LinAlgError: SVD did not converge

[jingc128]

Hi, we met the problem when we ran code: fs.tl.learn_intercellular_flows(adata, condition_key = condition_key, control_key = 'D1', flowsig_key = 'flowsig_network', flow_expr_key = 'X_flow', use_spatial = False, n_jobs = 32, n_bootstraps = 500) This is the error report:

_RemoteTraceback Traceback (most recent call last) _RemoteTraceback: """ Traceback (most recent call last): File "/home/cj123/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/externals/loky/process_executor.py", line 463, in _process_worker r = call_item() File "/home/cj123/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/externals/loky/process_executor.py", line 291, in call return self.fn(*self.args, self.kwargs) File "/home/cj123/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/parallel.py", line 598, in call return [func(*args, *kwargs) File "/home/cj123/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/parallel.py", line 598, in return [func(args, kwargs) File "/home/cj123/miniconda3/envs/flowsig/lib/python3.8/site-packages/flowsig/tools/_network.py", line 185, in run_utigsp obs_suffstat = partial_correlation_suffstat(control_resampled, invert=True) File "/home/cj123/miniconda3/envs/flowsig/lib/python3.8/site-packages/conditional_independence/suffstats/ci_suffstats/partial_correlation_suffstat.py", line 35, in partial_correlation_suffstat K = pinv(C) File "<__array_function__ internals>", line 200, in pinv File "/home/cj123/miniconda3/envs/flowsig/lib/python3.8/site-packages/numpy/linalg/linalg.py", line 1983, in pinv u, s, vt = svd(a, full_matrices=False, hermitian=hermitian) File "<__array_function__ internals>", line 200, in svd File "/home/cj123/miniconda3/envs/flowsig/lib/python3.8/site-packages/numpy/linalg/linalg.py", line 1642, in svd u, s, vh = gufunc(a, signature=signature, extobj=extobj) File "/home/cj123/miniconda3/envs/flowsig/lib/python3.8/site-packages/numpy/linalg/linalg.py", line 98, in _raise_linalgerror_svd_nonconvergence raise LinAlgError("SVD did not converge") numpy.linalg.LinAlgError: SVD did not converge """

The above exception was the direct cause of the following exception:

LinAlgError Traceback (most recent call last) Cell In[85], line 1 ----> 1 fs.tl.learn_intercellular_flows(adata, 2 condition_key = condition_key, 3 control_key = 'D1', 4 flowsig_key = 'flowsig_network', 5 flow_expr_key = 'X_flow', 6 use_spatial = False, 7 n_jobs = 32, 8 n_bootstraps = 500)

File ~/miniconda3/envs/flowsig/lib/python3.8/site-packages/flowsig/tools/_network.py:344, in learn_intercellular_flows(adata, condition_key, control_key, flowsig_key, flow_expr_key, use_spatial, block_key, n_jobs, n_bootstraps, alpha_ci, alpha_inv) 330 print(f'starting computations on {n_jobs} cores') 333 args = [(adata, 334 condition_key, 335 control_key, (...) 341 alpha_inv, 342 boot) for boot in range(n_bootstraps)] --> 344 bootstrap_results = Parallel(n_jobs=n_jobs)(delayed(run_utigsp)(*arg) for arg in args) 346 end = timer() 348 print(f'elapsed time: {end - start}')

File ~/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/parallel.py:2007, in Parallel.call(self, iterable) 2001 # The first item from the output is blank, but it makes the interpreter 2002 # progress until it enters the Try/Except block of the generator and 2003 # reaches the first yield statement. This starts the asynchronous 2004 # dispatch of the tasks to the workers. 2005 next(output) -> 2007 return output if self.return_generator else list(output)

File ~/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/parallel.py:1650, in Parallel._get_outputs(self, iterator, pre_dispatch) 1647 yield 1649 with self._backend.retrieval_context(): -> 1650 yield from self._retrieve() 1652 except GeneratorExit: 1653 # The generator has been garbage collected before being fully 1654 # consumed. This aborts the remaining tasks if possible and warn 1655 # the user if necessary. 1656 self._exception = True

File ~/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/parallel.py:1754, in Parallel._retrieve(self) 1747 while self._wait_retrieval(): 1748 1749 # If the callback thread of a worker has signaled that its task 1750 # triggered an exception, or if the retrieval loop has raised an 1751 # exception (e.g. GeneratorExit), exit the loop and surface the 1752 # worker traceback. 1753 if self._aborting: -> 1754 self._raise_error_fast() 1755 break 1757 # If the next job is not ready for retrieval yet, we just wait for 1758 # async callbacks to progress.

File ~/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/parallel.py:1789, in Parallel._raise_error_fast(self) 1785 # If this error job exists, immediately raise the error by 1786 # calling get_result. This job might not exists if abort has been 1787 # called directly or if the generator is gc'ed. 1788 if error_job is not None: -> 1789 error_job.get_result(self.timeout)

File ~/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/parallel.py:745, in BatchCompletionCallBack.get_result(self, timeout) 739 backend = self.parallel._backend 741 if backend.supports_retrieve_callback: 742 # We assume that the result has already been retrieved by the 743 # callback thread, and is stored internally. It's just waiting to 744 # be returned. --> 745 return self._return_or_raise() 747 # For other backends, the main thread needs to run the retrieval step. 748 try:

File ~/miniconda3/envs/flowsig/lib/python3.8/site-packages/joblib/parallel.py:763, in BatchCompletionCallBack._return_or_raise(self) 761 try: 762 if self.status == TASK_ERROR: --> 763 raise self._result 764 return self._result 765 finally:

LinAlgError: SVD did not converge

Thank you in advance for your reply.

[YuNong-Qiu]

@jingc128 Hi, Have you solved this problem? I also got this error when run flowsig. Can I ask for the solution?