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社区首页 >问答首页 >为什么员工在从外部“R”过程调用“`makePSOCKcluster`”时没有连接？

问为什么员工在从外部“R”过程调用“`makePSOCKcluster`”时没有连接？
EN

Stack Overflow用户
提问于 2022-10-05 14:40:23
回答 1查看 203关注 0票数 1

我正在经历一个在这里和这里之前已经提出的问题，但是在不同的背景下。

假设我有一个名为R的psock.R脚本文件，它包含以下代码：

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cat("Setup cluster...\n")
cluster <- parallel::makePSOCKcluster(
    rep("localhost", 2),
    master = "localhost",
    port = 11234,
    manual = FALSE,
    outfile = ""
)

cat("Sleep...\n")
Sys.sleep(1)

cat("Teardown cluster...\n")
parallel::stopCluster(cluster)

当我通过Rscript --vanilla psock.R运行脚本时，一切都如愿以偿，我看到：

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Setup cluster...
starting worker pid=11557 on localhost:11234 at 13:55:52.818
starting worker pid=11556 on localhost:11234 at 13:55:52.818
Sleep...
Teardown cluster...

但是，当我试图在外部R进程中执行同样的操作时，parallel::makePSOCKcluster会挂起。例如，假设psock.R现在包含以下代码：

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# Create a session.
session <- callr::r_session$new()

cat("Setup cluster...\n")
session$run(function() {
    # Create a cluster in the `.GlobalEnv`.
    cluster <<- parallel::makePSOCKcluster(
        rep("localhost", 2),
        master = "localhost",
        port = 11234,
        manual = FALSE,
        outfile = ""
    )
})

cat("Sleep...\n")
Sys.sleep(5)

cat("Teardown cluster...\n")
session$run(function() {
    # Stop it.
    parallel::stopCluster(cluster)
})

# Close session.
session$close()

运行psock.R现在在Setup cluster...挂起几分钟，然后退出时出现一个错误，即：

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Cluster setup failed. 1 worker of 2 failed to connect.

此外，运行htop --filter /exec/R可以确认第一个工作人员设法连接，但第二个工作人员没有连接。更具体地说，我看到以下进程(即由我添加的数字)：

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(1) └─ /Library/Frameworks/R.framework/Resources/bin/exec/R --no-echo --no-restore --vanilla --file=psock.R
(2)    └─ /Library/Frameworks/R.framework/Resources/bin/exec/R --no-readline --slave --no-save --no-restore
(3) ├─ /Library/Frameworks/R.framework/Resources/bin/exec/R --no-echo --no-restore -e tryCatch(parallel:::.workRSOCK,error=function(e)parallel:::.slaveRSOCK)() --args MASTER=localhost PORT=11234 OUT= SETUPTIMEOUT=120 TIMEOUT=2592000 XDR=TRUE SETUPSTRATEGY=parallel

其中(1)是psock.R脚本调用，(2)是callr::r_session$new()创建的外部进程，(3)是parallel::makePSOCKcluster生成的第一个成功连接的工作程序。

在史蒂夫·韦斯顿的答案这里和这里之后，我尝试进行一些调试。

我首先调整psock.R，将外部进程上的输出写入文件，并通过设置manual = TRUE启用手动模式，即：

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session$run(function() {
    # Connection.
    connection <- file("/some/path/log.txt", open = "wt")

    # Write anything to a log file.
    sink(connection, append = TRUE)
    sink(connection, append = TRUE, type = "message")

    # Create a cluster in the `.GlobalEnv`.
    cluster <<- parallel::makePSOCKcluster(
        rep("localhost", 2),
        master = "localhost",
        port = 11234,
        manual = TRUE,
        outfile = ""
    )
})

在上面的代码更改之后运行Rscript --vanilla psock.R，将以下命令记录到log.txt

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Manually start worker on localhost with
    '/Library/Frameworks/R.framework/Resources/bin/Rscript' --default-packages=datasets,utils,grDevices,graphics,stats,methods -e 'tryCatch(parallel:::.workRSOCK,error=function(e)parallel:::.slaveRSOCK)()' MASTER=localhost PORT=11234 OUT='' SETUPTIMEOUT=120 TIMEOUT=2592000 XDR=TRUE SETUPSTRATEGY=sequential

到目前为止，还没有创建任何工作人员，从htop --filter /exec/R的输出可以看出

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└─ /Library/Frameworks/R.framework/Resources/bin/exec/R --no-echo --no-restore --vanilla --file=psock.R
   └─ /Library/Frameworks/R.framework/Resources/bin/exec/R --no-readline --slave --no-save --no-restore

