TypeError due to the keyword 'cmdargs'

[ibrsam]

I got this error while running calphy.

Traceback (most recent call last):
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/bin/calphy_kernel", line 33, in <module>
    sys.exit(load_entry_point('calphy==1.2.5', 'console_scripts', 'calphy_kernel')())
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/queuekernel.py", line 150, in main
    _ = routine_ts(job)
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/routines.py",line 360, in routine_ts
    routine_fe(job)
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/routines.py",line 341, in routine_fe
    job.run_averaging()
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/solid.py", line 139, in run_averaging
    lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/helpers.py", line 54, in create_object
    lmp = LammpsLibrary(mode="local", cores=cores,
TypeError: LammpsLibrary.__init__() got an unexpected keyword argument 'cmdargs'

[srmnitc]

You need to update pylammpsmpi to 0.0.9. That will resolve the issue. If you installed using conda, you could do this with conda update pylammpsmpi command.

[ibrsam]

Thanks. Now I get this error.

Traceback (most recent call last):
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/pylammpsmpi/utils/../mpi/lmpmpi.py", line 48, in <module>
    job = lammps(cmdargs=args)
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/lammps/core.py", line 167, in __init__
    self.lib.lammps_flush_buffers.argtypes = [c_void_p]
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/ctypes/__init__.py", line 387, in __getattr__
    func = self.__getitem__(name)
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/ctypes/__init__.py", line 392, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: /home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/lib-dynload/../../liblammps.so: undefined symbol: lammps_flush_buffers
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[14634,1],0]
  Exit code:    1
--------------------------------------------------------------------------
Exception ignored in: <function LammpsBase.__del__ at 0x7fdd50f3a0e0>
Traceback (most recent call last):
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/pylammpsmpi/utils/lammps.py", line 677, in __del__
    self.close()
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/pylammpsmpi/utils/lammps.py", line 667, in close
    self._send(command="close")
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/pylammpsmpi/utils/lammps.py", line 68, in _send
    self._process.stdin.flush()
BrokenPipeError: [Errno 32] Broken pipe
Traceback (most recent call last):
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/bin/calphy_kernel", line 33, in <module>
    sys.exit(load_entry_point('calphy==1.2.5', 'console_scripts', 'calphy_kernel')())
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/queuekernel.py", line 144, in main
    job = Solid(calculation=calc, simfolder=simfolder)
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/solid.py", line 56, in __init__
    super().__init__(calculation=calculation,
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/phase.py", line 137, in __init__
    self.prepare_lattice()
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/phase.py", line 214, in prepare_lattice
    l, alat, apc, conc, dumpfile = pl.prepare_lattice(self.calc)
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/calphy-1.2.5-py3.10.egg/calphy/lattice.py", line 165, in prepare_lattice
    raise ValueError("An input file was provided but it was neither data or dump file")
ValueError: An input file was provided but it was neither data or dump file

[srmnitc]

The error comes from here:

Traceback (most recent call last):
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/pylammpsmpi/utils/../mpi/lmpmpi.py", line 48, in <module>
    job = lammps(cmdargs=args)
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/site-packages/lammps/core.py", line 167, in __init__
    self.lib.lammps_flush_buffers.argtypes = [c_void_p]
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/ctypes/__init__.py", line 387, in __getattr__
    func = self.__getitem__(name)
  File "/home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/ctypes/__init__.py", line 392, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: /home/eslam.ibrahim/miniconda3/envs/calphy/lib/python3.10/lib-dynload/../../liblammps.so: undefined symbol: lammps_flush_buffers

How did you install lammps? Seems like there is so issue with lammps libraries. Either what is wrong has to be figured out, or start in a new env from scratch.

[ibrsam]

Thank you. It works.