[gmx-developers] Removal of -noaddpart option from mdrun
t.piggot at soton.ac.uk
Thu Jul 15 18:36:25 CEST 2010
This is kind of the reason I asked. For me it would be useful if I could
easily maintain the same file naming convention in GROMACS 4 as I had
with GROMACS 3. For GROMACS 4 up to the latest development version I
could just use -noappend -noaddpart when the run crashed to control the
naming to be the way I wanted.
The only way I have found to easily do this in the development version
is to move the old files to another folder (apart from the .cpt) and
change -deffnm to the new name when restarting (without -noappend).
Maybe the -noaddpart option could be reinstated?
chris.neale at utoronto.ca wrote:
> Further, some of us have immensely complicated management scripts and
> programs in which it is important to know the name of the expected
> output .xtc file. For example, I run my own C-based server that can run REMD
> on a distributed computing platform (calling gromacs to do the run
> segments) and my client-side scripts needs to know what the output
> .xtc will be
> named. In this case, I always want name.xtc given -deffnm name,
> regardless of what part number the .cpt file has stored. Also, I can't
> allow any appending to
> any files that may exist. Backward compatibility is, in this case,
> pretty important to me. Perhaps it will be possible with some
> combinations of options and I'm just missing it, but resorting to an
> ls -ltr |tail -n 1 seems like too much of a risk for a distributed
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> Thomas Piggot wrote:
>>> But how can I get the new files, when using -noappend, to not have
>>> the 'part' bit in their names but just have the name as defined by
>>> Maybe I am missing something obvious, sorry if this is the case.
>> Per the documentation, this isn't possible. With -noappend, the "part"
>> number is always written.
>> Doesn't this create a problem if a run crashes? If a file has
>> ".part000X." and it goes down, starting from a new checkpoint will use
>> a different "part" number and thus one cannot append the output?
>> That's a bit inconvenient, unless I've understood the mechanism wrong.
>>> Justin A. Lemkul wrote:
>>>> Justin A. Lemkul wrote:
>>>>> Thomas Piggot wrote:
>>>>>> I was wondering what had happened to the -noaddpart option of
>>>>>> mdrun in the development version (downloaded yesterday). Has
>>>>>> this option been removed for a particular reason?
>>>>> Yes, it was removed about a month ago (6/16/2010). The option
>>>>> -noappend takes over. Now mdrun looks for all necessary files
>>>>> and will append to them, unless you tell it not to (with
>>>>> -noappend). If files are missing, mdrun generates an error.
>>>>> This should be explained in the mdrun -h information.
>>>> ...rather, if some files are missing mdrun generates an error. If
>>>> all files are missing, mdrun simply creates new ones with the
>>>> desired names.
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
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Dr Thomas Piggot
University of Southampton, UK.
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