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First let me preface this by stating that I'm pretty new to MATLAB and Linux, perhaps I'm missing something obvious, if that's the case please be patient with me.
I've been asked to help with a modeling project in my math department, so I've downloaded all the code, installed matlab on my computer, and after jumping through some hoops (had to install a library called "glu") the script itself actually runs. It gets to a point where I believe it's trying to render a plot where it crashes the system, I can't access other ttys with ctrl-alt-F(anything) and after a bit I get a blinking cursor in the top right, still unable to do anything, ctrl-alt-delete, nothing. So I hold the powerbutton down and shut down the computer.
I've found the crash dumps, and quite a few of them are just empty, some do have some info, here is "matlab_crash_dump.4121-1":
------------------------------------------------------------------------
Assertion detected at Sun Sep 18 17:13:44 2016
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Crash Mode : continue (default)
Current Graphics Driver: Intel Open Source Technology Center Mesa DRI Intel(R) Sandybridge Mobile Version 3.0 Mesa 11.0.6
Current Visual : 0x47 (class 4, depth 24)
Default Encoding : UTF-8
GNU C Library : 2.22 stable
Host Name : q
Java Crash Report : /home/d/hs_error_pid4121.log
Java Log : /home/d/java.log.4121
MATLAB Architecture : glnxa64
MATLAB Root : /usr/local/MATLAB/R2016a
MATLAB Version : 9.0.0.341360 (R2016a)
OpenGL : hardware
Operating System : Linux 4.4.6-gentoo #6 SMP Sun Sep 18 16:32:36 MDT 2016 x86_64
Processor ID : x86 Family 6 Model 42 Stepping 7, GenuineIntel
Virtual Machine : Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : The X.Org Foundation (11704000), display :0
Fault Count: 1
Assertion in void {anonymous}::mwJavaAbort() at javainit.cpp line 1389:
Fatal Java Exception. See Java Crash Report for details.
Register State (captured):
RAX = 00007f22a75e21e0 RBX = 00007f2329790878
RCX = 0000000000000000 RDX = 00007f2329770c20
RSP = 00007f22a75e2100 RBP = 00007f22a75e24c0
RSI = 00007f23295273b8 RDI = 00007f22a75e2110
R8 = 0000000000000000 R9 = 00007f230ec258e0
R10 = 0000000000000000 R11 = 000000000000000f
R12 = 00007f230ec251bb R13 = 00007f230ec258e0
R14 = 00007f23297807e8 R15 = 00007f22a75e2d30
RIP = 00007f232949459e EFL = 00007f232fa03500
CS = f0b8 FS = 2939 GS = 7f23
Stack Trace (captured):
[ 0] 0x00007f232949459e /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01082782 _ZN2fl4diag5linux6x86_6412context_base12capture_dataEv+00000030
[ 1] 0x00007f2329490541 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01066305
[ 2] 0x00007f2329491bd0 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01072080
[ 3] 0x00007f2329491c42 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01072194
[ 4] 0x00007f230ebe675a /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01099610
[ 5] 0x00007f230d8298bb /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+08513723
[ 6] 0x00007f230d6599f2 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06613490
[ 7] 0x00007f21f308ac02 /usr/local/MATLAB/R2016a/bin/glnxa64/libnativewindow_x11.so+00011266 NativewindowCommon_FatalError+00000268
[ 8] 0x00007f21f308b95a /usr/local/MATLAB/R2016a/bin/glnxa64/libnativewindow_x11.so+00014682
[ 9] 0x00007f232275edde /usr/lib64/libX11.so.6+00282078 _XIOError+00000078
[ 10] 0x00007f232275cebb /usr/lib64/libX11.so.6+00274107 _XReply+00001019
[ 11] 0x00007f2322743cb7 /usr/lib64/libX11.so.6+00171191 _XGetWindowAttributes+00000183
[ 12] 0x00007f2322743e31 /usr/lib64/libX11.so.6+00171569 XGetWindowAttributes+00000049
[ 13] 0x00007f22e16a3c44 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/xawt/libmawt.so+00109636
[ 14] 0x00007f22e19112f6 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/libawt.so+00209654 Java_sun_java2d_loops_Blit_Blit+00000534
[ 15] 0x00007f22fd012d98 <unknown-module>+00000000
[ 16] 0x00007f22fd006058 <unknown-module>+00000000
[ 17] 0x00007f22fd006058 <unknown-module>+00000000
