setenv fails to change environment variables on Linux

Hi,

I'm using Matlab on Ubuntu 16.04, and it seems that Matlab cannot run system calls:, because of an apparently failure of the Matlab command setenv to change the environment variables in the shell running below my Matlab session. To clarify what I mean, I copy and paste from my current session in Matlab:

>> ls /usr/local/bin/chimera
/usr/local/bin/chimera

This file /usr/local/bin/chimera is an executable that I would like to run from matlab without needing to pass the full path (i.e., as !chimera or system('chimera');). To make it visible to my Matlab session, I prepend it to the environment variable PATH of the linux shell through the matlab commands getenv and setenv

>> setenv('PATH',['/usr/local/bin/:',getenv('PATH')]);

However, the Linux shell cannot find the executable "chimera" when asked by Matlab:

>> !which chimera
>> 

In fact, looks like the PATH variable was never changed from the point of view of the Linux Shell

>> !echo $PATH
/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.

although Matlab finds the correct value through getenv:

>> getenv('PATH')
ans =
:/usr/local/bin/chimera:/usr/local/bsse/MATLAB_R2018a/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/puppetlabs/bin:'

In any case, this does not help me, as my Matlab session is unable to run system calls properly:

>> unix('chimera');
/bin/bash: chimera: command not found
>> system('chimera');
/bin/bash: chimera: command not found

So, what can be the reason that setenv is not working properly?

thanks in advance,

Daniel

matlab version: (R2018a)

Answer 1

[Jesse Hopkins]

Hello, I recently came across this same issue. While I wasn't able to directly solve it, I was able to workaround by setting up the PATH variable appropriately in my account's .cshrc file located in the account home directory, adding a line like

setenv PATH /my/new/path:${PATH}

That worked for future logins to my account. To refresh your current session, execute from your home directory:

source .cshrc