Running your example in Python 3 explains the problem.
result = get_dgms(2)
reports:
MaybeEncodingError: Error sending result: '[Diagram with 2 points]'. Reason: 'TypeError("can't pickle dionysus._dionysus.Diagram objects",)'
It seems joblib tries to pickle the return values and persistence diagrams are not pickleable. Why Python 2 fails silently, I don't know. The longterm solution is for me to add pickling to the diagram class (can you please file an issue on GitHub, so I don't forget about it?).
The quick fix for you would be to return a list rather than a diagram. So change the return line in computePD to
return [(p.birth, p.death) for p in dgms1[1]]
Dmitriy
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On Wed, Jun 20, 2018 at 1:27 PM, <cai.507@...> wrote: [Edited Message Follows]
Hi Dmitriy,
I am trying to compute persistence diagram for different graphs in parallel in python2. I use joblib to do multiprocessing computation. Here is a toy example:
def computePD(i):
import dionysus as d
import numpy as np np.random.seed(42)
f1 = d.fill_rips(np.random.random((i+10, 2)), 2, 1)
m1 = d.homology_persistence(f1)
dgms1 = d.init_diagrams(m1, f1)
return dgms1[1]
def get_dgms(n_jobs=1):
from joblib import delayed, Parallel
return Parallel(n_jobs=n_jobs)( delayed(computePD)(i) for i in range(10))
result = get_dgms(1)
However, when I change the n_jobs to 2(result = get_dgms(2)), I get a wired result.
[Diagram with 0 points,
Diagram with 6822207245174201887 points,
Diagram with 0 points,
Diagram with 6822207245174201887 points,
Diagram with 0 points,
Diagram with 6822207245174201887 points,
Diagram with 6148914691236517774 points,
Diagram with 0 points,
Diagram with 6822207245174201887 points,
Diagram with 0 points]
The correct result should be something like
[Diagram with 2 points,
Diagram with 2 points,
Diagram with 2 points,
Diagram with 1 points,
Diagram with 2 points,
Diagram with 2 points,
Diagram with 2 points,
Diagram with 2 points,
Diagram with 2 points,
Diagram with 4 points]
At first, I thought I didn't use joblib correctly so I change computePD to some simple function like the following def computePD(i): return i ** 2 then I call the same function with different n_jobs, the result is the same when I change the n_jobs, just as expected.
Again, I am not sure the problem lies in Dionysus or misuse of joblib. Any suggestions will be appreciated.
Best, Chen
