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What do I need to do to get Jira running? Here is the error log

Dawn Stencil

#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGBUS (0x7) at pc=0x00007f35d14c5b70, pid=7766, tid=139868609865472
#
# JRE version: Java(TM) SE Runtime Environment (8.0_11-b12) (build 1.8.0_11-b12)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.11-b03 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V [libjvm.so+0x785b70] _Copy_arrayof_conjoint_jlongs+0x30
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
# http://bugreport.sun.com/bugreport/crash.jsp
#

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

Current thread (0x00007f3574002000): JavaThread "localhost-startStop-1" daemon [_thread_in_vm, id=7812, stack(0x00007f35b2be6000,0x00007f35b2ce7000)]

siginfo:si_signo=SIGBUS: si_errno=0, si_code=2 (BUS_ADRERR), si_addr=0x00007f35a4090000

Registers:
RAX=0x00007f35a4090020, RBX=0x00007f3574002000, RCX=0x00000000f40e60a0, RDX=0xffffffffffffffff
RSP=0x00007f35b2ce3ed8, RBP=0x00007f35b2ce3f30, RSI=0x00000000f40e6080, RDI=0x00007f35a4090000
R8 =0x00007f35b2ce4010, R9 =0x0000000000000010, R10=0x00007f35bc7b46a2, R11=0x00007f35d1677300
R12=0x0000000000000000, R13=0x00007f35b2ce4010, R14=0x0000000000000010, R15=0x00007f35a4090000
RIP=0x00007f35d14c5b70, EFLAGS=0x0000000000010286, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00007f35b2ce3ed8)
0x00007f35b2ce3ed8: 00007f35d1747c6a 00007f3574002000
0x00007f35b2ce3ee8: 0000000000000004 00007f3574002000
0x00007f35b2ce3ef8: 00007f35d156917c 00000000000003d8
0x00007f35b2ce3f08: 00007f35b9bd0968 0000000000000000
0x00007f35b2ce3f18: 00007f35b9bd0968 00007f35b2ce4030
0x00007f35b2ce3f28: 00007f3574002000 00007f35b2ce3fd0
0x00007f35b2ce3f38: 00007f35bc7b46ce 0000000000000028
0x00007f35b2ce3f48: 00007f35d15693be 00007f35b2ce4158
0x00007f35b2ce3f58: 00007f3574001480 00007f35b9c95218
0x00007f35b2ce3f68: 00007f35cc02a950 00007f3574002000
0x00007f35b2ce3f78: 00007f3574002000 00007f35b2ce3fa0
0x00007f35b2ce3f88: 00007f35d157a441 00007f35b2ce3f90
0x00007f35b2ce3f98: 0000000000000000 00007f35b2ce4030
0x00007f35b2ce3fa8: 00007f35b9bea4e8 0000000000000000
0x00007f35b2ce3fb8: 00007f35b9bd0968 0000000000000000
0x00007f35b2ce3fc8: 00007f35b2ce3ff0 00007f35b2ce4078
0x00007f35b2ce3fd8: 00007f35bc7a72e0 0000000000000000
0x00007f35b2ce3fe8: 00007f35bc7aec18 0000000000000028
0x00007f35b2ce3ff8: 00007f35d15693be 0000000000000010
0x00007f35b2ce4008: 00007f3574001480 00000000f40e6070
0x00007f35b2ce4018: 00007f35a4090000 00007f35b2ce4078
0x00007f35b2ce4028: 0000000000000000 00000000d00d0e80
0x00007f35b2ce4038: 00007f35b2ce4038 00007f35b9c951fa
0x00007f35b2ce4048: 00007f35b2ce40e8 00007f35b9c95a30
0x00007f35b2ce4058: 0000000000000000 00007f35b9c95218
0x00007f35b2ce4068: 00007f35b2ce3ff0 00007f35b2ce40a8
0x00007f35b2ce4078: 00007f35b2ce4130 00007f35bc7a72e0
0x00007f35b2ce4088: 0000000000000028 0000000000000000
0x00007f35b2ce4098: 0000000000000010 0000000000000000
0x00007f35b2ce40a8: 0000000000000028 0000000000000028
0x00007f35b2ce40b8: 0000000000000000 0000000000000000
0x00007f35b2ce40c8: 0000000000000010 00007f35b2ce4130

