Segmentation violation on Docker using MCR

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Alessandro Aglietti
Alessandro Aglietti on 26 Jun 2017
Answered: Alessandro Aglietti on 26 Jun 2017
Hi there. I'm trying to run two function exported via Matlab Compiler in a Java application running inside a Docker container.
The installation of MCR inside the container is successful:
Step 37/67 : RUN ./install -destinationFolder /opt/mcr -agreeToLicense yes -mode silent
---> Running in 382605e4e0ac
Preparing installation files ...
Installing ...
(Jun 26, 2017 08:32:51) ##################################################################
(Jun 26, 2017 08:32:51) #
(Jun 26, 2017 08:32:51) # Today's Date:
(Jun 26, 2017 08:32:51) Mon Jun 26 08:32:51 UTC 2017
(Jun 26, 2017 08:32:51)
(Jun 26, 2017 08:32:51) System Info
(Jun 26, 2017 08:32:51) OS: Linux 4.4.0-81-generic
(Jun 26, 2017 08:32:51) Arch: amd64
(Jun 26, 2017 08:32:51) Data Model: 64
(Jun 26, 2017 08:32:51) Language: en
(Jun 26, 2017 08:32:51) Java Vendor: Oracle Corporation
(Jun 26, 2017 08:32:51) Java Home: /tmp/mathworks_5/sys/java/jre/glnxa64/jre
(Jun 26, 2017 08:32:51) Java Version: 1.7.0_60
(Jun 26, 2017 08:32:51) Java VM Name: Java HotSpot(TM) 64-Bit Server VM
(Jun 26, 2017 08:32:51) Java Class Path: /tmp/mathworks_5/java/config/installagent/pathlist.jar
(Jun 26, 2017 08:32:51) User Name: root
(Jun 26, 2017 08:32:51) Current Directory: /tmp/mathworks_5
(Jun 26, 2017 08:32:51) Input arguments:
(Jun 26, 2017 08:32:51) root /opt/mcr_installer
(Jun 26, 2017 08:32:51) libdir /tmp/mathworks_5
(Jun 26, 2017 08:32:51) destinationFolder /opt/mcr
(Jun 26, 2017 08:32:51) agreeToLicense yes
(Jun 26, 2017 08:32:51) mode silent
(Jun 26, 2017 08:32:51) standalone true
(Jun 26, 2017 08:32:51) connectionMode OFFLINE_ONLY
(Jun 26, 2017 08:32:52) Starting local product/component search in download directory
(Jun 26, 2017 08:32:52) Searching for archives...
(Jun 26, 2017 08:32:52) Reading /opt/mcr_installer/archives
(Jun 26, 2017 08:32:52) Assembling product list...
(Jun 26, 2017 08:32:52) 1467 files found in /opt/mcr_installer/archives
(Jun 26, 2017 08:32:52) Reading /opt/mcr_installer
(Jun 26, 2017 08:32:52) 9 files found in /opt/mcr_installer
(Jun 26, 2017 08:32:52) Archive search complete. 1476 total files found.
(Jun 26, 2017 08:32:55) Completed local product/component search
(Jun 26, 2017 08:32:55) Starting local product/component search in download directory
(Jun 26, 2017 08:32:55) Searching for archives...
(Jun 26, 2017 08:32:55) /opt/mcr/v92/archives doesn't exist ... skipping.
(Jun 26, 2017 08:32:55) Archive search complete. 0 total files found.
(Jun 26, 2017 08:32:55) Completed local product/component search
(Jun 26, 2017 08:32:56) Installing Product: MATLAB Runtime - Builder JA 9.2
(Jun 26, 2017 08:33:01) Installing Product: MATLAB Runtime - Core 9.2
(Jun 26, 2017 08:33:31) Installing Product: MATLAB Runtime - GPU 9.2
(Jun 26, 2017 08:33:55) Installing Product: MATLAB Runtime - Hadoop And Spark 9.2
(Jun 26, 2017 08:33:55) Installing Product: MATLAB Runtime - NET And XL 9.2
(Jun 26, 2017 08:33:55) Installing Product: MATLAB Runtime - Numerics 9.2
(Jun 26, 2017 08:34:11) Notes:
On the target computer, append the following to your LD_LIBRARY_PATH environment variable:
/opt/mcr/v92/runtime/glnxa64:/opt/mcr/v92/bin/glnxa64:/opt/mcr/v92/sys/os/glnxa64:
(Jun 26, 2017 08:34:11) Exiting with status 0
(Jun 26, 2017 08:34:11) End - Successful.
