Traceback (most recent call last):


 "/Applications/PyCharm.app/Contents/helpers/pydev/pydev_run_in_console.py", line 53, in run_file

pydev_imports.execfile(file, globals, locals)
# execute the script


 "/Applications/PyCharm.app/Contents/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile

exec(compile(contents+"\n", file, 'exec'), glob, loc)


 "/Users/davidal/GoogleDrive/code/tripathy/tests/visualize_test.py", line 641, in <module>

viz_w.check_if_matrix_is_found()


 "/Users/davidal/GoogleDrive/code/tripathy/tests/visualize_test.py", line 610, in check_if_matrix_is_found

W_hat, sn, l, s = Opt.try_two_step_optimization_with_restarts(self.kernel, self.X, self.Y)


 "/Users/davidal/GoogleDrive/code/tripathy/src/t_optimizer.py", line 79, in try_two_step_optimization_with_restarts

Y=Y


 "/Users/davidal/GoogleDrive/code/tripathy/src/t_optimizer.py", line 183, in run_two_step_optimization

l=self.l.copy()


 "/Users/davidal/GoogleDrive/code/tripathy/src/t_optimization_functions.py", line 41, in optimize_s_sn_l

gp_reg.optimize(optimizer="lbfgs")


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/GPy/core/gp.py", line 655, in optimize

ret = super(GP, self).optimize(optimizer, start, messages, max_iters, ipython_notebook, clear_after_finish, **kwargs)


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/paramz/model.py", line 115, in optimize

self.optimizer_array = opt.x_opt


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/paramz/parameterized.py", line 334, in __setattr__

return object.__setattr__(self, name, val)


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/paramz/core/parameter_core.py", line 124, in optimizer_array

self.trigger_update()


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/paramz/core/updateable.py", line 79, in trigger_update

self._trigger_params_changed(trigger_parent)


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/paramz/core/parameter_core.py", line 134, in _trigger_params_changed

self.notify_observers(None, None if trigger_parent else -np.inf)


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/paramz/core/observable.py", line 91, in notify_observers

[callble(self, which=which) for _, _, callble in self.observers]


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/paramz/core/observable.py", line 91, in <listcomp>

[callble(self, which=which) for _, _, callble in self.observers]


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/paramz/core/parameter_core.py", line 508, in _parameters_changed_notification

self.parameters_changed()


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/GPy/core/gp.py", line 255, in parameters_changed

self.posterior, self._log_marginal_likelihood, self.grad_dict = self.inference_method.inference(self.kern, self.X, self.likelihood, self.Y_normalized, self.mean_function, self.Y_metadata)


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/GPy/inference/latent_function_inference/exact_gaussian_inference.py", line 50, in inference

Wi, LW, LWi, W_logdet = pdinv(Ky)


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/GPy/util/linalg.py", line 204, in pdinv

L = jitchol(A, *args)


 "/Users/davidal/miniconda3/lib/python3.6/site-packages/GPy/util/linalg.py", line 72, in jitchol

raise linalg.LinAlgError("not positive definite, even with jitter.")
numpy.linalg.linalg.LinAlgError: not positive definite, even with jitter.

Traceback (most recent call last):

 "/usr/local/mylar/cherrypy/_cprequest.py", line 645, in respond
response.body = self.handler()

 "/usr/local/mylar/cherrypy/lib/encoding.py", line 188, in __call__
self.body = self.oldhandler(_args, *_kwargs)

 "/usr/local/mylar/cherrypy/_cpdispatch.py", line 29, in __call__
return self.callable(_self.args, *_self.kwargs)

 "/usr/local/mylar/mylar/webserve.py", line 609, in error_change
self.from_Exceptions(comicid=comicid,gcdid=errorgcd)

 "/usr/local/mylar/mylar/webserve.py", line 180, in from_Exceptions
with open('custom_exceptions.csv', 'a') as f:IOError: [Errno 13] Permission denied: 'custom_exceptions.csv'