VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 06 2020 - 14:20:06 CST

Hi,
  I haven't seen any further discussion of this issue since December 19th.

If there's any interest in actually resolving the problem, I will need
an example file that I can use to reproduce the behavior that Vlad
has reported. Vlad, can you (or anyone else) provide one?

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 19, 2019 at 08:22:10AM -0600, John Stone wrote:
> Hi,
> Newer VMD 1.9.4 alpha builds include HDF5, whereas older revs did not.
>
> It seems possible that we're observing an issue where the HDF5 version of
> NetCDF (or some shared internal routines used therein) is being picked
> up rather than the old standalone NetCDF I compiled from source,
> which is what was used for all prior builds.
>
> Vlad, I'm about to be offline for 2.5 days due to travel without network
> access, but once I'm back in civilization, if you can post an affected
> NetCDF file(s) that I can use for testing, I should be able to chase down
> if this is caused by linking with HDF5 libs or if something less
> obvious might be happening.
>
> Best,
> John
>
> On Thu, Dec 19, 2019 at 02:09:50PM +0100, Luthaf wrote:
> > Hi Vlad,
> >
> > What you are seeing is an assertion inside the netcdf library: https://github.com/Unidata/netcdf-c/blob/3acf69c6a01c9964532d85d9ec8a22acd6ca2488/libsrc/putget.m4#L821
> >
> > So either the the netcdf **library** version changed, or is was
> > compiled without assertions (-DNDEBUG) for 1.9.4a12, and with
> > assertions for 1.9.4a38.
> >
> > Anyway, hitting an assertion in the netcdf library might indicate
> > that the files you have are invalid netcdf files. Are you able to
> > open them outside of vmd? For example, using `ncdump file.nc`?
> >
> > Best,
> > Guillaume
> >
> > Vlad Cojocaru a écrit le 19.12.19 à 10:46 :
> > >Well, the only thing I can say at this point is that vmd 1.9.4a12
> > >reads the trajectories perfectly, whereas vmd 1.9.4a38 does not
> > >and gives the error I reported. First I thought its one trajectory
> > >that is corrupted but then I checked it with other programs and it
> > >was fine. After that I realized that the a38 version of vmd does
> > >not ready any other netcdf trajectory I have ...
> > >
> > >Except the VMD version, I have not changed anything to the system ...
> > >
> > >I will look further into it and see if I can figure out what is
> > >happening.
> > >
> > >Best,
> > >Vlad
> > >
> > >On 12/18/19 5:19 PM, John Stone wrote:
> > >>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/ 

-- 
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/