VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Mon Jan 06 2020 - 14:45:40 CST

I am sorry John, I was on vacation till yesterday and did not find the time to send you a file. I will do it in the next days

Best
Vlad

On 6 January 2020 21:20:06 CET, John Stone <johns_at_ks.uiuc.edu> wrote:
>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/ 

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