Hacktoberfest 2026: le issue che i maintainer hanno segnato per ottobre, aperte e adatte ai principianti. Sfoglia le issue Hacktoberfest

ModuleNotFoundError: No module named 'mdtraj

Aperta
  • Qualcosa non va?
#28 0 commenti 0 reazioni 0 assegnatari Vedi su GitHub

Nessuno ha ancora preso questa issue.

Valutazione

Difficoltà
4/5
Tempo stimato
3-5 giorni
Idoneità per principianti
30/100
Tipo di issue
Bug
Chiarezza
Da chiarire
Stato di attività
Ferma
Stack tecnologico
python
Ambito
infrastructure

Direzione di ricerca

Inizia riproducendo il comando rid submit con rid/template/rid_gmx_dih.json e il file modificato rid/template/machine_slurm_gpu_cpu.json. Esamina il passaggio prep-exploration che fallisce e lo script generato, insieme al ModuleNotFoundError segnalato; il lavoro è completato quando il workflow può avviarsi senza quell'errore di importazione.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Hi, after installing rid-kit in slurm computation environment, I encountered the following error output after running the command,

DFLOW_DEBUG=1 rid submit \
-i ./tests/data/000  \
-c ./rid/template/rid_gmx_dih.json \
-m ./rid/template/machine_slurm_gpu_cpu.json \
-d ala-dipeptide-1

In which I modified the machine_slurm_gpu_cpu.json part of the parameter,

{
    "resources": {
        "local_machine": {
            "executor":{
            "image": "dptechnology/dpdispatcher:latest",
            "merge_sliced_step": "True",
            "machine_dict":{
                "batch_type": "Slurm",
                "context_type": "Local",
                "local_root" : "./",
                "remote_root": ""
            },
            "resources_dict":{
                "number_node": 1,
                "cpu_per_node": 8,
                "gpu_per_node": 1,
                "queue_name": "gpu",
                "group_size": 1,
                "custom_flags": [
                    "#SBATCH --time=72:00:00",
		    "#SBATCH --exclude=gpu05,gpu07"
                   ],
                "source_list": [
			"export CONDA_PREFIX=/home/jygu/.conda/envs/rid-kit",
			"conda activate /home/jygu/.conda/envs/rid-kit",
			"export LIBRARY_PATH=/home/jygu/.conda/envs/rid-kit/lib:$LIBRARY_PATH",
    			"export LD_LIBRARY_PATH=/home/jygu/.conda/envs/rid-kit/lib:$LD_LIBRARY_PATH",
			"export LD_LIBRARY_PATH=/opt/ohpc/pub/compiler/gcc/12.2.0/lib64:$LD_LIBRARY_PATH",
			"export PYTHONPATH=/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages:$PYTHONPATH"
		]
            }
        }
        },
        "local_machine_cpu": {
            "executor":{
            "image": "dptechnology/dpdispatcher:latest",
            "merge_sliced_step": "True",
            "machine_dict":{
                "batch_type": "Slurm",
                "context_type": "Local",
                "local_root" : "./",
                "remote_root": ""
            },
            "resources_dict":{
                "number_node": 1,
                "cpu_per_node": 8,
                "gpu_per_node": 0,
                "queue_name": "cpu",
                "group_size": 1,
                "custom_flags": [
                    "#SBATCH --time=120:00:00"

                   ],
                "source_list": [
			"export CONDA_PREFIX=/home/jygu/.conda/envs/rid-kit",
			"conda activate /home/jygu/.conda/envs/rid-kit",
			"export LIBRARY_PATH=/home/jygu/.conda/envs/rid-kit/lib:$LIBRARY_PATH",
                        "export LD_LIBRARY_PATH=/home/jygu/.conda/envs/rid-kit/lib:$LD_LIBRARY_PATH",
			"export LD_LIBRARY_PATH=/opt/ohpc/pub/compiler/gcc/12.2.0/lib64:$LD_LIBRARY_PATH",
			"export PYTHONPATH=/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages:$PYTHONPATH"
		]
            }
        }
        }
    },
    "tasks": {
        "prep_exploration_config": "local_machine_cpu",
        "run_exploration_config": "local_machine",
        "prep_label_config": "local_machine_cpu",
        "run_label_config": "local_machine",
        "prep_select_config": "local_machine",
        "run_select_config": "local_machine",
        "prep_data_config": "local_machine",
        "run_train_config": "local_machine",
        "model_devi_config": "local_machine",
        "workflow_steps_config": "local_machine_cpu"
    }
}

