How to call MATLAB executable for Python on cluste

问题:

I am using a python-matlab-bridge that calls MATLAB from python by starting it on a ZMQ socket. On my own computer, I hand the bridge the location of the executable (in this case MATLAB 2014B):

executable='/Applications/MATLAB_R2014b.app/bin/matlab'

and everything works as required and the printed statement is:

Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge-49ce56ed-f5b4-43c4-8d53-8ae0cd30136d

Now I want to do the same on a cluster. Through module avail I find there are two MATLAB versions (2015a and 2016b) available and located at the following path:

/opt/ud/LOCAL/etc/modulefiles/matlab.

When I now call MATLAB using:

executable='/opt/ud/LOCAL/etc/modulefiles/matlab/MATLAB_R2015a.app/bin/matlab'

the error:

 Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge-95775445-359d-441f-803a-7193eedbf215    
Send 'exit' command to kill the server
............................................................MATLAB session timed out after 60 seconds

is returned. It cannot find the MATLAB executable. How to proceed?

回答1:

Step 0:

Check whether the code-segment responsible for "remote" launch of MATLAB goes well - for details about params, check pymatbridge.py:

    ### class _Session( object ): _____________________________
    ...

    def _run_server(self):
        code = self._preamble_code()
        code.extend([
            "matlabserver('%s')" % self.socket_addr
        ])
        command = '%s %s %s "%s"' % ( self.executable,
                                      self.startup_options,
                                      self._execute_flag(),
                                      ','.join( code )
                                      )
        subprocess.Popen( command,
                          shell  = True,
                          stdin  = subprocess.PIPE,
                          stdout = subprocess.PIPE
                          )

If such invocation works on any Cluster-Node you will try to harness in a massively distributed MATLAB scenario, the problem goes into ZeroMQ messaging part, if not, the remote server simply cannot launch a _Session, while the messaging ( and all it's { ipc:// | tcp:// | pgm:// | epgm:// | vmci:// } transport-classes available for a massively-distributed computing ) is not to be blamed.

Step 1:

If Step 0 ( a subprocess.Popen(...) invocation ) works well on all remote nodes, check all the ZeroMQ / pymatbridge pre-requisites ( dynamic loader settings - lines added to all remote cluster nodes' .bash_profile ( or similar file for respective shell ).

Yes, a tedious task to prove all remote nodes on the cluster meet these, but without checking these, there is no warranty a remote node can operate the remote MATLAB process connected via otherwise smart and powerful tool, like the pymatbridge is.

回答2:

In the end I found a method that works that is very simple. In the .pbs script I load the MATLAB module using

module load matlab/2015a

Then in the Python script the command

mlab = Matlab()

automatically detects the correct MATLAB path. I thus do not need to specify the path using the optional executable argument.