Hangs or crashes on ``initing''

[GoogleCodeExporter]

For which program(s) you want a new feature?
Simulator

Which build of the program(s)?
20101210

What operating system you use?
unix64

I'm trying to simulate 100,000,000 reads of length 150. NB_MOLECULES is 
200000000.
Everything seems to work fine until ``initing'' during the Sequencing step. 
Sometimes Flux hangs, and sometimes Java crashes (log in attachment).
I tried with a smaller number of reads and molecules to be simulated and it 
does not work either.

I attach one log from the JRE and my PAR file.

Original issue reported on code.google.com by mikael.s...@gmail.com on 7 Apr 2011 at 3:56

Attachments:

• hs_err_pid14267.log
• projet.150bp.par

[GoogleCodeExporter]

I tried to reproduce the problem, but unfortunately I was not able to get the 
JVM to crash.

The problem is that from the stacktrace I figured the problem occurs on

JRE version: 6.0_17-b17
# Java VM: OpenJDK 64-Bit Server VM (14.0-b16 mixed mode linux-amd64 )
# Derivative: IcedTea6 1.7.5
# Distribution: Custom build (Wed Oct 13 13:04:40 EDT 2010)

I was not able to quickly get my hand on exactly that Java version, but I tried 
with both, the SUN JVM

java version "1.6.0_24"
Java(TM) SE Runtime Environment (build 1.6.0_24-b07)
Java HotSpot(TM) Server VM (build 19.1-b02, mixed mode)
JRE version: 6.0_17-b17

and the current OpenJDK release:

java version "1.6.0_20"
OpenJDK Runtime Environment (IcedTea6 1.9.7) (6b20-1.9.7-0ubuntu1)
OpenJDK Server VM (build 19.0-b09, mixed mode)

The Flux Simulator is developed using the Sun JDK, and I suggest you switch 
from OpenJDK to Sun JDK/JRE. If the problem still occurs, I can take a more 
deeper look.

Original comment by thasso.g...@gmail.com on 15 Apr 2011 at 12:34

• Changed state: Unconfirmed
• Added labels: Simulator

[GoogleCodeExporter]

In fact I tried with both Sun JDK and Open JDK. Apparently Java crashes with 
Open JDK while the program hangs with Sun JDK.

When it hangs, ``initing'' is written on the output, but then the process 
doesn't do anything (it takes 0% of the CPU).

Original comment by mikael.s...@gmail.com on 17 Apr 2011 at 5:45

[GoogleCodeExporter]

I ran across the same problem. Also tried both Open JDK and Sun JDK, in both 
versions the program hangs after "initing".

It turned out to be problem with 64 bit Linux, at least for me. I tested 
FluxSimulator on different machines mostly 64 bit OS without much success (with 
really small number of reads and library sizes I did succeed occasionally).

However, on 32bit Linux I was able to run sequencing without problems. (it did 
hang once when I used .pro and .lib files generated on 64bit system - just a 
tip for developers)

Original comment by peter.gl...@gmail.com on 19 May 2011 at 4:00

[GoogleCodeExporter]

It has always been my problem when running flexsimulator: program hangs at 
random spot  at 'initing' step, no matter which version of flexsimulator I use.

will try 32-bit OS

Original comment by xyli...@gmail.com on 11 Jun 2011 at 11:47

[GoogleCodeExporter]

We uploaded a largely redesigned simulator version (1.0 RC1), which also 
excludes parallelization that seemed to cause JVM/OS-dependent crashes or 
deadlocks. I will try to update the webpages with new documentation ASAP, for 
the moment please refer to the readme file bundled in the tarball. Also, 
additional logging depth is provided by the --log DEBUG parameter, please post 
a corresponding stderr output if the problem persists for you. 

Issue remains open until confirmed to have disappeared in v1.0 RC1.

Original comment by gmicha@gmail.com on 17 Jun 2011 at 1:35

[GoogleCodeExporter]

No more comment on the topic since more than 6 weeks, closing issue.

Original comment by gmicha@gmail.com on 1 Sep 2011 at 12:57

• Changed state: Fixed