diff --git a/hs_err_pid23.log b/hs_err_pid23.log deleted file mode 100644 index 4b48e67..0000000 --- a/hs_err_pid23.log +++ /dev/null @@ -1,390 +0,0 @@ -# -# There is insufficient memory for the Java Runtime Environment to continue. -# Cannot create worker GC thread. Out of system resources. -# Possible reasons: -# The system is out of physical RAM or swap space -# The process is running with CompressedOops enabled, and the Java Heap may be blocking the growth of the native heap -# Possible solutions: -# Reduce memory load on the system -# Increase physical memory or swap space -# Check if swap backing store is full -# Decrease Java heap size (-Xmx/-Xms) -# Decrease number of Java threads -# Decrease Java thread stack sizes (-Xss) -# Set larger code cache with -XX:ReservedCodeCacheSize= -# JVM is running with Zero Based Compressed Oops mode in which the Java heap is -# placed in the first 32GB address space. The Java Heap base address is the -# maximum limit for the native heap growth. Please use -XX:HeapBaseMinAddress -# to set the Java Heap base and to place the Java Heap above 32GB virtual address. -# This output file may be truncated or incomplete. -# -# Out of Memory Error (workerManager.hpp:87), pid=23, tid=23 -# -# JRE version: (17.0.8.1+1) (build ) -# Java VM: OpenJDK 64-Bit Server VM (17.0.8.1+1-Ubuntu-0ubuntu122.04, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64) -# Core dump will be written. Default location: /storage1/fs1/dspencer/Active/spencerlab/mohamed/github/nf-core-wgsnano/core.23 -# - ---------------- S U M M A R Y ------------ - -Command Line: - -Host: Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz, 32 cores, 46G, Ubuntu 22.04.3 LTS -Time: Tue Nov 21 17:35:42 2023 UTC elapsed time: 0.013754 seconds (0d 0h 0m 0s) - ---------------- T H R E A D --------------- - -Current thread (0x000055696fe008e0): JavaThread "Unknown thread" [_thread_in_vm, id=23, stack(0x00007ffd10bf0000,0x00007ffd113ec000)] - -Stack: [0x00007ffd10bf0000,0x00007ffd113ec000], sp=0x00007ffd113e6c70, free space=8155k -Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) -V [libjvm.so+0xf560e5] VMError::report_and_die(int, char const*, char const*, __va_list_tag*, Thread*, unsigned char*, void*, void*, char const*, int, unsigned long)+0x175 -V [libjvm.so+0xf56c51] VMError::report_and_die(Thread*, char const*, int, unsigned long, VMErrorType, char const*, __va_list_tag*)+0x31 -V [libjvm.so+0x611430] report_vm_out_of_memory(char const*, int, unsigned long, VMErrorType, char const*, ...)+0xe0 -V [libjvm.so+0xf8a09f] WorkerManager::add_workers(WorkGang*, unsigned int, unsigned int, unsigned int, os::ThreadType, bool)+0x18f -V [libjvm.so+0xf8a25d] WorkGang::initialize_workers()+0x4d -V [libjvm.so+0x6f90c1] G1CollectedHeap::initialize()+0x6c1 -V [libjvm.so+0xf02846] universe_init()+0xd6 -V [libjvm.so+0x80b03b] init_globals()+0x3b -V [libjvm.so+0xed94a6] Threads::create_vm(JavaVMInitArgs*, bool*)+0x386 -V [libjvm.so+0x8d8e45] JNI_CreateJavaVM+0x55 -C [libjli.so+0x3d43] JavaMain+0x93 -C [libjli.so+0x8bc8] CallJavaMainInNewThread+0x98 -C [libjli.so+0x5c81] ContinueInNewThread+0x61 -C [libjli.so+0x72da] JLI_Launch+0x144a -C [java+0x12b4] - - ---------------- P R O C E S S --------------- - -Threads class SMR info: -_java_thread_list=0x00007fad3cee6a40, length=0, elements={ -} - -Java Threads: ( => current thread ) - -Other Threads: - -[error occurred during error reporting (printing all threads), id 0xb, SIGSEGV (0xb) at pc=0x00007fad3c2549a4] - -VM state: not at safepoint (not fully initialized) - -VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event]) -[0x000055696fdfe1d0] Heap_lock - owner thread: 0x000055696fe008e0 - -Heap address: 0x0000000512000000, size: 12000 MB, Compressed Oops mode: Zero based, Oop shift amount: 3 - -CDS archive(s) mapped at: [0x0000000000000000-0x0000000000000000-0x0000000000000000), size 0, SharedBaseAddress: 0x0000000800000000, ArchiveRelocationMode: 1. -Narrow klass base: 0x0000000000000000, Narrow klass shift: 0, Narrow klass range: 0x0 - -GC Precious Log: - - -Heap: - garbage-first heap total 0K, used 0K [0x0000000512000000, 0x0000000800000000) - region size 8192K, 0 young (0K), 0 survivors (0K) - -[error occurred during error reporting (printing heap information), id 0xb, SIGSEGV (0xb) at pc=0x00007fad3c825d1e] - -GC Heap History (0 events): -No events - -Dll operation events (1 events): -Event: 0.003 Loaded shared library /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so - -Deoptimization events (0 events): -No events - -Classes unloaded (0 events): -No events - -Classes redefined (0 events): -No events - -Internal exceptions (0 events): -No events - -VM Operations (0 events): -No events - -Events (1 events): -Event: 0.003 Protecting memory [0x00007ffd10bf0000,0x00007ffd10bf4000] with protection modes 0 - - -Dynamic libraries: -512000000-800000000 ---p 00000000 00:00 0 -55696f5cf000-55696f5d0000 r--p 00000000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -55696f5d0000-55696f5d1000 r-xp 00001000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -55696f5d1000-55696f5d2000 r--p 00002000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -55696f5d2000-55696f5d3000 r--p 00002000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -55696f5d3000-55696f5d4000 rw-p 00003000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -55696fdc4000-55696fe50000 rw-p 00000000 00:00 0 [heap] -7fad06fd9000-7fad073c2000 rw-p 00000000 00:00 0 -7fad073c2000-7fad073c3000 ---p 00000000 00:00 0 -7fad073c3000-7fad075e1000 rw-p 00000000 00:00 0 -7fad075e1000-7fad23331000 ---p 00000000 00:00 0 -7fad23331000-7fad24aab000 rw-p 00000000 00:00 0 -7fad24aab000-7fad24b8f000 ---p 00000000 00:00 0 -7fad24b8f000-7fad24b94000 rw-p 00000000 00:00 0 -7fad24b94000-7fad24c78000 ---p 00000000 00:00 0 -7fad24c78000-7fad24c7d000 rw-p 00000000 00:00 0 -7fad24c7d000-7fad24c88000 ---p 00000000 00:00 0 -7fad24c88000-7fad24ef8000 rwxp 00000000 00:00 0 -7fad24ef8000-7fad2c09f000 ---p 00000000 00:00 0 -7fad2c09f000-7fad2c30f000 rwxp 00000000 00:00 0 -7fad2c30f000-7fad2c870000 ---p 00000000 00:00 0 -7fad2c870000-7fad2cae0000 rwxp 00000000 00:00 0 -7fad2cae0000-7fad33c88000 ---p 00000000 00:00 0 -7fad33c88000-7fad33c94000 r--p 00000000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fad33c94000-7fad33ca7000 r-xp 0000c000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fad33ca7000-7fad33cad000 r--p 0001f000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fad33cad000-7fad33cae000 r--p 00024000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fad33cae000-7fad33caf000 rw-p 00025000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fad33caf000-7fad33cb0000 rw-p 00000000 00:00 0 -7fad33cb0000-7fad33cb8000 rw-s 00000000 fd:00 16751362 /tmp/hsperfdata_mmohamed/23 -7fad33cb8000-7fad3b713000 r--s 00000000 fd:00 162809986 /usr/lib/jvm/java-17-openjdk-amd64/lib/modules -7fad3b713000-7fad3b715000 r--p 00000000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fad3b715000-7fad3b718000 