fail to start MATLAB

[willard-yuan]

After installing the package python-matlab-bridge and pyzmq, I try to use the pymatbridge by the Usage instruction:

Python 2.7.6 (default, Nov 10 2013, 19:24:24) [MSC v.1500 64 bit (AMD64)] on win32
Type "copyright", "credits" or "license()" for more information.
>>> from pymatbridge import Matlab
>>> mlab = Matlab()
>>> mlab = Matlab(executable='D:\Program Files\MATLAB\R2014b\bin\matlab')
>>> mlab.start()
Starting MATLAB on ZMQ socket tcp://127.0.0.1:55555
Send 'exit' command to kill the server
............................................................MATLAB session timed out after 60 seconds
MATLAB failed to start
False

I don't know the reason, someone else has the problem?

[arokem]

Thanks for reporting your problems, and sorry to hear that this is not
working for you. What you should be seeing is something like the following:

    >>> from pymatbridge import Matlab

    >>> mlab = Matlab(executable='/Applications/MATLAB_R2014b.app/bin/matlab')

    >>> mlab.start()

    Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge

    Send 'exit' command to kill the server

    .MATLAB started and connected!

    True

    >>>

                            < M A T L A B (R) >

                  Copyright 1984-2014 The MathWorks, Inc.

                   R2014b (8.4.0.150421) 64-bit (maci64)

                             September 15, 2014




    To get started, type one of these: helpwin, helpdesk, or demo.

    For product information, visit www.mathworks.com.

     Socket created at: ipc:///tmp/pymatbridge

That is, the matlab application should start in that terminal. Just to be
sure, what happens when you type just this:

D:\Program Files\MATLAB\R2014b\bin\matlab

In your terminal (not in python)?

[willard-yuan]

when I type the 'D:\Program Files\MATLAB\R2014b\bin\matlab' in the DOS cmd, it says no command found. So I add the path 'D:\Program Files\MATLAB\R2014b\bin' to windows environment, then type it again. It works and open MATLAB.

Then I run the following commands:

>>> from pymatbridge import Matlab
>>> mlab = Matlab(executable='matlab')
>>> mlab.start()

after I type mlab.start() and press Enter button, a windows is opening. The content in the windows is as follows:

MATLAB is running in headless mode.  Figure windows will not be displayed.

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.


old_warning_state = 

16x1 struct array with fields:
    identifier
    state

Invalid MEX-file 'C:\Python27\lib\site-packages\pymatbridge\matlab\messenger.mexw64': XXXX

Error in matlabserver (line 7)
messenger('init', socket_address);

and still can't connect to matlab:

Starting MATLAB on ZMQ socket tcp://127.0.0.1:55555
Send 'exit' command to kill the server
............................................................MATLAB session timed
 out after 60 seconds
MATLAB failed to start
False

[arokem]

There seems to be something wrong with the Windows messenger. Might be
related to issue reported here:
#123. Unfortunately, I
don't have a Windows machine to figure this out with, but this page might
be helpful:

http://stackoverflow.com/questions/23716426/installing-pymatbridge-on-windows

On Mon, Feb 2, 2015 at 4:15 AM, Yong Yuan notifications@github.com wrote:

when I type the 'D:\Program Files\MATLAB\R2014b\bin\matlab' in the DOS
cmd, it says no command found. So I add the path 'D:\Program
Files\MATLAB\R2014b\bin' to windows environment, then type it again. It
works and open MATLAB.

Then I run the following commands:

from pymatbridge import Matlab>>> mlab = Matlab(executable='matlab')>>> mlab.start()

after I type mlab.start() and press Enter button, a windows is opening.
The content in the windows is as follows:

MATLAB is running in headless mode. Figure windows will not be displayed.

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

old_warning_state =

16x1 struct array with fields:
identifier
state

Invalid MEX-file 'C:\Python27\lib\site-packages\pymatbridge\matlab\messenger.mexw64': XXXX

Error in matlabserver (line 7)
messenger('init', socket_address);

and still can't connect to matlab:

Starting MATLAB on ZMQ socket tcp://127.0.0.1:55555
Send 'exit' command to kill the server
............................................................MATLAB session timed
out after 60 seconds
MATLAB failed to start
False

—
Reply to this email directly or view it on GitHub
#125 (comment)
.

[willard-yuan]

I try to run it in Ubuntu, and I still face a problem:

>>> mlab.start()
Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge
Send 'exit' command to kill the server
Invalid MEX-file
'/usr/local/lib/python2.7/dist-packages/pymatbridge/matlab/messenger.mexa64':
libzmq.so.3: cannot open shared object file: No such file or directory

But I have install the pyzmq. I have test it:

import zmq

It's ok. Can you tell me how to make it run?

