Hi John, I had to rebuild the h5utils package because conda forge released a new version of hdf5. It should work now if you do the following:
# make sure you're in the root environment source deactivate # Remove the old environments conda env remove -n mp conda env remove -n mp_test # Recreate them conda create -n mp -c chogan -c conda-forge pymeep conda create -n mp_test -c chogan/label/dev -c chogan -c conda-forge pymeep Thanks for reporting, Chris On Wed, Aug 15, 2018 at 7:44 AM, John Weiner <[email protected]> wrote: > Dear Chris and meep-discussion: > > I have run into a seemingly strange problem with h5topng, the program in > h5utils that converts h5 files to png. While working on a python tutorial > file in the parallel python meep environment (pmp) h5topng works with no > problem. However, when working with the identical python file in the > serial python meep environment (mp), I trigger a core dump when invoking > h5topng. The error message claims that the headers version is 1.10.1 while > the library version is 1.10.2., and the fact that the versions don't match > triggers the core dump. > > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > > (mp_test) john@Samba:~/pymeep/examples/myexamples$ h5topng -t 229 -R -Zc > dkbluered -a yarg -A right_angle_waveguide-eps-000000.00.h5 > right_angle_waveguide-ez.h5 > Warning! ***HDF5 library version mismatched error*** > The HDF5 header files used to compile this application do not match > the version used by the HDF5 library to which this application is linked. > Data corruption or segmentation faults may occur if the application > continues. > This can happen when an application was compiled by one version of HDF5 but > linked with a different version of static or shared HDF5 library. > You should recompile the application or check your shared library related > settings such as 'LD_LIBRARY_PATH'. > You can, at your own risk, disable this warning by setting the environment > variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. > Setting it to 2 or higher will suppress the warning messages totally. > Headers are 1.10.1, library is 1.10.2 > > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > > The LD_LIBRARY_PATH is not set and "which h5topng" shows that the command > points to the appropriate path for ~/miniconda/envs/mp and > ~/miniconda/envs/pmp. > > > I don't understand why I'm getting the core dump in the mp environment > (and in the mp_test environment) but not in the pmp environment. > > Any suggestions would be greatly appreciated. > > Best regards, > > John > >
_______________________________________________ meep-discuss mailing list [email protected] http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
