On 02/06/2012 12:45 PM, Jeroen Ooms wrote:
After upgrading my servers to 2.14, log files were filled warnings
that 'mem.limits' has been deprecated and to use gc instead. After
reading the NEWS for R 2.14.0 and PR#14795 I learned that it is
actually deprecated without replacement.
Hereby I just want to voice that this function was actually in use by
at least several users. Among other things, it is a useful to limit
per-session memory on a shared resource. I am not sure what the
assumption that 'these limits are nowadays almost never used' was
based on, but I would disagree.
These were also sometimes useful in our own use case, where setting
--min-n/vsize can speed start-up of scripts loading complicated packages
(e.g., Matrix or Bioconductor IRanges) that trigger dozens of garbage
collections before arriving at the > prompt, or needing to input large
data up-front; as a contrived example (70 garbage collections under
default values):
mtmorgan@linux-ibmc:~> time ~/bin/R-2-13-branch/bin/R --slave --vanilla
-e "library(IRanges)"
real 0m2.306s
user 0m2.270s
sys 0m0.028s
mtmorgan@linux-ibmc:~> time ~/bin/R-2-13-branch/bin/R
--min-nsize=2200000 --slave --vanilla -e "library(IRanges)"
real 0m1.931s
user 0m1.854s
sys 0m0.069s
mtmorgan@linux-ibmc:~> ~/bin/R-2-13-branch/bin/R --version
R version 2.13.1 Patched (2011-09-04 r56932)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
These were particularly useful in starting up nodes in an (Rmpi)
cluster, and perhaps more generally suggest that, for some use cases,
the default memory allocations could be revised (they have not for a
long time, from current R-devel):
29749 ripley #define Min_Nsize 220000
29749 ripley #define Min_Vsize (1*Mega)
Martin
Obviously this is message is late, the decision has been made and we
were not paying attention when we should have. However if there is
possibly anything that can be done to rescue some of this
functionality that would be greatly appreciated. E.g. by keeping some
of the support in the memory allocator and moving the R code into a
package or so.
Thank you
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