现在，我可以手动运行上面的命令，两次，创建工作人员并连接到主进程(即外部进程)。这将在终端中产生以下输出，确认已创建并连接了工作人员：

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starting worker pid=13065 on localhost:11234 at 14:59:38.185
starting worker pid=13201 on localhost:11234 at 14:59:38.185

我还可以通过htop --filter /exec/R验证这一点，它现在显示了以下内容：

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└─ /Library/Frameworks/R.framework/Resources/bin/exec/R --no-echo --no-restore --vanilla --file=psock.R
   └─ /Library/Frameworks/R.framework/Resources/bin/exec/R --no-readline --slave --no-save --no-restore
└─ /Library/Frameworks/R.framework/Resources/bin/exec/R --no-echo --no-restore -e tryCatch(parallel:::.workRSOCK,error=function(e)parallel:::.slaveRSOCK)() --args MASTER=localhost PORT=11234 OUT= SETUPTIMEOUT=120 TIMEOUT=2592000 XDR=TRUE SETUPSTRATEGY=sequential
└─ /Library/Frameworks/R.framework/Resources/bin/exec/R --no-echo --no-restore -e tryCatch(parallel:::.workRSOCK,error=function(e)parallel:::.slaveRSOCK)() --args MASTER=localhost PORT=11234 OUT= SETUPTIMEOUT=120 TIMEOUT=2592000 XDR=TRUE SETUPSTRATEGY=sequential

在这一点上，我感到困惑，因为我希望某些事情会失败。我唯一能想到的解释是，我为启动PSOCK集群而创建的进程的行为与在终端中手动运行该命令不同。可能是不同的权限还是缺少环境变量？这是意料之中的吗？

在手动模式打印的命令中，我还注意到使用了SETUPSTRATEGY=sequential。然而，当manual = FALSE时，htop过程显示使用了SETUPSTRATEGY=parallel。实际上，这与parallel::makePSOCKcluster的文档是一致的，该文档如下：

如果“并行”(默认)工作人员在可能的情况下在集群设置过程中并行启动，则现在用于本地计算机上所有工作人员自动启动的同构"PSOCK“集群(手动= FALSE)。工作人员将依次在其他集群、所有具有setup_strategy =“顺序”的集群和R3.6.0及更高版本的集群上启动。

出于好奇，我尝试运行手动模型打印的命令，而不是使用parallel策略(即SETUPSTRATEGY=parallel)。只运行一次之后，脚本将继续执行，并停止在Sys.sleep(5)部分。这也反映在htop进程列表中，其中我只能看到一个工作人员。

如果我禁用手动模式并将setup_strategy = "sequential"添加到parallel::makePSOCKcluster函数调用中，一切都会按预期工作。然而，我真的很想知道为什么它在parallel 安装策略中失败了。此外，在机器上运行良好，但在基于Debian的系统上挂起的情况完全一样。

就我正在运行的内容而言，这是我的R会话的样子：

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sessionInfo()

# R version 4.2.1 (2022-06-23)
# Platform: aarch64-apple-darwin20 (64-bit)
# Running under: macOS Monterey 12.6
#
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
#
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base
#
# loaded via a namespace (and not attached):
# [1] compiler_4.2.1 cli_3.3.0      jsonlite_1.8.0 rlang_1.0.5

而且，由于其他答案显示了与主机相关的问题，我的/etc/hosts看起来如下：

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───────┼─────────────────────────────────────────────────────────
   1   │ ##
   2   │ # Host Database
   3   │ #
   4   │ # localhost is used to configure the loopback interface
   5   │ # when the system is booting.  Do not change this entry.
   6   │ ##
   7   │ 127.0.0.1       localhost
   8   │ 255.255.255.255 broadcasthost
   9   │ ::1             localhost
───────┴─────────────────────────────────────────────────────────

而且，我的.Rprofile是空的。

最后，不确定这是否相关，但在运行netstat -i时，我的网络接口的Address列中的值是IPv6格式的，或者更确切地说是IPv6 4映射的。

在我屈服于setup_strategy = "sequential"之前，你知道发生了什么吗？

编辑1.

