[gmx-users] Can't build gromacs-4.5.3 with cmake

[Keith Callenberg]

Ah! "Outside the source tree" to me meant, outside "src/". I see now
that it means outside gromacs-4.5.3. It does indeed make a difference,
now I can build.

When I tried to compile with OpenMM I ran into an error that I was
missing libxml-2.0. I had libxml2 installed, but I needed to install
the headers using: sudo apt-get install libxml2-dev.

When I tried to compile I got this error:

$ make mdrun
[  0%] Building NVCC (Device) object
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
CMake Error at CMakeFiles/gmx_gpu_utils_generated_memtestG80_core.cu.o.cmake:256
(message):
 Error generating file
 /home/keithc/apps/gromacs-4.5.3-gpu/src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o

make[3]: *** [src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o]
Error 1
make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2

This comes from some permissions issue from when I compiled the CUDA
toolkit. I had just followed directions from a post on ubuntuforums,
so I think others could potentially run into this issue as well. The
(inelegant) workaround was to compile as sudo: sudo make mdrun (and)
sudo make install-mdrun. Now it works.

Thank you!

Keith