[ase-users] ase.io.read error with mpirun

[Zeeshan Ahmad]

On another cluster, the error on using mpirun with read is: TypeError: Not a proper NumPy array for MPI communication.

rank=000 L00: Traceback (most recent call last):
rank=000 L01:   File "/home/azeeshan/miniconda3/envs/gpaw/lib/python3.7/site-packages/ase/parallel.py", line 244, in new_generator
rank=000 L02:     broadcast((None, result))
rank=000 L03:   File "/home/azeeshan/miniconda3/envs/gpaw/lib/python3.7/site-packages/ase/parallel.py", line 181, in broadcast
rank=000 L04:     comm.broadcast(string, root)
rank=000 L05: TypeError: Not a proper NumPy array for MPI communication.
rank=000 L06: 
rank=000 L07: During handling of the above exception, another exception occurred:
rank=000 L08: 
rank=000 L09: Traceback (most recent call last):
rank=000 L10:   File "/home/azeeshan/miniconda3/envs/gpaw/lib/python3.7/site-packages/gpaw/__init__.py", line 201, in main
rank=000 L11:     runpy.run_path(gpaw_args.script, run_name='__main__')
rank=000 L12:   File "/home/azeeshan/miniconda3/envs/gpaw/lib/python3.7/runpy.py", line 263, in run_path
rank=000 L13:     pkg_name=pkg_name, script_name=fname)
rank=000 L14:   File "/home/azeeshan/miniconda3/envs/gpaw/lib/python3.7/runpy.py", line 96, in _run_module_code
rank=000 L15:     mod_name, mod_spec, pkg_name, script_name)
rank=000 L16:   File "/home/azeeshan/miniconda3/envs/gpaw/lib/python3.7/runpy.py", line 85, in _run_code
rank=000 L17:     exec(code, run_globals)
rank=000 L18:   File "F_str.py", line 7, in <module>
rank=000 L19:     atoms = read('../Lisurf_lc_rot_F_532.traj')
rank=000 L20:   File "/home/azeeshan/miniconda3/envs/gpaw/lib/python3.7/site-packages/ase/io/formats.py", line 498, in read
rank=000 L21:     parallel=parallel, **kwargs))
rank=000 L22:   File "/home/azeeshan/miniconda3/envs/gpaw/lib/python3.7/site-packages/ase/parallel.py", line 247, in new_generator
rank=000 L23:     broadcast((ex, None))
rank=000 L24:   File "/home/azeeshan/miniconda3/envs/gpaw/lib/python3.7/site-packages/ase/parallel.py", line 181, in broadcast
rank=000 L25:     comm.broadcast(string, root)
rank=000 L26: TypeError: Not a proper NumPy array for MPI communication.
GPAW CLEANUP (node 0): <class 'TypeError'> occurred.  Calling MPI_Abort!
application called MPI_Abort(MPI_COMM_WORLD, 42) - process 0
 

> On Aug 20, 2019, at 5:15 PM, Zeeshan Ahmad <azeeshan at cmu.edu> wrote:
> 
> Hi,
> 
> I am able to run the following file in serial (gpaw-python file.py) but not with mpirun:
> 
> from ase.io <http://ase.io/> import read, write
> from ase.build import bulk
> 
> atoms = read('anyfile.cif')
> 
> The error on running: mpirun -np 4 gpaw-python file.py is: (I have reproduced the same error with different cif and traj files.)
> 
> Fatal error in PMPI_Bcast: Other MPI error, error stack:
> PMPI_Bcast(1600)........: MPI_Bcast(buf=0x5653ca2b0f60, count=17432, MPI_BYTE, root=0, MPI_COMM_WORLD) failed
> MPIR_Bcast_impl(1452)...: 
> MPIR_Bcast(1476)........: 
> MPIR_Bcast_intra(1249)..: 
> MPIR_SMP_Bcast(1088)....: 
> MPIR_Bcast_binomial(250): message sizes do not match across processes in the collective routine: Received 8 but expected 17432
> Fatal error in PMPI_Bcast: Other MPI error, error stack:
> PMPI_Bcast(1600)........: MPI_Bcast(buf=0x555eb9c60020, count=17432, MPI_BYTE, root=0, MPI_COMM_WORLD) failed
> MPIR_Bcast_impl(1452)...: 
> MPIR_Bcast(1476)........: 
> MPIR_Bcast_intra(1249)..: 
> MPIR_SMP_Bcast(1088)....: 
> MPIR_Bcast_binomial(250): message sizes do not match across processes in the collective routine: Received 8 but expected 17432
> Fatal error in PMPI_Bcast: Other MPI error, error stack:
> PMPI_Bcast(1600)........: MPI_Bcast(buf=0x55b0603a7f60, count=17432, MPI_BYTE, root=0, MPI_COMM_WORLD) failed
> MPIR_Bcast_impl(1452)...: 
> MPIR_Bcast(1476)........: 
> MPIR_Bcast_intra(1249)..: 
> MPIR_SMP_Bcast(1088)....: 
> MPIR_Bcast_binomial(310): Failure during collective
> 
> The problem is with the read method. When I replace the file with:
> 
> from ase.io <http://ase.io/> import read, write
> from ase.build import bulk
> 
> atoms = bulk('Li', a=3.4)
> 
> I don't get any error. 
> I installed ase and gpaw using conda: conda install -c conda-forge gpaw
> 
> My gpaw and ase versions are: 1.5.2 and 3.18.0 respectively.
> 
> Thanks,
> -Zeeshan

--
Zeeshan Ahmad
PhD candidate, Mechanical Engineering
Carnegie Mellon University

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