HDF5File doesn't work with Fenics 2017.1

Question

Hi,

I was used to use the HDF5File function with Fenics 2016 (see example bollow).

from fenics import*
mesh = Mesh("grain.xml")
grains = MeshFunction("size_t", mesh,"grain_physical_region.xml")
hdf = HDF5File(mesh.mpi_comm(), "file.h5","w")
hdf.write(mesh,"/mesh")
hdf.write(grains,"/grains")

Now I use Fenics 2017.1 and it doesn't work anymore. I get this error :

Traceback (most recent call last):
File "HDF.py", line 8, in
hdf = HDF5File(mesh.mpi_comm(), "file.h5","w")
NameError: name 'HDF5File' is not defined
Abandon (core dumped)

I saw here Saving boundary-markers to HDF in FEniCS 2017.1 that it seems to work.
Can anybody help me with this issue?

Thanks

Comments

You probably have a DOLFIN installation without support for HDF5. How did you install FEniCS?

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Hey

we've installed this last version with Anaconda from Continuum Analytics and Python 2.7

conda create --name fenics                                  
conda info --envs                                       
source activate fenics                                          

conda install python=2.7.13                                 
conda install matplotlib numpy scipy mkl                            

conda install -c conda-forge fenics                     
conda install -c conda-forge mshr                                   

conda install -c conda-forge hdf5                                   

as explained on FEniCS website

we also have installed hdf5 package but there are only shared libraries with this package
no python file and HDF5File function

Thanks

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The conda package is not linked against HDF5 (see issue #5).

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This is fixed now. Please update to the latest fenics conda package.

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ok I'm going to update our FEniCS installations witch Anaconda, we'll make you a feedback