Hi,
One way (but by no means definitive) is to check the first three bytes
of the file, which should be 'C' 'D' 'F':
$ head -c 3 ../test/tz2.nc
CDF
Another way is to use the 'ncdump' utility and make sure the
"application" global attribute is AMBER.
Hope this helps,
-Dan
On Tue, Jan 22, 2019 at 9:56 AM Andreas Tosstorff
<andreas.tosstorff.cup.uni-muenchen.de> wrote:
>
> Sorry I think I need to rephrase my question:
>
> I am trying to recover netcdf trajectory files that are in a binary
> format as far as I know. So my question is if there's any clever way to
> identify a binary file as Amber Trajectory.
>
> Sorry for the confusion.
>
>
> Kind regards,
>
> Andreas
>
> On 22.01.19 14:41, Pratul Agarwal wrote:
> > Probably best to recompile AMBER for the long term.
> >
> > In the meantime here is a way to locate binaries:
> > find /path/to/lost+found -type f -print -exec ldd {} \;
> >
> > This will give you a list of dynamically linked libraries needed for files that are binaries
> > For pmemd.MPI (and other MPI programs) you will see libmpich.so.XX (if you compiled using MPICH) in the list of libraries
> > For pmemd.cuda (and other CUDA programs) you will see libcurand.so/libcufft.so etc.
> >
> > After some inspection and guess work you should be able to locate the binary files you want. Once located you can execute these binaries in a temporary folder -- the header/output/error will give you some more information. But if your libraries were also moved you will have additional issues while trying to execute these binary files.
> >
> > Good luck.
> >
> > Pratul K. Agarwal, Ph.D.
> > (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> > Web: http://www.agarwal-lab.org/
> >
> >
> > On 1/22/2019 7:12 AM, Andreas Tosstorff wrote:
> >
> > Hi all,
> >
> > today I received an email that said "Bad news". Turns out that a lot of
> > data on our cluster was lost.
> >
> > Does anybody have experience with data recovery?
> >
> > We may be able to recover files, however the folder structure and file
> > names are lost. Text files could be identified by string search. I was
> > wondering if there may be a way to identify amber binary files in a
> > similar way?
> >
> > Any help is highly appreciated!
> >
> >
> > Kind regards,
> >
> > Andreas
> >
> >
> > www.proteininteractions.eu<http://www.proteininteractions.eu>
> >
> > PIPPI conference
> >
> >
> > M.Sc. Andreas Tosstorff
> > Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> > Department Pharmazie
> > LMU München
> > Butenandtstr. 5-13 ( Haus B)
> > 81377 München
> > Germany
> >
> > Tel. +49 (0) 89 2180 77059
> > Email : andreas.tosstorff.cup.uni-muenchen.de<mailto:andreas.tosstorff.cup.uni-muenchen.de>
> > Homepage : http://www.cup.uni-muenchen.de/pb/aks/winter/
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> --
>
>
> www.proteininteractions.eu
>
> PIPPI conference
>
>
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> Department Pharmazie
> LMU München
> Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
>
> Tel. +49 (0) 89 2180 77059
> Email : andreas.tosstorff.cup.uni-muenchen.de
> Homepage : http://www.cup.uni-muenchen.de/pb/aks/winter/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jan 22 2019 - 17:00:02 PST