[willard-yuan]

After modifying the path in make.py and make the file, It's ok.

[arokem]

Seems like this is resolved. Closing it for now

[vaibhaw]

I installed pymatbridge using pip on Ubuntu 12.04 64bit machine with Python 2.7
I was also getting the following error:

Invalid MEX-file
'/usr/local/lib/python2.7/dist-packages/pymatbridge/matlab/messenger.mexa64':
libzmq.so.3: cannot open shared object file: No such file or directory

I think the reason for this error is that pip copies the precompiled messenger.mexa64 in python2.7/dist-packages/pymatbridge/matlab directory. This precompiled library was linked to libzmq.so.3 while I had lizmq.so.4 installed on my machine.

The solution is to compile this messenger binary on your machine. (Instructions for Linux)

# 1. Clone the python-matlab-bridge repo
git clone https://github.com/arokem/python-matlab-bridge.git
# 2. Change path of matlab/bin directory in python-matlab-bridge/messenger/mexa64/local.cfg
# In my case matlab was installed in /usr/local/MATLAB/R2013a/bin
# 3. Compile 
cd python-matlab-bridge/messenger
python make.py matlab

If libzmq and pyzmq is installed on your machine, new mex would be correctly linked to the libzmq binary installed on your machine.

Finally install python-matlab-bridge:

cd ..
python setup.py install

[arokem]

By the way, the compiled zmq4 binaries are now in the source distribution:

90fea89

so you don't even need to compile them yourself, but you will have to copy the messenger.mexa64.zmq4 file into messenger.mexa64 file, so that it's used.

[mnarayan]

The current master still isn't working for me. I still have linking issues with libzmq.so.3 despite having the library. I also tried to mex messenger as @vaibhawchandel suggested but I still get the following error.

Building messenger.mexa64...
"/opt/rice/matlab-2013b/bin/mex" -O -L. -I. -lzmq ./src/messenger.c

Traceback (most recent call last):
  File "make.py", line 108, in <module>
    build_matlab(static=args.static)
  File "make.py", line 93, in build_matlab
    do_build(make_cmd, 'messenger.%s' % extension)
  File "make.py", line 53, in do_build
    subprocess.check_output(shlex.split(make_cmd), shell=True)
  File "/opt/local/bin/anaconda/lib/python2.7/subprocess.py", line 573, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['/opt/rice/matlab-2013b/bin/mex', '-O', '-L.', '-I.', '-lzmq', './src/messenger.c']' returned non-zero exit status 255

Within matlab (version 2013b) I get this

>> cd pymatbridge/matlab
>> addpath(genpath('.'))
Warning: Function isrow has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name
conflict. 
> In path at 110
  In addpath at 87 
>> matlabserver('ipc:///tmp/pymatbridge')
Invalid MEX-file '/home/xxx/src/pymatbridge-0.4.3/pymatbridge/matlab/messenger.mexa64': libzmq.so.3: cannot open shared object
file: No such file or directory

Error in matlabserver (line 7)
messenger('init', socket_address);

[blink1073]

@mnarayan, can you try running that command directly from the shell prompt in the messenger directory and paste what you get?

[mnarayan]

It turns out that when I run the mex command from within matlab and link to libraries, I am able to compile messenger.mexa64.

mex -O -L/home/xxx/bin/lib/ -I/home/xxx/bin/include -lzmq src/messenger.c

However, matlabserver still cannot find libzmq.so.3 apparently; despite having the latest installation of pyzmq

>> matlabserver('ipc:/tmp/pymatbridge') 
Invalid MEX-file '/home/mn4/src/python-matlab-bridge/build/lib/pymatbridge/matlab/messenger.mexa64': libzmq.so.3: cannot open
shared object file: No such file or directory

Error in matlabserver (line 7)
messenger('init', socket_address);

[blink1073]

@mnarayan, it looks like you may need to set LD_LIBRARY_PATH to wherever zmq is located.

[mnarayan]

I do have LD_LIBRARY_PATH set to libzmq locations. This doesn't seem to resolve the linking issues.

I downgraded to pymatbridge 0.3 which seemed to resolve library linking issues. However ipython 3 notebooks don't seem to be able to return results from matlabserver to the notebook. This seems to be a notebook issues since I am able to use matlab magic within ipython. ipython 2 notebooks don't seem to have any problems however, so I will stick to that.

[blink1073]

Sorry @mnarayan, I'm out of ideas.