From nmcalder at verizon.net  Mon Dec 31 04:43:50 2007
From: nmcalder at verizon.net (Matt Calder)
Date: Sun, 30 Dec 2007 22:43:50 -0500
Subject: [Rd] Problem with dyn.load'ed code
In-Reply-To: <5C33CB00-7BE2-4169-8AD6-510BA58977D7@r-project.org>
References: <1199053522.17113.29.camel@calder-linux>
	<5C33CB00-7BE2-4169-8AD6-510BA58977D7@r-project.org>
Message-ID: <1199072630.17113.54.camel@calder-linux>

Simon,
	Thanks for the reply. Indeed, declaring the function static fixes the
example. Unfortunately, the real problem that gave rise to the example
arises in a large Fortran library that is not under my control (ARPACK).
The author is providing BLAS and LAPACK functionality intentionally.
That may or may not be good practice, but it is a given in this case.
	So, I have a set of Fortran code in which some BLAS functionality is
replicated. I am writing an interface to some of the functions in that
code (not to the BLAS part, that is used internally by ARPACK). I would
like it if that interface did not require alteration of the library
source code or build process (though it is open-source, so if need be I
can change it). 
	I still feel like the linker ought to be able to solve this problem for
me. My impression was that the static keyword passed to the linker
caused it to resolve all references at link time. So something like:

ld -o my_code_and_arpack.o -static my_code.o -larpack

would pull all the references from the two object files (my_code.o and
libarpack.a) and link them as needed, and unresolved references would
cause an error. I guess that impression is wrong, but how does one
accomplish the same thing? 
	Thanks for any help,

	Matt
	

On Sun, 2007-12-30 at 20:21 -0500, Simon Urbanek wrote:
> Matt,
> 
> On Dec 30, 2007, at 5:25 PM, Matt Calder wrote:
> 
> > 	I am still having trouble dyn.load'ing some code into R. I have  
> > isolated the problem, I wonder if someone could explain what I am  
> > seeing.
> > 	I think the problem is that a symbol defined in my compiled code  
> > clashes with one already defined in R.
> 
> The result of redefining a symbol is very much system-dependent. For  
> example on Mac OS X it has no adverse effects (i.e your symbols are  
> always private unless linked against), because it uses a two-level  
> namespace, but on Linux (and most other unices) it does as the  
> namespace of an executable is shared among all modules (dynamic and  
> static).
> 
> 
> > The result is that the function in my code is not called. Here is an  
> > example
> >
> > // lnktst.cc
> > extern "C"
> > {
> >  void func(double *out1, double *out2);
> >  void dnrm2_(double *out);
> >  void dnrm3_(double *out);
> > }
> >
> > void func(double *out1, double *out2)
> > {
> >  dnrm2_(out1);
> >  dnrm3_(out2);
> > }
> >
> > void dnrm2_(double *out)
> > {
> >  *out = 1234.5;
> > }
> >
> > void dnrm3_(double *out)
> > {
> >  *out = 6789.0;
> > }
> > // End of lnktst.cc
> >
> > When I compile:
> >
> > g++ -shared -static -o lnktst.so lnktst.cc
> >
> > and then in R I call "func"
> >
> >> dyn.load("lnktst.so")
> >> .C('func', double(1), double(1))
> > [[1]]
> > [1] 0
> >
> > [[2]]
> > [1] 6789
> >
> > So, as you can see, the function "dnrm2_" is not called whereas  
> > "dnrm3_" is, even though both functions are identical in form. Now,  
> > I believe dnrm2_ is a BLAS function, and so it is likely R already  
> > has a copy floating around.
> 
> Yes, indeed (it's a BLAS level 1 Fortran function, and usually to be  
> found in libRblas.so or the external BLAS implementation).
> 
> 
> > However, it surprises me that the "-static" option does
> > not force the call in my code to "dnrm2_" to be linked to the function
> > defined in my code.
> 
> You are confusing the purpose of -static: it only ensures that static  
> libraries are used at link time where possible, it doesn't affect your  
> code in any way. What you really want is to use
> static void dnrm2_(double *out);
> in your code instead.
> 
> In general, it is a bad idea to use external symbols that clash with  
> other libraries (in particular widespread ones such as BLAS),  
> especially if your function doesn't perform the same operation. It is  
> a good idea to declare all functions that you use internally (i.e.  
> that should not be visible to R) as static. However, all this is true  
> for C programming in general, not just in conjunction with R.
> 
> Cheers,
> Simon
> 
> 
> > 	I have been writing C code for Splus for quite a while and don't  
> > recall
> > ever running across this issue. However, I am new to R, so I wonder,  
> > am
> > I missing something obvious?
> > 	I am running this on Ubuntu Linux, the output of uname -a is:
> >
> > Linux calder-linux 2.6.22-14-generic #1 SMP Sun Oct 14 23:05:12 GMT  
> > 2007 i686 GNU/Linux
> >
> > Thanks for any help,
> >
> > 	Matt
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
>



[Rd] Problem with dyn.load'ed code
Matt Calder