[ 18] 0x00007f22fd006350 <unknown-module>+00000000
[ 19] 0x00007f22fd006350 <unknown-module>+00000000
[ 20] 0x00007f22fd0069fe <unknown-module>+00000000
[ 21] 0x00007f22fd0069fe <unknown-module>+00000000
[ 22] 0x00007f22fd006350 <unknown-module>+00000000
[ 23] 0x00007f22fd006350 <unknown-module>+00000000
[ 24] 0x00007f22fd006350 <unknown-module>+00000000
[ 25] 0x00007f22fd006706 <unknown-module>+00000000
[ 26] 0x00007f22fd006058 <unknown-module>+00000000
[ 27] 0x00007f22fd006058 <unknown-module>+00000000
[ 28] 0x00007f22fd006058 <unknown-module>+00000000
[ 29] 0x00007f22fd006058 <unknown-module>+00000000
[ 30] 0x00007f22fd006058 <unknown-module>+00000000
[ 31] 0x00007f22fd006058 <unknown-module>+00000000
[ 32] 0x00007f22fd006058 <unknown-module>+00000000
[ 33] 0x00007f22fd006058 <unknown-module>+00000000
[ 34] 0x00007f22fd006058 <unknown-module>+00000000
[ 35] 0x00007f22fd006058 <unknown-module>+00000000
[ 36] 0x00007f22fd006058 <unknown-module>+00000000
[ 37] 0x00007f22fd006058 <unknown-module>+00000000
[ 38] 0x00007f22fd006058 <unknown-module>+00000000
[ 39] 0x00007f22fd006058 <unknown-module>+00000000
[ 40] 0x00007f22fd006058 <unknown-module>+00000000
[ 41] 0x00007f22fd006706 <unknown-module>+00000000
[ 42] 0x00007f22fd006058 <unknown-module>+00000000
[ 43] 0x00007f22fd006058 <unknown-module>+00000000
[ 44] 0x00007f22fd006058 <unknown-module>+00000000
[ 45] 0x00007f22fd006058 <unknown-module>+00000000
[ 46] 0x00007f22fd006058 <unknown-module>+00000000
[ 47] 0x00007f22fd006058 <unknown-module>+00000000
[ 48] 0x00007f22fd006233 <unknown-module>+00000000
[ 49] 0x00007f22fd0004e7 <unknown-module>+00000000
[ 50] 0x00007f230d60a8f5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653
[ 51] 0x00007f230d609358 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120
[ 52] 0x00007f230d68fc74 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06835316 JVM_DoPrivileged+00000676
[ 53] 0x00007f22fd012d98 <unknown-module>+00000000
[ 54] 0x00007f22fd006233 <unknown-module>+00000000
[ 55] 0x00007f22fd006233 <unknown-module>+00000000
[ 56] 0x00007f22fd0068e1 <unknown-module>+00000000
[ 57] 0x00007f22fd006233 <unknown-module>+00000000
[ 58] 0x00007f22fd0004e7 <unknown-module>+00000000
[ 59] 0x00007f230d60a8f5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653
[ 60] 0x00007f230d609358 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120
[ 61] 0x00007f230d68fc74 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06835316 JVM_DoPrivileged+00000676
[ 62] 0x00007f22fd012d98 <unknown-module>+00000000
[ 63] 0x00007f22fd006233 <unknown-module>+00000000
[ 64] 0x00007f22fd0068e1 <unknown-module>+00000000
[ 65] 0x00007f22fd006058 <unknown-module>+00000000
[ 66] 0x00007f22fd006058 <unknown-module>+00000000
[ 67] 0x00007f22fd006058 <unknown-module>+00000000
[ 68] 0x00007f22fd006058 <unknown-module>+00000000
[ 69] 0x00007f22fd006058 <unknown-module>+00000000
[ 70] 0x00007f22fd006058 <unknown-module>+00000000
[ 71] 0x00007f22fd0004e7 <unknown-module>+00000000
[ 72] 0x00007f230d60a8f5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653
[ 73] 0x00007f230d609358 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120
[ 74] 0x00007f230d609627 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284839
[ 75] 0x00007f230d609747 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06285127
[ 76] 0x00007f230d6861d5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06795733
[ 77] 0x00007f230d963bdf /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+09800671
[ 78] 0x00007f230d963ce5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+09800933
[ 79] 0x00007f230d82a7f8 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+08517624
[ 80] 0x00007f232d73d494 /lib64/libpthread.so.0+00029844
[ 81] 0x00007f232d4825dd /lib64/libc.so.6+00955869 clone+00000109
[ 82] 0x0000000000000000 <unknown-module>+00000000
If this problem is reproducible, please submit a Service Request via:
http://www.mathworks.com/support/contact_us/
A technical support engineer might contact you with further information.
