[gmx-users] parallelization

pratibha kapoor kapoorpratibha7 at gmail.com
Thu Oct 17 14:25:08 CEST 2013

Dear gromacs users

I would like to run my simulations on all nodes(8) with full utilisation of
all cores(2 each). I have compiled gromacs version 4.6.3 using both thread
mpi and open mpi. I am using following command:
mpirun -np 8 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro
But I am getting following error:
Setting the total number of threads is only supported with thread-MPI and
Gromacs was compiled without thread-MPI .
Although during compilation I have used:

If I dont use -nt option, I could see that all the processors(8) are
utilised but I am not sure whether all cores are being utilised. For
version 4.6.3 without mpi, I Know by default gromacs uses all the threads
but not sure if mpi version uses all threads or not.
Any help is appreciated.

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