Error preventing me from calling bash script from Matlab

Hi,

I'm having a problem calling a bash script from within Matlab. I have a bash script that basically calls this line of code.

java -d64 -Xmx3G -jar GeneMANIA-v3.3.4.jar QueryRunner --data gmdata-2014-08-12-core --in flat --results result_dir --verbose InputFile.txt

I want to run this iteratively many many times, but with a different InputFile.txt each time, hence why I want to call it within a loop in Matlab (in Matlab, I'm doing various other things before and after that which are essential for my purposes, so I'd prefer to be able to call this one line as well directly from within Matlab).

However, I have tried several things for calling the script from within Matlab, and everytime I get this message:

Error: A JNI error has occurred, please check your installation and try again
Error: A JNI error has occurred, please check your installation and try again
bash runGeneManiaAnalysis.sh: Signal 127

I have tried calling it using:

fname = 'runGeneManiaAnalysis.sh'; 
unix(sprintf('bash %s',fname));
system(sprintf('bash %s',fname)); 
!bash runGeneManiaAnalysis.sh

This is a problem that I get only when I try to run it from within Matlab. If I go directly to the Terminal and run it from there, it runs fine without a problem. I'm using Matlab R2014b (8.4.0 150421) 64 bit (maci64).

So can anyone please help me ascertain what's going wrong and how I can fix this issue?

Thanks,

Mike

Answer 1

[Walter Roberson]

You could be having a PATH or java classpath difficulty. At the terminal prompt, give the command

printenv | egrep -i '(path|java)'

and then at the MATLAB prompt try

!printenv | egrep -i '(path|java)'

and compare the two.

[Michael]

Hi Walter,

Yes these do differ completely in what they return.

In the terminal, this:

printenv | egrep -i '(path|java)'

returns

DYLD_FALLBACK_LIBRARY_PATH=/Users/michael/abin
PATH=/Applications/fsl/bin:/Users/michael/Library/Enthought/Canopy_64bit/User/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/michael/abin

In Matlab, this:

!printenv | egrep -i '(path|java)'

returns

OSG_LD_LIBRARY_PATH=/Applications/MATLAB_R2014b.app/sys/openscenegraph/lib/maci64
PATH=/usr/bin:/bin:/usr/sbin:/sbin
XFILESEARCHPATH=/Applications/MATLAB_R2014b.app/sys/java/jre/maci64/jre/lib/locale/%L/%T/%N%S:
BASEMATLABPATH=
DYLD_FRAMEWORK_PATH=/Applications/MATLAB_R2014b.app/sys/os/maci64:/Applications/MATLAB_R2014b.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2014b.app/bin/maci64:/Applications/MATLAB_R2014b.app/extern/lib/maci64:/Applications/MATLAB_R2014b.app/sys/java/jre/maci64/jre/lib/./native_threads:/Applications/MATLAB_R2014b.app/sys/java/jre/maci64/jre/lib/./server:/Applications/MATLAB_R2014b.app/sys/java/jre/maci64/jre/lib/./lib/jli
DYLD_LIBRARY_PATH=/Applications/MATLAB_R2014b.app/sys/os/maci64:/Applications/MATLAB_R2014b.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2014b.app/bin/maci64:/Applications/MATLAB_R2014b.app/extern/lib/maci64:/Applications/MATLAB_R2014b.app/sys/java/jre/maci64/jre/lib/./native_threads:/Applications/MATLAB_R2014b.app/sys/java/jre/maci64/jre/lib/./server:/Applications/MATLAB_R2014b.app/sys/java/jre/maci64/jre/lib/./lib/jli

What should I do to fix this?

Mike

[Walter Roberson]

As an experiment, try adding these before your java invocation in your .sh file:

unset DYLD_FRAMEWORK_PATH DYLD_LIBRARY_PATH

I suspect that possibly the jre that are on the DYLD_LIBRARY_PATH are interfering with the functioning of java that expects a different jre.

[Michael]

Hi Walter,

This did the trick. Thanks so much for the help!

Mike

[Arturo Magana]

Walter, thank you so much for this answer. I was having the same issue as Michael, this solved everything!