FAQ

FAQ

With HALMD, I could do simulations of breath-taking quality and have obtained new scientific insight. How may I thank you?

Please acknowledge the use of HALMD in your publications by citing our article:

P. H. Colberg and F. Höfling, Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision, Comp. Phys. Comm. 182, 1120 (2011) [Link].

Why does HALMD abort with “[ERROR] potential energy diverged”?

An infinite potential energy sum of one or more particles indicates that the integration time-step is too large.

Try lowering the --timestep value.

Linking fails with: undefined reference to `boost::filesystem3::detail::copy_file(...)'

Check that the ABI version of the installed Boost C++ library conforms to
C++11. This can be achieved by building Boost C++ with the GCC option
``--std=c++11``.

nvcc fails with 'cudafe++' died due to signal 11 (Invalid memory reference)

This is due to a bug in the CUDA compiler, which may be circumvented by including --host-compilation=c in the NVCCFLAGS environment variable passed to cmake, or in CMAKE_CUDA_FLAGS using ccmake.

nvcc fails with error: inline function ‘__signbit’ cannot be declared weak

CUDA 3.0 (or less) is not compatible with GCC 4.4. As a work around install GCC 4.3 and place symlinks in the default CUDA compiler directory, e.g. if the CUDA toolkit is located in /opt/cuda, symlink /opt/cuda/bin/{gcc,g++} to /usr/bin/{gcc,g++}-4.3, respectively. The compiler directory may be overriden with the --compiler-bindir option.