VMD-L Mailing List
From: Luthaf (luthaf_at_luthaf.fr)
Date: Thu Dec 19 2019 - 07:09:50 CST
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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
>
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