Question: IGB is consistently crashing and I can't understand why
1
gravatar for Daniel
3.7 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

IGB has previously worked on my ubuntu 15.04 desktop, but within the last week it will load a genome from the default options, but die upon trying to load another track. Sometimes it will just crash during the time between loading the genome and doing anything else. I've tried with bed, gff3 and wig files. It appears that it has loaded the file from the log, but then crashes with the following error:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f3de2676714, pid=12777, tid=139903480776448
#
# JRE version: OpenJDK Runtime Environment (8.0_45-b14) (build 1.8.0_45-internal-b14)
# Java VM: OpenJDK 64-Bit Server VM (25.45-b02 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libawt_xawt.so+0x45714]
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/sbi6dap/Local/IGB/hs_err_pid12777.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
#

My java is 1.8 as is required (see above).

Has anyone else had this difficulty?

 

Edit: I've tried increasing the allocated ram with the '-Xmx4g' option in the .vmoptions file, but also turned it back to -'Xmx1280m' in consideration of 32bit limits (although I am running 64). My machine has 32gb available.

igb software • 1.3k views
ADD COMMENTlink modified 3.7 years ago by dcnorris270 • written 3.7 years ago by Daniel3.7k
4
gravatar for dcnorris
3.7 years ago by
dcnorris270
United States
dcnorris270 wrote:

Hi Daniel,

I'm very sorry to hear you are dealing with this bug.  This is a problem specific to some Ubuntu versions which we have now resolved on our development branch.  It is possible to work around this bug by dragging and dropping files to open them instead of using the normal "open file" action; however, we will be releasing an updated version of IGB very soon (early next week time frame) with a patch.  

 

ADD COMMENTlink written 3.7 years ago by dcnorris270

I can confirm that this was the problem, tracks are loaded if I drag the files into the window. What a strange bug! Thank you for the information, I only wish I could have found out sooner!

ADD REPLYlink written 3.7 years ago by Daniel3.7k
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