按照HenrikB的建议，我用parallelly::makeClusterPSOCK替换了parallel::makePSOCKcluster调用，在调用之前启用了调试日志options(parallelly.debug = TRUE)。

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session$run(function() {
    # Enable logging for `parallelly`.
    options(parallelly.debug = TRUE)

    # Connection.
    connection <- file("/some/path/log.txt", open = "wt")

    # Write anything to a log file.
    sink(connection, append = TRUE)
    sink(connection, append = TRUE, type = "message")

    # Create a cluster in the `.GlobalEnv`.
    cluster <<- parallelly::makeClusterPSOCK(
        rep("localhost", 2),
        master = "localhost",
        port = 11234,
        manual = FALSE,
        outfile = ""
    )
})

log.txt中的输出包含以下内容：

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[09:27:19.936] Set package option ‘parallelly.availableCores.methods’
[09:27:19.941] Environment variable ‘R_PARALLELLY_AVAILABLECORES_METHODS’ not set
[09:27:19.941] Set package option ‘parallelly.availableCores.fallback’
[09:27:19.941] Environment variable ‘R_PARALLELLY_AVAILABLECORES_FALLBACK’ not set
[09:27:19.941] Set package option ‘parallelly.availableCores.min’
[09:27:19.942] Environment variable ‘R_PARALLELLY_AVAILABLECORES_MIN’ not set
[09:27:19.942] Set package option ‘parallelly.availableCores.system’
[09:27:19.942] Environment variable ‘R_PARALLELLY_AVAILABLECORES_SYSTEM’ not set
[09:27:19.942] Set package option ‘parallelly.availableCores.logical’
[09:27:19.942] Environment variable ‘R_PARALLELLY_AVAILABLECORES_LOGICAL’ not set
[09:27:19.942] Set package option ‘parallelly.availableCores.omit’
[09:27:19.942] Environment variable ‘R_PARALLELLY_AVAILABLECORES_OMIT’ not set
[09:27:19.942] Set package option ‘parallelly.availableWorkers.methods’
[09:27:19.942] Environment variable ‘R_PARALLELLY_AVAILABLEWORKERS_METHODS’ not set
[09:27:19.942] Set package option ‘parallelly.fork.enable’
[09:27:19.942] Environment variable ‘R_PARALLELLY_FORK_ENABLE’ not set
[09:27:19.942] Set package option ‘parallelly.supportsMulticore.unstable’
[09:27:19.942] Environment variable ‘R_PARALLELLY_SUPPORTSMULTICORE_UNSTABLE’ not set
[09:27:19.943] Set package option ‘parallelly.makeNodePSOCK.setup_strategy’
[09:27:19.943] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_SETUP_STRATEGY’ not set
[09:27:19.943] Set package option ‘parallelly.makeNodePSOCK.validate’
[09:27:19.943] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_VALIDATE’ not set
[09:27:19.943] Set package option ‘parallelly.makeNodePSOCK.connectTimeout’
[09:27:19.943] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_CONNECTTIMEOUT’ not set
[09:27:19.943] Set package option ‘parallelly.makeNodePSOCK.timeout’
[09:27:19.943] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_TIMEOUT’ not set
[09:27:19.943] Set package option ‘parallelly.makeNodePSOCK.useXDR’
[09:27:19.943] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_USEXDR’ not set
[09:27:19.943] Set package option ‘parallelly.makeNodePSOCK.socketOptions’
[09:27:19.943] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_SOCKETOPTIONS’ not set
[09:27:19.943] Set package option ‘parallelly.makeNodePSOCK.rshcmd’
[09:27:19.943] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_RSHCMD’ not set
[09:27:19.944] Set package option ‘parallelly.makeNodePSOCK.rshopts’
[09:27:19.944] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_RSHOPTS’ not set
[09:27:19.944] Set package option ‘parallelly.makeNodePSOCK.tries’
[09:27:19.944] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_TRIES’ not set
[09:27:19.944] Set package option ‘parallelly.makeNodePSOCK.tries.delay’
[09:27:19.944] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_TRIES_DELAY’ not set
[09:27:19.944] Set package option ‘parallelly.makeNodePSOCK.rscript_label’
[09:27:19.944] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_RSCRIPT_LABEL’ not set
[09:27:19.944] Set package option ‘parallelly.makeNodePSOCK.sessionInfo.pkgs’
[09:27:19.944] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_SESSIONINFO_PKGS’ not set
[09:27:19.944] Set package option ‘parallelly.makeNodePSOCK.autoKill’
[09:27:19.944] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_AUTOKILL’ not set
[09:27:19.944] Set package option ‘parallelly.makeNodePSOCK.master.localhost.hostname’
[09:27:19.945] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_MASTER_LOCALHOST_HOSTNAME’ not set
[09:27:19.945] Set package option ‘parallelly.makeNodePSOCK.port.increment’
[09:27:19.945] Environment variable ‘R_PARALLELLY_MAKENODEPSOCK_PORT_INCREMENT’ not set
[09:27:19.945] parallelly-specific environment variables:
[09:27:19.961] [local output] Workers: [n = 2] ‘localhost’, ‘localhost’
[09:27:19.962] [local output] Base port: 11234
[09:27:19.962] [local output] Getting setup options for 2 cluster nodes ...
[09:27:19.963] [local output]  - Node 1 of 2 ...
[09:27:19.963] [local output] localMachine=TRUE => revtunnel=FALSE

