[gmx-users] run gromacs on a single machine with mutiple CPUs

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 21 10:23:06 CET 2006

Seaclear Theory wrote:
> I do not understand  why you are so upset. Are you the author of the 
> user manual :-)  Any way, let's go back for the issue, not person.

I'm not upset - I'm just communicating directly :-) I do get a little 
irritated when someone wanting help  doesn't describe their problem very 
well, but sometimes it is hard for them to know what to describe :-) 
Asserting "the manual doesn't describe much and it's wrong anyway" just 
makes most of us think you haven't looked hard enough and are trying to 
get us to do all of your work. Saying "I read A.5 in the manual, and 
when I tried <stuff>, then weird thing <this> happened... what's up?" is 
far better for everyone.

> The user manual said that "you don't have to use the mpirun command" if 
> you want to run gromacs on a single machine with multiple processors. 
> How should I understand this? By the way, the manual ( v.3.3) and the 
> reference does not have information about "mdrun_mpi". Thanks.

OK. configure --enable-mpi creates versions of all the executables that 
have an _mpi suffix... only mdrun actually needs this, however, so the 
usual best strategy is to do a configure without the MPI, install that, 
then configure with enable-mpi and then make install-mdrun. When you 
want a multi-processor mdrun, use the appropriate one..

If mdrun_mpi doesn't work as in A.5, then I suggest using an mpirun 
version anyway, since with the correct MPI configuration (and you're on 
your own here) you can run any combination of processes over processors.



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