JVM cannot be restarted

[xtrojak]

Restarting a node (eg. end and start again) resulted to the following error:

192.168.17.1 - - [24/Oct/2019 18:02:19] "POST /initiate HTTP/1.1" 200 -

Exception in thread 1PBR-checker:
Traceback (most recent call last):
  File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
    self.run()
  File "/home/pi/PBRcontrol/DataManager/executioner.py", line 48, in run
    device = interpreter.DeviceManager(*arguments)  # initiate the physical device and its interpreter
  File "/home/pi/PBRcontrol/DataManager/interpreterPBR.py", line 49, in __init__
    super(DeviceManager, self).__init__(device_details, device_class, log)
  File "/home/pi/PBRcontrol/DataManager/base_interpreter.py", line 9, in __init__
    self.device = device_class(self.device_details['device_type'], self.device_details['address'])
  File "/home/pi/PBRcontrol/HWdevices/PSI_java/PBR.py", line 7, in __init__
    super(PBR, self).__init__(ID, address, "/home/pi/PBRcontrol/HWdevices/PSI_java/lib/config/device_PBR.config")
  File "/home/pi/PBRcontrol/HWdevices/PSI_java/Device.py", line 16, in __init__
    self.device = self.connect(device_config)
  File "/home/pi/PBRcontrol/HWdevices/PSI_java/Device.py", line 20, in connect
    "-Djava.class.path=/home/pi/PBRcontrol/HWdevices/PSI_java/lib/jar/bioreactor-commander-0.8.7.jar")
  File "/home/pi/.local/lib/python3.5/site-packages/jpype/_core.py", line 157, in startJVM
    raise OSError('JVM cannot be restarted')
OSError: JVM cannot be restarted

[DanDayne]

Problem is in the implementation of PSI_java - if multiple nodes try to start JVM on the same system, PBRcontrol will fail as it is not possible. Only one JVM can be running at a time.

[DanDayne]

This introduces many problems regarding use of multiple java-bound PBRs and restarting PBRs

[mgeletka]

created PULL request #15

[DanDayne]

Once JVM is started, it is never turned off as there is currently no way of knowing whether other devices/nodes are using it. This should not afffect functionality, nor performance. My temporarily limited resources prevent me from thorough testing. @xtrojak, could you look into this?

[DanDayne]

Initiation of Java device resulted in following error:

/home/pi/.local/lib/python3.5/site-packages/jpype/_core.py:210: UserWarning:
-------------------------------------------------------------------------------
Deprecated: convertStrings was not specified when starting the JVM. The default
behavior in JPype will be False starting in JPype 0.8. The recommended setting
for new code is convertStrings=False.  The legacy value of True was assumed for
this session. If you are a user of an application that reported this warning,
please file a ticket with the developer.
-------------------------------------------------------------------------------
  """)
Exception in thread 19PBRPBR19-checker:
Traceback (most recent call last):
  File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
    self.run()
  File "/home/pi/PBRcontrol/DataManager/executioner.py", line 52, in run
    device = interpreter.DeviceManager(*arguments)  # initiate the physical device and its interpreter
  File "/home/pi/PBRcontrol/DataManager/interpreterPBR.py", line 48, in __init__
    super(DeviceManager, self).__init__(device_details, device_class, log)
  File "/home/pi/PBRcontrol/DataManager/base_interpreter.py", line 17, in __init__
    self.device = device_class(*args)
  File "/home/pi/PBRcontrol/HWdevices/PSI_java/PBR.py", line 7, in __init__
    super(PBR, self).__init__(ID, address, "/home/pi/PBRcontrol/HWdevices/PSI_java/lib/config/device_PBR.config")
  File "/home/pi/PBRcontrol/HWdevices/PSI_java/Device.py", line 16, in __init__
    self.device = self.connect(device_config)
  File "/home/pi/PBRcontrol/HWdevices/PSI_java/Device.py", line 19, in connect
    CommanderConnector = jpype.JClass("psi.bioreactor.commander.CommanderConnector")
  File "/home/pi/.local/lib/python3.5/site-packages/jpype/_jclass.py", line 130, in __new__
    return _JClassNew(args[0], **kwargs)
  File "/home/pi/.local/lib/python3.5/site-packages/jpype/_jclass.py", line 213, in _JClassNew
    javaClass = _jpype.PyJPClass(arg)
jpype._jclass.java.lang.NoClassDefFoundError: psi/bioreactor/commander/CommanderConnector

@mgeletka, do you have any idea what might be causing this issue?

[xtrojak]

Seems like problem in paths management.

[xtrojak]

Issue solved by manual addition of Java class path before the JVM is started (in Device.py file). It is not clear why this step is necessary, but it is working.