[Rd] mclapply returns NULLs on MacOS when running GAM

[Shian Su]

Yes I am running on Rstudio 1.2.5033. I was also running this code without error on Ubuntu in Rstudio. Checking again on the terminal and it does indeed work fine even with large data.frames.

Any idea as to what interaction between Rstudio and mclapply causes this?

Thanks,
Shian

On 28 Apr 2020, at 7:29 pm, Simon Urbanek <simon.urbanek using R-project.org<mailto:simon.urbanek using R-project.org>> wrote:

Sorry, the code works perfectly fine for me in R even for 1e6 observations (but I was testing with R 4.0.0). Are you using some kind of GUI?

Cheers,
Simon


On 28/04/2020, at 8:11 PM, Shian Su <su.s using wehi.edu.au<mailto:su.s using wehi.edu.au>> wrote:

Dear R-devel,

I am experiencing issues with running GAM models using mclapply, it fails to return any values if the data input becomes large. For example here the code runs fine with a df of 100 rows, but fails at 1000.

library(mgcv)
library(parallel)

df <- data.frame(
+     x = 1:100,
+     y = 1:100
+ )

mclapply(1:2, function(i, df) {
+         fit <- gam(y ~ s(x, bs = "cs"), data = df)
+     },
+     df = df,
+     mc.cores = 2L
+ )
[[1]]

Family: gaussian
Link function: identity

Formula:
y ~ s(x, bs = "cs")

Estimated degrees of freedom:
9  total = 10

GCV score: 0

[[2]]

Family: gaussian
Link function: identity

Formula:
y ~ s(x, bs = "cs")

Estimated degrees of freedom:
9  total = 10

GCV score: 0



df <- data.frame(
+     x = 1:1000,
+     y = 1:1000
+ )

mclapply(1:2, function(i, df) {
+         fit <- gam(y ~ s(x, bs = "cs"), data = df)
+     },
+     df = df,
+     mc.cores = 2L
+ )
[[1]]
NULL

[[2]]
NULL

There is no error message returned, and the code runs perfectly fine in lapply.

I am on a MacBook 15 (2016) running MacOS 10.14.6 (Mojave) and R version 3.6.2. This bug could not be reproduced on my Ubuntu 19.10 running R 3.6.1.

Kind regards,
Shian Su
----
Shian Su
PhD Student, Ritchie Lab 6W, Epigenetics and Development
Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville VIC 3052, Australia


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