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

Berk Hess hess at cbr.su.se
Mon Jul 19 12:45:31 CEST 2010

Ah, my stupid mistake.
I did not think of the situation where the output file names requested
from mdrun
would be different from those stored in the checkpoint file.
I fixed it.

Thanks for reporting this,


Thomas Piggot wrote:
> I thought this would be the case but if I do this then I get the
> following error:
> -------------------------------------------------------
> Program mdrun_git_13_7_10, VERSION 4.0.99-dev-20100713-721405b
> Source code file: gmxfio.c, line: 527
> Can not open file:
> aniso_test_LD2.trr
> For more information and tips for troubleshooting, please check the
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> My command is:
> mdrun_git_13_7_10 -s for-md_aniso_LD.tpr -deffnm aniso_test_LD2 -cpi
> aniso_test_LD1.cpt
> after having run the following until I got a checkpoint file:
> mdrun_git_13_7_10 -s for-md_aniso_LD.tpr -deffnm aniso_test_LD1 -cpt 1
> If I run the mdrun command with -noappend then it works fine but adds
> the part to the output files (as expected). The only way I can get
> what I want is if I move all the aniso_test_LD1 files (apart from the
> checkpoint) to another directory.
> Cheers
> Tom
> Berk Hess wrote:
>> 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 #...#.
>> Berk
>> 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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