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Old 10-25-2013, 10:44 AM   #1
RenéPaul
LQ Newbie
 
Registered: Oct 2013
Posts: 3

Rep: Reputation: Disabled
A fatal error has been detected by the Java Runtime Environment


Hello all,

I am facing the following problem:

I've installed the last Gephi release (Gephi 0.8.2-beta) for linux, which is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs (http://http://gephi.org/).

The Gephi documentation specifies that OpenJDK is not supported, Sun JDK is required. In addition, OPENGL is required.

My system is the following:

Distribution: Fedora 19 (i686) (32 bits)
Cinnamon 1.9.2
Kernel: 3-11-3_201.fc19.i686.PAE/# 1

Laptop: HP Pavillon dv6000
Processor: Intel Core 2 CPU T5500 1.66 GH
Memory: 2 GB
Graphic card: NVIDIA G72M GeForce Go 7400

My laptop is on dual boot Windows Vista Home on which I have no problem with Gephi. It's only under Fedora 19 Linux distribution that I have a problem.

On Fedora, I hope I have correctly installed java as shown here:

[rene@localhost bin]$ alternatives --config java

Il existe 3 programmes qui fournissent « java ».

Sélection Commande
-----------------------------------------------
* 1 /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.60-2.4.2.7.fc19.i386/jre/bin/java
2 /usr/java/jdk1.7.0_40/jre/bin/java
+ 3 /usr/java/jdk1.7.0_45/jre/bin/java

I use the two following commands to run Gephi:

cd /gephi/bin
LIBGL_DEBUG=verbose ./gephi &

I get the following log:

Loading native libraries
libGL: OpenDriver: trying /usr/lib/dri/tls/nouveau_dri.so
libGL: OpenDriver: trying /usr/lib/dri/nouveau_dri.so
Current Version is 082
libGL: OpenDriver: trying /usr/lib/dri/tls/nouveau_dri.so
libGL: OpenDriver: trying /usr/lib/dri/nouveau_dri.so
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x69dcf2f5, pid=11187, tid=1804266304
#
# JRE version: Java(TM) SE Runtime Environment (7.0_45-b18) (build 1.7.0_45-b18)
# Java VM: Java HotSpot(TM) Server VM (24.45-b08 mixed mode linux-x86 )
# Problematic frame:
# C [nouveau_dri.so+0x4222f5] nouveau_resource_map_offset+0x15
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#

In this forum, I found a thread very closed to my problem: "Getting 3D Acceleration working on Intel 82865G, no xorg.conf" (03-09-10, 03:46 AM)

I followed this thread without succeeding to fix my problem:

[rene@localhost ~]$ glxinfo | grep -i "direct rendering"
direct rendering: Yes
[rene@localhost ~]$ glxinfo | grep -i "renderer"
OpenGL renderer string: Gallium 0.4 on NV46
[rene@localhost ~]$ glxgears
Running synchronized to the vertical refresh. The framerate should be
approximately the same as the monitor refresh rate.
1199 frames in 5.0 seconds = 239.582 FPS
XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":0"
after 3927 requests (3927 known processed) with 0 events remaining.
[rene@localhost ~]$ glxgears
Running synchronized to the vertical refresh. The framerate should be
approximately the same as the monitor refresh rate.
1272 frames in 5.0 seconds = 254.058 FPS
1282 frames in 5.0 seconds = 256.177 FPS
1277 frames in 5.0 seconds = 255.102 FPS
1280 frames in 5.0 seconds = 255.963 FPS

LIBGL_DEBUG=verbose glxinfo
name of display: :0
libGL: OpenDriver: trying /usr/lib/dri/tls/nouveau_dri.so
libGL: OpenDriver: trying /usr/lib/dri/nouveau_dri.so
display: :0 screen: 0
direct rendering: Yes
server glx vendor string: SGI
server glx version string: 1.4
server glx extensions:
GLX_ARB_create_context, GLX_ARB_create_context_profile,
GLX_ARB_multisample, GLX_EXT_create_context_es2_profile,
GLX_EXT_import_context, GLX_EXT_texture_from_pixmap, GLX_EXT_visual_info,
GLX_EXT_visual_rating, GLX_INTEL_swap_event, GLX_MESA_copy_sub_buffer,
GLX_OML_swap_method, GLX_SGIS_multisample, GLX_SGIX_fbconfig,
GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group, GLX_SGI_swap_control
client glx vendor string: Mesa Project and SGI
client glx version string: 1.4

Could someone help me in solving this problem?

Many thanks in advance for your attention and your help.

René
 
Old 10-25-2013, 03:59 PM   #2
John VV
LQ Muse
 
Registered: Aug 2005
Location: A2 area Mi.
Posts: 17,623

Rep: Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651
Fedora 19
well you ARE going to have some problems
OpenJDK IS installed and USED by default

you can install Oracles Java1.7 ( there is NO sun java any longer )
and set "alternatives" to use Oracles java

right now you do not have oracles java installed , you only have openjdk

you might want to have a look at Mjmwired's quick guide page
-- for java--
http://www.mjmwired.net/resources/mj...-f19.html#java
 
Old 10-25-2013, 05:04 PM   #3
RenéPaul
LQ Newbie
 
Registered: Oct 2013
Posts: 3

Original Poster
Rep: Reputation: Disabled
Many thanks John VV for having taken time to study my post and for your help.

In my post, I mentioned that after having downloaded jdk1.7.0_45 and installed it (using alternatives -install not mentioned in my post) I swaped from OpenJDK to Sun Jdk using the "alternatives --config java" command. According to what you say I should have done something wrong.

Here is what I obtained from "alternatives --config java":

[root@localhost ~]# alternatives --config java

Il existe 3 programmes qui fournissent « java ».

Sélection Commande
-----------------------------------------------
* 1 /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.60-2.4.2.7.fc19.i386/jre/bin/java
2 /usr/java/jdk1.7.0_40/jre/bin/java
+ 3 /usr/java/jdk1.7.0_45/jre/bin/java

Entrez pour garder la sélection courante [+] ou saisissez le numéro de type de sélection :

You may note that I chose the 3rd option: /usr/java/jdk1.7.0_45/jre/bin/java

What's wrong in what did?

Following your suggestion, I'll take a deep look at Mjmwired's quick guide page -- for java--

I'll keep you informed of the followup.

Many thanks and good night.

René
 
  


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