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weird bug with parallel, RSQlite and tcltk

2 messages · Karl Forner, Simon Urbanek

Original
Karl Forner
# 
Hello,

I spent a lot of a time on a weird bug, and I just managed to narrow it down.

In parallel code (here with parallel::mclappy, but I got it
doMC/multicore too), if the library(tcltk) is loaded, R hangs when
trying to open a DB connection.
I got the same behaviour on two different computers, one dual-core,
and one 2 xeon quad-core.

Here's the code:

library(parallel)
library(RSQLite)
library(tcltk)
#unloadNamespace("tcltk")

res <- mclapply(1:2, function(x) {
	db <- DBI::dbConnect("SQLite", ":memory:")
}, mc.cores=2)
print("Done")	

When I execute it (R --vanilla  < test_parallel_db.R), it hangs
forever, and I have to type several times CTRL+C to interrupt it. I
then get this message:

Warning messages:
1: In selectChildren(ac, 1) : error 'Interrupted system call' in select
2: In selectChildren(ac, 1) : error 'Interrupted system call' in select

Then, just remove library(tcltk), or uncomment
unloadNamespace("tcltk"), and it works fine again.

I guess there's a bug somewhere, but where exactly ?

Best,

Karl Forner

Further info:


R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)

ubuntu 12.04 and 12.10

ubuntu package tk8.5
Simon Urbanek
#
On Dec 31, 2012, at 1:08 PM, Karl Forner wrote:

            

      
      
      
    

        
First, tcltk and multicore don't mix well, see the warning in the documentation (it mentions GUIs and AFAIR tcltk fires up a GUI event loop even if you don't actually create GUI elements). Second, using any kind of descriptors in parallel code is asking for trouble since those will be owned by multiple processes. If you use databases files, etc. they must be opened in the parallel code, they cannot be shared by multiple workers. The latter is ok in your code so you're probably bitten by the former.

Cheers,
Simon