Hi David,

This is a big piece of code where I solve nonlinear equations in a 2D domain with mixed systems involving vector functions.

I'd like to run the whole code in parallel except from some lines such as saving txt files, to avoid overwriting it or saving in several files. Is there a command to select a specific process? Andrew once mentioned using op2.MPI.comm.rank. Is that a solution? How can I use it?

The error when appending the array is not such an issue as I need it only for visualisation purpose.

For instance, I want to save a 1D function h_1D

mesh_1D = IntervalMesh(Nx,Lx)

V_1D = FunctionSpace(mesh_1D, "CG", 1)

h_1D = Function(V_1D)

on a 2D surface. So I define a 2D mesh as follows

mesh_2D = RectangleMesh(Nx,1,Lx,1.0,quadrilateral=True)

V_2D = FunctionSpace(mesh_2D, "CG", 1)

h_2D = Function(V_2D)

Then, I save in Indx[i] the indices for which x_2D[i] = x_1D[i]:

Indx = []

for i in range(Nx+1):

Indx.append([item for item in range(len(mesh_2D.coordinates.dat.data[:,0])) if mesh_2D.coordinates.dat.data[item,0] == mesh_1D.coordinates.dat.data[i]])

The idea is that I can then project h_1D to the 2D mesh through h_2D:

for i in range(Nx+1):

h_2D.dat.data[Indx[i]] = h_1D.dat.data[i]

This works fine when I run the code on one core, but when running in parallel I get an index error:

File "main.py", line 932, in <listcomp>

Indx.append([item for item in range(len(mesh_2D.coordinates.dat.data[:,0])) if mesh_2D.coordinates.dat.data[item,0] == mesh_1D.coordinates.dat.data[j]])

IndexError: index 125 is out of bounds for axis 0 with size 125

I can comment it, but then I get other (Firedrake-related) errors that I don't get otherwise, for example:

File "main.py", line 970, in <module>

mesh_WM = CubeMesh(1,1,1,1.0)

File "/home/ufaserv1_i/mmfg/firedrake/firedrake/src/firedrake/firedrake/utility_meshes.py", line 749, in CubeMesh

comm=comm)

File "/home/ufaserv1_i/mmfg/firedrake/firedrake/src/firedrake/firedrake/utility_meshes.py", line 725, in BoxMesh

return mesh.Mesh(plex, reorder=reorder, distribute=distribute)

File "<decorator-gen-259>", line 2, in Mesh

File "/home/ufaserv1_i/mmfg/firedrake/firedrake/src/PyOP2/pyop2/profiling.py", line 60, in wrapper

return f(*args, **kwargs)

File "/home/ufaserv1_i/mmfg/firedrake/firedrake/src/firedrake/firedrake/mesh.py", line 1249, in Mesh

topology = MeshTopology(plex, name=name, reorder=reorder, distribute=distribute)

File "<decorator-gen-257>", line 2, in __init__

File "/home/ufaserv1_i/mmfg/firedrake/firedrake/src/PyOP2/pyop2/profiling.py", line 60, in wrapper

return f(*args, **kwargs)

File "/home/ufaserv1_i/mmfg/firedrake/firedrake/src/firedrake/firedrake/mesh.py", line 377, in __init__

raise RuntimeError("Mesh must have at least one cell on every process")

RuntimeError: Mesh must have at least one cell on every process

I don't understand while running in parallel causes errors for the mesh definition?

Thank you,

Floriane

De : firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de Ham, David A <david.ham@imperial.ac.uk>
Envoyé : mardi 5 septembre 2017 09:42:44
À : firedrake
Objet : Re: [firedrake] running in Parallel

Hi Floriane,

can you provide a minimal example? Appending to an array isn't a Firedrake operation so it sounds like the issue is more a question of how you need to parallelise the surrounding code, and that will depend on exactly what it is you are doing.

Regards,

David

On Tue, 2017-09-05 at 08:05 +0000, Floriane Gidel [RPG] wrote:

Dear all,

I need to run my firedrake code in parallel but some of the commands (like appending an array) can't be executed in parallel. How can I force some lines to be executed by one core only?

Thanks in advance,

Floriane
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