OpenMP

PLUMED is partly parallelized using OpenMP. This should be enabled by default if your compiler supports it, and can be disabled with --disable-openmp.. At runtime, you should set the environment variable PLUMED_NUM_THREADS to the number of threads you wish to use with PLUMED. The number of OpenMP threads can be set either by the MD code, if implemented in the patch, or generally by setting PLUMED_NUM_THREADS. If they are not set openmp will be disabled at runtime.

E.g., to run with gromacs you can do:

export PLUMED_NUM_THREADS=8
mdrun -plumed


or as well

mdrun -plumed -ntomp 8


In the first case the number of OpenMP threads used by plumed is 8 while the one used by gromacs can be 1 or something else, this is usually sub optimal. In the second case GROMACS and plumed will use the same number of OpenMP threads.

Notice that:

• This option is likely to improve the performance, but could also slow down the code in some case.
• Results could be slightly different because of numerical round off and different order in summations. This should be harmless.
• The optimum number of threads is not necessary "all of them", nor should be equal to the number of threads used to parallelize MD.
• Only a few CVs are parallelized with openMP (currently, COORDINATION and DHENERGY).
• You might want to tune also the environmental variable PLUMED_CACHELINE_SIZE, by default 512, to set the size of cache lines on your machine. This is used by PLUMED to decrease the number of threads to be used in each loop so as to avoid clashes in memory access. This variable is expected to affect performance only, not results.