在R中使用bootMer()结合snow并行处理glmmTMB对象时出错

在R中尝试用bootMer()的snow参数对glmmTMB模型执行并行bootstrap时，所有模拟运行均失败。仅当设置parallel = "snow"且ncpus大于1时出现此问题，单核心运行无异常。参考相关解决方案后仍未解决，具体情况如下：

初始可复现代码 #

require(tidyverse)
require(glue)
require(lme4)
require(parallel) # 用于并行bootstrap步骤
require(glmmTMB)

m1 <- glmmTMB(count ~ DOY + mined + (1|site), 
              family = nbinom2, data = Salamanders)
summary(m1)

pred_data1 <- data.frame(mined = c("yes", "no")) %>% 
  group_by(mined) %>% 
  reframe(DOY = unique(Salamanders$DOY)) %>% 
  # 随机效应需要NA列
  mutate(site = NA)

pred_fun <- function(model) {
  predict(m1, newdata = pred_data1, type = "link", re.form = NA, 
          allow.new.levels = TRUE)
}

par_cores <- max(1, floor(detectCores()/2))
par_cluster <- makeCluster(rep("localhost", par_cores), outfile = "log.txt")
clusterEvalQ(par_cluster, library("glmmTMB"))
clusterExport(par_cluster, varlist = c("Salamanders"))

print(glue("Using {par_cores} cores."))

pred_bootMer <- bootMer(m1, nsim = 1, FUN = pred_fun,
                        parallel = "snow",
                        use.u = FALSE, type = "parametric",
                        ncpus = par_cores, cl = par_cluster)

stopCluster(par_cluster)

错误提示 #

运行后收到以下警告；实际设置1000次模拟时全部失败，pred_bootMer$t返回全NA：

Warning message:
In bootMer(m1, nsim = 1, FUN = pred_fun, parallel = "snow", use.u = FALSE,  :
  some bootstrap runs failed (1/1)

已尝试的解决操作 #

• 调整clusterEvalQ的包加载写法，包括：
  • clusterEvalQ(par_cluster, library("glmmTMB"))
  • clusterEvalQ(par_cluster, library(glmmTMB))
  • clusterEvalQ(par_cluster, {library(lme4); library(glmmTMB)})

2023年7月16日更新：修正代码后问题依旧 #

修正了预测函数的硬编码问题（将函数内的m1改为参数传入），并将原始模型对象加入集群导出列表，但仍提示bootstrap运行失败：

更新后的代码 #

pred_fun <- function(some_model) {
  predict(some_model, newdata = pred_data1, type = "link", re.form = NA, 
          allow.new.levels = TRUE)
}

par_cores <- max(1, floor(detectCores()/2))
par_cluster <- makeCluster(rep("localhost", par_cores), outfile = "log.txt")
clusterEvalQ(par_cluster, library("glmmTMB"))
clusterExport(par_cluster, varlist = c("Salamanders", "m1"))

print(glue("Using {par_cores} cores."))

pred_bootMer <- bootMer(m1, nsim = 2, FUN = pred_fun,
                        parallel = "snow",
                        use.u = FALSE, type = "parametric",
                        ncpus = 2, cl = par_cluster)

stopCluster(par_cluster)

疑问 #

1. 如何解决该并行bootstrap失败的问题？
2. 是否需要在glmmTMB的GitHub仓库提交相关issue？
3. 说明：使用的是bootMer()而非bootstrap_parameters

内容的提问来源于stack exchange，提问作者Karthik Thrikkadeeri