java SigBus (0x7) doing Clustering

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java SigBus (0x7) doing Clustering

ivan
Hello,

I'm getting sometime the error of Sigbus (0x7) core dumping while I'm
computing my clusterer.
I saw it's a problem about java trying to use allocate space in /tmp and no
more spaces
But when I do : "df -h /tmp" i got this
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda2       916G   28G  841G   4% /

So I suppose I have the spaces.
And I also tried the -Xss2m option but it's like I'm getting even more of
this error.
It's starting to get really annoying when I need to rerun my clusterer, but
I didn't find the solution.

Some help would be greatly appreciated.

Regards,

--
Ivan



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Re: java SigBus (0x7) doing Clustering

Eibe Frank-2
Administrator
Does this occur when you run a clustering algorithm from WEKA? Do you have any non-Java libraries for WEKA installed (e.g., wekaPython or RPlugin)?

Which version off Java are you using? And is there any other info that comes with the Sigbus error?

Cheers,
Eibe

> On 29/11/2019, at 5:23 AM, ivan <[hidden email]> wrote:
>
> Hello,
>
> I'm getting sometime the error of Sigbus (0x7) core dumping while I'm
> computing my clusterer.
> I saw it's a problem about java trying to use allocate space in /tmp and no
> more spaces
> But when I do : "df -h /tmp" i got this
> Filesystem      Size  Used Avail Use% Mounted on
> /dev/sda2       916G   28G  841G   4% /
>
> So I suppose I have the spaces.
> And I also tried the -Xss2m option but it's like I'm getting even more of
> this error.
> It's starting to get really annoying when I need to rerun my clusterer, but
> I didn't find the solution.
>
> Some help would be greatly appreciated.
>
> Regards,
>
> --
> Ivan
>
>
>
> --
> Sent from: https://weka.8497.n7.nabble.com/
> _______________________________________________
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Re: java SigBus (0x7) doing Clustering

ivan
I'm running my own clusterering algorithm I added to weka, i don't have any
non-Java libraries for WEKA installed and I m using java 8.

I have got also this header from my hs_err_pid30516.log file, i can also
send the whole file but I'm not sure you need it all.
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGBUS (0x7) at pc=0x00007f564a894d80, pid=30516, tid=0x00007f564e03a700
#
# JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build
1.8.0_222-8u222-b10-1ubuntu1~18.04.1-b10)
# Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode linux-amd64
compressed oops)
# Problematic frame:
# C  [libzip.so+0x4d80]
#
# 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.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

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

Current thread (0x00007f564400b000):  JavaThread "main" [_thread_in_native,
id=30517, stack(0x00007f564df3b000,0x00007f564e03b000)]

siginfo: si_signo: 7 (SIGBUS), si_code: 2 (BUS_ADRERR), si_addr:
0x00007f563407df68

Registers:
RAX=0x00007f564442ce30, RBX=0x00007f5644280d50, RCX=0x00007f56440008d0,
RDX=0x00007f564442ce30
RSP=0x00007f564e0374b0, RBP=0x00007f564e037520, RSI=0x00007f56440008e8,
RDI=0x0000000000000000
R8 =0x00000000b64f6156, R9 =0x0000000000000029, R10=0x00007f5635129218,
R11=0x0000000000000029
R12=0x0000000000000f4a, R13=0x00000000b64f6156, R14=0x00007f564442ce30,
R15=0x00007f563407df4a
RIP=0x00007f564a894d80, EFLAGS=0x0000000000010202,
CSGSFS=0x002b000000000033, ERR=0x0000000000000004
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00007f564e0374b0)
0x00007f564e0374b0:   0000000034a27288 0000000000000000
0x00007f564e0374c0:   ffffffffffffffff 0000000100000000
0x00007f564e0374d0:   00007f564400b000 00007f5600000000



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Re: java SigBus (0x7) doing Clustering

Eibe Frank-3
There is some info on this error here:


Upgrading to Java 9 or later could potentially help.

Cheers,
Eibe

On Tue, Dec 3, 2019 at 8:16 AM ivan <[hidden email]> wrote:
I'm running my own clusterering algorithm I added to weka, i don't have any
non-Java libraries for WEKA installed and I m using java 8.

I have got also this header from my hs_err_pid30516.log file, i can also
send the whole file but I'm not sure you need it all.
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGBUS (0x7) at pc=0x00007f564a894d80, pid=30516, tid=0x00007f564e03a700
#
# JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build
1.8.0_222-8u222-b10-1ubuntu1~18.04.1-b10)
# Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode linux-amd64
compressed oops)
# Problematic frame:
# C  [libzip.so+0x4d80]
#
# 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.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

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

Current thread (0x00007f564400b000):  JavaThread "main" [_thread_in_native,
id=30517, stack(0x00007f564df3b000,0x00007f564e03b000)]

siginfo: si_signo: 7 (SIGBUS), si_code: 2 (BUS_ADRERR), si_addr:
0x00007f563407df68

Registers:
RAX=0x00007f564442ce30, RBX=0x00007f5644280d50, RCX=0x00007f56440008d0,
RDX=0x00007f564442ce30
RSP=0x00007f564e0374b0, RBP=0x00007f564e037520, RSI=0x00007f56440008e8,
RDI=0x0000000000000000
R8 =0x00000000b64f6156, R9 =0x0000000000000029, R10=0x00007f5635129218,
R11=0x0000000000000029
R12=0x0000000000000f4a, R13=0x00000000b64f6156, R14=0x00007f564442ce30,
R15=0x00007f563407df4a
RIP=0x00007f564a894d80, EFLAGS=0x0000000000010202,
CSGSFS=0x002b000000000033, ERR=0x0000000000000004
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00007f564e0374b0)
0x00007f564e0374b0:   0000000034a27288 0000000000000000
0x00007f564e0374c0:   ffffffffffffffff 0000000100000000
0x00007f564e0374d0:   00007f564400b000 00007f5600000000



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