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josephdviviano / epitome

scriptit modules for fmri analysis
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matlab libraries linking problem #38

Closed josephdviviano closed 8 years ago

josephdviviano commented 8 years ago

on init_basic

* MODULE: init_basic. Reorients, phys regression, removes init TRs. * ++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Dec 10 2014) [64-bit] ++ Authored by: A cast of thousands

++ VERSION CHECK! This program = AFNI_2011_12_21_1014 ++ Current AFNI website = AFNI_16.0.00

++ Output dataset /scratch/colin/epitome/tmsfmri_study1/P105/TMS/SESS01//anat_EPI_tmp_initTR.nii.gz

Setting up environment variables

LD_LIBRARY_PATH is .:/opt/quarantine/matlab/matlab_concurrent_all/MATLAB_R2013b/runtime/glnxa64:/opt/quarantine/matlab/matlab_concurrent_all/MATLAB_R2013b/bin/glnxa64:/opt/quarantine/matlab/matlab_concurrent_all/MATLAB_R2013b/sys/os/glnxa64:/opt/quarantine/matlab/matlab_concurrent_all/MATLAB_R2013b/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/quarantine/matlab/matlab_concurrent_all/MATLAB_R2013b/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/quarantine/matlab/matlab_concurrent_all/MATLAB_R2013b/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/quarantine/matlab/matlab_concurrent_all/MATLAB_R2013b/sys/java/jre/glnxa64/jre/lib/amd64 /home/colin/epitome/tms_part1/bin/McRetroTS: error while loading shared libraries: libmwmclmcrrt.so.7.15: cannot open shared object file: No such file or directory

josephdviviano commented 8 years ago

This was a bug in erin's branch of the code -- no longer an issue.

hodaelcohen commented 5 years ago

how you fix that????? i have the same problem Exception in thread "main" java.lang.UnsatisfiedLinkError: Failed to find the required library libmwmclmcrrt.so.9.6 on java.library.path. This library is typically installed along with MATLAB or the MATLAB Runtime. Its absence may indicate an issue with that installation or the current path configuration, or a mismatch with the architecture of the Java interpreter on the path. MATLAB Runtime version this component is attempting to use: 9.6. Java interpreter architecture: glnxa64.

at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$ProxyLibraryDir.get(MCRConfiguration.java:185)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$ProxyLibraryDir.<clinit>(MCRConfiguration.java:195)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration.getProxyLibraryDir(MCRConfiguration.java:200)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$MCRRoot.get(MCRConfiguration.java:64)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$MCRRoot.<clinit>(MCRConfiguration.java:76)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration.getMCRRoot(MCRConfiguration.java:81)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration$ModuleDir.<clinit>(MCRConfiguration.java:53)
at com.mathworks.toolbox.javabuilder.internal.MCRConfiguration.getModuleDir(MCRConfiguration.java:58)
at com.mathworks.toolbox.javabuilder.internal.MWMCR.<clinit>(MWMCR.java:1711)
at makesqr.MakesqrMCRFactory.newInstance(MakesqrMCRFactory.java:44)
at makesqr.MakesqrMCRFactory.newInstance(MakesqrMCRFactory.java:55)
at makesqr.Class1.<init>(Class1.java:62)
at sqr.main(sqr.java:10)
josephdviviano commented 5 years ago

I don't know the details on your machine so I don't think I can help you.

This isn't the same issue, as you are reporting a missing libmwmclmcrrt.so.9.6 on java.library.path, i suspect it is a java installation / version issue.

josephdviviano commented 5 years ago

have a look here: https://www.mathworks.com/matlabcentral/answers/20124-missmatch-between-mcr-version-and-packaged-jar-failed-to-find-the-library-libmwmclmcrrt-so-7-13