[Rd] [External] svd For Large Matrix

[Dario Strbenac]

Good day,

Ah, I was confident it wouldn't be environment-specific but it is. My environment is

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

It crashes at about 180 GB RAM usage. The server has 1024 GB physical RAM in it. Modestly downsampling to 30 million cells avoids the segmentation fault. The segmentation fault originates from BLAS

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff7649c10 in ATL_dgecopy () from /usr/lib/x86_64-linux-gnu/libblas.so.3

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia