H5i_dec_ref hangs

HDF5 Library h5py
19

Hi Gerd,

I have tried an alternative solution with a single writer multiple reader where all processes send the preprocessed data to master, but unfortunately, it’s way too slow. The master rank spends all the time deserializing the MPI messages while the others are waiting for him (one image is cca 100MB in memory after preprocessing).

I am now trying to pinpoint the issue I’m experiencing. I have produced a minified example, see below:

import h5py
from mpi4py import MPI
import numpy as np

H5PATH = "../results/SDSS_cube_parallel.h5"
f = h5py.File(H5PATH, 'r+', driver='mpio', comm=MPI.COMM_WORLD)

rank = MPI.COMM_WORLD.Get_rank()

if rank == 0:
    ds = f["/semi_sparse_cube/5/22/90/362/1450/5802/23208/92832/4604806771.19/3551/(2048, 1489)/frame-u-004899-2-0260.fits"]
    ds.write_direct(np.ones((1489, 2048, 2)))
if rank == 1:
    ds = f["/semi_sparse_cube/5/22/90/362/1450/5802/23208/92832/4604806842.83/8932/(2048, 1489)/frame-z-004899-2-0260.fits"]
    ds.write_direct(np.ones((1489, 2048, 2)))
f.close()

use it with this h5 file (2.8 MB)
while running:

mpiexec -n 2 python script.py

The h5 file was produced in serial mode by just one process (without MPI).

Hope this helps you investigating the matter - you can also try C code on this file whether it produces the same issue?