[gmx-users] append does not work for me

Justin Lemkul jalemkul at vt.edu
Wed Apr 22 22:35:01 CEST 2015

On 4/22/15 4:23 PM, Michael Brunsteiner wrote:
> On 4/21/15 10:41 AM, Michael Brunsteiner wrote:
>  >>
>  >> Hi,
>  >> I just tried to continue a simulation, after having extended the total time
> using
>  >>
>  >> gmx convert-tpr -s original-xxx.tpr -o xxx.tpr -until 400000
>  >> mdrun -nt 4 -deffnm xxx -cpi xxx.cpt
>  >>
>  >> xxx.cpt, xxx.log, and xxx.trr are present  in the working directory and are
>  >> the original output files, i.e., they were NOT modified
>  >>
>  >> but instead of appending the new data gmx makes backups of theoriginal files
> (i.e. renames xxx.* to #xxx.*.1#)
>  >> and writes the data into new files xxx.*
>  >> this happens both with without the -append option to mdrun ...
>  >> the original files were produced with gmx 5.0.1 and for the extensioni tried
> to use gmx 5.0.4 ... can this be the problem?
>  >>if so, is there a work around?
>  >> other than using trjcat, which is tedious as here i am working with HUGE
> files...
>  >
>  > Did you enable large file support when you compiled GROMACS?
> no ... i wasn;'t aware there is such a thing ... some google-ing suggests
> that the limit is as low as 2Gb ... is that still true for gmx 5.0 ? ... and is
> it true
> that a checkpoint file written with an mdrun compiled without large file support
> and for a trr filesize greater than 2Gb cannot be used for a run continuation?
> is there no work around for that ??
>  >  Or maybe the file size is an OS limit?
> the trajectory files are about 20 Gb, which my 64 bit linux sould be able to
> handle ...

Which also means that the old 2 GB limit is not relevant here (the run literally 
would have stopped when any file reached 2 GB).  IIRC that was fixed, anyway. 
Large file support is detected automatically; I was hoping you knew offhand if 
your system supported it; sounds like it should.

The workaround is to concatenate later.  I would think you'd prefer to do that 
after the fact rather than waiting during run time while mdrun looks through all 
of those massive files before it starts appending.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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