Slurm 集群中的 R 代码无法正确读取

Question

我是运行 Slurm 集群上的 R 代码，具有以下“.sh”文件：

#!/bin/bash
#SBATCH --partition=p_parallel
#SBATCH --nodes=1
#SBATCH --cpus-per-task=16
#SBATCH --workdir=/work/uder2/ODE/lancio/
module load statistics/r-3.6.1
srun Rscript   TEST.R

R 代码非常简单。有时喜欢

DIRbase     = "/work/uder2/ODE/"
DIRdata     = paste(DIRbase,"data/",sep="")
list.files(DIRdata)
load(paste(DIRdata,"Data.Rdata",sep=""))


NAME = "PriorU" 
ialg = 3

nG  = 500  
LimEta = 40  

LimMu2  = 15 
LimMin = 500

LimMu = 0.1
LimSpike = 10
LimSigma2 = (8)^2/(-2*log(LimMu))*1.2


NAME = paste(NAME,"_ng",nG, sep="")

### ### ### ### ### ### ### ### 
### MODELS
### ### ### ### ### ### ### ### 

DATA = allGenesData
nrowData = nrow(DATA$premature)


sd1 = as.numeric(apply(DATA$premature,1,var))
sd2 = as.numeric(apply(DATA$mature,1,var))
sd3 = as.numeric(apply(DATA$nascent,1,var))

epsi = 0.000001
App = c(which(sd1<=epsi),which(sd2<=epsi),which(sd3<=epsi))
App2 = c(which(sd1>50),which(sd2>100000),which(sd3>1500))

minep = 0.1
xy1 = as.numeric(apply(DATA$premature,1,min))
xy2 = as.numeric(apply(DATA$mature,1,min))
xy3 = as.numeric(apply(DATA$nascent,1,min))
App3 = c(which(xy1<=minep),which(xy2<=minep),which(xy3<=minep))

实际上，代码要长得多，但我认为文件的内容并不重要。

发生的情况是，有时代码编写不正确。例如，而不是

App3 = c(which(xy1<=minep),which(xy2<=minep),which(xy3<=minep))

已读

App3  which(xy1<=minep),which(xy2<=minep),which(xy3<=minep))

然后，无需触及代码并再次启动“.sh”文件，即可正确读取代码。这种情况会发生 "randomly"，并且绝不会出现在代码的同一部分。

好像跟码长有关

有什么帮助吗？

谢谢

编辑 1：

例如，slurm 文件的输出是

[1] "Data.Rdata"
Loading required package: MASS
##
## Markov Chain Monte Carlo Package (MCMCpack)
## Copyright (C) 2003-2020 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
##
## Support provided by the U.S. National Science Foundation
## (Grants SES-0350646 and SES-0350613)
##
Loading required package: stats4
null device 
          1 
Error: unexpected symbol in:
"      Beta0   = rep(-4,3),
      Betagonale Psi"
Execution halted
srun: error: node02: task 0: Exited with exit code 1

密码是

priors  = list(
     Beta0 = list(
         type        = "Normal",
         Par1        = rep(-4,3),
         Par2        = rep(10,3)
       ),
       Beta1 = list(
         type        = "Normal",
         Par1        = rep(1.8,3), 
         Par2        = rep(10,3)
       ),
      VarK   = list(
        type        = "TruncatedNormal",
        Par1        = rep(0,3),
        Par2        = rep(100,3),
        Par3        = rep(0.0000000,3),
        Par4        = rep(LimSigma2,3), 
        Par5        = rep(2,3)
        #Par5        = rep(2,3)
      ), 
      RegCoef = list(
          type        = "Normal",
          Par1        = c(0,0,0,0,0), ## (1 o stessa dimension)
          Par2        = rep(100,5)
      ),
      sigmaMat = list(
          type        = "InverseWishart",
          Par1        = rep(10,3), 
          Par2        = c(diag(1,5)) ## diagonale Psi
      ),

      DPpar = list(
          type        = "Gamma",
          Par1        = 1, 
          Par2        = 1 ## diagonale Psi
      )
    )

Answer 1

此处描述的症状（存储在 NFS 服务器上的文件在读取时损坏）大部分时间与文件上的竞争条件相关。通常，文件会打开以供从一个 NFS 客户端（登录节点）写入，并打开以供从另一个客户端（计算节点）读取。由于NFS中没有全局锁机制，读取文件的客户端并不知道文件正在被写入。使用支持自动保存的高级编辑器，文件有时会以不一致的状态写入磁盘，例如在 copy/paste 操作的中间。

在这种情况下，一个选项是在提交作业时完全避免修改文件，或者至少停用自动保存。

另一种选择是在提交作业之前制作文件的副本，以便之后不会更新。

Slurm 集群中的 R 代码无法正确读取

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