From atp at piskorski.com  Mon Oct  5 23:22:02 2009
From: atp at piskorski.com (Andrew Piskorski)
Date: Mon, 5 Oct 2009 17:22:02 -0400
Subject: [Rd] R's --enable-threads does nothing?; gdb needs -lpthread
Message-ID: <20091005212202.GA49270@piskorski.com>

In the R-2-9-branch (svn revision 49914, 2009-09-24), R's configure
script has an "--enable-threads" option.  But, does it do anything
useful?  When I use "--enable-threads=posix", some of the configure
output changes slightly, but it seems to have no effect on the actual
link commands used when building R.  Is that a bug, or am I
misunderstanding what it's supposed to do?

Btw, ldd said that exactly these 4 objects are linked against
libpthread.so.0, regardless of whether I use --enable-threads or not:
 
  ./lib/R/modules/x86_64/R_X11.so
  ./lib/R/library/tcltk/libs/x86_64/tcltk.so
  ./lib/R/site-library/bigmemory/libs/x86_64/bigmemory.so
  ./lib/R/site-library/Rmpi/libs/x86_64/Rmpi.so

Next I tried setting the "LIBS=-lpthread" environment variable when
calling configure - that works.  (Perhaps I should have also set
FLIBS, I'm not sure.)  The generated Makeconf file now has this:

  LIBS =  -ldl -lm -lpthread 

and building with that links my libR.so against libpthread.so.0, which
fixes the gdb problem described below.  Is there any reason you know
of NOT to link R with -lpthread on Linux, any potential downside?

Now, why do I care about this -lpthread stuff in the first place?
It's to work around a gdb limitation.

I have a custom library of C code which I use from R, and my library
needs to be linked with -lpthread.  I know that R isn't thread-safe,
and my code is not itself using threads, but it in turn statically
links in some lower level libraries which insist on having the
-lpthread.

That has worked fine for me for a long time, no problems, except that
gdb won't work!  When I run R under the debugger with "R -d gdb", gdb
only works if my own linked-with-pthread package is NOT loaded.  As
soon as I load it, gdb stops with this error:

   [Thread debugging using libthread_db enabled] 
   Error while reading shared library symbols: 
   Cannot find new threads: generic error 

Googling says that happens because the R binary starts out without
thread support, and gdb doesn't know what to do when my *.so suddenly
brings in the thread stuff.  Since I can't stop using -lpthread in my
library, the obvious fix is for me to build R itself with -lpthread,
so gdb doesn't get confused.

-- 
Andrew Piskorski <atp at piskorski.com>
http://www.piskorski.com/



[Rd] R's --enable-threads does nothing?; gdb needs -lpthread
Andrew Piskorski