Memory allocation error (?) when running snap.pp.import_data
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- Python
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Description
I am trying to run snap.pp.import_data on my fragment file on a cluster, and I keep getting memory allocation errors, e.g.:
Processed 59,796 barcodes in 5m (226.7031/s) ...
memory allocation of 16384131072 bytes failed
Aborted (core dumped)
Processed 38,011 barcodes in 5m (65.6492/s) ...
memory allocation of 4718592 bytes failed
Aborted (core dumped)
The cluster I'm on has plenty of memory and should be sufficient for this step:
total used free shared buff/cache available
Mem: 755Gi 5.3Gi 252Gi 2.0Mi 496Gi 745Gi
Swap: 8.0Gi 23Mi 8.0Gi
My dataset has about 90k cell barcodes.
I've tried regenerating the fragment file and running snap.pp.import_data, but I still get the error.
I appreciate any help with this issue!
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Research direction
Start by reproducing the reported snap.pp.import_data run with a fragment file containing about 90k cell barcodes and compare the allocation failure with available cluster memory. No source file or test is named; done means identifying the cause of the allocation error and documenting or implementing a verified fix.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100