ssh: connect to host 2 port 22: Network is unreachable

[Sherry520]

I used foreach and dopar to replace for. If I use an R script in the slurm cluster, it will report an error. If I go directly to a compute node, open R, and enter the code, there is no such error.

[Sherry520]

command:

Rscript 7131-d_eff_pval.R --trait PH --thread 4 --path ./

cat 7131-d_eff_pval.R
# library(BGLR) # R package BGLR is required
library(data.table)
library(foreach)
library(doParallel)
library(getopt)

# 准备读入参数
spec <- matrix(
  c("trait",  "t", 1, "character",  "trait name",
    "thread", "n", 1, "character",  "thread number for doparallel",
    "path",  "p", 2, "character",  "working path",
    "help",   "h", 0, "logical",  "This is Help!"),
  byrow=TRUE, ncol=5)

## 使用getopt方法
opt <- getopt(spec=spec)

if (is.null(opt$trait) || is.null(opt$thread)) {
  cat(paste(getopt(spec, usage = T), "\n"))
  q(status = 1)
}

# 默认值
if (is.null(opt$path)) {
  opt$path = "./"
}

# 赋值读入的参数
trait <- opt$trait
no_cores <- opt$thread

# 设置工作目录
setwd(opt$path)

# 载入trDdata
# trAdata <- as.matrix(read.table(paste0("trAdata_",trait,".txt")))
trDdata <- as.matrix(read.table(paste0("trDdata_",trait,".txt")))
Y <- (read.table(paste0("Y_",trait,".txt")))$V1
# TRAN <- as.matrix(read.table(paste0("TRAN_",trait,".txt")))
load(file = "total_ma_names.rdata")

source("SNP_eff_pval_fun.R")
d_eff_pval(trDdata = trDdata,total_ma_names = total_ma_names,trait = trait,Y=Y,no_cores = no_cores)

cat SNP_eff_pval_fun.R
## calculater domiance effect and pval
d_eff_pval <- function(trDdata, total_ma_names, trait, Y, no_cores) {
  cl <- makeCluster(no_cores)
  registerDoParallel(cl)

  nmar <- length(total_ma_names)
  result <- foreach(m = 1:nmar, .combine = "rbind", .inorder = TRUE) %dopar%
    {
      subfinalDATA <- data.frame(y = Y, trDdata[, m])
      colnames(subfinalDATA)[2] <- total_ma_names[m]
      fit.lm <- lm(as.formula(paste("y ~", total_ma_names[m], "-1")),
        data = subfinalDATA)
      c(summary(fit.lm)$coefficient[1, 1], summary(fit.lm)$coefficient[1,
        4])
    }
  stopCluster(cl)

  colnames(result) <- c("Effect", "Pvalue")
  rownames(result) <- total_ma_names

  write.table(result, paste0("test.MapQTL_MPH_pval_effect_d_", trait,
    ".txt"), quote = FALSE)
}

[Sherry520]

I found that I entered the wrong datatype, the datatype of the number of threads should be an integer, and the number of threads I set in getopt's argument is a character.

spec <- matrix(
  c("trait",  "t", 1, "character",  "trait name",
    "thread", "n", 1, "integer",  "thread number for doparallel")