slurmR 尝试运行示例作业“调用 `silent_system2` 时发生错误：”

如何解决slurmR 尝试运行示例作业“调用 `silent_system2` 时发生错误：”

我设置了一个 slurm 集群，我可以发出 srun -N4 主机名就好了。

我一直看到“silent_system2”错误。我已经使用 devtools::install_github("USCbiostats/slurmR") 安装了 slurmR

我正在关注第二个示例 3：https://github.com/USCbiostats/slurmR

这是我的文件

cat slurmR.R

library(doParallel)
library(slurmR)

cl <- makeSlurmCluster(4)

registerDoParallel(cl)
m <- matrix(rnorm(9),3,3)
foreach(i=1:nrow(m),.combine=rbind)

StopCluster(cl)
print(m)

cat rscript.slurm

#!/bin/bash
#SBATCH --output=slurmR.out

cd /mnt/nfsshare/tankpve0/
Rscript --vanilla slurmR.R

cat slurmR.out

Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
slurmR default option for `tmp_path` (used to store auxiliar files) set to:
  /mnt/nfsshare/tankpve0
You can change this and checkout other slurmR options using: ?opts_slurmR,or you could just type "opts_slurmR" on the terminal.
Submitting job... jobid:18.
Slurm accounting storage is disabled
Error: An error has occurred when calling `silent_system2`:
Warning: An error was detected before returning the cluster object. If submitted,we will try to cancel the job and stop the cluster object.
Execution halted

解决方法

不完全与 slurmR 相关，但如果目标是 slurm + 集群的...那么只需将 slurmR 用作批处理并修改 slurmR.R（不是相同的内部函数，但您会看到聚类是如何完成的）

>

library(parallel)
primary <- 'slurmw01'
spec <- c(rep(primary,4),rep('slurmw02',rep('slurmw03',rep('slurmw04',4))
cl <- makeCluster(master=primary,spec=spec)
#load libraries,load files
simpi <- function(n) {
  points <- matrix(runif(n*2),ncol=2)
  mean(rowSums(points^2) <= 1)*4
 }

clusterEvalQ(cl,{
        ## set up each worker.  Could also use clusterExport()
          library(parallel)
  })
#copy vars,functions
clusterExport(cl,ls(all.names=TRUE),envir = .GlobalEnv)
rest <- clusterApplyLB(cl,rep(1e6,100),simpi)
print(mean(unlist(rest)))
stopCluster(cl)