Instructions: (pc=0x00007f35d14c5b70)
0x00007f35d14c5b50: 00 00 00 48 8d 4c d6 f8 48 f7 da eb 39 48 8b 74
0x00007f35d14c5b60: d0 08 48 89 74 d1 08 48 83 c2 01 75 f0 c3 66 90
0x00007f35d14c5b70: 48 8b 74 d0 e8 48 89 74 d1 e8 48 8b 74 d0 f0 48
0x00007f35d14c5b80: 89 74 d1 f0 48 8b 74 d0 f8 48 89 74 d1 f8 48 8b

RAX=0x00007f35a4090020 is an unknown value
RBX=0x00007f3574002000 is a thread
RCX=0x00000000f40e60a0 is an oop

Accepted answers

All comments

Nic Brough -Adaptavist-

There's something wrong at an OS level if it can't write core dumps, and that error is probably masking the real one.

Can you try doing what it suggests? Use the ulimit setting so that it can write a core dump, and hence show us the actual error?

Dawn Stencil

A fatal error has been detected by the Java Runtime Environment:
#
# SIGBUS (0x7) at pc=0x00007f40a8405b70, pid=10665, tid=139915031504640
#
# JRE version: Java(TM) SE Runtime Environment (8.0_11-b12) (build 1.8.0_11-b12)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.11-b03 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V [libjvm.so+0x785b70] _Copy_arrayof_conjoint_jlongs+0x30
#
# Core dump written. Default location: /opt/atlassian/jira/bin/core or core.10665
#
# If you would like to submit a bug report, please visit:
# http://bugreport.sun.com/bugreport/crash.jsp
#

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

Current thread (0x00007f4044002000): JavaThread "localhost-startStop-1" daemon [_thread_in_vm, id=10711, stack(0x00007f4081b06000,0x00007f4081c07000)]

siginfo:si_signo=SIGBUS: si_errno=0, si_code=2 (BUS_ADRERR), si_addr=0x00007f3fcd7d8000

