Open Microscopy Environment

Hi there,

I'm trying to call a compiled Matlab executable from Omero server using Python script service.

In my Python script, I use the fucntion:

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subprocess.Popen(['/home/yuh5/Desktop/magicsquare/for_testing/magicsquare', '5'])

However, I got error:

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omero script launch 354
Using session 869c89d4-c0a5-44a1-9205-6aa49a300d47 (yuh5@localhost:4064). Idle timeout: 10 min. Current group: system
Enter value for "IDs": 1
Job 311 ready
Waiting....
Callback received: FINISHED

   *** start stdout (id=361)***
   * Color of each channel:
   *
   *** end stdout ***


   *** start stderr (id=362)***
   * Traceback (most recent call last):
   *   File "./script", line 122, in <module>
   *     run_script()
   *   File "./script", line 100, in run_script
   *     subprocess.Popen(['/home/yuh5/Desktop/magicsquare/for_testing/magicsquare', '5'])
   *   File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
   *     errread, errwrite)
   *   File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
   *     raise child_exception
   * OSError: [Errno 13] Permission denied
   *
   *** end stderr ***


   *** out parameters ***
   ***  done ***

I'm sure I have the permission to execute file under that path. And I was able to run that executable with:

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omero@ceb-cad2:/usr/local/MATLAB$ python
Python 2.7.12 (default, Dec  4 2017, 14:50:18)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import subprocess
>>> subprocess.Popen(['/home/yuh5/Desktop/magicsquare/for_testing/magicsquare', '5'])
<subprocess.Popen object at 0x7f879a9f8f90>
>>>
m =

    17    24     1     8    15
    23     5     7    14    16
     4     6    13    20    22
    10    12    19    21     3
    11    18    25     2     9



FYI:
ceb-cad2 is my Linux server. Omero.server is installed on ceb-cad2. Matlab executable is placed under ~/Desktop/ on ceb-cad2.

1. Do y'all know why I get this error?

2. When I call: "omero script launch...", what group is this executed under? Root? my user account on the Linux machine? or Omero?

Hi Hang,

the OMERO script should be executed by the owner of the Processor process

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$ ps aux | grep runProcessor.py


What are the ownership and the permissions of your executable file as shown by:

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$ ls -alh /home/yuh5/Desktop/magicsquare/for_testing/magicsquare


Best,
Sebastien

For each of the two commands, I got the following. The first one I don't quite understand what it's telling me. The second the permissions seems fine to me.

1.

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ps aux | grep runProcessor.py
yuh5      3230  0.0  0.0  14224  1020 pts/1    S+   11:17   0:00 grep --color=auto runProcessor.py
omero     3288  0.0  0.2 1205716 83280 ?       Sl   Apr27   8:13 python lib/python/runProcessor.py --Ice.Config=/home/omero/OMERO.server-5.4.4-ice36-b82/var/master/servers/Processor-0/config/config

2.

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ls -alh /home/yuh5/Desktop/magicsquare/for_testing/magicsquare
-rwxrwxr-x 1 yuh5 yuh5 87K Apr 11 17:22 /home/yuh5/Desktop/magicsquare/for_testing/magicsquare


Hang

See also discussion in viewtopic.php?f=6&t=8473&p=19262#p19262