[R] Issue with gc() on Ubuntu 20.04

John Logsdon j@|og@don @end|ng |rom qu@ntex-re@e@rch@com
Sun Aug 27 20:54:23 CEST 2023


I have come across an issue with gc() hogging the processor according to 

Platform is Ubuntu 20.04 all up to date
R version 4.3.1
libraries: survival, MASS, gtools and openxlsx.

With default gc.auto options, the profiler notes the garbage collector 
as self.pct 99.39%.

So I have tried switching it off using options(gc.auto=Inf) in the R 
session before running my program using source().

This lowered self.pct to 99.36.  Not much there.

After some pondering, I added an options(gc.auto=Inf) at the beginning 
of each function, not resetting it at exit, but expecting the offending 
function(s) to plead guilty.

Not so although it did lower the gc() time to 95.84%.

This was on a 16 core Threadripper 1950X box so I was intending to use 
library parallel but I tried it on my lowly windows box that is years 
old and got it down to 88.07%.

The only thing I can think of is that there are quite a lot of cases 
where a function is generated on the fly as in:

eval(parse(t=paste("dprob <- 

I haven't added the options to any of these.

The highest time used by any of my functions is 0.05% - the rest is 
dominated by gc().

There may not be much point in parallising the code until I can reduce 
the garbage collection.

I am not short of memory and would like to disable it fully but despite 
adding to all routines, I haven't managed to do this yet.

Can anyone advise me?

And why is the Linux version so much worse than Windows?


John Logsdon
Quantex Research Ltd

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