|
Main /
MatlabNotes about the Ptolemy Matlab interface. GLIBXCXX_3.4.15 not found1/12/15: While running the nightly build under RHEL 6 on sisyphus using hudson In addition, loadLibrary("ptmatlab") was called, the exception for the loadLibrary() call was:
java.lang.UnsatisfiedLinkError: /home/hudson/jobs/ptII/workspace/lib/libptmatlab.so:
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/matlab/recent/bin/glnxa64/libut.so)
1/25/2015 SolutionThe problem is triggered when I run Java 3D and the load a shared library that uses Matlab. A possible workaround: # Add /usr/local/matlab/recent/sys/os/glnxa64 and avoid problems with Matlab after Java3D
export LD_LIBRARY_PATH=/usr/local/matlab/recent/sys/os/glnxa64:${LD_LIBRARY_PATH}
What's happening is that something is loading /usr/lib64/libstdc++.so.6 which is not up to date enough for Matlab. Running I ran: lsof -p 24726 >& /tmp/o
awk '{print $NF}' /tmp/o | egrep '\.so' | xargs ldd >& /tmp/l
/tmp/l says: /usr/lib64/dri/swrast_dri.so:
linux-vdso.so.1 => (0x00007fffa2fff000)
libdrm_intel.so.1 => /usr/lib64/libdrm_intel.so.1 (0x00007fcdc52db000)
libdrm_radeon.so.1 => /usr/lib64/libdrm_radeon.so.1 (0x00007fcdc50ce000)
libdrm.so.2 => /usr/lib64/libdrm.so.2 (0x00007fcdc4ec3000)
libexpat.so.1 => /usr/local/matlab/recent/bin/glnxa64/libexpat.so.1 (0x00007fcdc4c9b000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fcdc4a5d000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fcdc4859000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007fcdc463a000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fcdc4333000)
libm.so.6 => /lib64/libm.so.6 (0x00007fcdc40af000)
libc.so.6 => /lib64/libc.so.6 (0x00007fcdc3d1b000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fcdc3b04000)
libpciaccess.so.0 => /usr/lib64/libpciaccess.so.0 (0x00007fcdc38fb000)
librt.so.1 => /lib64/librt.so.1 (0x00007fcdc36f3000)
/lib64/ld-linux-x86-64.so.2 (0x0000003236a00000)
http://dri.freedesktop.org/wiki/glxinfo/ indicates that swrast_dri is part of OpenGL. 1/23/2015 Yet another attempt
The idea now is to narrow the problem down. As running the one model by hand does not work, now we try running all the export tests as hudson on sisyphus: Xvfb :3 -screen 0 1024x768x24 & export DISPLAY=localhost:3.0 cd $PTII nohup ant test.longest >& /tmp/m1.out & The above takes about 90 minutes and reproduces the bug! Narrowing down the problem: Line 4Placing the test early in the file: $CLASSPATH/lbnl/demo/CRoom/CRoom.xml $CLASSPATH/lbnl/demo/MatlabRoom/MatlabRoom.xml $CLASSPATH/lbnl/demo/SystemCommand/SystemCommand.xml $CLASSPATH/ptolemy/domains/wireless/demo/MatlabWirelessSoundDetection/MatlabWirelessSoundDetection.xml $CLASSPATH/org/ptolemy/machineImprovisation/demo/JazzImprovisation/JazzImprovisation.xml $CLASSPATH/org/ptolemy/machineLearning/hmm/demo/CommunicationAnomalyDetectionAOM/CommunicationAnomalyDetectionAOM.xml Does not replicate the problem. Ok, so perhaps something is messing with the environment? Or the process is getting large? Narrowing: Line 249:Trying it at the middle of the file. $CLASSPATH/ptolemy/domains/continuous/demo/NewtonsCradle/NewtonsCradleAnimated.xml $CLASSPATH/ptolemy/domains/wireless/demo/MatlabWirelessSoundDetection/MatlabWirelessSoundDetection.xml $CLASSPATH/ptolemy/domains/continuous/demo/NewtonsCradle/NewtonsCradleComplicated.xml Line 249 Failed. Line 64 