Use command line in matlab using ! and zsh:1: command not found: is displayed

Hi

I'm using MATLAB 2020b and Big sur OSX

before catalina version, in my memory...

I was using well with ! for call mac command line

but now in big sur when I use ! and matlab display zsh:1: command not found: brew or other package!

so...how can I solve it?

[KSSV]

What is zsh?

[Walter Roberson]

zsh is the Z shell, which is one of the successors to ksh (Korne Shell). Apple made it the default.

[KSSV]

Ohk.. I have no idea.

Answer 1

[Walter Roberson]

Open terminal on the Mac. Give the command

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

See https://brew.sh/

This is not MATLAB specific: you happen to be asking to execute commands that need the third-party package "brew" installed.

[Chang-Soo Yun]

Oh! I think my question is not cleared for delivering what I ask!

I mean this problem! I'm a novice of programmer so... please understand me

Top image is in the MATLAB and buttom image is in the terminal

[Walter Roberson]

OpenMPI was removed from MacOS in the Leopard time frame. You can install it yourself.

Download https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.0.tar.gz and let it expand into a directory automatically. In terminal, cd to that directory and look at the INSTALL instructions starting from the lines about "User Builds" -- you will need to run a ./configure step and an install step. You will need to choose where you want to install it to. If you install to a system location such as /usr/lib/ then you may need to use "sudo" for the install step.

[Chang-Soo Yun]

OK I got it! thank you for answer!:)

[Michael]

@Walter Roberson I am getting the same problem on a command that runs fine in terminal, but not in Matlab. I tried both system and ! execution with the same result:

zsh:1: command not found: airspy_rx

The command works fine in terminal. Any ideas why that might be?

[Michael]

FYI - Related issue here:

https://www.mathworks.com/matlabcentral/answers/669363-cannot-run-system-commands-from-matlab-macos-catalina-zsh-1-command-not-found-blastp

[Walter Roberson]

When you start a terminal session, then that is considered "interactive", and various shell initialization files are run. It is common that those initialization files may set the shell PATH environment variable.

When you system() from MATLAB, then that is not considered "interactive", and several of the shell initialization files are skipped. If one of those files added the location of airspy_rx to your PATH environment variable, then the executable would not be located by the shell process.

The easiest way to solve the problem is to change what you system() to give the full path to the executable,

system('/usr/local/bin/airspy_rx whatever')

The second easiest way to solve the problem is to

system('export PATH="$PATH:/usr/local/bin"; airspy_rx whatever')

in the above, "export" is a shell keyword, but /usr/local/bin should be replaced by the directory that airspy_rx is located in.

There are other approaches as well. One is to force the shell to believe that it is interactive so that the initialization files are run. Another is to change a MacOS system configuration file to add the directory for airspy_rx to the list of directories put on the PATH of all processes.

[Michael]

@Walter Roberson I just answered in the other related issue before seeing your answer here. It seems that I stumbled across your first easiest method. I had noticed your second method in the documentation file for system.m. I did not know that each shell session could have their own PATH. Part of the issue I am dealing with is that I am trying to incorporate this into a standalone application I built in App Designer. In that case, having the users manually look up the location of airspy_rx is not preferable.

If I use your second method with the export call within system.m, will that permanantly add the path for future system calls or only update the PATH for that particulare system call?

Thanks.

[Walter Roberson]

The shell export command only affects the environment for that shell and the subprocesses of the shell, and each system() call is a different process.

At the MATLAB level you can do things like

setenv('PATH', getenv('PATH')+":/usr/local/bin")

and that should affect anything started using system() or the ! operator. But that does not tell you where your executable is.

To locate the executable, you can try:

[status, msg] = system('exec -a -ksh /bin/ksh -c "which airspy_rx"');
if status == 0
   airpath = string(regexprep(msg, '\r?\n', ''));
   setenv('PATH', getenv('PATH')+":"+airpath);
else
   error('Failed to locate airspy_rx because "%s"', msg);
end

This should work if the user has ksh or zsh configured as their login shell, and someone has configured the appropriate configuration files so that airspy_rx is normally on their path when they log in.

If they happen to have configured bash instead, then

 bash -l -c "which airspy_rx"

would be appropriate.. you could try that within the "else".

But at some point you are going to encounter a user whose shell configuration does not have the executable on the path, and you going to have to uigetfile() or something similar.

You might want to use the MATLAB preferences system https://www.mathworks.com/help/matlab/ref/setpref.html to remember the setting for each user.