[gmx-users] Why does the -append option exist?

[Mark Abraham]

On 5/06/2011 11:08 PM, Francesco Oteri wrote:
> Dear Dimitar,
> I'm following the debate regarding:
>
>
>> The point was not "why" I was getting the restarts, but the fact 
>> itself that I was getting restarts close in time, as I stated in my 
>> first post. I actually also don't know whether jobs are deleted or 
>> suspended. I've thought that a job returned back to the queue will 
>> basically start from the beginning when later moved to an empty slot 
>> ... so don't understand the difference from that perspective.
>
> In the second mail yoo say:
>
> Submitted by:
> ========================
> ii=1
> ifmpi="mpirun -np $NSLOTS"
> --------
>    if [ ! -f run${ii}-i.tpr ];then
>       cp run${ii}.tpr run${ii}-i.tpr
>       tpbconv -s run${ii}-i.tpr -until 200000 -o run${ii}.tpr
>    fi
>
>    k=`ls md-${ii}*.out | wc -l`
>    outfile="md-${ii}-$k.out"
>    if [[ -f run${ii}.cpt ]]; then
> * $ifmpi `which mdrun` *-s run${ii}.tpr -cpi run${ii}.cpt -v -deffnm 
> run${ii} -npme 0 > $outfile  2>&1
>
>    fi
> =========================
>
>
> If I understand well, you are submitting the SERIAL  mdrun. This means 
> that multiple instances of mdrun are running at the same time.
> Each instance of mdrun is an INDIPENDENT instance. Therefore 
> checkpoint files, one for each instance (i.e. one for each CPU),  are 
> written at the same time.

Good thought, but Dimitar's stdout excerpts from early in the thread do 
indicate the presence of multiple execution threads. Dynamic load 
balancing gets turned on, and the DD is 4x2x1 for his 8 processors. 
Conventionally, and by default in the installation process, the 
MPI-enabled binaries get an "_mpi" suffix, but it isn't enforced - or 
enforceable :-)

Mark
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