如何使用foreach在Windows上实现并行jags？

Question

我想在我的带有4个内核的Windows计算机上并行运行jags模型,但是我们无法弄清楚为什么我的模型不会运行.我在网上广泛搜索了这些帖子:

http://andrewgelman.com/2011/07/23/parallel-jags-rngs/

http://users.soe.ucsc.edu/~draper/eBay-Google-2013-parallel-rjags-example.txt

当我运行一个简单的例子(见下面的代码)时%do%,模型运行正常(当然是连续的).当我使用时%dopar%,我收到错误: Error in { : task 1 failed - "Symbol table is empty"

library(rjags)
library(coda)
library(foreach)              
library(doParallel)
library(random)     
load.module("lecuyer")

###  Data generation 
y <- rnorm(100)
n <- length(y)
win.data <- list(y=y, n=n)

# Define model
sink("model.txt")
cat("
    model {
    # Priors
    mu ~ dnorm(0, 0.001)
    tau <- 1 / (sigma * sigma)
    sigma ~ dunif(0, 10)
    # Likelihood
    for (i in 1:n) {
      y[i] ~ dnorm(mu, tau)
    }
}
",fill=TRUE)
sink()

inits <- function(){ list(mu=rnorm(1), sigma=runif(1, 0, 10),
                 .RNG.name = "lecuyer::RngStream", 
                 .RNG.seed = as.numeric(randomNumbers( n = 1, min = 1, max = 1e+06, col = 1 )) ) }
params <- c('mu','sigma')  

cl <- makePSOCKcluster(3)              
clusterSetRNGStream(cl)
registerDoParallel(cl)      
model.wd <- paste(getwd(), '/model.txt', sep='')     # I wondered if the cores were having trouble finding the model.         

m <- foreach(i=1:3, .packages=c('rjags','random','coda'), .multicombine=TRUE) %dopar% {  
                load.module( "lecuyer" )  
                model.jags <- jags.model(model.wd, win.data, inits=inits, n.chains=1, n.adapt=1000, quiet=TRUE)
                result <- coda.samples(model.jags, params, 1000, thin=5)
                return(result)
              }            
stopCluster(cl)
# Error in { : task 1 failed - "Symbol table is empty


sessionInfo()
# R version 3.0.1 (2013-05-16)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# 
# locale:
#   [1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252
# [4] LC_NUMERIC=C                    LC_TIME=English_Canada.1252    
# 
# attached base packages:
#   [1] parallel  stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
#   [1] random_0.2.1     doParallel_1.0.3 iterators_1.0.6  foreach_1.4.1    rjags_3-10       coda_0.16-1     
# [7] lattice_0.20-21 
# 
# loaded via a namespace (and not attached):
#   [1] codetools_0.2-8 compiler_3.0.1  grid_3.0.1      tools_3.0.1  

---

更多细节:

在没有管理员权限的Windows 7计算机上会出现此问题,但在具有管理员权限的计算机上则不会出现此问题.问题出现在Rgui和Rterm以及新的rjags打包3-11.该函数内出现错误消息jags.model

问题似乎源于写入和读取文件到临时目录的不匹配.当我启动R时,它会自动创建一个临时文件夹.当我关闭R时,该文件夹会自动删除,除非它包含文件.

例如,当我启动R时,它会创建此文件夹: C:\Users\jesse whittington\AppData\Local\Temp\RtmpoBe1gw.

当我运行rjags模型时

m <- jags.model(file='model.txt', data=win.data, inits=inits, n.chains=3, n.adapt=1000, quiet=FALSE)

没有文件写入此临时目录.

当我使用foreach串行运行3个链时,会将%do%3个临时文件写入此文件夹.这些文件大小为1 kb,当我用文本编辑器打开时,它们显示为空白.

wd <- getwd()                   
cl <- makePSOCKcluster(3, outfile=paste(wd,'/Out_messages.txt', sep=''))   # 3 chains           
clusterSetRNGStream(cl)
registerDoParallel(cl)   
m <- foreach(i=1:3, .packages=c('rjags','random','coda'), .multicombine=TRUE) %do% {  
                load.module( "lecuyer" ) 
                result <- jags.model(file='model.txt', data=win.data, inits=inits, n.chains=1, n.adapt=1000, quiet=FALSE)
                return(result)
              }  
stopCluster(cl) 

当我与foreach并行运行3个链时,会将%dopar%3个临时文件写入该文件夹..Temp\RtmpoBe1gw.outfile中的错误消息表明该函数正在DIFFERENT临时目录中查找不同的文件.当我包含一行来创建临时文件目录和名称时,我看到创建了3个新的临时文件夹(稍后将其删除stopCluster). jags.model在这3个文件夹中查找临时文件并失败,因为它们中没有任何内容.因此,我怀疑tempfiles被写入一个临时目录(与父R会话相关联),然后在尝试在foreach中创建的3个临时目录中打开不同的tmpfiles时失败.

