In lammps job executable file, lammps potential file name is lmp mpi vs the actuall name is lmp

[sepidbgh]

alledProcessError                        Traceback (most recent call last)
File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:936, in execute_command_with_error_handling(executable, shell, working_directory, cores, threads, gpus, conda_environment_name, conda_environment_path, accepted_return_codes, accept_crash)
    935 try:
--> 936     shell_output = execute_subprocess(
    937         executable=executable,
    938         shell=shell,
    939         working_directory=working_directory,
    940         conda_environment_name=conda_environment_name,
    941         conda_environment_path=conda_environment_path,
    942         cores=cores,
    943         threads=threads,
    944         gpus=gpus,
    945     )
    946 except (subprocess.CalledProcessError, FileNotFoundError) as error:

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:745, in execute_subprocess(executable, shell, working_directory, cores, threads, gpus, conda_environment_name, conda_environment_path)
    744 if conda_environment_name is None and conda_environment_path is None:
--> 745     out = subprocess.run(
    746         executable,
    747         cwd=working_directory,
    748         shell=shell,
    749         stdout=subprocess.PIPE,
    750         stderr=subprocess.STDOUT,
    751         universal_newlines=True,
    752         check=True,
    753         env=environment_dict,
    754     ).stdout
    755 else:

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/subprocess.py:571, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    570     if check and retcode:
--> 571         raise CalledProcessError(retcode, process.args,
    572                                  output=stdout, stderr=stderr)
    573 return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '/home/users/baghasq1/anaconda3/envs/workflow-rdf-v0.2/share/pyiron/lammps/bin/run_lammps_2024.02.07.sh' returned non-zero exit status 134.

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:978, in execute_job_with_calculate_function(job)
    973 try:
    974     (
    975         shell_output,
    976         parsed_output,
    977         job_crashed,
--> 978     ) = job.get_calculate_function()(**job.calculate_kwargs)
    979 except RuntimeError:

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:139, in CalculateFunctionCaller.__call__(self, working_directory, input_parameter_dict, executable_script, shell_parameter, cores, threads, gpus, conda_environment_name, conda_environment_path, accept_crash, accepted_return_codes, output_parameter_dict)
    135     self.write_input_funct(
    136         input_dict=input_parameter_dict,
    137         working_directory=working_directory,
    138     )
--> 139 job_crashed, shell_output = execute_command_with_error_handling(
    140     executable=executable_script,
    141     shell=shell_parameter,
    142     working_directory=working_directory,
    143     cores=cores,
    144     threads=threads,
    145     gpus=gpus,
    146     conda_environment_name=conda_environment_name,
    147     conda_environment_path=conda_environment_path,
    148     accepted_return_codes=accepted_return_codes,
    149     accept_crash=accept_crash,
    150 )
    151 parsed_output = None

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:953, in execute_command_with_error_handling(executable, shell, working_directory, cores, threads, gpus, conda_environment_name, conda_environment_path, accepted_return_codes, accept_crash)
    952         f.write(error.output)
--> 953     raise RuntimeError("External executable failed")
    954 else:

RuntimeError: External executable failed

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
Cell In[13], line 1
----> 1 job.run()

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_snippets/deprecate.py:158, in Deprecator.__deprecate_argument.<locals>.decorated(*args, **kwargs)
    148     if kw in self.arguments:
    149         warnings.warn(
    150             message_format.format(
    151                 "{}.{}({}={})".format(
   (...)
    156             stacklevel=2,
    157         )
--> 158 return function(*args, **kwargs)

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:880, in GenericJob.run(self, delete_existing_job, repair, debug, run_mode, run_again)
    878     self._run_if_repair()
    879 elif status == "initialized":
--> 880     self._run_if_new(debug=debug)
    881 elif status == "created":
    882     self._run_if_created()

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:1402, in GenericJob._run_if_new(self, debug)
   1394 def _run_if_new(self, debug=False):
   1395     """
   1396     Internal helper function the run if new function is called when the job status is 'initialized'. It prepares
   1397     the hdf5 file and the corresponding directory structure.
   (...)
   1400         debug (bool): Debug Mode
   1401     """
-> 1402     run_job_with_status_initialized(job=self, debug=debug)

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:189, in run_job_with_status_initialized(job, debug)
    187 else:
    188     job.save()
--> 189     job.run()

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_snippets/deprecate.py:158, in Deprecator.__deprecate_argument.<locals>.decorated(*args, **kwargs)
    148     if kw in self.arguments:
    149         warnings.warn(
    150             message_format.format(
    151                 "{}.{}({}={})".format(
   (...)
    156             stacklevel=2,
    157         )
--> 158 return function(*args, **kwargs)

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:882, in GenericJob.run(self, delete_existing_job, repair, debug, run_mode, run_again)
    880     self._run_if_new(debug=debug)
    881 elif status == "created":
--> 882     self._run_if_created()
    883 elif status == "submitted":
    884     run_job_with_status_submitted(job=self)

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:1413, in GenericJob._run_if_created(self)
   1404 def _run_if_created(self):
   1405     """
   1406     Internal helper function the run if created function is called when the job status is 'created'. It executes
   1407     the simulation, either in modal mode, meaning waiting for the simulation to finish, manually, or submits the
   (...)
   1411         int: Queue ID - if the job was send to the queue
   1412     """
-> 1413     return run_job_with_status_created(job=self)

When I install atomrdf with the help pf yml file of workflow environment and try to run a simple lammps job I got this error.

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:212, in run_job_with_status_created(job)
    210     run_job_with_runmode_manually(job=job, _manually_print=True)
    211 elif job.server.run_mode.modal:
--> 212     job.run_static()
    213 elif job.server.run_mode.srun:
    214     run_job_with_runmode_srun(job=job)

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:917, in GenericJob.run_static(self)
    913 """
    914 The run static function is called by run to execute the simulation.
    915 """
    916 if self._job_with_calculate_function:
--> 917     execute_job_with_calculate_function(job=self)
    918 else:
    919     return execute_job_with_external_executable(job=self)

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:717, in run_time_decorator.<locals>.wrapper(job)
    715 if not state.database.database_is_disabled and job.job_id is not None:
    716     job.project.db.item_update({"timestart": datetime.now()}, job.job_id)
--> 717     output = func(job)
    718     job.project.db.item_update(job._runtime(), job.job_id)
    719 else:

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:980, in execute_job_with_calculate_function(job)
    974     (
    975         shell_output,
    976         parsed_output,
    977         job_crashed,
    978     ) = job.get_calculate_function()(**job.calculate_kwargs)
    979 except RuntimeError:
--> 980     raise_runtimeerror_for_failed_job(job=job)
    981 else:
    982     job.set_input_to_read_only()

File ~/anaconda3/envs/workflow-rdf-v0.2/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:873, in raise_runtimeerror_for_failed_job(job)
    871 if job.server.run_mode.non_modal:
    872     state.database.close_connection()
--> 873 raise RuntimeError("Job aborted")

RuntimeError: Job aborted

[srmnitc]

@sepidbgh I am not sure what is wrong here. Could you please mention how you informed lammps, and what is the version installed? Thanks!