First time using Pyiron - lammps

[fmfaraujo]

Hi everyone,

I am a student starting with molecular dynamics. I am using Ubuntu and created a miniconda envinroment where I installed pyiron (https://pyiron.readthedocs.io/en/latest/source/installation.html#conda-installation). I also used "pyiron install" to perform the first configurations. I am facing a problem with the lmp_serial:

2023-02-23 14:40:36,436 - pyiron_log - WARNING - Job aborted
2023-02-23 14:40:36,437 - pyiron_log - WARNING - /home/fmfaraujo/pyiron/resources/lammps/bin/run_lammps_2020.03.03.sh: line 2: exec: lmp_serial: not found


CalledProcessError                        Traceback (most recent call last)
File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:476, in execute_job_with_external_executable(job)

File ~/envs/miniconda3/envs/CMS/lib/python3.11/subprocess.py:569, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    568     if check and retcode:
--> 569         raise CalledProcessError(retcode, process.args,
    570                                  output=stdout, stderr=stderr)
    571 return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '/home/fmachado/pyiron/resources/lammps/bin/run_lammps_2020.03.03.sh' returned non-zero exit status 127.

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)

I tried installing again, adding different paths, but nothing is working. I never used different environments, and the paths above are different, my guess is that something is going wrong there.

I am sure I am doing something wrong, but I am stuck with this quite a while, would be happy with some help.

Thanks a lot in advance :)

[jan-janssen]

@fmfaraujo Did you install lammps via conda ?

conda install -c conda-forge lammps

[fmfaraujo]

hi @jan-janssen, thanks for the reply! Yes I did install lammps via conda

[pmrv]

Can you check if there's a error.msg file in the working directory of the job? Also is that the full traceback? Seems like there's something cut off at the bottom.

[fmfaraujo]

This is the error.msg :

/home/fmachado/pyiron/resources/lammps/bin/run_lammps_2020.03.03.sh: line 2: exec: lmp_serial: not found

And this would be the complete traceback

CalledProcessError                        Traceback (most recent call last)
File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:476, in execute_job_with_external_executable(job)
    475 try:
--> 476     out = subprocess.run(
    477         executable,
    478         cwd=job.project_hdf5.working_directory,
    479         shell=shell,
    480         stdout=subprocess.PIPE,
    481         stderr=subprocess.STDOUT,
    482         universal_newlines=True,
    483         check=True,
    484     ).stdout
    485 except subprocess.CalledProcessError as e:

File ~/envs/miniconda3/envs/CMS/lib/python3.11/subprocess.py:569, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    568     if check and retcode:
--> 569         raise CalledProcessError(retcode, process.args,
    570                                  output=stdout, stderr=stderr)
    571 return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '/home/fmachado/pyiron/resources/lammps/bin/run_lammps_2020.03.03.sh' returned non-zero exit status 127.

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
Cell In[8], line 1
----> 1 job.run()

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/utils/deprecate.py:171, in Deprecator.__deprecate_argument.<locals>.decorated(*args, **kwargs)
    161     if kw in self.arguments:
    162         warnings.warn(
    163             message_format.format(
    164                 "{}.{}({}={})".format(
   (...)
    169             stacklevel=2,
    170         )
--> 171 return function(*args, **kwargs)

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:693, in GenericJob.run(self, delete_existing_job, repair, debug, run_mode, run_again)
    691     self._run_if_repair()
    692 elif status == "initialized":
--> 693     self._run_if_new(debug=debug)
    694 elif status == "created":
    695     self._run_if_created()

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:1217, in GenericJob._run_if_new(self, debug)
   1209 def _run_if_new(self, debug=False):
   1210     """
   1211     Internal helper function the run if new function is called when the job status is 'initialized'. It prepares
   1212     the hdf5 file and the corresponding directory structure.
   (...)
   1215         debug (bool): Debug Mode
   1216     """
-> 1217     run_job_with_status_initialized(job=self, debug=debug)

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:76, in run_job_with_status_initialized(job, debug)
     74 else:
     75     job.save()
---> 76     job.run()

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/utils/deprecate.py:171, in Deprecator.__deprecate_argument.<locals>.decorated(*args, **kwargs)
    161     if kw in self.arguments:
    162         warnings.warn(
    163             message_format.format(
    164                 "{}.{}({}={})".format(
   (...)
    169             stacklevel=2,
    170         )
--> 171 return function(*args, **kwargs)

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:695, in GenericJob.run(self, delete_existing_job, repair, debug, run_mode, run_again)
    693     self._run_if_new(debug=debug)
    694 elif status == "created":
--> 695     self._run_if_created()
    696 elif status == "submitted":
    697     run_job_with_status_submitted(job=self)

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:1228, in GenericJob._run_if_created(self)
   1219 def _run_if_created(self):
   1220     """
   1221     Internal helper function the run if created function is called when the job status is 'created'. It executes
   1222     the simulation, either in modal mode, meaning waiting for the simulation to finish, manually, or submits the
   (...)
   1226         int: Queue ID - if the job was send to the queue
   1227     """
-> 1228     return run_job_with_status_created(job=self)

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:99, in run_job_with_status_created(job)
     97     job.run_if_manually(_manually_print=False)
     98 elif job.server.run_mode.modal:
---> 99     job.run_static()
    100 elif job.server.run_mode.srun:
    101     job.run_if_srun()

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:729, in GenericJob.run_static(self)
    725 def run_static(self):
    726     """
    727     The run static function is called by run to execute the simulation.
    728     """
--> 729     execute_job_with_external_executable(job=self)

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:448, in run_time_decorator.<locals>.wrapper(job)
    446 if job.job_id is not None:
    447     job.project.db.item_update({"timestart": datetime.now()}, job.job_id)
--> 448     func(job)
    449     job.project.db.item_update(job._runtime(), job.job_id)
    450 else:

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:486, in execute_job_with_external_executable(job)
    476     out = subprocess.run(
    477         executable,
    478         cwd=job.project_hdf5.working_directory,
   (...)
    483         check=True,
    484     ).stdout
    485 except subprocess.CalledProcessError as e:
--> 486     out, job_crashed = handle_failed_job(job=job, error=e)
    488 job._logger.info(
    489     "{}, status: {}, output: {}".format(job.job_info_str, job.status, out)
    490 )
    491 with open(
    492     posixpath.join(job.project_hdf5.working_directory, "error.out"), mode="w"
    493 ) as f_err:

File ~/envs/miniconda3/envs/CMS/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:540, in handle_failed_job(job, error)
    538     if job.server.run_mode.non_modal:
    539         state.database.close_connection()
--> 540     raise RuntimeError("Job aborted")
    541 else:
    542     return True, out

RuntimeError: Job aborted

[jan-janssen]

This is the error.msg :

/home/fmachado/pyiron/resources/lammps/bin/run_lammps_2020.03.03.sh: line 2: exec: lmp_serial: not found

This basically means that the executable lmp_serial is not found. This executable is included in the lammps conda package. So You might have to add a conda activate command to the /home/fmachado/pyiron/resources/lammps/bin/run_lammps_2020.03.03.sh script as it does not seem to be loaded.

[fmfaraujo]

That worked!! Thank you so much :)