306796 kB
- Inactive(file): 13535248 kB
- Unevictable: 33554444 kB
- Mlocked: 33554444 kB
- SwapTotal: 8388604 kB
- SwapFree: 96 kB
- Dirty: 44 kB
- Writeback: 0 kB
- AnonPages: 109299908 kB
- Mapped: 2241092 kB
- Shmem: 44222224 kB
- Slab: 2586620 kB
- SReclaimable: 1593012 kB
- SUnreclaim: 993608 kB
- KernelStack: 41040 kB
- PageTables: 237716 kB
- NFS_Unstable: 0 kB
- Bounce: 0 kB
- WritebackTmp: 0 kB
- CommitLimit: 272407804 kB
- Committed_AS: 168204192 kB
- VmallocTotal: 34359738367 kB
- VmallocUsed: 3101396 kB
- VmallocChunk: 34087995224 kB
- Percpu: 50176 kB
- HardwareCorrupted: 0 kB
- AnonHugePages: 26949632 kB
- CmaTotal: 0 kB
- CmaFree: 0 kB
- HugePages_Total: 0
- HugePages_Free: 0
- HugePages_Rsvd: 0
- HugePages_Surp: 0
- Hugepagesize: 2048 kB
- DirectMap4k: 1248344 kB
- DirectMap2M: 187351040 kB
- DirectMap1G: 348127232 kB
- /sys/kernel/mm/transparent_hugepage/enabled:
- [always] madvise never
- /sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts parameter):
- [always] madvise never
- Process Memory:
- Virtual Size: 28118700K (peak: 36260348K)
- Resident Set Size: 930184K (peak: 930184K) (anon: 904488K, file: 25696K, shmem: 0K)
- Swapped out: 0K
- C-Heap outstanding allocations: 27623K, retained: 27176K
- glibc malloc tunables: (default)
- /proc/sys/kernel/threads-max (system-wide limit on the number of threads):
- 4125135
- /proc/sys/vm/max_map_count (maximum number of memory map areas a process may have):
- 65530
- /proc/sys/kernel/pid_max (system-wide limit on number of process identifiers):
- 131072
- container information not found.
- Steal ticks since vm start: 0
- Steal ticks percentage since vm start: 0.000
- CPU:total 128 (initial active 1) (64 cores per cpu, 1 threads per core) family 23 model 49 stepping 0 microcode 0x830104d, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, mmxext, 3dnowpref, lzcnt, sse4a, tsc, tscinvbit, tscinv, bmi1, bmi2, adx, sha, fma
- CPU Model and flags from /proc/cpuinfo:
- model name : AMD EPYC 7742 64-Core Processor
- 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 mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc art rep_good nopl nonstop_tsc extd_apicid aperfmperf eagerfpu pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_l2 cpb cat_l3 cdp_l3 hw_pstate sme retpoline_amd ssbd ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif umip overflow_recov succor smca
- Online cpus:
- 0-127
- Offline cpus:
- BIOS frequency limitation:
- 2250000
- Frequency switch latency (ns):
- 0
- Available cpu frequencies:
- 2250000 2000000 1500000
- Current governor:
- conservative
- Core performance/turbo boost:
- 1
- Memory: 4k page, physical 528038404k(312735396k free), swap 8388604k(96k free)
- vm_info: OpenJDK 64-Bit Server VM (11.0.19+7-post-Ubuntu-0ubuntu118.04.1) for linux-amd64 JRE (11.0.19+7-post-Ubuntu-0ubuntu118.04.1), built on May 10 2023 00:54:54 by "unknown" with gcc 8.4.0
- END.
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