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Cluster setup failed. 2 of 2 workers failed to connect. #5

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Roger-GOAT opened this issue Jan 8, 2021 · 1 comment
Open

Cluster setup failed. 2 of 2 workers failed to connect. #5

Roger-GOAT opened this issue Jan 8, 2021 · 1 comment

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@Roger-GOAT
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hi, I am going to build a ts file from a matrix. It has 7274 cells with 22457 genes. It is running in rstudio server with 8 CPU and 64G RAM.
Code:
library(tSpace)
Idents(scRNA) <- "orig.ident"
df <- subset(scRNA, idents = 'day5')
df <- GetAssayData(df,slot="data",assay="RNA")
ts <- tSpace(df = df,
K = 20, L = 15,
D = 'pearson_correlation',
graph = 5,
trajectories = 200,
wp = 15, dr = 'pca', core_no = 2)
It shown error like below:
Step 1:Finding graphError in makePSOCKcluster(names = spec, ...) : Cluster setup failed. 2 of 2 workers failed to connect.
In addition: Warning messages: 1: In system(cmd, wait = FALSE) : system call failed: Cannot allocate memory 2: In system(cmd, wait = FALSE) : error in running command Error in save(list = names(.GlobalEnv), file = outfile, version = version, : error writing to connection Error saving session (search_path): R code execution error Error in system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE) : cannot popen '/usr/bin/which 'pdflatex' 2>/dev/null', probable reason 'Cannot allocate memory' Error in system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE) : cannot popen '/usr/bin/which 'pdflatex' 2>/dev/null', probable reason 'Cannot allocate memory'

Hope some one would give me some suggestion!
Best!

@Roger-GOAT
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PS: this is the information about df:

str(df)
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
..@ i : int [1:17528373] 8 11 16 35 54 60 79 96 100 108 ...
..@ p : int [1:7275] 0 1835 3637 5791 8919 11855 13622 16696 19530 22302 ...
..@ Dim : int [1:2] 22457 7274
..@ Dimnames:List of 2 .. ..$ : chr [1:22457] "Xkr4" "Gm37381" "Rp1" "Sox17" ... .. ..$ : chr [1:7274] "day5_AAACCCACAGGCCCTA-1" "day5_AAACCCACATAGGAGC-1" "day5_AAACCCACATTCCTAT-1" "day5_AAACCCAGTCCAGCAC-1" ...
..@ x : num [1:17528373] 1.18 1.18 2.05 1.7 2.05 ... ..@ factors : list()
--

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