[ase-users] EOF Error Vibrational Modes Espresso
Ask Hjorth Larsen
asklarsen at gmail.com
Sun Dec 3 01:06:32 CET 2017
Hi.
2017-12-02 23:12 GMT+01:00 Lance Kavalsky <lance.kavalsky at mail.utoronto.ca>:
> Hello,
>
>
> Below is the traceback. It reaches this point and then hangs. I am running
> the script with mpirun on 4 processors (mpirun -np 4 python trans_ase.py).
>
>
> As for the pseudopotentials, I am using Na.pbe-mt_fhi.UPF and
> P.pbe-mt_fhi.UPF which were obtained from the Quantum Espresso webpage.
>
>
> Writing vib.log.0x+.pckl
> Writing vib.log.eq.pckl
> Writing vib.log.0y-.pckl
> Writing vib.log.0x-.pckl
> Writing vib.log.0y+.pckl
> Writing vib.log.0z+.pckl
> Writing vib.log.1x-.pckl
> Writing vib.log.0z-.pckl
> Writing vib.log.1z-.pckl
> Writing vib.log.1y+.pckl
> Writing vib.log.1y-.pckl
> Writing vib.log.1x+.pckl
> Traceback (most recent call last):
> File "trans_ase.py", line 23, in <module>
> vib.summary(log='vib.txt')
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 292, in summary
> hnu = self.get_energies(method, direction)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 256, in get_energies
> self.read(method, direction)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 210, in read
> fplus = load(name + '+.pckl')
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 195, in load
> f = pickleload(fl)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py",
> line 1384, in load
> Traceback (most recent call last):
> File "trans_ase.py", line 23, in <module>
> vib.summary(log='vib.txt')
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 292, in summary
> hnu = self.get_energies(method, direction)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 256, in get_energies
> self.read(method, direction)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 210, in read
> fplus = load(name + '+.pckl')
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 195, in load
> f = pickleload(fl)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py",
> line 1384, in load
> Traceback (most recent call last):
> File "trans_ase.py", line 23, in <module>
> vib.summary(log='vib.txt')
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 292, in summary
> hnu = self.get_energies(method, direction)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 256, in get_energies
> self.read(method, direction)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 210, in read
> fplus = load(name + '+.pckl')
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/site-packages/ase/vibrations/vibrations.py",
> line 195, in load
> f = pickleload(fl)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py",
> line 1384, in load
> return Unpickler(file).load()
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py",
> line 864, in load
> return Unpickler(file).load()
> return Unpickler(file).load()
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py",
> line 864, in load
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py",
> line 864, in load
> dispatch[key](self)
> dispatch[key](self)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py",
> line 886, in load_eof
> dispatch[key](self)
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py",
> line 886, in load_eof
> File
> "/bg01/homescinet/c/csingh/kavalsky/CONDA_ENVS/ase/lib/python2.7/pickle.py",
> line 886, in load_eof
> raise EOFError
> raise EOFError
> EOFError
> raise EOFError
> EOFError
> EOFError
This contains repetitive lines. I infer that it ran on multiple
cores, and that probably the simultaneous opening of the same files
lead to garbled data.
I believe the Vibrations class should work in parallel, so this is
probably a bug. However it is somewhat unusual to run ASE scripts in
parallel except with GPAW and ASAP, so I suspect you should be doing
something else.
Did you run this in e.g. slurm through "srun python ...."? Perhaps
what you want is to not put the srun command in the submit script, but
rather inside the Python script:
calc = Espresso(command='srun my-espresso-command', ...)
or equivalently export ASE_ESPRESSO_COMMAND="srun my-espresso-command".
That way ASE will run in serial, but invoke QE in parallel.
ASE may run indeed correctly in parallel with mpi4py, but it appears
to me that the Vibrations class is not quite fit for the task at the
moment.
Best regards
Ask
>
>
>
> Thanks,
>
> Lance
>
>
>
> ________________________________
> From: Ask Hjorth Larsen <asklarsen at gmail.com>
> Sent: Saturday, December 2, 2017 7:42:51 AM
> To: Lance Kavalsky
> Cc: ase-users at listserv.fysik.dtu.dk
> Subject: Re: [ase-users] EOF Error Vibrational Modes Espresso
>
> Hi,
>
> 2017-12-01 18:39 GMT+01:00 Lance Kavalsky via ase-users
> <ase-users at listserv.fysik.dtu.dk>:
>> Hello,
>>
>>
>> My end goal is to calculate the vibrational energies (and subsequently ZPE
>> and TS) of an adatom on a fixed substrate using ase.vibrations.
>>
>>
>> As a test case, I have been trying to reduce my system to only 2 atoms (1
>> P
>> and 1 Na) to ensure my script is functioning properly (attached). The
>> script
>> successfully reads from the Quantum Espresso input file, and vib.run()
>> will
>> write the pckl displacement files, but it returns EOFError when trying to
>> execute vib.summary().
>>
>>
>> Any advice or guidance would be very much appreciated.
>
> I don't know if I can help with vibrations, but in case someone can,
> could you give the full stack trace please? It would be useful to
> know what it was reading when it caused EOF.
>
> The pseudopotentials and version numbers might also prove useful.
>
> Best regards
> Ask
>
>>
>>
>> Thanks,
>>
>> Lance Kavalsky
>>
>> HBSc., MASc. Student
>>
>> Dept. of Materials Science and Engineering
>>
>> University of Toronto
>>
>>
>>
>> _______________________________________________
>> ase-users mailing list
>> ase-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
More information about the ase-users
mailing list