[gmx-developers] Removal of -noaddpart option from mdrun

Berk Hess hess at cbr.su.se
Mon Jul 19 11:31:34 CEST 2010

I don't understand the issue.

If you request new file names, the will be no old files with matching
names to append to
and mdrun will by default write the requested file names without the
part number added.

The only thing that is not possible with the new setup, as far as I can
see, is to write to
the same file names as before, without appending, and have the old files
backed up to #...#.


Thomas Piggot wrote:
> 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?
> Cheers
> Tom
> 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
>> environment.
>> Chris.
>> 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   -deffnm?
>>>> 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
>>>> Tom
>>>> Justin A. Lemkul wrote:
>>>>> Justin A. Lemkul wrote:
>>>>>> Thomas Piggot wrote:
>>>>>>> Hi,
>>>>>>> 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
>>> -- 
>>> ========================================
>>> 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
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> ========================================
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