[09:27:19.963] Testing if worker's PID can be inferred: ‘'/Library/Frameworks/R.framework/Resources/bin/Rscript' -e 'try(suppressWarnings(cat(Sys.getpid(),file="/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=1.parallelly.parent=3664.e504deb9152.pid")), silent = TRUE)' -e 'file.exists("/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=1.parallelly.parent=3664.e504deb9152.pid")'’
[09:27:19.978] - Possible to infer worker's PID: FALSE
[09:27:19.978] [local output] Rscript port: 11234

[09:27:19.978] [local output]  - Node 2 of 2 ...
[09:27:19.979] [local output] localMachine=TRUE => revtunnel=FALSE

[09:27:19.979] Testing if worker's PID can be inferred: ‘'/Library/Frameworks/R.framework/Resources/bin/Rscript' -e 'try(suppressWarnings(cat(Sys.getpid(),file="/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=2.parallelly.parent=3664.e502491c675.pid")), silent = TRUE)' -e 'file.exists("/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=2.parallelly.parent=3664.e502491c675.pid")'’
[09:27:19.995] - Possible to infer worker's PID: FALSE
[09:27:19.995] [local output] Rscript port: 11234

[09:27:19.995] [local output] Getting setup options for 2 cluster nodes ... done
[09:27:19.995] [local output]  - Parallel setup requested for some PSOCK nodes
[09:27:19.996] [local output] Setting up PSOCK nodes in parallel
[09:27:19.996] List of 20
[09:27:19.996]  $ local_cmd     : chr "'/Library/Frameworks/R.framework/Resources/bin/Rscript' --default-packages=datasets,utils,grDevices,graphics,st"| __truncated__
[09:27:19.996]  $ worker        : chr "localhost"
[09:27:19.996]   ..- attr(*, "localhost")= logi TRUE
[09:27:19.996]  $ rank          : int 1
[09:27:19.996]  $ rshlogfile    : NULL
[09:27:19.996]  $ port          : int 11234
[09:27:19.996]  $ connectTimeout: num 120
[09:27:19.996]  $ timeout       : num 2592000
[09:27:19.996]  $ useXDR        : logi FALSE
[09:27:19.996]  $ pidfile       : chr "/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=1.parallelly.parent=3664.e504deb9152.pid"
[09:27:19.996]  $ setup_strategy: chr "parallel"
[09:27:19.996]  $ outfile       : chr ""
[09:27:19.996]  $ rshcmd_label  : NULL
[09:27:19.996]  $ rsh_call      : NULL
[09:27:19.996]  $ cmd           : chr "'/Library/Frameworks/R.framework/Resources/bin/Rscript' --default-packages=datasets,utils,grDevices,graphics,st"| __truncated__
[09:27:19.996]  $ localMachine  : logi TRUE
[09:27:19.996]  $ manual        : logi FALSE
[09:27:19.996]  $ dryrun        : logi FALSE
[09:27:19.996]  $ quiet         : logi FALSE
[09:27:19.996]  $ rshcmd        : NULL
[09:27:19.996]  $ revtunnel     : logi FALSE
[09:27:19.996]  - attr(*, "class")= chr [1:2] "makeNodePSOCKOptions" "makeNodeOptions"
[09:27:20.001] [local output] System call to launch all workers:
[09:27:20.001] [local output] '/Library/Frameworks/R.framework/Resources/bin/Rscript' --default-packages=datasets,utils,grDevices,graphics,stats,methods -e 'try(suppressWarnings(cat(Sys.getpid(),file="/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=1.parallelly.parent=3664.e504deb9152.pid")), silent = TRUE)' -e 'options(socketOptions = "no-delay")' -e 'workRSOCK <- tryCatch(parallel:::.workRSOCK, error=function(e) parallel:::.slaveRSOCK); workRSOCK()' MASTER=localhost PORT=11234 OUT= TIMEOUT=2592000 XDR=FALSE SETUPTIMEOUT=120 SETUPSTRATEGY=parallel
[09:27:20.001] [local output] Starting PSOCK main server
[09:27:20.003] [local output] Workers launched
[09:27:20.003] [local output] Waiting for workers to connect back
[09:27:20.003] [local output] 0 workers out of 2 ready
[09:27:20.120] [local output] 0 workers out of 2 ready
[09:27:20.121] [local output] 1 workers out of 2 ready
[09:29:20.126] [local output] 1 workers out of 2 ready
[09:31:20.133] [local output] 1 workers out of 2 ready
Error in parallelly::makeClusterPSOCK(rep("localhost", 2), master = "localhost",  : 
  Cluster setup failed. 1 worker of 2 failed to connect.
In addition: Warning messages:
1: In system(test_cmd, intern = TRUE, input = input) :
  running command ''/Library/Frameworks/R.framework/Resources/bin/Rscript' -e 'try(suppressWarnings(cat(Sys.getpid(),file="/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=1.parallelly.parent=3664.e504deb9152.pid")), silent = TRUE)' -e 'file.exists("/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=1.parallelly.parent=3664.e504deb9152.pid")'' had status 2
2: In system(test_cmd, intern = TRUE, input = input) :
  running command ''/Library/Frameworks/R.framework/Resources/bin/Rscript' -e 'try(suppressWarnings(cat(Sys.getpid(),file="/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=2.parallelly.parent=3664.e502491c675.pid")), silent = TRUE)' -e 'file.exists("/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=2.parallelly.parent=3664.e502491c675.pid")'' had status 2

