提交作业后运行 R 代码时出错

问题描述

如果我只是运行 R 代码，那么它就可以工作。但是，当我提交作业时它不起作用。

我正在尝试通过提交作业来运行 myRcode.R 文件。以下是 .sh 文件：

#!/bin/bash
#PBS -N myRexample # Set job name to myjob
#PBS -l nodes=1:ppn=2 # Request 1 node with 2 processors
#PBS -l mem=8gb # Request 8gb memory
#PBS -l walltime=1:00:00 # Request 1hr job time
#PBS -V # Use submission environment
cd "$PBS_O_WORKDIR"
Rscript myRcode.R 

以下是我的 R 代码 (myRcode.R)：

#!/usr/bin/env Rscript
#Call the required functions and library
source("function1.R") 
library(R2jags)

#Function to be used in parallel computation  
mysim <- function(sim_number){
  set.seed(sim_number)
  outs <- function1() #rjags is called inside function1.
    return(list(outs[[1]],outs[[2]]))
}
 
#Parallel Computation
library(parallel)
library(doParallel)
registerDoParallel(cl <- parallel::makeCluster(2,outfile="test.txt"));

    results <- foreach(x = 1:2,.packages = c('MASS','R2jags'))%dopar% { mysim(sim_number=x)} 
  stopCluster(cl)

以下是我得到的错误：

Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.0.0
Loaded modules: basemod,bugs

Attaching package: ‘R2jags’

The following object is masked from ‘package:coda’:

    traceplot

Loading required package: foreach
Loading required package: iterators
Error in unserialize(socklist[[n]]) : error reading from connection
Calls: %dopar% ... recvOneData -> recvOneData.SOCKcluster -> unserialize
Execution halted

以下是 test.txt 文件：

starting worker pid=59438 on localhost:11788 at 08:55:04.422
starting worker pid=59451 on localhost:11788 at 08:55:04.799
Loading required package: rjags
Loading required package: rjags
Loading required package: coda
Loading required package: coda
Linked to JAGS 4.0.0
Loaded modules: basemod,bugs
Linked to JAGS 4.0.0
Loaded modules: basemod,bugs

Attaching package: ‘R2jags’


Attaching package: ‘R2jags’

The following object is masked from ‘package:coda’:

    traceplot

The following object is masked from ‘package:coda’:

    traceplot


 *** caught illegal operation ***
address 0x7f51ceed1917,cause 'illegal operand'

 *** caught illegal operation ***
address 0x7fe45c73d917,cause 'illegal operand'

解决方法

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