This will attempt to restart the R session, reloading all packages, and
saving and reloading the simList.
Currently, this is not intended for general use: it has many specialized
pieces for using inside a spades call.
The main purpose for doing this is to clear memory leaks (possibly deep
in R https://github.com/r-lib/fastmap) that are not fully diagnosed.
This is still very experimental.
This should only be used if there are RAM limitations being hit with long running simulations.
It has been tested to work Linux within Rstudio and at a terminal R session.
The way to initiate restarting of R is simply setting the spades.restartRInterval or
setting the equivalent parameter in the restartR core module via:
simInit(..., params = list(.restartR = list(.restartRInterval = 1)), ...)
greater than 0, which is the default,
e.g., options("spades.restartRInterval" = 100).
This is only intended to restart a simulation in exactly the same place as it was
(i.e., cannot change machines), and because of the restart, the assignment of the spades
call will be either to sim or the user must make such an assignment manually,
e.g., sim <- SpaDES.core:::.pkgEnv$.sim.
This is stated in a message.
restartR(
sim,
reloadPkgs = TRUE,
.First = NULL,
.RDataFile = getOption("spades.restartR.RDataFilename"),
restartDir = getOption("spades.restartR.restartDir", NULL)
)invoked for side effect of restarting the R session
Required. A simList to be retained through the restart
Logical. If TRUE, it will attempt to reload all the packages
as they were in previous session, in the same order. If FALSE, it will
load no packages beyond normal R startup. Default TRUE
A function to save to ~/.qs which will
be loaded at restart from ~/.qs and run. Default is NULL,
meaning it will use the non-exported SpaDES.core:::First. If a
user wants to make a custom First file, it should built off that one.
A filename for saving the simList.
Defaults to getOption("spades.restartR.filename"), and the directory will
be in restartDir. The simulation time will be mid-pended to this
name, as in: basename(file), "_time",
paddedFloatToChar(time(sim), padL = nchar(as.character(end(sim))))))
A character string indicating root directory to
save simList and other ancillary files during restart.
Defaults to getOption("spades.restartR.restartDir", NULL).
If NULL, then it will try, in order, outputPath(sim),
modulePath(sim), inputPath(sim), cachePath(sim),
taking the first one that is not inside the tempdir(), which will
disappear during restart of R.
The actual directory for a given spades call that is restarting will be:
file.path(restartDir, "restartR", paste0(sim$._startClockTime, "_", .rndString)).
The random string is to prevent parallel processes that started at the same clock
time from colliding.
The process responds to several options. Though under most cases,
the default behaviour should suffice. These are of 3 types: restartRInterval
the arguments to restartR and the arguments to saveSimList, these latter two
using a dot to separate the function name and its argument. The defaults for
two key options are: options("spades.restartR.restartDir" = NULL, meaning
use file.path(restartDir, "restartR", paste0(sim$._startClockTime, "_", .rndString))
and options("spades.saveSimList.fileBackend" = 0), which means don't do anything
with raster-backed files.
See specific functions for defaults and argument meanings.
The only difference from the default function values is with saveSimList argument
fileBackend = FALSE during restartR by default, because it is assumed that
the file backends will still be intact after a restart, so no need to move them all to memory.