Thank you for your help.
and here is the corresponding "java.log.4121"
Operating System: Linux 4.4.6-gentoo #6 SMP Sun Sep 18 16:32:36 MDT 2016 x86_64
Processor ID: x86 Family 6 Model 42 Stepping 7, GenuineIntel
Host Name: q
FATAL ERROR in native method: Nativewindow X11 IOError: Display 0x7f230b054450 (:0): Resource temporarily unavailable
at sun.java2d.loops.Blit.Blit(Native Method)
at sun.java2d.pipe.DrawImage.blitSurfaceData(Unknown Source)
at sun.java2d.pipe.DrawImage.renderImageCopy(Unknown Source)
at sun.java2d.pipe.DrawImage.copyImage(Unknown Source)
at sun.java2d.pipe.DrawImage.copyImage(Unknown Source)
at sun.java2d.pipe.ValidatePipe.copyImage(Unknown Source)
at sun.java2d.SunGraphics2D.copyImage(Unknown Source)
at sun.java2d.SunGraphics2D.drawImage(Unknown Source)
at sun.java2d.SunGraphics2D.drawImage(Unknown Source)
at com.jogamp.opengl.awt.GLJPanel$OffscreenBackend.doPaintComponent(GLJPanel.java:2101)
at com.jogamp.opengl.awt.GLJPanel.paintComponent(GLJPanel.java:568)
at com.mathworks.hg.peer.JavaSceneServerGLJPanel.paintComponent(JavaSceneServerGLJPanel.java:147)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
- locked <0x00000000e81d1210> (a java.awt.Component$AWTTreeLock)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
- locked <0x00000000e81d1210> (a java.awt.Component$AWTTreeLock)
at javax.swing.JComponent.paint(Unknown Source)
at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source)
at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source)
at sun.awt.SunGraphicsCallback.runComponents(Unknown Source)
at java.awt.Container.paint(Unknown Source)
at java.awt.Window.paint(Unknown Source)
at sun.awt.RepaintArea.paintComponent(Unknown Source)
at sun.awt.X11.XRepaintArea.paintComponent(Unknown Source)
at sun.awt.RepaintArea.paint(Unknown Source)
at sun.awt.X11.XComponentPeer.handleEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$200(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
At this point I'm pretty sure its a graphics problem, I've tried opengl software rendering as well. The director of the project suggested that there could be a problem with the kernel since it's taking out my whole system, at this point he wants me to switch to a different environment so that we can just move on, though I would still like to know whats going on with gentoo here.
One thing I was thinking about was I don't have a DE, just a tiling WM (awesome 3.5), I don't know if this would cause a problem, just a thought
Here's what I'm working with:
Matlab2016a
Awesome 3.5
gentoo-4.4.6
intel 2760M
Quadro 2000M (I don't think it's using this)
20GB RAM
Along with whatever the standard drivers are for these parts
Let me know if there's anything else you need.
uvsvdu
Posted 2016-09-19T19:29:03.553
Reputation: 1
This problem more then likely, is caused by Matlab, attempting to use the iGPU instead of your Quadro 2000M. – Ramhound – 2016-09-19T19:33:04.637
Do you think that the system is expecting it to use the Quadro? How can I tell matlab to do that instead? I'm not actually sure but I think the default for the system is the iGPU, thought I'm not sure how to check. – uvsvdu – 2016-09-19T19:48:48.430
I am thinking Matlab is doing something the iGPU isn't compatable of actually doing. I don't know linux enough to tell you how to force Matlab to use the Quadro GPU instead. – Ramhound – 2016-09-19T19:50:44.360
I just told matlab to plot sin(x) from 0 to pi and it handled that just fine. Wondering if there's something going on with java instead. – uvsvdu – 2016-09-19T19:52:34.860
I am not sure what plotting 0 to pi proves, iGPU will be fine for some things, the script that isn't working isn't as simple I gather. – Ramhound – 2016-09-19T19:54:36.653
Oh, alright. Like I said, I'm new to this :). Is there a way to test to see if it's for sure the iGPU that's not handling it that you know of? Thanks for your help :) – uvsvdu – 2016-09-19T20:09:41.767