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

Thomas Piggot t.piggot at soton.ac.uk
Mon Jul 19 11:55:54 CEST 2010

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:
For more information and tips for troubleshooting, please check the GROMACS
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 

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.



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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Dr Thomas Piggot
University of Southampton, UK.

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