Welcome to IDTxl Discussions!

[pwollstadt]

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[mwibral]

Hi Patricia,
nice tool. Seems like the right place to discuss, share tips and plan the future of IDTxl :-)

[pwollstadt]

Thought so as well :) let's see how it goes!

[hswchung860603]

Hi,I am a student doing project about multivariate-TE. And this is my first time using this package.
After the installation I tried the multivariateTE example and this error ran out.
I search for help but still got no idea for this.
It would be a huge favor if someone can fix this problem.

Adding data with properties: 5 processes, 1000 samples, 5 replications
overwriting existing data
JVMNotFoundException Traceback (most recent call last)
in
16
17 # c) Run analysis
---> 18 results = network_analysis.analyse_network(settings=settings, data=data)
19
20 # d) Plot inferred network to console and via matplotlib

c:\users\yaolab\idtxl\idtxl\multivariate_te.py in analyse_network(self, settings, data, targets, sources)
156 print('\n####### analysing target with index {0} from list {1}'
157 .format(t, targets))
--> 158 res_single = self.analyse_single_target(
159 settings, data, targets[t], sources[t])
160 results.combine_results(res_single)

c:\users\yaolab\idtxl\idtxl\multivariate_te.py in analyse_single_target(self, settings, data, target, sources)
268 """
269 # Check input and clean up object if it was used before.
--> 270 self._initialise(settings, data, sources, target)
271
272 # Main algorithm.

c:\users\yaolab\idtxl\idtxl\network_inference.py in _initialise(self, settings, data, sources, target)
369
370 # Set CMI estimator.
--> 371 self._set_cmi_estimator()
372
373 # Check the provided target and sources.

c:\users\yaolab\idtxl\idtxl\network_analysis.py in _set_cmi_estimator(self)
207 self._cmi_estimator_local = EstimatorClass(self.settings)
208 else:
--> 209 self._cmi_estimator = EstimatorClass(self.settings)
210
211 def _separate_realisations(self, idx_full, idx_single):

c:\users\yaolab\idtxl\idtxl\estimators_jidt.py in init(self, settings)
1323 settings = self._check_settings(settings)
1324 # Start JAVA virtual machine and create JAVA object.
-> 1325 self._start_jvm()
1326 CalcClass = (jp.JPackage('infodynamics.measures.continuous.gaussian').
1327 ConditionalMutualInfoCalculatorMultiVariateGaussian)

c:\users\yaolab\idtxl\idtxl\estimators_jidt.py in _start_jvm(self)
59 jar_location = resource_filename(name, 'infodynamics.jar')
60 if not jp.isJVMStarted():
---> 61 jp.startJVM(jp.getDefaultJVMPath(), '-ea', ('-Djava.class.path=' +
62 jar_location))
63

~\Anaconda3\envs\idtxl\lib\site-packages\jpype_jvmfinder.py in getDefaultJVMPath()
72 else:
73 finder = LinuxJVMFinder()
---> 74 return finder.get_jvm_path()
75
76

~\Anaconda3\envs\idtxl\lib\site-packages\jpype_jvmfinder.py in get_jvm_path(self)
210 if jvm_notsupport_ext is not None:
211 raise jvm_notsupport_ext
--> 212 raise JVMNotFoundException("No JVM shared library file ({0}) "
213 "found. Try setting up the JAVA_HOME "
214 "environment variable properly."

JVMNotFoundException: No JVM shared library file (jvm.dll) found. Try setting up the JAVA_HOME environment variable properly.

[mwibral]

Dear hswchung860603, could you give some more information on your installation, i.e. OS version, and the java virtual machine (jvm) your are using? Best, Michael

…

On 17.01.21 17:11, hswchung860603 wrote: Hi,I am a student doing project about multivariate-TE. And this is my first time using this package. After the installation I tried the multivariateTE example and this error ran out. I search for help but still got no idea for this. It would be a huge favor if someone can fix this problem. Adding data with properties: 5 processes, 1000 samples, 5 replications overwriting existing data JVMNotFoundException Traceback (most recent call last) in 16 17 # c) Run analysis ---> 18 results = network_analysis.analyse_network(settings=settings, data=data) 19 20 # d) Plot inferred network to console and via matplotlib c:\users\yaolab\idtxl\idtxl\multivariate_te.py in analyse_network(self, settings, data, targets, sources) 156 print('\n####### analysing target with index {0} from list {1}' 157 .format(t, targets)) --> 158 res_single = self.analyse_single_target( 159 settings, data, targets[t], sources[t]) 160 results.combine_results(res_single) c:\users\yaolab\idtxl\idtxl\multivariate_te.py in analyse_single_target(self, settings, data, target, sources) 268 """ 269 # Check input and clean up object if it was used before. --> 270 self._initialise(settings, data, sources, target) 271 272 # Main algorithm. c:\users\yaolab\idtxl\idtxl\network_inference.py in _initialise(self, settings, data, sources, target) 369 370 # Set CMI estimator. --> 371 self._set_cmi_estimator() 372 373 # Check the provided target and sources. c:\users\yaolab\idtxl\idtxl\network_analysis.py in _set_cmi_estimator(self) 207 self._cmi_estimator_local = EstimatorClass(self.settings) 208 else: --> 209 self._cmi_estimator = EstimatorClass(self.settings) 210 211 def _separate_realisations(self, idx_full, idx_single): c:\users\yaolab\idtxl\idtxl\estimators_jidt.py in *init*(self, settings) 1323 settings = self._check_settings(settings) 1324 # Start JAVA virtual machine and create JAVA object. -> 1325 self._start_jvm() 1326 CalcClass = (jp.JPackage('infodynamics.measures.continuous.gaussian'). 1327 ConditionalMutualInfoCalculatorMultiVariateGaussian) c:\users\yaolab\idtxl\idtxl\estimators_jidt.py in _start_jvm(self) 59 jar_location = resource_filename(*name*, 'infodynamics.jar') 60 if not jp.isJVMStarted(): ---> 61 jp.startJVM(jp.getDefaultJVMPath(), '-ea', ('-Djava.class.path=' + 62 jar_location)) 63 ~\Anaconda3\envs\idtxl\lib\site-packages\jpype_jvmfinder.py in getDefaultJVMPath() 72 else: 73 finder = LinuxJVMFinder() ---> 74 return finder.get_jvm_path() 75 76 ~\Anaconda3\envs\idtxl\lib\site-packages\jpype_jvmfinder.py in get_jvm_path(self) 210 if jvm_notsupport_ext is not None: 211 raise jvm_notsupport_ext --> 212 raise JVMNotFoundException("No JVM shared library file ({0}) " 213 "found. Try setting up the JAVA_HOME " 214 "environment variable properly." JVMNotFoundException: No JVM shared library file (jvm.dll) found. Try setting up the JAVA_HOME environment variable properly. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#61 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFJQGSABMYY2UTIFZ2JF5LS2MDZVANCNFSM4UWOWJYQ>.