Registers:
RAX=0x00007f3fcd7d8020, RBX=0x00007f4044002000, RCX=0x00000000f906a5f0, RDX=0xffffffffffffffff
RSP=0x00007f4081c04018, RBP=0x00007f4081c04070, RSI=0x00000000f906a5d0, RDI=0x00007f3fcd7d8000
R8 =0x00007f4081c04150, R9 =0x0000000000000010, R10=0x00007f40910146a2, R11=0x00007f40a85b7300
R12=0x0000000000000000, R13=0x00007f4081c04150, R14=0x0000000000000010, R15=0x00007f3fcd7d8000
RIP=0x00007f40a8405b70, EFLAGS=0x0000000000010286, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00007f4081c04018)
0x00007f4081c04018: 00007f40a8687c6a 00007f4044002000
0x00007f4081c04028: 0000000000000004 00007f4044002000
0x00007f4081c04038: 00007f40a84a917c 00000000000003d8
0x00007f4081c04048: 00007f4090876968 0000000000000000
0x00007f4081c04058: 00007f4090876968 00007f4081c04170
0x00007f4081c04068: 00007f4044002000 00007f4081c04110
0x00007f4081c04078: 00007f40910146ce 0000000000000028
0x00007f4081c04088: 00007f40a84a93be 00007f4081c04298
0x00007f4081c04098: 00007f4044001480 00007f409093b218
0x00007f4081c040a8: 00007f40a002a950 00007f4044002000
0x00007f4081c040b8: 00007f4044002000 00007f4081c040e0
0x00007f4081c040c8: 00007f40a84ba441 00007f4081c040d0
0x00007f4081c040d8: 0000000000000000 00007f4081c04170
0x00007f4081c040e8: 00007f40908904e8 0000000000000000
0x00007f4081c040f8: 00007f4090876968 0000000000000000
0x00007f4081c04108: 00007f4081c04130 00007f4081c041b8
0x00007f4081c04118: 00007f40910072e0 0000000000000000
0x00007f4081c04128: 00007f409100ec18 0000000000000028
0x00007f4081c04138: 00007f40a84a93be 0000000000000010
0x00007f4081c04148: 00007f4044001480 00000000f906a5c0
0x00007f4081c04158: 00007f3fcd7d8000 00007f4081c041b8
0x00007f4081c04168: 0000000000000000 00000000d00e2670
0x00007f4081c04178: 00007f4081c04178 00007f409093b1fa
0x00007f4081c04188: 00007f4081c04228 00007f409093ba30
0x00007f4081c04198: 0000000000000000 00007f409093b218
0x00007f4081c041a8: 00007f4081c04130 00007f4081c041e8
0x00007f4081c041b8: 00007f4081c04270 00007f40910072e0
0x00007f4081c041c8: 0000000000000028 0000000000000000
0x00007f4081c041d8: 0000000000000010 0000000000000000
0x00007f4081c041e8: 0000000000000028 0000000000000028
0x00007f4081c041f8: 0000000000000000 0000000000000000
0x00007f4081c04208: 0000000000000010 00007f4081c04270

Instructions: (pc=0x00007f40a8405b70)
0x00007f40a8405b50: 00 00 00 48 8d 4c d6 f8 48 f7 da eb 39 48 8b 74
0x00007f40a8405b60: d0 08 48 89 74 d1 08 48 83 c2 01 75 f0 c3 66 90
0x00007f40a8405b70: 48 8b 74 d0 e8 48 89 74 d1 e8 48 8b 74 d0 f0 48
0x00007f40a8405b80: 89 74 d1 f0 48 8b 74 d0 f8 48 89 74 d1 f8 48 8b

RAX=0x00007f3fcd7d8020 is an unknown value
RBX=0x00007f4044002000 is a thread
RCX=0x00000000f906a5f0 is an oop

Nic Brough -Adaptavist-

Ok, with the core-dump problem returning the same message, that tells me it's not that particular problem.

What you are seeing tends to happen when there is a memory error, and about 90% of the times these happen, the error is either that there is not enough for the process to run properly, or the OS is struggling with memory.

Could you tell us how much physical memory is available on the machine, and what the maximum is for the Java process running Jira?

In case you're not a system admin, and I apologise if I am "trying to teach you to suck eggs", because I don't know:

By "physical memory", I mean "what would the server tell you if you asked it how much memory it has" (one of my Atlassian servers reports 4Gb because it has 4 1Gb memory sticks in a box the cat sleeps on because it is warm, and the other says it has 2Gb because that's what I granted the virtual machine it runs on).
The maximum heap size for a java process is set by the -Xmx parameter. If Jira is running "ps -ef" will expose that. If it won't start at all, then look at <jira install>/bin/setenv.sh - it should try to set -Xmx in there

Dawn Stencil

There are 16GB of memory on the system. About 13.5 of which are in use. The vast majority that is in use is being used by Confluence and BitBucket. The xmx value was set at around 700mb and we since changed it to 2gb in case it wasn't enough to start it, but nothing changed.

Nic Brough -Adaptavist-

Ok, so how much memory does the process appear to consume? The ps -ef while it runs before failing?

Dawn Stencil

I was misreading the in use memory as it included the cache. In reality there about 12GB of unused memory. I don't think it has to do with running out of memory. We have reinstalled the software and it is still giving the same error.

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