Finished
---> 58937614b2e4
Also the
MWApplication.initialize(MWMCROption.NODISPLAY, MWMCROption.logFile("/opt/matlab_from_java.log"))
is executed without problems and the
MWApplication.isMCRInitialized()
return true, see there: https://matlab-dot-growbit-0.appspot.com/matlab .
When the application try to use the exported Class1 I got a Segmentation violation during CFT reading I think.
------------------------------------------------------------------------
Segmentation violation detected at Mon Jun 26 08:59:48 2017
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled - No sandbox or build area path
Crash Mode : continue (default)
Default Encoding : UTF-8
GNU C Library : 2.19 stable
Host Name : 7603c1c623d7
MATLAB Architecture : glnxa64
MATLAB Root : /opt/mcr/v92
MATLAB Version : 9.2.0.538062 (R2017a)
Operating System : Linux 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2 (2017-04-30) x86_64
Processor ID : x86 Family 6 Model 45 Stepping 7, GenuineIntel
Fault Count: 1
Abnormal termination:
Segmentation violation
Register State (from fault):
RAX = 00007fa072311e40 RBX = 0000000000000000
RCX = 0000000000000000 RDX = 0000000000000001
RSP = 00007fa072311720 RBP = 00007fa07231af80
RSI = 0000000000000000 RDI = 00007fa07231176f
R8 = 0000000000000000 R9 = 00007fa0a412fbd0
R10 = 00007fa0a41a5080 R11 = 0000000000000000
R12 = 00007fa07231176f R13 = 00007fa07231b2a0
R14 = 00007fa0d10919e8 R15 = 00007fa07231b610
RIP = 00007fa0c55d33a3 EFL = 0000000000010202
CS = 0033 FS = 0000 GS = 0000
Stack Trace (from fault):
[ 0] 0x00007fa0c55d33a3 /opt/mcr/v92/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00537507 _ZNSi6sentryC2ERSib+00000019
[ 1] 0x00007fa0c55d46fa /opt/mcr/v92/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00542458 _ZNSi5tellgEv+00000026
[ 2] 0x00007fa089efaa65 bin/glnxa64/libmwmclmcr.so+03119717 _ZN6mclmcr12CtfExtractorC1EN5boost10shared_ptrISiEENS1_8functionIFmPKcS6_EEE+00000117
[ 3] 0x00007fa089e87cc6 bin/glnxa64/libmwmclmcr.so+02649286 _Z25mclMakeCtfStreamExtractorN5boost10shared_ptrISiEE+00000118
[ 4] 0x00007fa08bae5e59 /opt/mcr/v92/bin/glnxa64/libnativemcl.so+01121881 Java_com_mathworks_toolbox_javabuilder_internal_MWMCR_mclInitializeComponentInstance+00001081
[ 5] 0x00007fa0cd012d98 <unknown-module>+00000000
[ 6] 0x00007fa0cd006233 <unknown-module>+00000000
[ 7] 0x00007fa0cd006233 <unknown-module>+00000000
[ 8] 0x00007fa0cd0004e7 <unknown-module>+00000000
[ 9] 0x00007fa0d7a950a5 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06299813
[ 10] 0x00007fa0d7a93b08 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06294280
[ 11] 0x00007fa0d7d29caf /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+09006255
[ 12] 0x00007fa0d7d2aa60 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+09009760
[ 13] 0x00007fa0d7b11383 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06808451 JVM_InvokeMethod+00000483
[ 14] 0x00007fa0cd012d98 <unknown-module>+00000000
[ 15] 0x00007fa0cd006233 <unknown-module>+00000000
[ 16] 0x00007fa0cd006233 <unknown-module>+00000000
[ 17] 0x00007fa0cd0068e1 <unknown-module>+00000000
[ 18] 0x00007fa0cd006233 <unknown-module>+00000000
[ 19] 0x00007fa0cd0068e1 <unknown-module>+00000000
