I know you're convinced but just want to add 5th point to Case's comment.
netcdf file is self-describable. You can extract metadata easily. This is
example from extracting information from Amber simulation in python
In [40]: from scipy.io import netcdf_file
In [41]: fh = netcdf_file("./rem.nc.000")
In [42]: fh.variables
Out[42]:
{'coordinates': <scipy.io.netcdf.netcdf_variable at 0x2aaac971e8d0>,
'spatial': <scipy.io.netcdf.netcdf_variable at 0x2aaac971ebe0>,
'temp0': <scipy.io.netcdf.netcdf_variable at 0x2aaac971ecc0>,
'time': <scipy.io.netcdf.netcdf_variable at 0x2aaac971ea58>}
In [43]: fh.variables['temp0'].data # extract temperature in REMD run.
Out[43]:
array([ 300. , 630.5, 630.5, 630.5, 630.5, 630.5, 630.5, 630.5,
492.2, 384.3])
Hai
On Wed, Jun 17, 2015 at 4:20 PM, Gerald Monard <
Gerald.Monard.univ-lorraine.fr> wrote:
> OK. OK. You all convinced me. I'm going to change my old habits.
>
> Gerald.
>
> On 06/17/2015 10:03 PM, Marion, Antoine wrote:
> > Hi Gérald,
> >
> > I did the same tests as you did and got similar results for the files
> size.
> > A compressed ascii file is smaller than the corresponding netcdf one.
> >
> > However, I agree with Prof. Case about the efficiency of post-processing
> netcdf files.
> >
> > Here are some timings for 200 frames of a ~160000 atoms system with PBC.
> >
> > For a series of distances and rmsd analysis using cpptraj :
> > - ascii :TIME: Total execution time: 16.3310 seconds.
> > - ascii.gz : TIME: Total execution time: 21.6712 seconds.
> > - netcdf : TIME: Total execution time: 2.4660 seconds.
> >
> > The difference is also quite striking when loading a trajectory into a
> visualization program.
> > Using vmd :
> >
> > -- ascii
> >>> time vmd -parm7 md.prmtop -crdbox md.crd << eof
> > quit
> > eof
> >
> > real 0m34.124s
> > user 0m33.038s
> > sys 0m0.732s
> >
> > -- netcdf
> >>> time vmd -parm7 md.prmtop -netcdf md.nc << eof
> > quit
> > eof
> >
> > real 0m2.132s
> > user 0m1.657s
> > sys 0m0.369s
> >
> > Also to run the trajectory itself, it feels like it is faster to write
> netcdf files.
> > I cannot give you the exact timings since the two simulations ran on
> different machines and with different output setting for the velocities,
> but it seems so.
> > Anyone else did such a comparison ?
> >
> > Best wishes,
> >
> > Antoine
> > ________________________________________
> > From: David A Case <case.biomaps.rutgers.edu>
> > Sent: Wednesday, June 17, 2015 9:27 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not
> recognized
> >
> > On Wed, Jun 17, 2015, Gerald Monard wrote:
> >
> >> What's the advantage, except size, of using the NetCDF format?
> >
> > Loading netcdf files into cpptraj can be *much* faster than uncompressing
> > an ASCII file, then converting those to the internal representation.
> >
> > Second, code can skip frames efficiently, rather than having to read the
> > intervening frames.
> >
> > Third, values are stored in floating point format, so you avoid the
> dreaded
> > problem of finding '****' in the 5075'th frame.
> >
> > Fourth, you can skip corrupted frames (which *do* happen occasionally)
> much
> > more robustly with netcdf than with ASCII.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
>
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> SRSMC, Université de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
>
> ____________________________________________________________________________
>
>
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Received on Wed Jun 17 2015 - 13:30:04 PDT