failedLine 32 passed$CLASSPATH/org/ptolemy/ptango/demo/UCBPower/UCBPower.xml $CLASSPATH/ptolemy/domains/wireless/demo/MatlabWirelessSoundDetection/MatlabWirelessSoundDetection.xml $CLASSPATH/org/ptolemy/ptango/demo/UCBPower/UCBPowerAnalyzerServer.xml Line 48 failed$CLASSPATH/ptolemy/actor/gt/demo/ModelGeneration/ModelGenerationDE.xml $CLASSPATH/ptolemy/domains/wireless/demo/MatlabWirelessSoundDetection/MatlabWirelessSoundDetection.xml $CLASSPATH/ptolemy/actor/gt/demo/PublisherTest/PublisherTest.xml Line 40 failed$CLASSPATH/ptolemy/actor/gt/demo/ConstOptimization/ConstOptimizationDE.xml $CLASSPATH/ptolemy/domains/wireless/demo/MatlabWirelessSoundDetection/MatlabWirelessSoundDetection.xml $CLASSPATH/ptolemy/actor/gt/demo/DiningPhilosophers/DiningPhilosophers.xml Line 36 passed$CLASSPATH/org/ptolemy/qss/demo/RLC/RLC.xml $CLASSPATH/ptolemy/domains/wireless/demo/MatlabWirelessSoundDetection/MatlabWirelessSoundDetection.xml $CLASSPATH/ptolemy/actor/gt/demo/BouncingBallX2/BouncingBallX2.xml Line 38 failed$CLASSPATH/ptolemy/actor/gt/demo/ConstOptimization/ConstOptimization.xml $CLASSPATH/ptolemy/domains/wireless/demo/MatlabWirelessSoundDetection/MatlabWirelessSoundDetection.xml $CLASSPATH/ptolemy/actor/gt/demo/ConstOptimization/ConstOptimizationDDF.xml Line 37 failed:$CLASSPATH/ptolemy/actor/gt/demo/BouncingBallX2/BouncingBallX2.xml $CLASSPATH/ptolemy/domains/wireless/demo/MatlabWirelessSoundDetection/MatlabWirelessSoundDetection.xml $CLASSPATH/ptolemy/actor/gt/demo/ConstOptimization/ConstOptimization.xml Success!The issue here is that running a model that loads Java3D results in an error when subsequently loading a Matlab model. Searching the webSearch for
Steps to reproduce
Unfortunately, this does not reproduce the problem. Setting export LD_LIBRARY_PATH=/usr/lib64:/usr/local/matlab/recent/bin/glnxa64/:/home/hudson/jobs/ptII/workspace/lib does not reproduce the problem. lddWhere is the message coming from? Running ldd does not reproduce the problem bash-4.1$ /usr/bin/ldd /usr/local/matlab/recent/bin/glnxa64/libut.so | grep stdc++ libstdc++.so.6 => /usr/local/matlab/recent/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6 (0x00007fc2c96ff000) bash-4.1$ /usr/lib64/libstdc++.so.6The message is about GLIBCXX_3.4.15 missing. Indeed, it is missing from that library: bash-4.1$ strings /usr/lib64/libstdc++.so.6 | grep GLIBCXX GLIBCXX_3.4 GLIBCXX_3.4.1 GLIBCXX_3.4.2 GLIBCXX_3.4.3 GLIBCXX_3.4.4 GLIBCXX_3.4.5 GLIBCXX_3.4.6 GLIBCXX_3.4.7 GLIBCXX_3.4.8 GLIBCXX_3.4.9 GLIBCXX_3.4.10 GLIBCXX_3.4.11 GLIBCXX_3.4.12 GLIBCXX_3.4.13 GLIBCXX_FORCE_NEW GLIBCXX_DEBUG_MESSAGE_LENGTH bash-4.1$ RHEL does not keep up with GLib, so this is not that surprising. LD_LIBRARY_PATHAt the start of the hudson run, we echo LD_LIBRARY_PATH: echo 'LD_LIBRARY_PATH: /usr/local/certi/lib:/home/hudson/jobs/ptII/workspace/lbnl/lib/util:/home/hudson/jobs/ptII/workspace/lib:/usr/local/matlab/recent/bin/glnxa64:/home/hudson/jobs/ptII/workspace/vendors/misc/dbxml-2.5.16/install/lib:/usr/local/lib:/usr/lib64:/usr/local/certi/lib:/home/hudson/jobs/ptII/workspace/lbnl/lib/util:/home/hudson/jobs/ptII/workspace/lib:/usr/local/matlab/recent/bin/glnxa64:/home/hudson/jobs/ptII/workspace/vendors/misc/dbxml-2.5.16/install/lib:/usr/local/lib:/usr/lib64:/usr/local/certi/lib:${WORKSPACE}/lbnl/lib/util:${WORKSPACE}/lib:/usr/local/matlab/recent/bin/glnxa64:${WORKSPACE}/vendors/misc/dbxml-2.5.16/install/lib:/usr/local/lib:/usr/lib64:/usr/local/certi/lib:${WORKSPACE}/lbnl/lib/util:${WORKSPACE}/lib:/usr/local/matlab/recent/bin/glnxa64:${WORKSPACE}/vendors/misc/dbxml-2.5.16/install/lib:/usr/local/lib:/usr/lib64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.33.