[ 20] 0x00007fa0cd0068e1 <unknown-module>+00000000
[ 21] 0x00007fa0cd006233 <unknown-module>+00000000
[ 22] 0x00007fa0cd006233 <unknown-module>+00000000
[ 23] 0x00007fa0cd006233 <unknown-module>+00000000
[ 24] 0x00007fa0cd006058 <unknown-module>+00000000
[ 25] 0x00007fa0cd006058 <unknown-module>+00000000
[ 26] 0x00007fa0cd006058 <unknown-module>+00000000
[ 27] 0x00007fa0cd006233 <unknown-module>+00000000
[ 28] 0x00007fa0cd0004e7 <unknown-module>+00000000
[ 29] 0x00007fa0d7a950a5 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06299813
[ 30] 0x00007fa0d7a93b08 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06294280
[ 31] 0x00007fa0d7d29caf /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+09006255
[ 32] 0x00007fa0d7d2aa60 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+09009760
[ 33] 0x00007fa0d7b11383 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06808451 JVM_InvokeMethod+00000483
[ 34] 0x00007fa0cd012d98 <unknown-module>+00000000
[ 35] 0x00007fa0cd006233 <unknown-module>+00000000
[ 36] 0x00007fa0cd006233 <unknown-module>+00000000
[ 37] 0x00007fa0cd0068e1 <unknown-module>+00000000
[ 38] 0x00007fa0cd006233 <unknown-module>+00000000
[ 39] 0x00007fa0cd006233 <unknown-module>+00000000
[ 40] 0x00007fa0cd006233 <unknown-module>+00000000
[ 41] 0x00007fa0cd006058 <unknown-module>+00000000
[ 42] 0x00007fa0cd006233 <unknown-module>+00000000
[ 43] 0x00007fa0cd006233 <unknown-module>+00000000
[ 44] 0x00007fa0cd0068e1 <unknown-module>+00000000
[ 45] 0x00007fa0cd006058 <unknown-module>+00000000
[ 46] 0x00007fa0cd006058 <unknown-module>+00000000
[ 47] 0x00007fa0cd006058 <unknown-module>+00000000
[ 48] 0x00007fa0cd006058 <unknown-module>+00000000
[ 49] 0x00007fa0cd006058 <unknown-module>+00000000
[ 50] 0x00007fa0cd006058 <unknown-module>+00000000
[ 51] 0x00007fa0cd006706 <unknown-module>+00000000
[ 52] 0x00007fa0cd006058 <unknown-module>+00000000
[ 53] 0x00007fa0cd006706 <unknown-module>+00000000
[ 54] 0x00007fa0cd006706 <unknown-module>+00000000
[ 55] 0x00007fa0cd006058 <unknown-module>+00000000
[ 56] 0x00007fa0cd006706 <unknown-module>+00000000
[ 57] 0x00007fa0cd006058 <unknown-module>+00000000
[ 58] 0x00007fa0cd006706 <unknown-module>+00000000
[ 59] 0x00007fa0cd006058 <unknown-module>+00000000
[ 60] 0x00007fa0cd006706 <unknown-module>+00000000
[ 61] 0x00007fa0cd006058 <unknown-module>+00000000
[ 62] 0x00007fa0cd006706 <unknown-module>+00000000
[ 63] 0x00007fa0cd006058 <unknown-module>+00000000
[ 64] 0x00007fa0cd006706 <unknown-module>+00000000
[ 65] 0x00007fa0cd006058 <unknown-module>+00000000
[ 66] 0x00007fa0cd006706 <unknown-module>+00000000
[ 67] 0x00007fa0cd006058 <unknown-module>+00000000
[ 68] 0x00007fa0cd006706 <unknown-module>+00000000
[ 69] 0x00007fa0cd006058 <unknown-module>+00000000
[ 70] 0x00007fa0cd006706 <unknown-module>+00000000
[ 71] 0x00007fa0cd006058 <unknown-module>+00000000
[ 72] 0x00007fa0cd006058 <unknown-module>+00000000
[ 73] 0x00007fa0cd006706 <unknown-module>+00000000
[ 74] 0x00007fa0cd006706 <unknown-module>+00000000
[ 75] 0x00007fa0cd006706 <unknown-module>+00000000
[ 76] 0x00007fa0cd006706 <unknown-module>+00000000
[ 77] 0x00007fa0cd006706 <unknown-module>+00000000
