GROMACS version:
GROMACS modification: Yes/No
Here post your question
I am using single node workstation where i have 64 core in total. now i want to submit total 8 jobs simultaneously so that each job get 8core with 100% cpu time, what should be the ideal command line for that.
Second question is that I found in gmx manual something like pinoffset, pinstride, but i am unable to understand that properly, if anyone can explain that with proper example it would be very beneficial to me.
The simplest solution is to put you 8 run inputs in different directories and then use the -multidir option of mdrun. Then the thread pinning is fully automated.
If you don’t use -multidir, the answer depends on if SMT (hyperthreading on Intel) is enabled or not and if you want to use SMT or not.
thanks a lot for your reply, I will use different directories for 8jobs. But I have a question, since using -multidir option the thread pinning is fully automated, then is there any need of using -nt option.
And one more question is during the use of -multidir option i have to use -pinoffset -pinstride all these option or not.
I just realized that you will need an MPI build for using -multidir.
With -multidir you need to decide the number of MPI ranks, which should be a multiple of the number of simulations. Usually setting this equal to the number of simulations gives the best performance. The thread count and pinning is automated when you don’t supply any of those options.
mdrun -multidir is only supported when GROMACS has been configured with a
proper external MPI library.
when I am going to use -multidir option, this type of error coming. But in gromacs manual it is written that using external mpi runs slowly than the thread mpi