From ggrothendieck at gmail.com  Thu Jan  3 12:14:28 2013
From: ggrothendieck at gmail.com (Gabor Grothendieck)
Date: Thu, 3 Jan 2013 06:14:28 -0500
Subject: [Rd] weird bug with parallel, RSQlite and tcltk
In-Reply-To: <CAMd4_Af2FihaiMYsv8vKL4z_V+X4oWUtce4HDH5iqZa-V4ji7A@mail.gmail.com>
References: <CAMd4_Ac0+CgORVFfhFAXTttAza1iG1aagZ08j_E-U-rYZspLXg@mail.gmail.com>
	<52B72508-C480-4DF3-B1E6-8B9DDA0DFD78@r-project.org>
	<CAMd4_Af2FihaiMYsv8vKL4z_V+X4oWUtce4HDH5iqZa-V4ji7A@mail.gmail.com>
Message-ID: <CAP01uR=pczw-KCZAkJFju0WJ5kut++oxNvxyReHgF+D8-ehEEw@mail.gmail.com>

On Thu, Jan 3, 2013 at 4:32 AM, Karl Forner <karl.forner at gmail.com> wrote:
> Hello,
>
> The point is that I do not use tcltk, it gets loaded probably as a
> dependency of a dependency of a package.
> When I unload it all work perfectly fine. I just found it because one
> of my computer did not have tk8.5 installed, and did not exhibit the
> mentioned bug. So I really think something should be done about this.
> Maybe the "gui loop" should not be run a the the loading of the tcltk
> package, but
> at the first function ran, or something like this.
>
> As you can see in my example code, the in-memory database is opened in
> the parallel code...
>
> Best,
> Karl

If the package you are referring to is gsubfn or a package dependent
on it such as sqldf then you can ask it to use the R engine rather
than the tcltk engine by using this option:

options(gsubfn.engine = "R")

There is more in the FAQs on the gsubfn home page: http://gsubfn.googlecode.com

>
> On Mon, Dec 31, 2012 at 10:58 PM, Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>>
>> On Dec 31, 2012, at 1:08 PM, Karl Forner wrote:
>>
>>> Hello,
>>>
>>> I spent a lot of a time on a weird bug, and I just managed to narrow it down.
>>>
>>
>> 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
>>
>>
>>
>>> 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
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



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[Rd] weird bug with parallel, RSQlite and tcltk
Gabor Grothendieck