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/
>
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>
>
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--
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/
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Received on Tue Jan 22 2019 - 07:00:04 PST
