search

amnsbr / cubnm

A toolbox for biophysical network modeling on GPUs
https://cubnm.readthedocs.io
BSD 3-Clause "New" or "Revised" License
7 stars 3 forks source link

[BUG] Linking to pre-existing GSL libraries compiled without `-fPIC` #2

Closed amnsbr closed 2 months ago

amnsbr commented 8 months ago

When building from source setup.py searches for libgsl.a and libgslcblas.a in some known paths which will be linked in compilation of bnm.cu and run_simulations.cpp. If there are preexisting GSL libraries but they have not been compiled with -fPIC compilation fails with this error message:

  /bin/ld: /usr/lib/x86_64-linux-gnu/libgslcblas.a(xerbla.o): warning: relocation against `stderr@@GLIBC_2.2.5' in read-only section `.text'
  /bin/ld: /usr/lib/x86_64-linux-gnu/libgslcblas.a(xerbla.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC

To fix this the setup needs to identify if GSL libraries are compiled without -fPIC and if this is the case avoid using them.

amnsbr commented 2 months ago

I just added a note in the installation instructions that GSL must be built with --enable-shared option in this commit