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h5md / VMD-h5mdplugin

This plugin enables VMD to display data stored in h5 files that are structured according to the H5MD specifications (http://nongnu.org/h5md/)
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error when loading H5MD file #22

Closed anyuzx closed 8 years ago

anyuzx commented 8 years ago

Hi

My system is MAC 10.11. Since VMD 1.9.1 on MAC is still 32-bit. I did a universal 32/64 built of hdf5 using homebrew. VMD can load plugin with no issues. However when I tried to read a trajectory. It shows error like this:

vmd > HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
  #000: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #001: H5Tconv.c line 8585 in H5T__conv_double_ulong(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #002: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #003: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #004: H5Tconv.c line 8531 in H5T__conv_float_ulong(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #005: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #006: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #007: H5Tconv.c line 8612 in H5T__conv_ldouble_long(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #008: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #009: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #010: H5Tconv.c line 8558 in H5T__conv_double_long(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #011: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #012: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #013: H5Tconv.c line 8504 in H5T__conv_float_long(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #014: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #015: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #016: H5Tconv.c line 7838 in H5T__conv_ulong_ldouble(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #017: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #018: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #019: H5Tconv.c line 7813 in H5T__conv_ulong_double(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #020: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #021: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #022: H5Tconv.c line 7788 in H5T__conv_ulong_float(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #023: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #024: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #025: H5Tconv.c line 7763 in H5T__conv_long_ldouble(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #026: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #027: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #028: H5Tconv.c line 7738 in H5T__conv_long_double(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
  #029: H5T.c line 2290 in H5T_register(): unable to locate/allocate conversion path
    major: Datatype
    minor: Unable to initialize object
  #030: H5T.c line 4508 in H5T_path_find(): unable to initialize conversion function
    major: Datatype
    minor: Unable to initialize object
  #031: H5Tconv.c line 7713 in H5T__conv_long_float(): disagreement about datatype size
    major: Datatype
    minor: Unable to initialize object
HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
  #000: H5F.c line 604 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: H5Fint.c line 1133 in H5F_open(): problems closing file
    major: File accessibilty
    minor: Unable to close file
  #002: H5Fint.c line 844 in H5F_dest(): can't get property list
    major: Invalid arguments to routine
    minor: Inappropriate type
  #003: H5Fint.c line 1087 in H5F_open(): unable to read superblock
    major: File accessibilty
    minor: Read failed
  #004: H5Fsuper.c line 271 in H5F_super_read(): can't get property list
    major: Invalid arguments to routine
    minor: Inappropriate type
Info) Using plugin h5md for structure file /Users/gs27722/Desktop/Chr5_145870001_157870001_G2.5_SC_1_traj.h5
ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0
ERROR) molecule_structure: Unable to read structure for molecule 0
ERROR) molecule_structure: severe error indicated by plugin aborting loading of molecule 0

Does it have something to do with the fact I did a universal build of HDF5 rather than only 32-bit build? Thanks!

jonaslandsgesell commented 8 years ago

Is the file valid? Just to check this, could you please zip a h5 file that produces the above error and drag and drop it into this thread? On Github this should work for files up to 25 MB.

anyuzx commented 8 years ago

My original trajectory is huge(11Gb). I select subset of frames and made a short version of it. Please see the zip file. The original trajectory is generated from LAMMPS short_h5.zip

jonaslandsgesell commented 8 years ago

The file is valid. I suppose that the problem arises from your universal build. At compile time the types e.g. H5T_NATIVE_INT are identified. This could be the problem you are running into. It should be fixed when you compile the plugin on the machine you want to use it.

anyuzx commented 8 years ago

I now build the plugin with "32-bit only" HDF5. VMD can correctly load the trajectory!