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

[Francesco Oteri]

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.
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