看起来，Rscript命令的退出状态为2，从文档发出的退出状态听起来像是发生了一些神秘的事情：

错误状态2用于R‘自杀’，这是灾难性的故障，而其他一些小数字则由特定端口用于初始化失败。

r
parallel-processing
cluster-computing
snow
EN

回答 1

Stack Overflow用户

回答已采纳

发布于 2022-10-07 19:24:25

更新2022-10-10:根本的问题是由于R本身的一个错误，这个问题已经在R-devel r83051 (2022-10-10) https://github.com/wch/r-source/commit/97b3dfb71aeff4a6acb72d400bb1fba8e6b2ed37中修复了。不确定，但我怀疑这一修正也会进入Rv4.2.2(2022年10月底)。

对于固定版本的R，OP的示例也适用于processx 3.7.0当前在CRAN上。

更新2022-10-09：

该问题与processx包和R本身有关，后者需要工作标准输入(stdin)流。具体来说，callr (当使用processx <= 3.7.0时)将所有文件描述符标记为接近exec，system2()假定stdin (等等)。将在子进程中继承，而不是显式复制它。这导致system()失败，cf。https://github.com/r-lib/callr/issues/236。因此，processx包(>= 3.7.0-9000)被更新为默认不关闭标准流(stdin、stdout和stderr)。这解决了OP报告的问题( 2022-10-08T21:05:46由OP确认)。

在processx包的固定版本在克拉恩上之前，开发人员版本可以安装如下：

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remotes::install_github("r-lib/processx")

由于您更新了来自parallelly::makeClusterPSOCK()的调试输出(*)，我已经将其缩小到了当前callr中的一个bug。我在https://github.com/r-lib/callr/issues/236向上游报告了这一点，这也说明了问题的核心。

(*)引起我注意的确切原因是：

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[09:27:19.963] Testing if worker's PID can be inferred: ‘'/Library/Frameworks/R.framework/Resources/bin/Rscript' -e 'try(suppressWarnings(cat(Sys.getpid(),file="/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=1.parallelly.parent=3664.e504deb9152.pid")), silent = TRUE)' -e 'file.exists("/var/folders/v9/yftkgjms78qdx9vz7mll88mw0000gn/T//RtmpRVw8vP/worker.rank=1.parallelly.parent=3664.e504deb9152.pid")'’
[09:27:19.978] - Possible to infer worker's PID: FALSE

更准确地说，当使用后台回调进程调用时，它无法推断工人的PID。如果您在主R会话中执行相同的操作，您将得到：

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[09:27:19.978] - Possible to infer worker's PID: TRUE
票数 2
EN
页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：

https://stackoverflow.com/questions/73962109

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