Skip to content

fastMNN causing timeout in hca-bone-marrow.Rmd when testing with openblas-openmp #6

@PeteHaitch

Description

@PeteHaitch

From #bioc-builds > Books now being built on macOS in devel? @ 💬

The timeout happens in OSCA.workflows in the hca-bone-marrow.Rmd chapter in the integration chunk when batchelor::fastMNN() is called. This call spans five R processes that use 14.1g each and the load falls to < 1. So it looks like batchelor::fastMNN() gets stuck, but it's stuck doing what? It doesn't seem to be I/O. This only happens with openblas-openmp. I want to investigate this more. Note that this indirectly causes the timeouts you see for the other sub-books (OSCA.basic, OSCA.multisample and *OSCA.advanced) because for all of them rebook::preCompileBook() gets stuck waiting for OSCA.workflows to compute and cache the stuff that they need in order to proceed.

```{r integration}
library(batchelor)
library(BiocNeighbors)
set.seed(1010001)
merged.bone <- fastMNN(sce.bone, batch = sce.bone$Donor, subset.row = top.bone,
BSPARAM=BiocSingular::RandomParam(deferred = TRUE),
BNPARAM=AnnoyParam(),
BPPARAM=bpp)
reducedDim(sce.bone, 'MNN') <- reducedDim(merged.bone, 'corrected')
```

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions