Error: cannot allocate vector of size 294.0 Gb #1
Description
Hi All,
More looking for information, I was trying to run this pipeline after finding your cellsegmentationevaluator. I managed to get it running without issue. However, whilst it is processing I run into an error:
`> cytospatio(input_file = "./data.csv", output_dir = "./results/", TR, IR, HR)
Error: object 'IR' not found
cytospatio(input_file = "./data.csv", output_dir = "./results", TR = 500, IR = 100, HR = 1)
Generating quadrature scheme of range 100
Marked planar point pattern: 78580 points
Multitype, with levels =
AEC (DRA) AEC (PBS) Alveolar Fibroblast Alveolar Macrophages ATI (DRA) ATI (PBS) ATII (DRA) ATII (PBS) B Cells CD11b+ Cells CD11b+CD44+ Cells CD11b+Ly6C+ Endothelial Infiltrating Cells Intraepithelial Cells MHCII+B220-S100a4+
cells Neutrophils S100a4Hi Fibroblasts SMA+ Stromal Cells Smooth Muscle
window: rectangle = [0.3333, 688.6667] x [0.3333, 658.6667] units
List of spatial objects
Component 1:
Quadrature scheme (Berman-Turner)
78580 data points, 1493100 dummy points
0 x 0 grid of dummy points, plus 4 corner points
dummy spacing: Inf units
Total weight 9063055.55576
[1] "tomogram" "1"
Large quadrature scheme split into blocks to avoid memory size limits; 1493100 dummy points split into 299 blocks, the first 298 blocks containing 4994 dummy points and the last block containing 4888 dummy points
[1] 0
Error: cannot allocate vector of size 294.0 Gb`
Our dataset is just under 80,000 cells total. I just tried again with it cut down to 20,000 cells and it seems to be working fine. Just wondered what the system requirements were likely to be in relation to input data size?