r-xp 00002000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fad3b718000-7fad3b719000 r--p 00005000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fad3b719000-7fad3b71a000 ---p 00006000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fad3b71a000-7fad3b71b000 r--p 00006000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fad3b71b000-7fad3b71c000 rw-p 00007000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fad3b71c000-7fad3b81c000 rw-p 00000000 00:00 0 -7fad3b81c000-7fad3b81f000 r--p 00000000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fad3b81f000-7fad3b836000 r-xp 00003000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fad3b836000-7fad3b83a000 r--p 0001a000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fad3b83a000-7fad3b83b000 r--p 0001d000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fad3b83b000-7fad3b83c000 rw-p 0001e000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fad3b83c000-7fad3b84a000 r--p 00000000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fad3b84a000-7fad3b8c6000 r-xp 0000e000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fad3b8c6000-7fad3b921000 r--p 0008a000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fad3b921000-7fad3b922000 r--p 000e4000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fad3b922000-7fad3b923000 rw-p 000e5000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fad3b923000-7fad3b9bd000 r--p 00000000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fad3b9bd000-7fad3bace000 r-xp 0009a000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fad3bace000-7fad3bb3d000 r--p 001ab000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fad3bb3d000-7fad3bb3e000 ---p 0021a000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fad3bb3e000-7fad3bb49000 r--p 0021a000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fad3bb49000-7fad3bb4c000 rw-p 00225000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fad3bb4c000-7fad3bb4f000 rw-p 00000000 00:00 0 -7fad3bb4f000-7fad3bda0000 r--p 00000000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fad3bda0000-7fad3cb26000 r-xp 00251000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fad3cb26000-7fad3cda9000 r--p 00fd7000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fad3cda9000-7fad3cdaa000 ---p 0125a000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fad3cdaa000-7fad3ce62000 r--p 0125a000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fad3ce62000-7fad3ce97000 rw-p 01312000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fad3ce97000-7fad3cef3000 rw-p 00000000 00:00 0 -7fad3cef3000-7fad3cf1b000 r--p 00000000 fd:00 162809015 /usr/lib/x86_64-linux-gnu/libc.so.6 -7fad3cf1b000-7fad3d0b0000 r-xp 00028000 fd:00 162809015 /usr/lib/x86_64-linux-gnu/libc.so.6 -7fad3d0b0000-7fad3d108000 r--p 001bd000 fd:00 162809015 /usr/lib/x86_64-linux-gnu/libc.so.6 -7fad3d108000-7fad3d10c000 r--p 00214000 fd:00 162809015 /usr/lib/x86_64-linux-gnu/libc.so.6 -7fad3d10c000-7fad3d10e000 rw-p 00218000 fd:00 162809015 /usr/lib/x86_64-linux-gnu/libc.so.6 -7fad3d10e000-7fad3d11b000 rw-p 00000000 00:00 0 -7fad3d11b000-7fad3d11d000 r--p 00000000 fd:00 162809967 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjli.so -7fad3d11d000-7fad3d127000 r-xp 00002000 fd:00 162809967 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjli.so -7fad3d127000-7fad3d12a000 r--p 0000c000 fd:00 162809967 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjli.so -7fad3d12a000-7fad3d12b000 r--p 0000e000 fd:00 162809967 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjli.so -7fad3d12b000-7fad3d12c000 rw-p 0000f000 fd:00 162809967 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjli.so -7fad3d12c000-7fad3d12e000 r--p 00000000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fad3d12e000-7fad3d13f000 r-xp 00002000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fad3d13f000-7fad3d145000 r--p 00013000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fad3d145000-7fad3d146000 ---p 00019000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fad3d146000-7fad3d147000 r--p 00019000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fad3d147000-7fad3d148000 rw-p 0001a000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fad3d14a000-7fad3d14b000 ---p 00000000 00:00 0 -7fad3d14b000-7fad3d14c000 r--p 00000000 00:00 0 -7fad3d14c000-7fad3d14e000 rw-p 00000000 00:00 0 -7fad3d14e000-7fad3d150000 r--p 00000000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7fad3d150000-7fad3d17a000 r-xp 00002000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7fad3d17a000-7fad3d185000 r--p 0002c000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7fad3d185000-7fad3d186000 ---p 00000000 00:00 0 -7fad3d186000-7fad3d188000 r--p 00037000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7fad3d188000-7fad3d18a000 rw-p 00039000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7ffd10bf0000-7ffd10bf4000 ---p 00000000 00:00 0 -7ffd113cd000-7ffd113f0000 rw-p 00000000 00:00 0 [stack] -7ffd113f0000-7ffd113f2000 r-xp 00000000 00:00 0 [vdso] -ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] - - -VM Arguments: -java_command: -java_class_path (initial): -Launcher Type: SUN_STANDARD - -[Global flags] - intx CICompilerCount = 15 {product} {ergonomic} - uint ConcGCThreads = 6 {product} {ergonomic} - uint G1ConcRefinementThreads = 23 {product} {ergonomic} - size_t G1HeapRegionSize = 8388608 {product} {ergonomic} - uintx GCDrainStackTargetSize = 64 {product} {ergonomic} - size_t InitialHeapSize = 788529152 {product} {ergonomic} - size_t MarkStackSize = 4194304 {product} {ergonomic} - size_t MaxHeapSize = 12582912000 {product} {ergonomic} - size_t MinHeapDeltaBytes = 8388608 {product} {ergonomic} - size_t MinHeapSize = 8388608 {product} {ergonomic} - uintx NonNMethodCodeHeapSize = 8192380 {pd product} {ergonomic} - uintx NonProfiledCodeHeapSize = 121732930 {pd product} {ergonomic} - uintx ProfiledCodeHeapSize = 121732930 {pd product} {ergonomic} - uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic} - bool SegmentedCodeCache = true {product} {ergonomic} - size_t SoftMaxHeapSize = 12582912000 {manageable} {ergonomic} - bool UseCompressedClassPointers = true {product lp64_product} {ergonomic} - bool UseCompressedOops = true {product lp64_product} {ergonomic} - bool UseG1GC = true {product} {ergonomic} - -Logging: -Log output configuration: - #0: stdout all=warning uptime,level,tags - #1: stderr all=off uptime,level,tags - -Environment Variables: -JAVA_HOME=/opt/ibm/jre -PATH=/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/rust/.cargo/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/aws-cli/v2/2.9.10/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw-agent:/opt/conda/bin:/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw-agent:/opt/conda/bin:/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc:/opt/ibm/lsfsuite/ext/ppm/10.2/bin:/opt/ibm/lsfsuite/ext/ppm/10.2/linux2.6-glibc2.3-x86_64/bin:/opt/ibm/jre/bin:/usr/lpp/mmfs/bin:/opt/thpc/bin:/rdcw/fs2/dspencer/Active/spencerlab/mohamed/apps/vscode/.vscode-server/bin/1a5daa3a0231a0fbba4f14db7ec463cf99d7768e/bin/remote-cli:/home/mmohamed/.cargo/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/rust/.cargo/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/aws-cli/v2/2.9.10/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw-agent:/opt/conda/bin:/opt/ibm/lsfsuite/ext/ppm/10.2/bin:/opt/ibm/lsfsuite/ext/ppm/10.2/linux2.6-glibc2.3-x86_64/bin:/opt/ibm/jre/bin:/usr/lpp/mmfs/bin:/opt/thpc/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/bin:/usr/bin:/bin:/home/mmohamed/.local/bin:/home/mmohamed/bin:/bin:/usr/bin:/bin:/home/mmohamed/.local/bin:/home/mmohamed/bin -USERNAME=mmohamed -SHELL=/bin/bash -HOSTTYPE=X86_64 -LANG=en_US.UTF-8 -TERM=xterm-256color -TMPDIR=/tmp/444113.tmpdir - -Active Locale: -LC_ALL=C -LC_COLLATE=C -LC_CTYPE=C -LC_MESSAGES=C -LC_MONETARY=C -LC_NUMERIC=C -LC_TIME=C - -Signal Handlers: - SIGSEGV: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGBUS: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGFPE: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGPIPE: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked - SIGXFSZ: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked - SIGILL: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGUSR2: SR_handler in libjvm.so, mask=00000000000000000000000000000000, flags=SA_RESTART|SA_SIGINFO, blocked - SIGHUP: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked - SIGINT: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked - SIGTERM: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked - SIGQUIT: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked - SIGTRAP: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - - ---------------- S Y S T E M --------------- - -OS: -DISTRIB_ID=Ubuntu -DISTRIB_RELEASE=22.04 -DISTRIB_CODENAME=jammy -DISTRIB_DESCRIPTION="Ubuntu 22.04.3 LTS" -uname: Linux 3.10.0-1160.53.1.el7.x86_64 #1 SMP Thu Dec 16 10:19:28 UTC 2021 x86_64 -OS uptime: 256 days 6:59 hours -libc: glibc 2.35 NPTL 2.35 -rlimit (soft/hard): STACK 8192k/infinity , CORE infinity/infinity , NPROC infinity/infinity , NOFILE 1048576/1048576 , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK infinity/infinity -load average: 0.55 0.30 0.42 - -/proc/meminfo: -MemTotal: 394630832 kB -MemFree: 310954136 kB -MemAvailable: 338863804 kB -Buffers: 9160 kB -Cached: 23215012 kB -SwapCached: 34544 kB -Active: 16331564 kB -Inactive: 17663420 kB -Active(anon): 11911848 kB -Inactive(anon): 3121460 kB -Active(file): 4419716 kB -Inactive(file): 14541960 kB -Unevictable: 31457280 kB -Mlocked: 31457280 kB -SwapTotal: 1048572 kB -SwapFree: 961084 kB -Dirty: 80 kB -Writeback: 0 kB -AnonPages: 42195620 kB -Mapped: 838480 kB -Shmem: 4262488 kB -Slab: 11609004 kB -SReclaimable: 9879312 kB -SUnreclaim: 1729692 kB -KernelStack: 44352 kB -PageTables: 104252 kB -NFS_Unstable: 0 kB -Bounce: 0 kB -WritebackTmp: 0 kB -CommitLimit: 198363988 kB -Committed_AS: 56218852 kB -VmallocTotal: 34359738367 kB -VmallocUsed: 1725496 kB -VmallocChunk: 34055980748 kB -Percpu: 169984 kB -HardwareCorrupted: 0 kB -AnonHugePages: 37324800 kB -CmaTotal: 0 kB -CmaFree: 0 kB -HugePages_Total: 0 -HugePages_Free: 0 -HugePages_Rsvd: 0 -HugePages_Surp: 0 -Hugepagesize: 2048 kB -DirectMap4k: 2610860 kB -DirectMap2M: 209858560 kB -DirectMap1G: 190840832 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: 13175204K (peak: 13175204K) -Resident Set Size: 12980K (peak: 12980K) (anon: 6360K, file: 6620K, shmem: 0K) -Swapped out: 0K -C-Heap outstanding allocations: 28692K, retained: 79K -glibc malloc tunables: (default) - -/proc/sys/kernel/threads-max (system-wide limit on the number of threads): 3082856 -/proc/sys/vm/max_map_count (maximum number of memory map areas a process may have): 1048480 -/proc/sys/kernel/pid_max (system-wide limit on number of process identifiers): 262144 - -container (cgroup) information: -container_type: cgroupv1 -cpu_cpuset_cpus: 0-31 -cpu_memory_nodes: 0-3 -active_processor_count: 32 -cpu_quota: no quota -cpu_period: 100000 -cpu_shares: 24 -memory_limit_in_bytes: 49152000 k -memory_and_swap_limit_in_bytes: unlimited -memory_soft_limit_in_bytes: unlimited -memory_usage_in_bytes: 8448 k -memory_max_usage_in_bytes: 8636 k -kernel_memory_usage_in_bytes: unlimited -kernel_memory_max_usage_in_bytes: unlimited -kernel_memory_limit_in_bytes: unlimited -maximum number of tasks: unlimited -current number of tasks: 5 - -Steal ticks since vm start: 0 -Steal ticks percentage since vm start: 0.000 - -CPU: total 32 (initial active 32) (16 cores per cpu, 2 threads per core) family 6 model 85 stepping 7 microcode 0x5003103, cx8, cmov, fxsr, ht, mmx, 3dnowpref, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, lzcnt, tsc, tscinvbit, avx, avx2, aes, erms, clmul, bmi1, bmi2, rtm, adx, avx512f, avx512dq, avx512cd, avx512bw, avx512vl, fma, vzeroupper, avx512_vnni, clflush, clflushopt, clwb -CPU Model and flags from /proc/cpuinfo: -model name : Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz -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 art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single intel_ppin intel_pt ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke avx512_vnni md_clear spec_ctrl intel_stibp flush_l1d arch_capabilities - -Online cpus: 0-31 -Offline cpus: 32-255 -BIOS frequency limitation: -Frequency switch latency (ns): 4294967295 -Available cpu frequencies: -Current governor: performance -Core performance/turbo boost: - -Memory: 4k page, physical 49152000k(49143552k free), swap 1048572k(961084k free) -Page Sizes: 4k - -vm_info: OpenJDK 64-Bit Server VM (17.0.8.1+1-Ubuntu-0ubuntu122.04) for linux-amd64 JRE (17.0.8.1+1-Ubuntu-0ubuntu122.04), built on Aug 24 2023 23:23:28 by "buildd" with gcc 11.4.0 - -END. diff --git a/hs_err_pid38.log b/hs_err_pid38.log deleted file mode 100644 index bc87147..0000000 --- a/hs_err_pid38.log +++ /dev/null @@ -1,390 +0,0 @@ -# -# There is insufficient memory for the Java Runtime Environment to continue. -# Cannot create worker GC thread. Out of system resources. -# Possible reasons: -# The system is out of physical RAM or swap space -# The process is running with CompressedOops enabled, and the Java Heap may be blocking the growth of the native heap -# Possible solutions: -# Reduce memory load on the system -# Increase physical memory or swap space -# Check if swap backing store is full -# Decrease Java heap size (-Xmx/-Xms) -# Decrease number of Java threads -# Decrease Java thread stack sizes (-Xss) -# Set larger code cache with -XX:ReservedCodeCacheSize= -# JVM is running with Zero Based Compressed Oops mode in which the Java heap is -# placed in the first 32GB address space. The Java Heap base address is the -# maximum limit for the native heap growth. Please use -XX:HeapBaseMinAddress -# to set the Java Heap base and to place the Java Heap above 32GB virtual address. -# This output file may be truncated or incomplete. -# -# Out of Memory Error (workerManager.hpp:87), pid=38, tid=38 -# -# JRE version: (17.0.8.1+1) (build ) -# Java VM: OpenJDK 64-Bit Server VM (17.0.8.1+1-Ubuntu-0ubuntu122.04, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64) -# Core dump will be written. Default location: /storage1/fs1/dspencer/Active/spencerlab/mohamed/github/nf-core-wgsnano/core.38 -# - ---------------- S U M M A R Y ------------ - -Command Line: - -Host: Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz, 32 cores, 46G, Ubuntu 22.04.3 LTS -Time: Tue Nov 21 17:35:52 2023 UTC elapsed time: 0.016650 seconds (0d 0h 0m 0s) - ---------------- T H R E A D --------------- - -Current thread (0x0000563710c6e8e0): JavaThread "Unknown thread" [_thread_in_vm, id=38, stack(0x00007fffc2b99000,0x00007fffc3395000)] - -Stack: [0x00007fffc2b99000,0x00007fffc3395000], sp=0x00007fffc338f8a0, free space=8154k -Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) -V [libjvm.so+0xf560e5] VMError::report_and_die(int, char const*, char const*, __va_list_tag*, Thread*, unsigned char*, void*, void*, char const*, int, unsigned long)+0x175 -V [libjvm.so+0xf56c51] VMError::report_and_die(Thread*, char const*, int, unsigned long, VMErrorType, char const*, __va_list_tag*)+0x31 -V [libjvm.so+0x611430] report_vm_out_of_memory(char const*, int, unsigned long, VMErrorType, char const*, ...)+0xe0 -V [libjvm.so+0xf8a09f] WorkerManager::add_workers(WorkGang*, unsigned int, unsigned int, unsigned int, os::ThreadType, bool)+0x18f -V [libjvm.so+0xf8a25d] WorkGang::initialize_workers()+0x4d -V [libjvm.so+0x6f90c1] G1CollectedHeap::initialize()+0x6c1 -V [libjvm.so+0xf02846] universe_init()+0xd6 -V [libjvm.so+0x80b03b] init_globals()+0x3b -V [libjvm.so+0xed94a6] Threads::create_vm(JavaVMInitArgs*, bool*)+0x386 -V [libjvm.so+0x8d8e45] JNI_CreateJavaVM+0x55 -C [libjli.so+0x3d43] JavaMain+0x93 -C [libjli.so+0x8bc8] CallJavaMainInNewThread+0x98 -C [libjli.so+0x5c81] ContinueInNewThread+0x61 -C [libjli.so+0x72da] JLI_Launch+0x144a -C [java+0x12b4] - - ---------------- P R O C E S S --------------- - -Threads class SMR info: -_java_thread_list=0x00007fa6b3ef6a40, length=0, elements={ -} - -Java Threads: ( => current thread ) - -Other Threads: - -[error occurred during error reporting (printing all threads), id 0xb, SIGSEGV (0xb) at pc=0x00007fa6b32649a4] - -VM state: not at safepoint (not fully initialized) - -VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event]) -[0x0000563710c6c1d0] Heap_lock - owner thread: 0x0000563710c6e8e0 - -Heap address: 0x0000000512000000, size: 12000 MB, Compressed Oops mode: Zero based, Oop shift amount: 3 - -CDS archive(s) mapped at: [0x0000000000000000-0x0000000000000000-0x0000000000000000), size 0, SharedBaseAddress: 0x0000000800000000, ArchiveRelocationMode: 1. -Narrow klass base: 0x0000000000000000, Narrow klass shift: 0, Narrow klass range: 0x0 - -GC Precious Log: - - -Heap: - garbage-first heap total 0K, used 0K [0x0000000512000000, 0x0000000800000000) - region size 8192K, 0 young (0K), 0 survivors (0K) - -[error occurred during error reporting (printing heap information), id 0xb, SIGSEGV (0xb) at pc=0x00007fa6b3835d1e] - -GC Heap History (0 events): -No events - -Dll operation events (1 events): -Event: 0.002 Loaded shared library /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so - -Deoptimization events (0 events): -No events - -Classes unloaded (0 events): -No events - -Classes redefined (0 events): -No events - -Internal exceptions (0 events): -No events - -VM Operations (0 events): -No events - -Events (1 events): -Event: 0.002 Protecting memory [0x00007fffc2b99000,0x00007fffc2b9d000] with protection modes 0 - - -Dynamic libraries: -512000000-800000000 ---p 00000000 00:00 0 -56370faf4000-56370faf5000 r--p 00000000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -56370faf5000-56370faf6000 r-xp 00001000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -56370faf6000-56370faf7000 r--p 00002000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -56370faf7000-56370faf8000 r--p 00002000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -56370faf8000-56370faf9000 rw-p 00003000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -563710c32000-563710cbe000 rw-p 00000000 00:00 0 [heap] -7fa67dfe9000-7fa67e3d2000 rw-p 00000000 00:00 0 -7fa67e3d2000-7fa67e3d3000 ---p 00000000 00:00 0 -7fa67e3d3000-7fa67e5f1000 rw-p 00000000 00:00 0 -7fa67e5f1000-7fa69a341000 ---p 00000000 00:00 0 -7fa69a341000-7fa69babb000 rw-p 00000000 00:00 0 -7fa69babb000-7fa69bb9f000 ---p 00000000 00:00 0 -7fa69bb9f000-7fa69bba4000 rw-p 00000000 00:00 0 -7fa69bba4000-7fa69bc88000 ---p 00000000 00:00 0 -7fa69bc88000-7fa69bc8d000 rw-p 00000000 00:00 0 -7fa69bc8d000-7fa69bc98000 ---p 00000000 00:00 0 -7fa69bc98000-7fa69bf08000 rwxp 00000000 00:00 0 -7fa69bf08000-7fa6a30af000 ---p 00000000 00:00 0 -7fa6a30af000-7fa6a331f000 rwxp 00000000 00:00 0 -7fa6a331f000-7fa6a3880000 ---p 00000000 00:00 0 -7fa6a3880000-7fa6a3af0000 rwxp 00000000 00:00 0 -7fa6a3af0000-7fa6aac98000 ---p 00000000 00:00 0 -7fa6aac98000-7fa6aaca4000 r--p 00000000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fa6aaca4000-7fa6aacb7000 r-xp 0000c000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fa6aacb7000-7fa6aacbd000 r--p 0001f000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fa6aacbd000-7fa6aacbe000 r--p 00024000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fa6aacbe000-7fa6aacbf000 rw-p 00025000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7fa6aacbf000-7fa6aacc0000 rw-p 00000000 00:00 0 -7fa6aacc0000-7fa6aacc8000 rw-s 00000000 fd:00 16751362 /tmp/hsperfdata_mmohamed/38 -7fa6aacc8000-7fa6b2723000 r--s 00000000 fd:00 162809986 /usr/lib/jvm/java-17-openjdk-amd64/lib/modules -7fa6b2723000-7fa6b2725000 r--p 00000000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fa6b2725000-7fa6b2728000 r-xp 00002000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fa6b2728000-7fa6b2729000 r--p 00005000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fa6b2729000-7fa6b272a000 ---p 00006000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fa6b272a000-7fa6b272b000 r--p 00006000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fa6b272b000-7fa6b272c000 rw-p 00007000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7fa6b272c000-7fa6b282c000 rw-p 00000000 00:00 0 -7fa6b282c000-7fa6b282f000 r--p 00000000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fa6b282f000-7fa6b2846000 r-xp 00003000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fa6b2846000-7fa6b284a000 r--p 0001a000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fa6b284a000-7fa6b284b000 r--p 0001d000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fa6b284b000-7fa6b284c000 rw-p 0001e000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7fa6b284c000-7fa6b285a000 r--p 00000000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fa6b285a000-7fa6b28d6000 r-xp 0000e000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fa6b28d6000-7fa6b2931000 r--p 0008a000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fa6b2931000-7fa6b2932000 r--p 000e4000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fa6b2932000-7fa6b2933000 rw-p 000e5000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7fa6b2933000-7fa6b29cd000 r--p 00000000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fa6b29cd000-7fa6b2ade000 r-xp 0009a000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fa6b2ade000-7fa6b2b4d000 r--p 001ab000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fa6b2b4d000-7fa6b2b4e000 ---p 0021a000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fa6b2b4e000-7fa6b2b59000 r--p 0021a000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fa6b2b59000-7fa6b2b5c000 rw-p 00225000 fd:00 162809124 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.30 -7fa6b2b5c000-7fa6b2b5f000 rw-p 00000000 00:00 0 -7fa6b2b5f000-7fa6b2db0000 r--p 00000000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fa6b2db0000-7fa6b3b36000 r-xp 00251000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fa6b3b36000-7fa6b3db9000 r--p 00fd7000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fa6b3db9000-7fa6b3dba000 ---p 0125a000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fa6b3dba000-7fa6b3e72000 r--p 0125a000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fa6b3e72000-7fa6b3ea7000 rw-p 01312000 fd:00 16100791 /usr/lib/jvm/java-17-openjdk-amd64/lib/server/libjvm.so -7fa6b3ea7000-7fa6b3f03000 rw-p 00000000 00:00 0 -7fa6b3f03000-7fa6b3f2b000 r--p 00000000 fd:00 162809015 /usr/lib/x86_64-linux-gnu/libc.so.6 -7fa6b3f2b000-7fa6b40c0000 r-xp 00028000 fd:00 162809015 /usr/lib/x86_64-linux-gnu/libc.so.6 -7fa6b40c0000-7fa6b4118000 r--p 001bd000 fd:00 162809015 /usr/lib/x86_64-linux-gnu/libc.so.6 -7fa6b4118000-7fa6b411c000 r--p 00214000 fd:00 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/usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fa6b4155000-7fa6b4156000 ---p 00019000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fa6b4156000-7fa6b4157000 r--p 00019000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fa6b4157000-7fa6b4158000 rw-p 0001a000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7fa6b415a000-7fa6b415b000 ---p 00000000 00:00 0 -7fa6b415b000-7fa6b415c000 r--p 00000000 00:00 0 -7fa6b415c000-7fa6b415e000 rw-p 00000000 00:00 0 -7fa6b415e000-7fa6b4160000 r--p 00000000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7fa6b4160000-7fa6b418a000 r-xp 00002000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7fa6b418a000-7fa6b4195000 r--p 0002c000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7fa6b4195000-7fa6b4196000 ---p 00000000 00:00 0 -7fa6b4196000-7fa6b4198000 r--p 00037000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7fa6b4198000-7fa6b419a000 rw-p 00039000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7fffc2b99000-7fffc2b9d000 ---p 00000000 00:00 0 -7fffc3376000-7fffc3399000 rw-p 00000000 00:00 0 [stack] -7fffc33d5000-7fffc33d7000 r-xp 00000000 00:00 0 [vdso] -ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] - - -VM Arguments: -java_command: -java_class_path (initial): -Launcher Type: SUN_STANDARD - -[Global flags] - intx CICompilerCount = 15 {product} {ergonomic} - uint ConcGCThreads = 6 {product} {ergonomic} - uint G1ConcRefinementThreads = 23 {product} {ergonomic} - size_t G1HeapRegionSize = 8388608 {product} {ergonomic} - uintx GCDrainStackTargetSize = 64 {product} {ergonomic} - size_t InitialHeapSize = 788529152 {product} {ergonomic} - size_t MarkStackSize = 4194304 {product} {ergonomic} - size_t MaxHeapSize = 12582912000 {product} {ergonomic} - size_t MinHeapDeltaBytes = 8388608 {product} {ergonomic} - size_t MinHeapSize = 8388608 {product} {ergonomic} - uintx NonNMethodCodeHeapSize = 8192380 {pd product} {ergonomic} - uintx NonProfiledCodeHeapSize = 121732930 {pd product} {ergonomic} - uintx ProfiledCodeHeapSize = 121732930 {pd product} {ergonomic} - uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic} - bool SegmentedCodeCache = true {product} {ergonomic} - size_t SoftMaxHeapSize = 12582912000 {manageable} {ergonomic} - bool UseCompressedClassPointers = true {product lp64_product} {ergonomic} - bool UseCompressedOops = true {product lp64_product} {ergonomic} - bool UseG1GC = true {product} {ergonomic} - -Logging: -Log output configuration: - #0: stdout all=warning uptime,level,tags - #1: stderr all=off uptime,level,tags - -Environment Variables: -JAVA_HOME=/opt/ibm/jre -PATH=/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/rust/.cargo/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/aws-cli/v2/2.9.10/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw-agent:/opt/conda/bin:/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw-agent:/opt/conda/bin:/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc:/opt/ibm/lsfsuite/ext/ppm/10.2/bin:/opt/ibm/lsfsuite/ext/ppm/10.2/linux2.6-glibc2.3-x86_64/bin:/opt/ibm/jre/bin:/usr/lpp/mmfs/bin:/opt/thpc/bin:/rdcw/fs2/dspencer/Active/spencerlab/mohamed/apps/vscode/.vscode-server/bin/1a5daa3a0231a0fbba4f14db7ec463cf99d7768e/bin/remote-cli:/home/mmohamed/.cargo/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/rust/.cargo/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/aws-cli/v2/2.9.10/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw-agent:/opt/conda/bin:/opt/ibm/lsfsuite/ext/ppm/10.2/bin:/opt/ibm/lsfsuite/ext/ppm/10.2/linux2.6-glibc2.3-x86_64/bin:/opt/ibm/jre/bin:/usr/lpp/mmfs/bin:/opt/thpc/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/bin:/usr/bin:/bin:/home/mmohamed/.local/bin:/home/mmohamed/bin:/bin:/usr/bin:/bin:/home/mmohamed/.local/bin:/home/mmohamed/bin -USERNAME=mmohamed -SHELL=/bin/bash -HOSTTYPE=X86_64 -LANG=en_US.UTF-8 -TERM=xterm-256color -TMPDIR=/tmp/444113.tmpdir - -Active Locale: -LC_ALL=C -LC_COLLATE=C -LC_CTYPE=C -LC_MESSAGES=C -LC_MONETARY=C -LC_NUMERIC=C -LC_TIME=C - -Signal Handlers: - SIGSEGV: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGBUS: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGFPE: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGPIPE: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked - SIGXFSZ: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked - SIGILL: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGUSR2: SR_handler in libjvm.so, mask=00000000000000000000000000000000, flags=SA_RESTART|SA_SIGINFO, blocked - SIGHUP: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked - SIGINT: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked - SIGTERM: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked - SIGQUIT: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked - SIGTRAP: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - - ---------------- S Y S T E M --------------- - -OS: -DISTRIB_ID=Ubuntu -DISTRIB_RELEASE=22.04 -DISTRIB_CODENAME=jammy -DISTRIB_DESCRIPTION="Ubuntu 22.04.3 LTS" -uname: Linux 3.10.0-1160.53.1.el7.x86_64 #1 SMP Thu Dec 16 10:19:28 UTC 2021 x86_64 -OS uptime: 256 days 7:00 hours -libc: glibc 2.35 NPTL 2.35 -rlimit (soft/hard): STACK 8192k/infinity , CORE infinity/infinity , NPROC infinity/infinity , NOFILE 1048576/1048576 , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK infinity/infinity -load average: 0.46 0.29 0.42 - -/proc/meminfo: -MemTotal: 394630832 kB -MemFree: 310959564 kB -MemAvailable: 338869252 kB -Buffers: 9160 kB -Cached: 23215024 kB -SwapCached: 34544 kB -Active: 16332904 kB -Inactive: 17657100 kB -Active(anon): 11906848 kB -Inactive(anon): 3121460 kB -Active(file): 4426056 kB -Inactive(file): 14535640 kB -Unevictable: 31457280 kB -Mlocked: 31457280 kB -SwapTotal: 1048572 kB -SwapFree: 961084 kB -Dirty: 116 kB -Writeback: 0 kB -AnonPages: 42188980 kB -Mapped: 841412 kB -Shmem: 4262488 kB -Slab: 11608752 kB -SReclaimable: 9879312 kB -SUnreclaim: 1729440 kB -KernelStack: 44304 kB -PageTables: 104800 kB -NFS_Unstable: 0 kB -Bounce: 0 kB -WritebackTmp: 0 kB -CommitLimit: 198363988 kB -Committed_AS: 56216828 kB -VmallocTotal: 34359738367 kB -VmallocUsed: 1725496 kB -VmallocChunk: 34055980748 kB -Percpu: 169984 kB -HardwareCorrupted: 0 kB -AnonHugePages: 37318656 kB -CmaTotal: 0 kB -CmaFree: 0 kB -HugePages_Total: 0 -HugePages_Free: 0 -HugePages_Rsvd: 0 -HugePages_Surp: 0 -Hugepagesize: 2048 kB -DirectMap4k: 2610860 kB -DirectMap2M: 209858560 kB -DirectMap1G: 190840832 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: 13175204K (peak: 13175204K) -Resident Set Size: 12984K (peak: 12984K) (anon: 6364K, file: 6620K, shmem: 0K) -Swapped out: 0K -C-Heap outstanding allocations: 28692K, retained: 79K -glibc malloc tunables: (default) - -/proc/sys/kernel/threads-max (system-wide limit on the number of threads): 3082856 -/proc/sys/vm/max_map_count (maximum number of memory map areas a process may have): 1048480 -/proc/sys/kernel/pid_max (system-wide limit on number of process identifiers): 262144 - -container (cgroup) information: -container_type: cgroupv1 -cpu_cpuset_cpus: 0-31 -cpu_memory_nodes: 0-3 -active_processor_count: 32 -cpu_quota: no quota -cpu_period: 100000 -cpu_shares: 24 -memory_limit_in_bytes: 49152000 k -memory_and_swap_limit_in_bytes: unlimited -memory_soft_limit_in_bytes: unlimited -memory_usage_in_bytes: 8536 k -memory_max_usage_in_bytes: 8636 k -kernel_memory_usage_in_bytes: unlimited -kernel_memory_max_usage_in_bytes: unlimited -kernel_memory_limit_in_bytes: unlimited -maximum number of tasks: unlimited -current number of tasks: 5 - -Steal ticks since vm start: 0 -Steal ticks percentage since vm start: 0.000 - -CPU: total 32 (initial active 32) (16 cores per cpu, 2 threads per core) family 6 model 85 stepping 7 microcode 0x5003103, cx8, cmov, fxsr, ht, mmx, 3dnowpref, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, lzcnt, tsc, tscinvbit, avx, avx2, aes, erms, clmul, bmi1, bmi2, rtm, adx, avx512f, avx512dq, avx512cd, avx512bw, avx512vl, fma, vzeroupper, avx512_vnni, clflush, clflushopt, clwb -CPU Model and flags from /proc/cpuinfo: -model name : Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz -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 art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single intel_ppin intel_pt ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke avx512_vnni md_clear spec_ctrl intel_stibp flush_l1d arch_capabilities - -Online cpus: 0-31 -Offline cpus: 32-255 -BIOS frequency limitation: -Frequency switch latency (ns): 4294967295 -Available cpu frequencies: -Current governor: performance -Core performance/turbo boost: - -Memory: 4k page, physical 49152000k(49143464k free), swap 1048572k(961084k free) -Page Sizes: 4k - -vm_info: OpenJDK 64-Bit Server VM (17.0.8.1+1-Ubuntu-0ubuntu122.04) for linux-amd64 JRE (17.0.8.1+1-Ubuntu-0ubuntu122.04), built on Aug 24 2023 23:23:28 by "buildd" with gcc 11.4.0 - -END. diff --git a/hs_err_pid52.log b/hs_err_pid52.log deleted file mode 100644 index 5fef787..0000000 --- a/hs_err_pid52.log +++ /dev/null @@ -1,390 +0,0 @@ -# -# There is insufficient memory for the Java Runtime Environment to continue. -# Cannot create worker GC thread. Out of system resources. -# Possible reasons: -# The system is out of physical RAM or swap space -# The process is running with CompressedOops enabled, and the Java Heap may be blocking the growth of the native heap -# Possible solutions: -# Reduce memory load on the system -# Increase physical memory or swap space -# Check if swap backing store is full -# Decrease Java heap size (-Xmx/-Xms) -# Decrease number of Java threads -# Decrease Java thread stack sizes (-Xss) -# Set larger code cache with -XX:ReservedCodeCacheSize= -# JVM is running with Zero Based Compressed Oops mode in which the Java heap is -# placed in the first 32GB address space. The Java Heap base address is the -# maximum limit for the native heap growth. Please use -XX:HeapBaseMinAddress -# to set the Java Heap base and to place the Java Heap above 32GB virtual address. -# This output file may be truncated or incomplete. -# -# Out of Memory Error (workerManager.hpp:87), pid=52, tid=52 -# -# JRE version: (17.0.8.1+1) (build ) -# Java VM: OpenJDK 64-Bit Server VM (17.0.8.1+1-Ubuntu-0ubuntu122.04, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64) -# Core dump will be written. Default location: /storage1/fs1/dspencer/Active/spencerlab/mohamed/github/nf-core-wgsnano/core.52 -# - ---------------- S U M M A R Y ------------ - -Command Line: - -Host: Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz, 32 cores, 46G, Ubuntu 22.04.3 LTS -Time: Tue Nov 21 17:37:55 2023 UTC elapsed time: 0.029770 seconds (0d 0h 0m 0s) - ---------------- T H R E A D --------------- - -Current thread (0x0000564d49ff98e0): JavaThread "Unknown thread" [_thread_in_vm, id=52, stack(0x00007ffd87f31000,0x00007ffd8872e000)] - -Stack: [0x00007ffd87f31000,0x00007ffd8872e000], sp=0x00007ffd887284b0, free space=8157k -Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) -V [libjvm.so+0xf560e5] VMError::report_and_die(int, char const*, char const*, __va_list_tag*, Thread*, unsigned char*, void*, void*, char const*, int, unsigned long)+0x175 -V [libjvm.so+0xf56c51] VMError::report_and_die(Thread*, char const*, int, unsigned long, VMErrorType, char const*, __va_list_tag*)+0x31 -V [libjvm.so+0x611430] report_vm_out_of_memory(char const*, int, unsigned long, VMErrorType, char const*, ...)+0xe0 -V [libjvm.so+0xf8a09f] WorkerManager::add_workers(WorkGang*, unsigned int, unsigned int, unsigned int, os::ThreadType, bool)+0x18f -V [libjvm.so+0xf8a25d] WorkGang::initialize_workers()+0x4d -V [libjvm.so+0x6f90c1] G1CollectedHeap::initialize()+0x6c1 -V [libjvm.so+0xf02846] universe_init()+0xd6 -V [libjvm.so+0x80b03b] init_globals()+0x3b -V [libjvm.so+0xed94a6] Threads::create_vm(JavaVMInitArgs*, bool*)+0x386 -V [libjvm.so+0x8d8e45] JNI_CreateJavaVM+0x55 -C [libjli.so+0x3d43] JavaMain+0x93 -C [libjli.so+0x8bc8] CallJavaMainInNewThread+0x98 -C [libjli.so+0x5c81] ContinueInNewThread+0x61 -C [libjli.so+0x72da] JLI_Launch+0x144a -C [java+0x12b4] - - ---------------- P R O C E S S --------------- - -Threads class SMR info: -_java_thread_list=0x00007f401fd94a40, length=0, elements={ -} - -Java Threads: ( => current thread ) - -Other Threads: - -[error occurred during error reporting (printing all threads), id 0xb, SIGSEGV (0xb) at pc=0x00007f401f1029a4] - -VM state: not at safepoint (not fully initialized) - -VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event]) -[0x0000564d49ff71d0] Heap_lock - owner thread: 0x0000564d49ff98e0 - -Heap address: 0x0000000512000000, size: 12000 MB, Compressed Oops mode: Zero based, Oop shift amount: 3 - -CDS archive(s) mapped at: [0x0000000000000000-0x0000000000000000-0x0000000000000000), size 0, SharedBaseAddress: 0x0000000800000000, ArchiveRelocationMode: 1. -Narrow klass base: 0x0000000000000000, Narrow klass shift: 0, Narrow klass range: 0x0 - -GC Precious Log: - - -Heap: - garbage-first heap total 0K, used 0K [0x0000000512000000, 0x0000000800000000) - region size 8192K, 0 young (0K), 0 survivors (0K) - -[error occurred during error reporting (printing heap information), id 0xb, SIGSEGV (0xb) at pc=0x00007f401f6d3d1e] - -GC Heap History (0 events): -No events - -Dll operation events (1 events): -Event: 0.003 Loaded shared library /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so - -Deoptimization events (0 events): -No events - -Classes unloaded (0 events): -No events - -Classes redefined (0 events): -No events - -Internal exceptions (0 events): -No events - -VM Operations (0 events): -No events - -Events (1 events): -Event: 0.003 Protecting memory [0x00007ffd87f31000,0x00007ffd87f35000] with protection modes 0 - - -Dynamic libraries: -512000000-800000000 ---p 00000000 00:00 0 -564d497e2000-564d497e3000 r--p 00000000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -564d497e3000-564d497e4000 r-xp 00001000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -564d497e4000-564d497e5000 r--p 00002000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -564d497e5000-564d497e6000 r--p 00002000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -564d497e6000-564d497e7000 rw-p 00003000 fd:00 421172336 /usr/lib/jvm/java-17-openjdk-amd64/bin/java -564d49fbd000-564d4a049000 rw-p 00000000 00:00 0 [heap] -7f3fe9e87000-7f3fea270000 rw-p 00000000 00:00 0 -7f3fea270000-7f3fea271000 ---p 00000000 00:00 0 -7f3fea271000-7f3fea48f000 rw-p 00000000 00:00 0 -7f3fea48f000-7f40061df000 ---p 00000000 00:00 0 -7f40061df000-7f4007959000 rw-p 00000000 00:00 0 -7f4007959000-7f4007a3d000 ---p 00000000 00:00 0 -7f4007a3d000-7f4007a42000 rw-p 00000000 00:00 0 -7f4007a42000-7f4007b26000 ---p 00000000 00:00 0 -7f4007b26000-7f4007b2b000 rw-p 00000000 00:00 0 -7f4007b2b000-7f4007b36000 ---p 00000000 00:00 0 -7f4007b36000-7f4007da6000 rwxp 00000000 00:00 0 -7f4007da6000-7f400ef4d000 ---p 00000000 00:00 0 -7f400ef4d000-7f400f1bd000 rwxp 00000000 00:00 0 -7f400f1bd000-7f400f71e000 ---p 00000000 00:00 0 -7f400f71e000-7f400f98e000 rwxp 00000000 00:00 0 -7f400f98e000-7f4016b36000 ---p 00000000 00:00 0 -7f4016b36000-7f4016b42000 r--p 00000000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7f4016b42000-7f4016b55000 r-xp 0000c000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7f4016b55000-7f4016b5b000 r--p 0001f000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7f4016b5b000-7f4016b5c000 r--p 00024000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7f4016b5c000-7f4016b5d000 rw-p 00025000 fd:00 162809962 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjava.so -7f4016b5d000-7f4016b5e000 rw-p 00000000 00:00 0 -7f4016b5e000-7f4016b66000 rw-s 00000000 fd:00 16751362 /tmp/hsperfdata_mmohamed/52 -7f4016b66000-7f401e5c1000 r--s 00000000 fd:00 162809986 /usr/lib/jvm/java-17-openjdk-amd64/lib/modules -7f401e5c1000-7f401e5c3000 r--p 00000000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7f401e5c3000-7f401e5c6000 r-xp 00002000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7f401e5c6000-7f401e5c7000 r--p 00005000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7f401e5c7000-7f401e5c8000 ---p 00006000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7f401e5c8000-7f401e5c9000 r--p 00006000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7f401e5c9000-7f401e5ca000 rw-p 00007000 fd:00 162809966 /usr/lib/jvm/java-17-openjdk-amd64/lib/libjimage.so -7f401e5ca000-7f401e6ca000 rw-p 00000000 00:00 0 -7f401e6ca000-7f401e6cd000 r--p 00000000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7f401e6cd000-7f401e6e4000 r-xp 00003000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7f401e6e4000-7f401e6e8000 r--p 0001a000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7f401e6e8000-7f401e6e9000 r--p 0001d000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7f401e6e9000-7f401e6ea000 rw-p 0001e000 fd:00 162809040 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 -7f401e6ea000-7f401e6f8000 r--p 00000000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 -7f401e6f8000-7f401e774000 r-xp 0000e000 fd:00 162809067 /usr/lib/x86_64-linux-gnu/libm.so.6 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/usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7f401fff3000-7f401fff4000 ---p 00019000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7f401fff4000-7f401fff5000 r--p 00019000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7f401fff5000-7f401fff6000 rw-p 0001a000 fd:00 162809146 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11 -7f401fff8000-7f401fff9000 ---p 00000000 00:00 0 -7f401fff9000-7f401fffa000 r--p 00000000 00:00 0 -7f401fffa000-7f401fffc000 rw-p 00000000 00:00 0 -7f401fffc000-7f401fffe000 r--p 00000000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7f401fffe000-7f4020028000 r-xp 00002000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7f4020028000-7f4020033000 r--p 0002c000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7f4020033000-7f4020034000 ---p 00000000 00:00 0 -7f4020034000-7f4020036000 r--p 00037000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7f4020036000-7f4020038000 rw-p 00039000 fd:00 162808997 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 -7ffd87f31000-7ffd87f35000 ---p 00000000 00:00 0 -7ffd8870e000-7ffd88731000 rw-p 00000000 00:00 0 [stack] -7ffd887a0000-7ffd887a2000 r-xp 00000000 00:00 0 [vdso] -ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] - - -VM Arguments: -java_command: -java_class_path (initial): -Launcher Type: SUN_STANDARD - -[Global flags] - intx CICompilerCount = 15 {product} {ergonomic} - uint ConcGCThreads = 6 {product} {ergonomic} - uint G1ConcRefinementThreads = 23 {product} {ergonomic} - size_t G1HeapRegionSize = 8388608 {product} {ergonomic} - uintx GCDrainStackTargetSize = 64 {product} {ergonomic} - size_t InitialHeapSize = 788529152 {product} {ergonomic} - size_t MarkStackSize = 4194304 {product} {ergonomic} - size_t MaxHeapSize = 12582912000 {product} {ergonomic} - size_t MinHeapDeltaBytes = 8388608 {product} {ergonomic} - size_t MinHeapSize = 8388608 {product} {ergonomic} - uintx NonNMethodCodeHeapSize = 8192380 {pd product} {ergonomic} - uintx NonProfiledCodeHeapSize = 