On Thu, 8 Sep 2011, Steve Lianoglou wrote:
Hi Simon,
Thanks for the quick response.
Comments in line:
On Thu, Sep 8, 2011 at 4:11 PM, Simon Urbanek
<simon.urba...@r-project.org> wrote:
On Sep 8, 2011, at 3:59 PM, Steve Lianoglou wrote:
Hi,
Essentially: subject line says it all.
I've created a package that wraps an external c++ library (which I didn't
write) that only successfully compiles on 64bit machines.
That doesn't sound right, it contradicts your subject line - x86_64
is just one of many 64-bit architectures ...
Ok, sorry for being imprecise. Let's see if we can figure out what it
is (more precise details are at the bottom of the email). I see x86_64
on every 64bit machine I touch (linux or mac), so I thought they were
interchangeable (as names).
Not so. That's not what Windows uses (it mainly uses x64, sometimes
amd64 or x86-64, almost never x86_64), and although it is what Solaris
uses, your Linux x86_64 assembler (presumably GNU) will not work
there.
My hunch is that it really is about the architecture, not x86_64
but from what you describe it's not about an architecture at all -
it's about the library .. (see below).
[snip]
I see hints in how to limit which architecture a package is built
against in the R-ext and R-admin manuals where they seem to suggest to
include a src/Makefile in order to do that ... but I'm not sure what I
should put in it.
No, that's not the purpose.
Well, the r-admin doc does suggest using your own Makefile in close
proximity to targetting specific architectures several times ... eg.
section 2.6, 6.3.1, 6.3.4.
No, it suggests there is an interaction: *if* you use your own
src/Makefile it interacts with multiarch builds. And so does having a
configure file ....
In fact, if you search that document for "src/Makefile" it's almost
always found next to something that talks about compiling architecture
specific builds ... I'm sure it's used for a lot more than that, but
r-admin repeatedly suggests that this is one of its functions.
But let's get to the good stuff.
Even if it can't go on CRAN as 64-bit only, it would be great if I can
put up some easy install instructions for people to d/l my source
package externally and use it that way.
The configure script is designed to figure out things like that, so all you
need to do is to add a configure script that will check whether the package can
be built for that architecture or not.
OK ... I was hoping I could avoid getting into configure/autoconf
stuff, but at some point I'll have to bite the bullet and read up on
it much more than I really want to, so I guess that will happen sooner
than later.
In fact, it should really check whatever the C++ library does that
prevents it from working elsewhere. The particularities depends on
the library so you'll need to provide more info in oder to help you
better ...
It's doing some inline assembly. The problematic code is here:
https://github.com/lianos/buckshot/blob/master/src/cas_array.h#L90
Compiling the 32bit version of the library on my mac complains about
the call to `cmpxchg`, specifically:
/var/folders/C2/C2bsTekpH-qdLj5psUvjtk+++TM/-Tmp-//cc7q88qD.s:785:suffix
or operands invalid for `cmpxchg'
Doing surgery on the code to actually fix it is a bit above my pay
grade right now as the last time I had to write in assembly was > 10
years ago for an undergraduate class, so I'd just like to sidestep the
issue.
I'm not sure how to properly check if this call to cmpxchg can work
inside a configure script or using autoconf. If it's relatively
simple, I'd appreciate a hint if you've got one to spare, otherwise
I'll just keep compiling the 64bit only version of the library until I
can figure out how to sort it out.
The library also compiles fine on our linux compute servers, which
`uname -a` tells me are also of the x86_64 64bit variety. I'm not sure
if that's helpful to know, but thought I'd just put it out there.
You try to compile the crucial fragament of code in configure: there
are lots of examples of that in the R sources (mainly in the m4
directory).
Thanks,
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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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)
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