--use-fast-tsne segfaults

[ghuls]

I get a segfault when running SC__SCANPY__DIM_REDUCTION__UMAP on my data

Multicore-TSNE segfault bug report: DmitryUlyanov/Multicore-TSNE#59

Maybe it is worth to look if https://github.com/pavlin-policar/openTSNE/ can be used instead of Multicore-TSNE in scanpy.

Error executing process > 'single_sample:SINGLE_SAMPLE:DIM_REDUCTION:SC__SCANPY__DIM_REDUCTION__UMAP (1)'

Caused by:
  Process `single_sample:SINGLE_SAMPLE:DIM_REDUCTION:SC__SCANPY__DIM_REDUCTION__UMAP (1)` terminated with an error exit status (139)

Command executed:

  /staging/leuven/stg_00002/lcb/ghuls/software/SingleCellTxBenchmark/src/scanpy/bin/dim_reduction/sc_dim_reduction.py          --method UMAP                              --n-comps 20                              --use-fast-tsne          TEW__7b2a3b__scNuc_Liver_Habib.SC__SCANPY__DIM_REDUCTION_TSNE.h5ad          "TEW__7b2a3b__scNuc_Liver_Habib.SC__SCANPY__DIM_REDUCTION_UMAP.h5ad"

Command exit status:
  139

Command output:
  (empty)

Command error:
  /opt/venv/lib/python3.7/site-packages/louvain/Optimiser.py:349: SyntaxWarning: assertion is always true, perhaps remove parentheses?
    assert(issubclass(partition_type, LinearResolutionParameterVertexPartition),
  /staging/leuven/stg_00002/lcb/ghuls/software/SingleCellTxBenchmark/src/scanpy/bin/dim_reduction/sc_dim_reduction.py:96: UserWarning: The neighborhood graph of observations has not been computed. Computing...
    warnings.warn("The neighborhood graph of observations has not been computed. Computing...")
  .command.sh: line 2:  4807 Segmentation fault      (core dumped) /staging/leuven/stg_00002/lcb/ghuls/software/SingleCellTxBenchmark/src/scanpy/bin/dim_reduction/sc_dim_reduction.py --method UMAP --n-comps 20 --use-fast-tsne TEW__7b2a3b__scNuc_Liver_Habib.SC__SCANPY__DIM_REDUCTION_TSNE.h5ad "TEW__7b2a3b__scNuc_Liver_Habib.SC__SCANPY__DIM_REDUCTION_UMAP.h5ad"

Work dir:
  /.../analysis_ghuls/work/d8/909b46cf55fe12d36e3977738e167c

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

[KrisDavie]

That process is the UMAP one, so unless I'm mistaken, it isn't even running the tSNE. Must be something to do with the UMAP instead.

[ghuls]

Pull request #21 fixes the error.