writing h5 file

Question

Hello

I want to write mesh in h5 file format. There is an explanation for this;

http://fenicsproject.org/qa/274/consistent-io-of-mesh-and-function-in-parallel

when I use this commend i get this error;

In 1: from dolfin import *
In [2]: mesh = UnitSquareMesh(5, 5)
In [3]: V = FunctionSpace(mesh, 'CG', 1)
In [4]: u = project(Expression('x[0]'), V)
Solving linear system of size 36 x 36 (PETSc Krylov solver).

In [5]: f = HDF5File('u.h5', 'w')

TypeError Traceback (most recent call last)
in ()
----> 1 f = HDF5File('u.h5', 'w')

/usr/lib/python2.7/dist-packages/dolfin/cpp/io.pyc in init(self, args)
909
910 """
--> 911 _io.HDF5File_swiginit(self,_io.new_HDF5File(args))
912 swig_destroy = _io.delete_HDF5File
913 def close(self):

TypeError: new_HDF5File expected 3 arguments, got 2

In [6]: f.write(mesh, 'mesh')

NameError Traceback (most recent call last)
in ()
----> 1 f.write(mesh, 'mesh')
NameError: name 'f' is not defined

In [7]: f.write(u, 'u')

NameError Traceback (most recent call last)
in ()
----> 1 f.write(u, 'u')
NameError: name 'f' is not defined

Any idea for this?
Thanks

Answer 1

Hi, try

f = HDF5File(mesh.mpi_comm(), 'u.h5', 'w')

The error message

TypeError: new_HDF5File expected 3 arguments, got 2

tells you that in call to HDF5File()you were missing one argument. Check out constructor's
signature here to see that the first argument must by MPI communicator.

Comments

thanks, it works now!

---

Hi

if i put this in a python module, like this;

def write_solution(ouput_filename):

    g = HDF5File(mesh.mpi_comm(),ouput_filename,'w')
    g.write(u,'u')
    return u

i have an error;

AttributeError: 'module' object has no attribute 'mpi_comm'

any idea for this?

thanks

Burak

---

Check the type of mesh in my code and your code

print type(mesh)

In my previous post it yields <class 'dolfin.cpp.mesh.UnitSquareMesh'>. In your case now, the answer is most likely <type module> and that's the cause of error.

---

Hi

Type of the mesh is;

<class 'dolfin.cpp.mesh.Mesh'>

I also try to do something like Mesh.mpi_comm() or **mesh.Mesh.mpi_comm()**** but both do not work. Any idea for this?

Thanks

Burak