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
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?
Thanks,
Andy
