Open aageo25 opened 9 months ago
I noticed that pyrion does not recognize my configuration file (.pyiron)
Running "s._configuration" outputs:
{'user': 'pyiron',
'resource_paths': ['/opt/conda/share/pyiron'],
'project_paths': [],
'connection_timeout': 60,
'sql_connection_string': None,
'sql_table_name': 'jobs_pyiron',
'sql_view_connection_string': None,
'sql_view_table_name': None,
'sql_view_user': None,
'sql_view_user_key': None,
'sql_file': '/cephyr/users/ageo/Vera/pyiron.db',
'sql_host': None,
'sql_type': 'SQLite',
'sql_user_key': None,
'sql_database': None,
'project_check_enabled': False,
'disable_database': False,
'credentials_file': None,
'write_work_dir_warnings': True,
'config_file_permissions_warning': True}
I managed to run a LAMMPS calculation and generate a trajectory, but not through squeue. I guess it used the lammps from the container.
Summarise the answers we discussed during the meeting:
Friday afternoon follow-up:
virtualev
, the recommended for the cluster. Thus, I install pyiron via pip
(not recommended according to pyiron docs).Pyiron is installed. Now I can move on.
The first issue I encountered was on how to make pyiron recognize the .pyiron
configuration file that it is not allocated in $HOME
.
PYIRONCONFIG
variableThe current issue is now when I try creating the structure. It raised an error ValueError(Was not able to locate a periodic table)
.
pyiron_atomistics/atomistics/structure/periodic_table.py
, but I did not find how this error is raised.JupyterLab
log, I notice that kite
was not found. Does this have something to do with this error?
- I looked into the source code of
pyiron_atomistics/atomistics/structure/periodic_table.py
, but I did not find how this error is raised.
This is similar to the issue discussed in https://github.com/pyiron/FAQs/issues/6 can you try to download the potential files as explained in https://pyiron.readthedocs.io/en/latest/source/installation.html#download-pyiron-parameter-files ?
> import pyiron
> pyiron.install()
>>> It appears that pyiron is not yet configured, do you want to create a default start configuration (recommended: yes). [yes/no]:
> yes
> exit()
- I looked into the source code of
pyiron_atomistics/atomistics/structure/periodic_table.py
, but I did not find how this error is raised.
When I run pyiron.install()
, I get "pyiron is already installed"
At the moment this function only works when pyiron is not yet configured: https://github.com/pyiron/pyiron_base/blob/main/pyiron_base/state/install.py#L97
Still it anyway does nothing else than downloading https://github.com/pyiron/pyiron-resources/releases and creating an initial pyiron resources file.
- I looked into the source code of
pyiron_atomistics/atomistics/structure/periodic_table.py
, but I did not find how this error is raised.This is similar to the issue discussed in #6 can you try to download the potential files as explained in https://pyiron.readthedocs.io/en/latest/source/installation.html#download-pyiron-parameter-files ?
> import pyiron > pyiron.install() >>> It appears that pyiron is not yet configured, do you want to create a default start configuration (recommended: yes). [yes/no]: > yes > exit()
After cleaning up my environment, I was able to succesfully run pyiron.install()
.
I created the queues
folders and files. For now I only have the work
queue.
I continued to run my notebook. I prepared my queue, defining the number of cores, and modifying the run_lammps_2020.03.03_mpi.sh
to submit a job to the cluster. When I fire job.run(run_mode='work', delete_existing_job=True)
, I get The job Al_T800K was saved and received the ID: 2
followed by the error message starting with 2023-11-30 18:27:09,968 - pyiron_log - WARNING - Job aborted
and in the end ValueError: run_queue.sh crashed
.
- I looked into the source code of
pyiron_atomistics/atomistics/structure/periodic_table.py
, but I did not find how this error is raised.This is similar to the issue discussed in #6 can you try to download the potential files as explained in https://pyiron.readthedocs.io/en/latest/source/installation.html#download-pyiron-parameter-files ?
> import pyiron > pyiron.install() >>> It appears that pyiron is not yet configured, do you want to create a default start configuration (recommended: yes). [yes/no]: > yes > exit()
After cleaning up my environment, I was able to succesfully run
pyiron.install()
.I created the
queues
folders and files. For now I only have thework
queue.I continued to run my notebook. I prepared my queue, defining the number of cores, and modifying the
run_lammps_2020.03.03_mpi.sh
to submit a job to the cluster. When I firejob.run(run_mode='work', delete_existing_job=True)
, I getThe job Al_T800K was saved and received the ID: 2
followed by the error message starting with2023-11-30 18:27:09,968 - pyiron_log - WARNING - Job aborted
and in the endValueError: run_queue.sh crashed
.
The reason was a misconfigured sbatch
submission template file. After adjusting the keywords, I was able to submit a lammps
job to the queue.
I want to install pyiron on the HPC at Chalmers. Some remarks:
I prepared my container based on the pyiron docker image. I succesfully launched JupyterLab and created a first project database. Can that be used in production?
What I want to do now is to launch an example calculation (lammps) to the slurm system. I want to know if my basic configuration is correct. Probably it is not.