121732930 {pd product} {ergonomic} - uintx ProfiledCodeHeapSize = 121732930 {pd product} {ergonomic} - uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic} - bool SegmentedCodeCache = true {product} {ergonomic} - size_t SoftMaxHeapSize = 12582912000 {manageable} {ergonomic} - bool UseCompressedClassPointers = true {product lp64_product} {ergonomic} - bool UseCompressedOops = true {product lp64_product} {ergonomic} - bool UseG1GC = true {product} {ergonomic} - -Logging: -Log output configuration: - #0: stdout all=warning uptime,level,tags - #1: stderr all=off uptime,level,tags - -Environment Variables: -JAVA_HOME=/opt/ibm/jre -PATH=/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/rust/.cargo/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/aws-cli/v2/2.9.10/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw-agent:/opt/conda/bin:/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw-agent:/opt/conda/bin:/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc:/opt/ibm/lsfsuite/ext/ppm/10.2/bin:/opt/ibm/lsfsuite/ext/ppm/10.2/linux2.6-glibc2.3-x86_64/bin:/opt/ibm/jre/bin:/usr/lpp/mmfs/bin:/opt/thpc/bin:/rdcw/fs2/dspencer/Active/spencerlab/mohamed/apps/vscode/.vscode-server/bin/1a5daa3a0231a0fbba4f14db7ec463cf99d7768e/bin/remote-cli:/home/mmohamed/.cargo/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/rust/.cargo/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/aws-cli/v2/2.9.10/bin:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw:/storage1/fs1/dspencer/Active/spencerlab/mohamed/apps/tw-agent:/opt/conda/bin:/opt/ibm/lsfsuite/ext/ppm/10.2/bin:/opt/ibm/lsfsuite/ext/ppm/10.2/linux2.6-glibc2.3-x86_64/bin:/opt/ibm/jre/bin:/usr/lpp/mmfs/bin:/opt/thpc/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/bin:/usr/bin:/bin:/home/mmohamed/.local/bin:/home/mmohamed/bin:/bin:/usr/bin:/bin:/home/mmohamed/.local/bin:/home/mmohamed/bin -USERNAME=mmohamed -SHELL=/bin/bash -HOSTTYPE=X86_64 -LANG=en_US.UTF-8 -TERM=xterm-256color -TMPDIR=/tmp/444113.tmpdir - -Active Locale: -LC_ALL=C -LC_COLLATE=C -LC_CTYPE=C -LC_MESSAGES=C -LC_MONETARY=C -LC_NUMERIC=C -LC_TIME=C - -Signal Handlers: - SIGSEGV: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGBUS: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGFPE: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGPIPE: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked - SIGXFSZ: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked - SIGILL: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - SIGUSR2: SR_handler in libjvm.so, mask=00000000000000000000000000000000, flags=SA_RESTART|SA_SIGINFO, blocked - SIGHUP: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked - SIGINT: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked - SIGTERM: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked - SIGQUIT: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked - SIGTRAP: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked - - ---------------- S Y S T E M --------------- - -OS: -DISTRIB_ID=Ubuntu -DISTRIB_RELEASE=22.04 -DISTRIB_CODENAME=jammy -DISTRIB_DESCRIPTION="Ubuntu 22.04.3 LTS" -uname: Linux 3.10.0-1160.53.1.el7.x86_64 #1 SMP Thu Dec 16 10:19:28 UTC 2021 x86_64 -OS uptime: 256 days 7:02 hours -libc: glibc 2.35 NPTL 2.35 -rlimit (soft/hard): STACK 8192k/infinity , CORE infinity/infinity , NPROC infinity/infinity , NOFILE 1048576/1048576 , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK infinity/infinity -load average: 0.18 0.22 0.38 - -/proc/meminfo: -MemTotal: 394630832 kB -MemFree: 310974352 kB -MemAvailable: 338884188 kB -Buffers: 9160 kB -Cached: 23215108 kB -SwapCached: 34544 kB -Active: 16333648 kB -Inactive: 17659580 kB -Active(anon): 11907496 kB -Inactive(anon): 3123952 kB -Active(file): 4426152 kB -Inactive(file): 14535628 kB -Unevictable: 31457280 kB -Mlocked: 31457280 kB -SwapTotal: 1048572 kB -SwapFree: 961084 kB -Dirty: 44 kB -Writeback: 0 kB -AnonPages: 42194016 kB -Mapped: 838820 kB -Shmem: 4262488 kB -Slab: 11608664 kB -SReclaimable: 9879376 kB -SUnreclaim: 1729288 kB -KernelStack: 44464 kB -PageTables: 104852 kB -NFS_Unstable: 0 kB -Bounce: 0 kB -WritebackTmp: 0 kB -CommitLimit: 198363988 kB -Committed_AS: 55939304 kB -VmallocTotal: 34359738367 kB -VmallocUsed: 1725496 kB -VmallocChunk: 34055980748 kB -Percpu: 169984 kB -HardwareCorrupted: 0 kB -AnonHugePages: 37322752 kB -CmaTotal: 0 kB -CmaFree: 0 kB -HugePages_Total: 0 -HugePages_Free: 0 -HugePages_Rsvd: 0 -HugePages_Surp: 0 -Hugepagesize: 2048 kB -DirectMap4k: 2610860 kB -DirectMap2M: 209858560 kB -DirectMap1G: 190840832 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: 13175204K (peak: 13175204K) -Resident Set Size: 13032K (peak: 13032K) (anon: 6364K, file: 6668K, shmem: 0K) -Swapped out: 0K -C-Heap outstanding allocations: 28692K, retained: 79K -glibc malloc tunables: (default) - -/proc/sys/kernel/threads-max (system-wide limit on the number of threads): 3082856 -/proc/sys/vm/max_map_count (maximum number of memory map areas a process may have): 1048480 -/proc/sys/kernel/pid_max (system-wide limit on number of process identifiers): 262144 - -container (cgroup) information: -container_type: cgroupv1 -cpu_cpuset_cpus: 0-31 -cpu_memory_nodes: 0-3 -active_processor_count: 32 -cpu_quota: no quota -cpu_period: 100000 -cpu_shares: 24 -memory_limit_in_bytes: 49152000 k -memory_and_swap_limit_in_bytes: unlimited -memory_soft_limit_in_bytes: unlimited -memory_usage_in_bytes: 8336 k -memory_max_usage_in_bytes: 8636 k -kernel_memory_usage_in_bytes: unlimited -kernel_memory_max_usage_in_bytes: unlimited -kernel_memory_limit_in_bytes: unlimited -maximum number of tasks: unlimited -current number of tasks: 5 - -Steal ticks since vm start: 0 -Steal ticks percentage since vm start: 0.000 - -CPU: total 32 (initial active 32) (16 cores per cpu, 2 threads per core) family 6 model 85 stepping 7 microcode 0x5003103, cx8, cmov, fxsr, ht, mmx, 3dnowpref, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, lzcnt, tsc, tscinvbit, avx, avx2, aes, erms, clmul, bmi1, bmi2, rtm, adx, avx512f, avx512dq, avx512cd, avx512bw, avx512vl, fma, vzeroupper, avx512_vnni, clflush, clflushopt, clwb -CPU Model and flags from /proc/cpuinfo: -model name : Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz -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 art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single intel_ppin intel_pt ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke avx512_vnni md_clear spec_ctrl intel_stibp flush_l1d arch_capabilities - -Online cpus: 0-31 -Offline cpus: 32-255 -BIOS frequency limitation: -Frequency switch latency (ns): 4294967295 -Available cpu frequencies: -Current governor: performance -Core performance/turbo boost: - -Memory: 4k page, physical 49152000k(49143664k free), swap 1048572k(961084k free) -Page Sizes: 4k - -vm_info: OpenJDK 64-Bit Server VM (17.0.8.1+1-Ubuntu-0ubuntu122.04) for linux-amd64 JRE (17.0.8.1+1-Ubuntu-0ubuntu122.04), built on Aug 24 2023 23:23:28 by "buildd" with gcc 11.4.0 - -END.