VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 18 2019 - 10:19:26 CST

Vlad,
 The only change to the NetCDF plugin (since 2016 actually) has been
to correct a memory leak for a cell angles unit string in the AMBER
reader code, nothing that would impact the eror you reported:

@@ -133,6 +133,9 @@
   if (cdf->amber.cell_lengths_units)
     free(cdf->amber.cell_lengths_units);
 
+ if (cdf->amber.cell_angles_units)
+ free(cdf->amber.cell_angles_units);
+
   /* MMTK stuff */
   if (cdf->mmtk.comment)
     free(cdf->mmtk.comment);
@@ -1121,7 +1124,7 @@
   plugin.prettyname = "NetCDF (AMBER, MMTK)";
   plugin.author = "Konrad Hinsen, John Stone";
   plugin.majorv = 1;
- plugin.minorv = 1;
+ plugin.minorv = 2;
   plugin.is_reentrant = VMDPLUGIN_THREADSAFE;
   plugin.filename_extension = "nc,ncrst";
   plugin.open_file_read = open_cdf_read;

I expect that the problem you're seeing is something deeper in
the NetCDF library itself.

Best,
  John Stone

On Wed, Dec 18, 2019 at 02:25:11PM +0100, Vlad Cojocaru wrote:
> Dear all,
>
> Did VMD change the netcdf plugin between version 1.9.4a12 and 1.9.4a38 ?
> I am using netcdf trajectories created with CPPTRAJ program from
> AmberTools 19.
>
> When I load these trajectories in VMD 1.9.4a12, everything works well ....
>
> However, with VMD 1.9.4a38, I cannot load exactly the same
> trajectories loaded correctly with the a12 version. I am getting the
> error below. I will revert for now to the a12 version, but maybe
> this is worth investigating.
>
> Best wishes
> Vlad
>
> netcdfplugin) conventions: 'AMBER'
> netcdfplugin) trajectory follows AMBER conventions version '1.0'
> netcdfplugin) AMBER: program 'cpptraj'
> netcdfplugin) AMBER: program version 'V18.01'
> netcdfplugin) AMBER: title 'Cpptraj Generated trajectory'
> netcdfplugin) AMBER: application 'AMBER'
> netcdfplugin) AMBER: spatial dimension: 3
> netcdfplugin) AMBER: atom dimension: 13042
> netcdfplugin) AMBER: frame dimension: 80000
> netcdfplugin) AMBER: coordinates units: 'angstrom'
> netcdfplugin) AMBER: no coordinates scalefactor attribute, 1.0 assumed
> netcdfplugin) AMBER: coordinates scalefactor: 1.000000
> netcdfplugin) AMBER trajectory contains periodic cell information
> netcdfplugin) AMBER: cell lengths units: 'angstrom'
> netcdfplugin) AMBER: no cell lengths scalefactor attribute, 1.0 assumed
> netcdfplugin) AMBER: cell lengths scalefactor: 1.000000
> netcdfplugin) AMBER: cell angles units: 'degree'
> netcdfplugin) AMBER: no cell angles scalefactor attribute, 1.0 assumed
> netcdfplugin) AMBER: cell angles scalefactor: 1.000000
> Info) Using plugin netcdf for coordinates from file ../test.ncdf
> vmd_LINUXAMD64: putget.c:3593: getNCvx_float_float: Assertion `value
> != ((void *)0)' failed.
> Abort (core dumped)
>
> --
> Vlad Cojocaru, PD (Habil.), Ph.D.
> -----------------------------------------------
> Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> -----------------------------------------------
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/