[gmx-users] Mdrun kills all other(single CPU)mdrun processes started by same father process?

[David van der Spoel]

Peter Mueller wrote:
> Dear Gromacs users,
> 
> on a smaller cluster I start with a small C + MPI program via a system call several single CPU Gromacs mdrun jobs.
> (For the cluster admin it's OK, because my system does not scale well and I need lots of small independent trajectories.)
> All the mdrun jobs are independent and shouldn't know from each other.
> Just to make sure that the jobs don't kill each I included a "MPI_Barrier(MPI_COMM_WORLD)" before the process call "MPI_Finalize()".
> Now I realized that when the first single CPU mdrun finishes a TERM signal is send to all other mdrun jobs which are started by my C program.
> After getting the TERM signal this mdrun jobs do one additional md-step and then write out a summary before stopping.
> 
> In the manual page of mdrun I found following hint:
>    "When mdrun receives a TERM signal, it will
>      set nsteps to the current step plus one
>     ... all the usual output will be written to file.
>     When running with MPI, a signal to one of
>     the mdrun processes is sufficient, this signal
>      should not be sent to mpirun or the mdrun
>     process that is the parent of the others."
> 
> I think mdrun is to clever :-). When it finishes it checks if the father process started any other mdrun jobs. If this is the case it send a TERM single to all this corresponding mdrun jobs.
> Because my mdrun jobs are independent this behavior is my case wrong.
> Is there any flag for "mdrun" to avoid this behavior?
> 
> 
> Thanks
> Peter
> 
Why not use  a script or queueing system?
Much easier for the user.

-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se