Henrik,
See https://github.com/duncantl/CodeDepends (as used by used by
https://github.com/gmbecker/RCacheSuite). It will identify
necessarily defined symbols (input variables) for code that is
not doing certain tricks (eg get(), mixing data.frame columns and
gobal variables in formulas, etc ).
Tierney's codetools package also does things along these lines
but there are some situations where it has trouble. I can give
more detail if desired.
~G
On Sun, Nov 3, 2013 at 3:04 PM, Ryan <r...@thompsonclan.org
<mailto:r...@thompsonclan.org>> wrote:
Another potential easy step we can do is that if FUN function
in the user's workspace, we automatically export that
function under the same name in the children. This would make
recursive functions just work, but it might be a bit too
magical.
On 11/3/13, 2:38 PM, Ryan wrote:
Here's an easy thing we can add to BiocParallel in the
short term. The following code defines a wrapper function
"withBPExtraErrorText" that simply appends an additional
message to the end of any error that looks like it is
about a missing variable. We could wrap every evaluation
in a similar tryCatch to at least provide a more
informative error message when a subprocess has a missing
variable.
-Ryan
withBPExtraErrorText <- function(expr) {
tryCatch({
expr
}, simpleError = function(err) {
if (grepl("^object '(.*)' not found$",
err$message, perl=TRUE)) {
## It is an error due to a variable not found.
err$message <- paste0(err$message, ". Maybe
you forgot to export this variable from the main R
session using \"bpexport\"?")
}
stop(err)
})
}
x <- 5
## Succeeds
withBPExtraErrorText(x)
## Fails with more informative error message
withBPExtraErrorText(y)
On Sun Nov 3 14:01:48 2013, Henrik Bengtsson wrote:
On Sun, Nov 3, 2013 at 1:29 PM, Michael Lawrence
<lawrence.mich...@gene.com
<mailto:lawrence.mich...@gene.com>> wrote:
An analog to clusterExport is a good idea. To
make it even easier, we could
have a dynamic environment based on object tables
that would catch missing
symbols and download them from the parent thread.
But maybe there's some
benefit to being explicit?
A first step to fully automate this would be to
provide some (opt
in/out) mechanism for code inspection and warn about
non-defined
objects (cf. 'R CMD check'). That is of course major
work, but will
certainly spare the community/users 1000's of hours
in troubleshooting
and the mailing lists from "why doesn't my parallel
code not work"
messages. Such protection may be better suited for
the 'parallel'
package though. Unfortunately, it's beyond my
skills/time to pull
such a thing together.
/Henrik
Michael
On Sun, Nov 3, 2013 at 12:39 PM, Henrik Bengtsson
<h...@biostat.ucsf.edu <mailto:h...@biostat.ucsf.edu>>
wrote:
Hi,
in BiocParallel, is there a suggested (or
planned) best standards for
making *locally* assigned variables (e.g.
functions) available to the
applied function when it runs in a separate R
process (which will be
the most common use case)? I understand that
avoid local variables
should be avoided and it's preferred to put
as mush as possible in
packages, but that's not always possible or
very convenient.
EXAMPLE:
library('BiocParallel')
library('BatchJobs')
# Here I pick a recursive functions to make
the problem a bit harder, i.e.
# the function needs to call itself ("itself"
= see below)
fib <- function(n=0) {
if (n < 0) stop("Invalid 'n': ", n)
if (n == 0 || n == 1) return(1)
fib(n-2) + fib(n-1)
}
# Executing in the current R session
cluster.functions <-
makeClusterFunctionsInteractive()
bpParams <-
BatchJobsParam(cluster.functions=cluster.functions)
register(bpParams)
values <- bplapply(0:9, FUN=fib)
## SubmitJobs
|++++++++++++++++++++++++++++++++++| 100%
(00:00:00)
## Waiting [S:0 R:0 D:10 E:0]
|+++++++++++++++++++| 100% (00:00:00)
# Executing in a separate R process, where
fib() is not defined
# (not specific to BiocParallel)
cluster.functions <- makeClusterFunctionsLocal()
bpParams <-
BatchJobsParam(cluster.functions=cluster.functions)
register(bpParams)
values <- bplapply(0:9, FUN=fib)
## SubmitJobs
|++++++++++++++++++++++++++++++++++| 100%
(00:00:00)
## Waiting [S:0 R:0 D:10 E:0]
|+++++++++++++++++++| 100% (00:00:00)
Error in LastError$store(results = results,
is.error = !ok, throw.error =
TRUE)
:
Errors occurred during execution. First
error message:
Error in FUN(...): could not find function "fib"
[...]
# The following illustrates that the solution
is not always
straightforward.
# (not specific to BiocParallel; must have
been discussed previously)
values <- bplapply(0:9, FUN=function(n, fib) {
fib(n)
}, fib=fib)
Error in LastError$store(results = results,
is.error = !ok,
throw.error = TRUE) :
Errors occurred during execution. First
error message:
Error in fib(n): could not find function "fib"
[...]
# Workaround; make fib() aware of itself
# (this is something the user need to do, and
would be very
# hard for BiocParallel et al. to automate.
BTW, should all
# recursive functions be implemented this way?).
fib <- function(n=0) {
if (n < 0) stop("Invalid 'n': ", n)
if (n == 0 || n == 1) return(1)
fib <- sys.function() # Make function
aware of itself
fib(n-2) + fib(n-1)
}
values <- bplapply(0:9, FUN=function(n, fib) {
fib(n)
}, fib=fib)
WISHLIST:
Considering the above recursive issue solved,
a slightly more explicit
and standardized solution is then:
values <- bplapply(0:9, FUN=function(n,
BPGLOBALS=NULL) {
for (name in names(BPGLOBALS))
assign(name, BPGLOBALS[[name]])
fib(n)
}, BPGLOBALS=list(fib=fib))
Could the above be generalized into something
as neat as:
bpExport("fib")
values <- bplapply(0:9, FUN=function(n) {
BiocParallel::bpImport("fib")
fib(n)
})
or ideally just (analogously to
parallel::clusterExport()):
bpExport("fib")
values <- bplapply(0:9, FUN=fib)
/Henrik
_______________________________________________
Bioc-devel@r-project.org
<mailto:Bioc-devel@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org
<mailto:Bioc-devel@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis
