Unfamiliar errors running methylKit on mox

[yaaminiv]

TL;DR R module on mox producing new errors when running randomization tests

I'm running some pretty computationally-intensive methylKit randomization tests. This is my R script, and this is the SLURM script I'm using to load the R module and run the R script.

When running this code, I encountered the errors below:

for (i in 1:1000) {
  pHRandTreat <- sample(sampleMetadataFem$pHTreatment,
                        size = length(sampleMetadataFem$pHTreatment),
                        replace = FALSE)
  pHRandDML <- methylKit::reorganize(methylationInformationFilteredCov5Fem,
                                     sample.ids = sampleMetadataFem$sampleID,
                                     treatment = pHRandTreat) %>%
    methylKit::calculateDiffMeth(., covariates = covariateMetadataFem,
                                 overdispersion = "MN",
                                 test = "Chisq", mc.cores = 40) %>%
    methylKit::getMethylDiff(., difference = 75, qvalue = 0.01) %>%
    nrow() -> pHRandTest75Fem[i]
}

I haven't encountered the "non-existent physical address" or cores not delivering results errors previously. I did try running this code on the R Studio server without the mc.cores argument. However, it took 2 days to make it through 6 iterations, and when I included the mc.cores argument, the R Studio server browser interface froze (see notebook here).

What do these errors mean, and how do I not get them?

[yaaminiv]

I'm currently running the randomization test WITHOUT mc.cores on mox to see if I still encounter the "non-existent physical address" errors and will update this discussion accordingly.

[yaaminiv]

Running without mc.cores and I have yet to encounter the same error. For reference, I got the previous error ~10 minutes after I started running the script. My guess is that mc.cores is the issue.

Should I try running with mc.cores = 28, since we're usually allowed 28 cores? When I tried running without mc.cores on the R Studio server, I only made it through 6 iterations in 2 days, and I need to get through 1000 iterations...