wd <- getwd()                   
cl <- makePSOCKcluster(3, outfile=paste(wd,'/Out_messages.txt', sep=''))   # 3 chains           
clusterSetRNGStream(cl)
registerDoParallel(cl)   
m <- foreach(i=1:3, .packages=c('rjags','random','coda'), .multicombine=TRUE) %dopar% {  
                load.module( "lecuyer" ) 
        tmp <- tempfile()
                print(tmp)
                result <- jags.model(file='model.txt', data=win.data, inits=inits, n.chains=1, n.adapt=1000, quiet=FALSE)
                return(result)
              }  
stopCluster(cl) 

来自Out_messages.txt

starting worker pid=4396 on localhost:11109 at 08:34:06.430
starting worker pid=6548 on localhost:11109 at 08:34:06.879
starting worker pid=6212 on localhost:11109 at 08:34:07.418
Loading required package: coda
Loading required package: lattice
Loading required package: coda
Loading required package: lattice
Loading required package: coda
Loading required package: lattice
Linked to JAGS 3.3.0
Loaded modules: basemod,bugs
Linked to JAGS 3.3.0
Loaded modules: basemod,bugs
Linked to JAGS 3.3.0
Loaded modules: basemod,bugs
module lecuyer loaded
module lecuyer loaded
module lecuyer loaded
[1] "C:\\Users\\JESSEW~1\\AppData\\Local\\Temp\\RtmpQbPAVC\\file112c8077a0"  # Note this is from: tmp <- tempfile()
[1] "C:\\Users\\JESSEW~1\\AppData\\Local\\Temp\\RtmpMPMpcY\\file199489564c6"
[1] "C:\\Users\\JESSEW~1\\AppData\\Local\\Temp\\Rtmpk9vMR5\\file18445f6b2fd4"
Compiling model graph
Compiling model graph
Compiling model graph

Warning messages:
1: In jags.model(file = "model.txt", data = win.data, inits = inits,  :
  Unused variable "y" in data
2: In jags.model(file = "model.txt", data = win.data, inits = inits,  :
  Unused variable "n" in data
3: In jags.model(file = "model.txt", data = win.data, inits = inits,  :
  Failed to open file C:\Users\JESSEW~1\AppData\Local\Temp\RtmpQbPAVC\file112c394b4eef
Nothing to compile

4: In jags.model(file = "model.txt", data = win.data, inits = inits,  :
  Unused initial value for "mu" in chain 1
5: In jags.model(file = "model.txt", data = win.data, inits = inits,  :
  Unused initial value for "sigma" in chain 1
6: In jags.model(file = "model.txt", data = win.data, inits = inits,  :
  Can't initialize. No nodes in graph (Have you compiled the model?)

该文件夹RtmpQbPAVC已创建,但该文件file112c394b4eef不存在.

Answer 1

我已经确定了问题的根源。正常使用 R 时，我可以在临时目录中写入和读取文件。并行时，我可以将文件写入临时目录，但我没有读取文件的权限。

写入和读取文本文件（使用 writeLines 和 readLines）以及 csv 文件时都会出现此问题。

我发现如果收到此消息：“{ 中的错误：任务 1 失败 - 无法打开连接”，我可以通过删除 TEMP 中的所有临时文件来纠正问题。对于某些锁定的文件，我必须关闭并重新启动计算机才能删除必要的文件。即便如此，在同一个 R 会话中，我可能会收到错误消息，然后能够在下次尝试时成功运行该程序。该问题可能源于我们的政府防病毒软件和/或远程网络访问的结构。

为了简单起见，下面是一个写入和读取文本文件的示例。

library(foreach)              
library(doParallel)
wd <- getwd()
data <- data.frame(x=1:10, y=1:10)

这很好用。

modfile <- tempfile()
print(modfile)
# "C:\\Users\\JESSEW~1\\AppData\\Local\\Temp\\RtmpsvYfFk\\filef38a272022"
write.csv(data, modfile, row.names=F)
m <- read.csv(modfile) 

这不起作用

cl <- makePSOCKcluster(3, outfile=paste(wd,'/Out_messages.txt', sep=''))   # 3 chains           
clusterSetRNGStream(cl)
registerDoParallel(cl)   
m <- foreach(i=1:3) %dopar% {  
  modfile <- tempfile()
  write.csv(data, modfile, row.names=F)
  x <- read.csv(modfile)
  return(x)
}  
# Error in { : task 1 failed - "cannot open the connection"
stopCluster(cl) 

这是 Out_message.txt 的输出。请注意最右侧的“权限被拒绝”。

starting worker pid=6852 on localhost:11611 at 22:09:19.488
starting worker pid=6984 on localhost:11611 at 22:09:19.926
starting worker pid=3384 on localhost:11611 at 22:09:20.441
Warning message:
  Warning message:
  In file(con, "r") :
  cannot open file 'C:\Users\JESSEW~1\AppData\Local\Temp\Rtmp6dEZLP\file1ac44a506032': Permission denied
In file(con, "r") :
  cannot open file 'C:\Users\JESSEW~1\AppData\Local\Temp\RtmpuydRvR\file1b48185f2a2d': Permission denied
Warning message:
  In file(con, "r") :
  cannot open file 'C:\Users\JESSEW~1\AppData\Local\Temp\RtmpAbOIng\filed382ef37d51': Permission denied