[gmx-developers] About the multi-simulation

Yukun Wang wangykoo at gmail.com
Wed Mar 16 08:46:29 CET 2011

Hi all:
    I want to run a group of simulations which are weakly coupled, like
REMD,but with different algorithm. I find there is a data structure called
'gmx_multisim_t' whose definition is below:
                 typedef struct {
  int nsim;
  int sim;
  MPI_Group mpi_group_masters;
  MPI_Comm mpi_comm_masters;
  /* these buffers are used as destination buffers if MPI_IN_PLACE isn't
  mpi_in_place_buf_t *mpb;
} gmx_multisim_t;

Then I have three questions:
1. If a command line is writen as for GROMACS 4.0 and a seires of input .tpr
files is named as 'prefix_0.tpr, prefix_1.tpr ... prefix_9.tpr',
[...] $ mpirun -np 10 mdrun -s prefix_.tpr -multi *(number of steps)*
by output options)*
Are those simulation are mutually independent? ( Attention no -replex here
2. I know Gromacs from 4.0version have a ablility that each replica can be
parallelly simulated. Then I want to know if they are intra-commucation for
each replica and inter-communication between replicas.
3. What is the means of  'nsim','sim','mpi_group_masters' and
'mpi_comm_masters'  in the above structure?

Thank you for your patience!
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