[Rd] Does dlltools in 64-bit rtools for windows support 64-bit machine type?
Hi,
I've been trying to get the python bridge (rpy2) to build for 64-bit R
and python. The current stumbling block is that mingw can't use the
python27.lib file that comes with CPython and so I need to generate
libpython27.a.
When I use dlltool from rtools to do that however, I end up with a 32-bit file:
>"G:\Rtools\gcc-4.6.3\i686-w64-mingw32\bin\dlltool" -e libpython27.a -d
>python27.def python27.dll
>objdump -f libpython27.a
libpython27.a: file format pe-i386
More problematically, x86_64 is not listed as supported by objdump:
Usage G:\Rtools\gcc-4.6.3\i686-w64-mingw32\bin\dlltool
-m --machine Create as DLL for . [default: i386]
possible : arm[_interwork], i386,
mcore[-elf]{-le|-be}, ppc, thumb
Am I doing it wrong?
Regards,
Johan
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[Rd] weird bug with parallel, RSQlite and tcltk
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
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Re: [Rd] Does dlltools in 64-bit rtools for windows support 64-bit machine type?
On 12-12-30 9:07 AM, Johan Johansson wrote:
Hi,
I've been trying to get the python bridge (rpy2) to build for 64-bit R
and python. The current stumbling block is that mingw can't use the
python27.lib file that comes with CPython and so I need to generate
libpython27.a.
When I use dlltool from rtools to do that however, I end up with a 32-bit file:
"G:\Rtools\gcc-4.6.3\i686-w64-mingw32\bin\dlltool" -e libpython27.a -d
python27.def python27.dll
objdump -f libpython27.a
libpython27.a: file format pe-i386
More problematically, x86_64 is not listed as supported by objdump:
Usage G:\Rtools\gcc-4.6.3\i686-w64-mingw32\bin\dlltool
-m --machine Create as DLL for . [default: i386]
possible : arm[_interwork], i386,
mcore[-elf]{-le|-be}, ppc, thumb
Am I doing it wrong?
You aren't using the same flags as R uses in its builds. For 64 bit
builds, it uses these flags (from MkRules.rules):
DLLTOOLFLAGS=--as $(BINPREF)as $(DT_ARCH) -k
DT_ARCH = -m i386:x86-64 --as-flags --64
Duncan Murdoch
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Re: [Rd] Does dlltools in 64-bit rtools for windows support 64-bit machine type?
On 31/12/2012 18:19, Duncan Murdoch wrote:
On 12-12-30 9:07 AM, Johan Johansson wrote:
Hi,
I've been trying to get the python bridge (rpy2) to build for 64-bit R
and python. The current stumbling block is that mingw can't use the
python27.lib file that comes with CPython and so I need to generate
libpython27.a.
BTW, 'mingw' is irrelevant as it has not been used by R for a long time.
Mingw's dlltool is indeed 32-bit only.
When I use dlltool from rtools to do that however, I end up with a
32-bit file:
"G:\Rtools\gcc-4.6.3\i686-w64-mingw32\bin\dlltool" -e libpython27.a
-d python27.def python27.dll
objdump -f libpython27.a
libpython27.a: file format pe-i386
More problematically, x86_64 is not listed as supported by objdump:
Usage G:\Rtools\gcc-4.6.3\i686-w64-mingw32\bin\dlltool
-m --machine Create as DLL for . [default:
i386]
possible : arm[_interwork], i386,
mcore[-elf]{-le|-be}, ppc, thumb
Am I doing it wrong?
You aren't using the same flags as R uses in its builds. For 64 bit
builds, it uses these flags (from MkRules.rules):
DLLTOOLFLAGS=--as $(BINPREF)as $(DT_ARCH) -k
DT_ARCH = -m i386:x86-64 --as-flags --64
The irrational mess of flags in GNU bintools is not our doing, and
suggestions upstream to support e.g. -m64 have fallen on deaf ears. At
least a useR does not need to divine this from the bintools
documentation (at least at the time I had to read the sources as it was
not in the bintools manual).
Duncan Murdoch
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [Rd] weird bug with parallel, RSQlite and tcltk
Dear Karl, I get exactly the same warning messages with an Rmpi minimal example (also took me a while to narrow it down). I posted it on R-sig-hpc (more appropriate for these issues I believe), some days ago, but haven't received an answer yet. Cheers, Marius PS: https://stat.ethz.ch/pipermail/r-sig-hpc/2012-December/001572.html __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] weird bug with parallel, RSQlite and tcltk
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
>
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> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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Re: [Rd] weird bug with parallel, RSQlite and tcltk
On Dec 31, 2012, at 4:20 PM, Marius Hofert wrote: > Dear Karl, > > I get exactly the same warning messages with an Rmpi minimal example (also > took > me a while to narrow it down). I posted it on R-sig-hpc (more appropriate for > these issues I believe), some days ago, but haven't received an answer yet. > AFAIR MPI doesn't support forking. Cheers, Simon > Cheers, > > Marius > > PS: https://stat.ethz.ch/pipermail/r-sig-hpc/2012-December/001572.html > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
