<br><font size=2 face="sans-serif">Hi,</font>
<br>
<br><font size=2 face="sans-serif">Espresso file format, like most other
ascii formats has a serious problem,</font>
<br><font size=2 face="sans-serif">if you worry about parallel IO: They
are hardly parallelizable.</font>
<br><font size=2 face="sans-serif">Even though IO may not be a problem
today, given time, it will,</font>
<br><font size=2 face="sans-serif">as simulated systems and number of compute
nodes get larger</font>
<br><font size=2 face="sans-serif">and serial CPU power for ASCII formatting
on rank 0 no longer scales.</font>
<br><font size=2 face="sans-serif">I would seriously recommend to consider
John's suggestion and go for HDF5,</font>
<br><font size=2 face="sans-serif">which parallelizes well and offers high
flexibility.</font>
<br><font size=2 face="sans-serif">For those who want the simplicity of
Fortran array IO, I would rather spend</font>
<br><font size=2 face="sans-serif">a bit of extra effort to develop a comfortable
reader tool, that can extract ascii</font>
<br><font size=2 face="sans-serif">readable data for those who don't want
the complexity of having to deal</font>
<br><font size=2 face="sans-serif">with HDF5 directly (although HDF5 comes
with it's own flexible ascii readers</font>
<br><font size=2 face="sans-serif">which might be sufficientfor most tasks).</font>
<br>
<br><tt><font size=2>> Message: 5<br>
> Date: Mon, 31 Mar 2008 13:42:41 -0700<br>
> From: "John Chodera" <jchodera@gmail.com><br>
> Subject: Re: [gmx-developers] Shall we ditch gro and g96 files?<br>
> To: "Discussion list for GROMACS development"<br>
> <gmx-developers@gromacs.org><br>
> Message-ID:<br>
> <14cc10610803311342i7f9ed758r8ed8fe95569573da@mail.gmail.com><br>
> Content-Type: text/plain; charset=ISO-8859-1<br>
> <br>
> Gentlemen,<br>
> <br>
> I know I don't chime in very often here, but I wanted to take this<br>
> opportunity to say that I very much support the idea of replacing
the<br>
> limited-precision text-based formats like .gro, .pdb, and .g96 with<br>
> more flexible, portable, full-precision file formats.<br>
> <br>
> Berk's suggestions of Espresso sounds very reasonable, but I would<br>
> encourage you to instead look at netCDF and HDF5:<br>
> <br>
> netCDF:<br>
> http://www.unidata.ucar.edu/software/netcdf/<br>
> <br>
> HDF5:<br>
> http://hdf.ncsa.uiuc.edu/HDF5/<br>
> <br>
> Both of these formats provide easy-to-use libraries with APIs that<br>
> support nearly every language you could want to use (including C,<br>
> Fortran, and Python). They provide platform-independent, extensible<br>
> formats for storing numerical information. Both provide attribute<br>
> support, and HDF5 even allows hierarchical organization of objects,<br>
> making it very much like XML but with support for multidimensional<br>
> arrays of the same precision as used internally in gromacs. The<br>
> libraries are robust, efficient, and well-supported.<br>
> <br>
> AMBER, for example, has already moved to netCDF for their trajectory<br>
> format, though (unfortunately) not yet for their coordinate/restart<br>
> files.<br>
> <br>
> http://amber.scripps.edu/netcdf/nctraj.html<br>
> <br>
> Cheers,<br>
> <br>
> John<br>
> <br>
> --<br>
> Dr. John D. Chodera <jchodera@gmail.com> |
Mobile : 415.867.7384<br>
> Postdoctoral researcher, Pande lab
| Lab phone : 650.723.1097<br>
> Department of Chemistry, Stanford University | Lab fax
: 650.724.4021<br>
> http://www.dillgroup.ucsf.edu/~jchodera<br>
> <br>
> On 29/03/2008, David van der Spoel <spoel@xray.bmc.uu.se> wrote:<br>
> > Hi,<br>
> ><br>
> > as you are aware all coordinate files have their drawbacks.<br>
> > - gro & pdb have limited space for coordinates which
is problematic for<br>
> > simulating large systems<br>
> > - pdb has no velocities<br>
> > - gro & g96 can not store information on the element
(i.e. can not<br>
> > distinguish between Calpha and Calcium or Hgamma and Mercury,
pdb can do<br>
> > this)<br>
> > - gro stores non-rectanular boxes in an awkward manner<br>
> ><br>
> > I would therefore propose to make better coordinate file
format that has<br>
> > - coordinates<br>
> > - velocities<br>
> > - box as three edges and three angles (as in pdb file)<br>
> > - atom name (and number)<br>
> > - residue name and number<br>
> > - element type (we could also introduce special elements
for united<br>
> > atoms or course grained particles, but they should not
overlap with real<br>
> > elements)<br>
> > - variable format (no fixed column widths)<br>
> ><br>
> > In order to encourage the use of such a more flexible file
format I<br>
> > would then propose that we remove the facility for writing
gro and g96<br>
> > files.<br>
> ><br>
> > Please let me know what you think.<br>
> ><br>
> > --<br>
> > David van der Spoel, Ph.D.<br>
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol.,
Uppsala University.<br>
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
Fax: +4618511755.<br>
> > spoel@xray.bmc.uu.se spoel@gromacs.org
http://folding.bmc.uu.se<br>
> > _______________________________________________<br>
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> ><br>
> <br>
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> End of gmx-developers Digest, Vol 48, Issue 1<br>
> *********************************************<br>
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