[jlizier]

I think the suggestion in the error message from jpype "Try setting up the JAVA_HOME environment variable properly" is key. Try googling how to do that in your environment, try it, and if it doesn't work then send more info.

…

--joe

On Sat, 23 Jan 2021 at 00:21, mwibral ***@***.***> wrote: Dear hswchung860603, could you give some more information on your installation, i.e. OS version, and the java virtual machine (jvm) your are using? Best, Michael On 17.01.21 17:11, hswchung860603 wrote: > > Hi,I am a student doing project about multivariate-TE. And this is my > first time using this package. > After the installation I tried the multivariateTE example and this > error ran out. > I search for help but still got no idea for this. > It would be a huge favor if someone can fix this problem. > > Adding data with properties: 5 processes, 1000 samples, 5 replications > overwriting existing data > JVMNotFoundException Traceback (most recent call last) > in > 16 > 17 # c) Run analysis > ---> 18 results = network_analysis.analyse_network(settings=settings, > data=data) > 19 > 20 # d) Plot inferred network to console and via matplotlib > > c:\users\yaolab\idtxl\idtxl\multivariate_te.py in > analyse_network(self, settings, data, targets, sources) > 156 print('\n####### analysing target with index {0} from list {1}' > 157 .format(t, targets)) > --> 158 res_single = self.analyse_single_target( > 159 settings, data, targets[t], sources[t]) > 160 results.combine_results(res_single) > > c:\users\yaolab\idtxl\idtxl\multivariate_te.py in > analyse_single_target(self, settings, data, target, sources) > 268 """ > 269 # Check input and clean up object if it was used before. > --> 270 self._initialise(settings, data, sources, target) > 271 > 272 # Main algorithm. > > c:\users\yaolab\idtxl\idtxl\network_inference.py in _initialise(self, > settings, data, sources, target) > 369 > 370 # Set CMI estimator. > --> 371 self._set_cmi_estimator() > 372 > 373 # Check the provided target and sources. > > c:\users\yaolab\idtxl\idtxl\network_analysis.py in > _set_cmi_estimator(self) > 207 self._cmi_estimator_local = EstimatorClass(self.settings) > 208 else: > --> 209 self._cmi_estimator = EstimatorClass(self.settings) > 210 > 211 def _separate_realisations(self, idx_full, idx_single): > > c:\users\yaolab\idtxl\idtxl\estimators_jidt.py in *init*(self, settings) > 1323 settings = self._check_settings(settings) > 1324 # Start JAVA virtual machine and create JAVA object. > -> 1325 self._start_jvm() > 1326 CalcClass = > (jp.JPackage('infodynamics.measures.continuous.gaussian'). > 1327 ConditionalMutualInfoCalculatorMultiVariateGaussian) > > c:\users\yaolab\idtxl\idtxl\estimators_jidt.py in _start_jvm(self) > 59 jar_location = resource_filename(*name*, 'infodynamics.jar') > 60 if not jp.isJVMStarted(): > ---> 61 jp.startJVM(jp.getDefaultJVMPath(), '-ea', ('-Djava.class.path=' + > 62 jar_location)) > 63 > > ~\Anaconda3\envs\idtxl\lib\site-packages\jpype_jvmfinder.py in > getDefaultJVMPath() > 72 else: > 73 finder = LinuxJVMFinder() > ---> 74 return finder.get_jvm_path() > 75 > 76 > > ~\Anaconda3\envs\idtxl\lib\site-packages\jpype_jvmfinder.py in > get_jvm_path(self) > 210 if jvm_notsupport_ext is not None: > 211 raise jvm_notsupport_ext > --> 212 raise JVMNotFoundException("No JVM shared library file ({0}) " > 213 "found. Try setting up the JAVA_HOME " > 214 "environment variable properly." > > JVMNotFoundException: No JVM shared library file (jvm.dll) found. Try > setting up the JAVA_HOME environment variable properly. > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > < #61 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ACFJQGSABMYY2UTIFZ2JF5LS2MDZVANCNFSM4UWOWJYQ >. > — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#61 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAMKXQZYEYH6BOVJOP6II63S3F3VVANCNFSM4UWOWJYQ> .

[jlizier]

Actually, I see this is a duplicate of another discussion thread #63 and that's a more appropriate place to follow this through. I'll move mine and Michael's comments over there.