[ 78] 0x00007fa0cd006706 <unknown-module>+00000000
[ 79] 0x00007fa0cd006706 <unknown-module>+00000000
[ 80] 0x00007fa0cd006233 <unknown-module>+00000000
[ 81] 0x00007fa0cd0068e1 <unknown-module>+00000000
[ 82] 0x00007fa0cd0068e1 <unknown-module>+00000000
[ 83] 0x00007fa0cd006058 <unknown-module>+00000000
[ 84] 0x00007fa0cd006706 <unknown-module>+00000000
[ 85] 0x00007fa0cd006058 <unknown-module>+00000000
[ 86] 0x00007fa0cd006706 <unknown-module>+00000000
[ 87] 0x00007fa0cd006706 <unknown-module>+00000000
[ 88] 0x00007fa0cd0004e7 <unknown-module>+00000000
[ 89] 0x00007fa0d7a950a5 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06299813
[ 90] 0x00007fa0d7a93b08 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06294280
[ 91] 0x00007fa0d7a93dd7 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06294999
[ 92] 0x00007fa0d7a93ef7 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06295287
[ 93] 0x00007fa0d7b128d5 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+06813909
[ 94] 0x00007fa0d7deefff /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+09814015
[ 95] 0x00007fa0d7def105 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+09814277
[ 96] 0x00007fa0d7cb68c8 /opt/jdk1.7.0_80/jre/lib/amd64/server/libjvm.so+08534216
[ 97] 0x00007fa0d8ad9064 /lib/x86_64-linux-gnu/libpthread.so.0+00032868
[ 98] 0x00007fa0d83f562d /lib/x86_64-linux-gnu/libc.so.6+00951853 clone+00000109
[ 99] 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.** This crash report has been saved to disk as /root/matlab_crash_dump.1-1 **
MATLAB is exiting because of fatal error
This is the bean that use Matlab Java utilities https://github.com/growingabit/appengine-matlab-service/blob/master/src/main/java/it/growbit/matlab/controller/MatlabController.java
The Dockerfile https://github.com/growingabit/appengine-matlab-service/blob/master/Dockerfile
Thank you,
  1 Comment
Alessandro Aglietti
Alessandro Aglietti on 26 Jun 2017
Also using the libstdc++ from OS cause same error
Stack Trace (from fault):
[ 0] 0x00007ff6ccb938b3 /usr/lib/x86_64-linux-gnu/libstdc++.so.6+00518323 _ZNSi6sentryC1ERSib+00000019
[ 1] 0x00007ff6ccb94c0 /usr/lib/x86_64-linux-gnu/libstdc++.so.6+00523274 _ZNSi5tellgEv+00000026
[ 2] 0x00007ff6891d5a65 bin/glnxa64/libmwmclmcr.so+03119717 _ZN6mclmcr12CtfExtractorC1EN5boost10shared_ptrISiEENS1_8functionIFmPKcS6_EEE+00000117
[ 3] 0x00007ff689162cc6 bin/glnxa64/libmwmclmcr.so+02649286 _Z25mclMakeCtfStreamExtractorN5boost10shared_ptrISiEE+00000118
[ 4] 0x00007ff68adc0e59 /opt/mcr/v92/bin/glnxa64/libnativemcl.so+01121881 Java_com_mathworks_toolbox_javabuilder_internal_MWMCR_mclInitializeComponentInstance+00001081
[ 5] 0x00007ff6d0398d98 <unknown-module>+00000000
[...]

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Accepted Answer

Alessandro Aglietti
Alessandro Aglietti on 26 Jun 2017
Resolved, the problem was the decompiler I used for extract the Matlab Compiler generated jar.
It fail to decompress the ctf file, resulting in an empty file...
As a workaround I use unzip.
You can see the Dockerfile diff there
https://github.com/growingabit/appengine-matlab-service/compare/2895970d45bc...b37bc50e1467
Regards

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