Enable export of environment variables plus lobster run as a command #326
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@janosh would be great if you could have a look at it. Ideally, we have this in the next custodian and atomate2 version as it would simplify running automated bonding analysis runs quite a lot. I changed 2 lines of code here. Any suggestions welcome. Alternative to this solution: changing both atomate and atomate2 code base to not convert the command into a list. I am a bit hesitant to do that as atomate is not very frequently updated. |
custodian/lobster/jobs.py
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| @@ -87,7 +87,8 @@ def run(self, directory="./"): | |||
| zopen(os.path.join(directory, self.stderr_file), "w", buffering=1) as f_err, | |||
| ): | |||
| # use line buffering for stderr | |||
| return subprocess.Popen(cmd, cwd=directory, stdout=f_std, stderr=f_err) # pylint: disable=R1732 | |||
| cmd = " ".join(cmd) # to join split commands (e.g., from atomate and atomate2) | |||
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| cmd = " ".join(cmd) # to join split commands (e.g., from atomate and atomate2) | |
| if isinstance(cmd, list): | |
| cmd = " ".join(cmd) # to join split commands (e.g., from atomate and atomate2) |
We could also do this to make it safer in case a string is transferred or replace it with one of the shlex commands:
| cmd = " ".join(cmd) # to join split commands (e.g., from atomate and atomate2) | |
| import shlex | |
| if isinstance(cmd, list): | |
| cmd = shlex.join(cmd) |
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@janosh maybe Sequence is better than list but I am not sure if we ever pass anything other than a list
custodian/lobster/jobs.py
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| @@ -78,16 +78,16 @@ def setup(self, directory="./"): | |||
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| def run(self, directory="./"): | |||
| """Runs the job.""" | |||
| cmd = self.lobster_cmd | |||
| cmd = " ".join(self.lobster_cmd) # join split commands (e.g., from atomate and atomate2) | |||
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do we want to support both str and Sequence for lobster_cmd?
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Yes, I think it would be good. Just made a comment on that with two alternatives. You were faster :D
janosh
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enhancement
lobster
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Thanks, @janosh ! |
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Would be great if a new version could be released when the next pymatgen version is released as well. |
Summary
This will enable using "NUM_OMP_THREADS=48 /bin/lobster-command" as a command. With this, running VASP and LOBSTER within one job-script with jobflow and atomate2 only (without installing fireworks or jobflow remote) will be possible. If users rely on one 1 CPU node only, this should ensure good run times.
(cc @naik-aakash )