build issue relocation R_X86_64_32 against symbol __gxx_personality_v0@@CXXABI_1.3' can not be used when making a PIE object; recompile with -fPIE`

[alisterburt]

Me again, struggling to build AT2 following the instructions

I'm working in a conda environment with the following dependencies:

channels:
  - conda-forge
  - defaults
dependencies:
  - torchvision
  - libtiff
  - python=3.10.6
  - pytorch-gpu
  - cmake
  - cudatoolkit=11.4
  - pytorch
  - fftw
  - cudatoolkit-dev
  - cxx-compiler=1.3
  - cudnn
  - dotnet=6.0

And getting the following error whilst building

software/AreTomo2/Lib/libmrcfile.a(CLoadExtHeader.o): relocation R_X86_64_32 against symbol `__gxx_personality_v0@@CXXABI_1.3' can not be used when making a PIE object; recompile with -fPIE`

Any ideas?

[mpibpc-mroose]

I had the same problem. I fixed it by editing makefile11:

[sroet]

just mentioning I also ran into this issue and seemed to be solved by the solution off @mpibpc-mroose (haven't tested it completely yet, but was able to run AreTomo2 --version after moving the binary)

[tthersleff]

I also had this issue when compiling it and was able to solve it by adding the -no-pie flag, just as @mpibpc-mroose mentioned above. Thanks!

[mpm896]

Following up on this, I was able to successfully compile it as well with @mpibpc-mroose suggestion, but was anything added to your PATH variable? I'm not able to run AreTomo2 --version or any of the other commands in the doc, just say command not found. Thanks!

Edit: Found the executable and added it to the PATH, works fine now!