Error running calphy from conda install in a clean conda environment

[wuziqi-cmu]

Hi there, as described I encountered a problem running calphy from conda install in a clean conda environment. The environment was created using:
conda create --name=only_calphy python=3.9
then within the environment, calphy was installed using:
conda install -c conda-forge calphy

When running calphy using calphy -i input.yaml, it gave me the following error:
[mpiexec@MacBook-Pro.local] match_arg (utils/args/args.c:163): unrecognized argument oversubscribe [mpiexec@MacBook-Pro.local] HYDU_parse_array (utils/args/args.c:178): argument matching returned error [mpiexec@MacBook-Pro.local] parse_args (ui/mpich/utils.c:1603): error parsing input array [mpiexec@MacBook-Pro.local] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1655): unable to parse user arguments [mpiexec@MacBook-Pro.local] main (ui/mpich/mpiexec.c:128): error parsing parameters Traceback (most recent call last): File "/Users/Michael_wang/opt/anaconda3/envs/only_calphy/bin/calphy_kernel", line 10, in <module> sys.exit(main()) File "/Users/Michael_wang/.local/lib/python3.9/site-packages/calphy-0.8.0-py3.9.egg/calphy/queuekernel.py", line 254, in main _ = routine_fe(job) File "/Users/Michael_wang/.local/lib/python3.9/site-packages/calphy-0.8.0-py3.9.egg/calphy/queuekernel.py", line 50, in routine_fe job.run_averaging() File "/Users/Michael_wang/.local/lib/python3.9/site-packages/calphy-0.8.0-py3.9.egg/calphy/solid.py", line 86, in run_averaging lmp = ph.create_object(self.cores, self.simfolder, self.options["md"]["timestep"]) File "/Users/Michael_wang/.local/lib/python3.9/site-packages/calphy-0.8.0-py3.9.egg/calphy/helpers.py", line 61, in create_object lmp.units("metal") File "/Users/Michael_wang/opt/anaconda3/envs/only_calphy/lib/python3.9/site-packages/pylammpsmpi/lammps_wrapper.py", line 81, in command_wrapper fut = self.lmp.command(cmd) File "/Users/Michael_wang/opt/anaconda3/envs/only_calphy/lib/python3.9/site-packages/pylammpsmpi/utils/lammps.py", line 487, in command _ = self._receive() File "/Users/Michael_wang/opt/anaconda3/envs/only_calphy/lib/python3.9/site-packages/pylammpsmpi/utils/lammps.py", line 72, in _receive output = pickle.load(self._process.stdout) EOFError: Ran out of input Exception ignored in: <function LammpsBase.__del__ at 0x7f96a4c1ae50> Traceback (most recent call last): File "/Users/Michael_wang/opt/anaconda3/envs/only_calphy/lib/python3.9/site-packages/pylammpsmpi/utils/lammps.py", line 628, in __del__ self.close() File "/Users/Michael_wang/opt/anaconda3/envs/only_calphy/lib/python3.9/site-packages/pylammpsmpi/utils/lammps.py", line 618, in close self._send(command="close") File "/Users/Michael_wang/opt/anaconda3/envs/only_calphy/lib/python3.9/site-packages/pylammpsmpi/utils/lammps.py", line 57, in _send self._process.stdin.flush() BrokenPipeError: [Errno 32] Broken pipe

It is the same on either Mac OS or Linux, either install from conda or create an environment using environment.yml and then python setup.py install

[srmnitc]

@wuziqi-cmu Thanks for posting this issue. This issue is due to pylammpsmpi, the parallel python LAMMPS version used in calphy. LAMMPS is installed from conda. It looks like the currently installed LAMMPS is the mpich version which does not work with pylammpsmpi. The solution is to install the openmpi version of LAMMPS. Please see the correct package here.

[srmnitc]

Changing the LAMMPS version in the environment.yml file to lammps =2021.09.21=*openmpi*_2 should fix the problem.

[wuziqi-cmu]

@srmnitc Thanks a lot for the help! The version you provided seems to be a Linux version, whereas I'm running on a Mac platform. It is quite easy to find a version that works for Mac though: lammps[build=py39h64223d6_openmpi_2] solves the installation issue, and now it runs. I just saw you updated the environment.yml file, maybe could consider adding a note somewhere.