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.33.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.33.x86_64/jre/../lib/amd64' Update I modified the Build Environment plugin and now LD_LIBRARY_PATH is java.library.pathThe error message includes the value of the [junit] The java.library.path property was: /usr/lib/jvm/jdk1.8.0_25/jre/lib/amd64/server:/usr/lib/jvm/jdk1.8.0_25/jre/lib/amd64:/usr/lib/jvm/jdk1.8.0_25/jre/../lib/amd64:/usr/local/certi/lib:/home/hudson/jobs/ptII/workspace/lbnl/lib/util:/home/hudson/jobs/ptII/workspace/lib:/usr/local/matlab/recent/bin/glnxa64:/home/hudson/jobs/ptII/workspace/vendors/misc/dbxml-2.5.16/install/lib:/usr/local/lib:/usr/lib64:/usr/local/certi/lib:/home/hudson/jobs/ptII/workspace/lbnl/lib/util:/home/hudson/jobs/ptII/workspace/lib:/usr/local/matlab/recent/bin/glnxa64:/home/hudson/jobs/ptII/workspace/vendors/misc/dbxml-2.5.16/install/lib:/usr/local/lib:/usr/lib64:/usr/local/certi/lib:${WORKSPACE}/lbnl/lib/util:${WORKSPACE}/lib:/usr/local/matlab/recent/bin/glnxa64:${WORKSPACE}/vendors/misc/dbxml-2.5.16/install/lib:/usr/local/lib:/usr/lib64:/usr/local/certi/lib:${WORKSPACE}/lbnl/lib/util:${WORKSPACE}/lib:/usr/local/matlab/recent/bin/glnxa64:${WORKSPACE}/vendors/misc/dbxml-2.5.16/install/lib:/usr/local/lib:/usr/lib64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.33.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.33.x86_64/jre/lib/amd64:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.33.x86_64/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib Update Now the [junit] The java.library.path property was: /usr/local/certi/lib:/home/hudson/jobs/ptII/workspace/lbnl/lib/util:/home/hudson/jobs/ptII/workspace/lib:/usr/local/matlab/recent/bin/glnxa64:/home/hudson/jobs/ptII/workspace/vendors/misc/dbxml-2.5.16/install/lib:/usr/local/lib:/usr/lib64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
The above might account for the ${WORKSPACE}, so for the next run, I've substituted PTII_DIR and set PTII_DIR to a path.
A hint from Stack Overflow:Not much there suggests sudo ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 /usr/local/MATLAB/R2012a/bin/glnxa64/libstdc++.so.6 R2014b has different files: bash-4.1$ ls -l /usr/local/matlab/recent/bin/glnxa64/../../sys/os/glnxa64/ | grep stdc++ lrwxrwxrwx 1 cxh gopher 19 Nov 26 08:15 libstdc++.so.6 -> libstdc++.so.6.0.17 -r-xr-xr-x 1 cxh gopher 6345639 Jul 26 01:52 libstdc++.so.6.0.17 -r--r--r-- 1 cxh gopher 291 Jul 26 01:52 README.libstdc++ bash-4.1$ cat /usr/local/matlab/recent/bin/glnxa64/../../sys/os/glnxa64/README.libstdc++ The GCC runtime libraries included here: libstdc++.so.6.0.17 libgcc_s.so.1 libgfortran.so.3.0.0 libquadmath.so.0.0.0 and associated symlinks are part of gcc-4.7.2, available from ftp.gnu.org. They are included with MATLAB in the event that your distribution does not provide them. I'm hesitant to do the link because I can't reproduce the problem from the command line. /usr/lib64I believe I added /usr/lib64 to support OpenModelica. So, I'll try removing it and see what happens. |