On Thu, 22 Sep 2005, Charles Geyer wrote:
> On Tue, Sep 20, 2005 at 09:43:51PM -0500, Luke Tierney wrote:
>> On Tue, 20 Sep 2005, Charles Geyer wrote:
>>>
>>> I still don't understand why gcc -shared even bothers to look in *.a
>>> (on AMD64) when it won't do the slightest bit of good. Maybe I'm still
>>> ignorant of some important technical issue (maybe? more like with very
>>> high probability!)
>>>
>>
>> The issue is not the library but whether the code is compiled as
>> position-independent code (PIC) or not. Many .a libraries are built
>> as PIC and they can be used to create shared objects, you just get
>> copies of the modules you use linked in. PIC code can be slower,
>> which is why some prefer to build .a libraries as non-PIC.
>
> Oh. Thanks. That makes it all clear. If I compile cddlib with
>
> export CXX=gcc
> export CFLAGS="-O -fPIC"
> ./configure --prefix=/APPS/64/
>
> then I can build rcdd and it works! (And, you're right, the fact that
> cddlib builds libcddgmp.a instead of libcddgmp.so is irrelevant, it's
> the -fPIC that matters.)
>
>> I'm not sure why one rarely runs into non-PIC issues on i386--it may
>> be that gcc at least is always producing PIC code there. It does come
>> up on other architectures though, in particular on x86_64. It seems
>> that most Linux distros that provide pvm only provide .a libraries,
>> but some build these with PIC some don't. Red Hat Enterprise WS4
>> seems to be non-PIC, FC3 and FC4 seem to be PIC. If your distro is
>> non-PIC you will need to build your own PIC version of pvm and tell
>> rpvm where to find it.
>
> snowbank$ locate pvm | grep -E '\.so|\.a$'
> /usr/lib/pvm3/lib/LINUX64/libfpvm3.a
> /usr/lib/pvm3/lib/LINUX64/libgpvm3.a
> /usr/lib/pvm3/lib/LINUX64/libpvm3.a
> /usr/lib/pvm3/lib/LINUX64/libpvmtrc.a
> /usr/lib64/libpvm3.so
> /usr/lib64/libpvm3.so.3
> /usr/lib64/libpvm3.so.3.4
>
> I think I've got the libraries, so
>
> > install.packages("rpvm", repos = "http://www.biometrics.mtu.edu/CRAN/";)
> trying URL 'http://www.biometrics.mtu.edu/CRAN/src/contrib/rpvm_0.6-5.tar.gz'
>
> [lots of blather deleted]
>
> gcc -shared -L/usr/local/lib64 -o rpvm.so rpvm_core.o rpvm_ser.o utils.o
> -L/usr/lib/pvm3/lib/LINUX64 -lpvm3 -lgpvm3 -lreadline -lncurses
>
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/bin/ld:
> /usr/lib/pvm3/lib/LINUX64/libpvm3.a(lpvmgen.o): relocation R_X86_64_32
> against `a local symbol' can not be used when making a shared object;
> recompile with -fPIC
>
> same problem, I have a .so (presumably PIC), but it's picked another library.
> Reading the help for install.packages, I don't find anything about how to
> make it link against /usr/lib64/libpvm3.so instead
> of /usr/lib/pvm3/lib/LINUX64/libpvm3.a so I guess that means do it by hand.
>
> I'm a little puzzled by that too. Apparently the configure in rpvm wants
> to use PVM_ROOT which for this (SuSE 9.3 AMD64) box is /usr/lib/pvm3 (which
> is the default) to find the libraries it wants to link to, but that won't
> work. The appropriate library is /usr/lib64/libpvm3.so -- maybe.
> I just noticed the -lpvm3 -lgpvm3 in the link that failed. I'm not
> sure /usr/lib64/libpvm3.so contains everything rpvm needs.
> This just isn't going to work with the SuSE provided pvm stuff right?
>
> I untarred the rpvm package and did R CMD check on it and it really
> doesn't give any way to link to a library in an odd place -- at least
> not that I can see.
I would run configure in the untarred package then edit src/Makevars
to remove the -L bit and the -lgpvm and see if that works. If not,
I'd get the pvm source, build libpvm.a and liggpvm.a with -fPIC files,
and fix src/Makevars to use them. I'm sure there are more elegant
alternatives, but ...
luke
--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: [EMAIL PROTECTED]
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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