Dear Andy,
On Mon, Sep 15, 2008 at 11:22 PM, Andrew Fant <[email protected]> wrote:
> I'm building rdkit on an ubuntu 8.04 lts intel pc and am running into a
> really annoying link error. For several reasons, I'm using a hand-built
> atlas that works with the other applications, but any time one of the
> rdkit routines attempts to link to blas/lapack routines, I get a link
> error of the form:
>
> /usr/bin/ld:
> Numerics/EigenSolvers/bin/gcc-4.2.3/release/threading-multi/main.exe:
> hidden symbol `__stack_chk_fail_local' in
> /usr/lib/libc_nonshared.a(stack_chk_fail_local.oS) is referenced by DSO
> /usr/bin/ld: final link failed: Nonrepresentable section on output
> collect2: ld returned 1 exit status
> ...failed gcc.link
> Numerics/EigenSolvers/bin/gcc-4.2.3/release/threading-multi/main.exe...
> gcc.link Numerics/EigenSolvers/testExecs/main.exe
>
> Googling for this error indicates that it usually comes from using ld
> -shared rather than gcc -shared to build shared libraries, which doesn't
> appear to be the immediate issue at hand here. Another post suggested a
> modification to the compile and link flags to mask the problem. Sadly,
> setting the new flags on the bjam command line "cflags=-foo" only
> succeeded in getting bjam to run all night without building anything
> before segfaulting at dawn.
>
> Has anyone butted heads with this one before? Alternately, is there a
This is a new one to me.
I'm going to be out of town until the end of the week, but I will take
a look at linking against ATLAS when I get back. In the meantime, if
you can find a "normal" BLAS to link against, that should clear up the
problem and won't affect runtimes too much: the use of the linear
algebra routines in the RDKit is very limited.
> good introduction to bjam for people who are used to using make and who
> don't want to delve into the BNF of the language just to change some
> compile flags?
I don't know any good introductions. BJam is a nice tool, but the docs
are not so pleasant for beginners. If you look in the Jamroot file in
$RDBASE/Code, the project RDKit has an illustration of how to add
compiler flags:
-----
project RDKit
: requirements <include>. <threading>multi
<include>$(BOOSTHOME)
# <library>/boost/log//boost_log
<include>$(RDBASE)/External/Lapack++/include
<include>$(RDBASE)/External/vflib-2.0/include
<toolset>gcc:<cflags>-Wno-unused-function
<toolset>gcc:<cflags>-fno-strict-aliasing
<toolset>msvc:<define>WIN32
<address-model>64:<cflags>-fPIC
: default-build release ;
-----
Best regards,
-greg
