[ase-users] ase-users Digest, Vol 134, Issue 21
Toma Susi
toma.susi at univie.ac.at
Wed Aug 21 16:23:18 CEST 2019
Hi,
I have seen the same error crop up with ASE 3.18 on the Vienna cluster. The solution for me was to give the paramater "parallel = False" to any ase.io calls during parallel runs. But this seems like it might be a bug, and definitely did not occur before this version.
-Toma
> On 21.08.2019, at 16:12, ase-users-request at listserv.fysik.dtu.dk wrote:
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> 1. Re: ase.io.read error with mpirun (Zeeshan Ahmad)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 21 Aug 2019 10:12:19 -0400
> From: Zeeshan Ahmad <azeeshan at cmu.edu>
> To: ase users <ase-users at listserv.fysik.dtu.dk>
> Subject: Re: [ase-users] ase.io.read error with mpirun
> Message-ID: <CF97074A-D002-445F-B471-B282F568BADB at cmu.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> 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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