_search_dim_red_parameters: TSNE option sets the run to permanent sleep
While writing tests I encountered that the function _search_dim_red_parameters is send to permanent sleep. At least this what I suspect. CPU usage is 0 and it runs at least 1 hour, which is a lot for a 200*100 anndata object.
With the option set to umap there are no problems. When interupting the process it stops here:
KeyboardInterrupt Traceback (most recent call last)
Cell In [7], line 1
----> 1 sctoolbox.plotting.search_tsne_parameters(adata, color="condition")
File /mnt/workspace/rwiegan/conda_envs/sctoolbox/lib/python3.10/site-packages/sctoolbox/plotting/embedding.py:168, in search_tsne_parameters(adata, perplexity_range, learning_rate_range, color, verbose, threads, save, **kwargs)
165 args["method"] = "tsne"
166 kwargs = args.pop("kwargs")
--> 168 return _search_dim_red_parameters(**args, **kwargs)
File /mnt/workspace/rwiegan/conda_envs/sctoolbox/lib/python3.10/site-packages/sctoolbox/plotting/embedding.py:255, in _search_dim_red_parameters(adata, method, perplexity_range, learning_rate_range, min_dist_range, spread_range, color, verbose, threads, save, **kwargs)
252 jobs[(i, j)] = job
253 pool.close()
--> 255 utils.monitor_jobs(jobs, f"Computing {method.upper()}s")
256 pool.join()
258 # Figure with rows=spread, cols=dist
File /mnt/workspace/rwiegan/conda_envs/sctoolbox/lib/python3.10/site-packages/sctoolbox/utils/multiprocessing.py:53, in monitor_jobs(jobs, description)
51 pbar.n = n_ready
52 pbar.refresh()
---> 53 time.sleep(1)
54 n_ready = sum([job.ready() for job in jobs])
56 pbar.n = n_ready # update progress bar to 100%
Not sure what is the exact cause
Edited by Rene Wiegandt