Please help me to resolve it at your convenience

nohup: ignoring input
2024-11-27 11:30:37 | INFO | rid.entrypoint.main | Preparing RiD ...
Traceback (most recent call last):
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1672, in run
    self.exec(scope, parameters, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1854, in exec
    self.exec_pod(scope, parameters, item)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 2100, in exec_pod
    raise RuntimeError("Run %s failed" % args)
RuntimeError: Run ['python3', '/home/jygu/wxy/rid_kit/rid-kit-master/ala-dipeptide-1/iter-001-prep-exploration-0/script'] failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1919, in exec_steps
    steps.run(scope.workflow_id, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/steps.py", line 291, in run
    step.run(self, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1676, in run
    raise RuntimeError("Step %s failed" % self)
RuntimeError: Step prep-exploration failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1672, in run
    self.exec(scope, parameters, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1852, in exec
    self.exec_steps(scope, parameters, item, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1924, in exec_steps
    raise RuntimeError("Step %s failed" % self)
RuntimeError: Step Exploration failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1919, in exec_steps
    steps.run(scope.workflow_id, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/steps.py", line 291, in run
    step.run(self, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1676, in run
    raise RuntimeError("Step %s failed" % self)
RuntimeError: Step Exploration failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1672, in run
    self.exec(scope, parameters, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1852, in exec
    self.exec_steps(scope, parameters, item, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1924, in exec_steps
    raise RuntimeError("Step %s failed" % self)
RuntimeError: Step reinforced-dynamics-block failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1919, in exec_steps
    steps.run(scope.workflow_id, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/steps.py", line 291, in run
    step.run(self, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1676, in run
    raise RuntimeError("Step %s failed" % self)
RuntimeError: Step reinforced-dynamics-block failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1672, in run
    self.exec(scope, parameters, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1852, in exec
    self.exec_steps(scope, parameters, item, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1924, in exec_steps
    raise RuntimeError("Step %s failed" % self)
RuntimeError: Step rid-procedure failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/workflow.py", line 337, in submit
    entrypoint.run(self.id, self.context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/steps.py", line 291, in run
    step.run(self, context)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dflow/step.py", line 1676, in run
    raise RuntimeError("Step %s failed" % self)
RuntimeError: Step rid-procedure failed
Workflow is running locally (ID: ala-dipeptide-1)
2024-11-27 11:31:29,697 - INFO : info:check_all_finished: False
2024-11-27 11:31:29,740 - INFO : job: a9d7d4853786fd5eacd7be7238065c476b953af3 submit; job_id is 803892
2024-11-27 11:46:33,688 - INFO : job: a9d7d4853786fd5eacd7be7238065c476b953af3 803892 finished
2024-11-27 11:46:38,665 - INFO : info:check_all_finished: False
2024-11-27 11:46:38,692 - INFO : job: f4007d8c7fd7061241ccf4088f7083376cf1d0f3 submit; job_id is 803893
2024-11-27 12:02:11,216 - INFO : job: f4007d8c7fd7061241ccf4088f7083376cf1d0f3 803893 finished
2024-11-27 12:02:13,472 - INFO : info:check_all_finished: False
2024-11-27 12:02:13,516 - INFO : job: 26dad25f1e072c05c7b3c041933108bd8515ec3c submit; job_id is 803896
2024-11-27 12:02:13,534 - INFO : job: bc817200d66825111065f773a821b7170a88bf87 submit; job_id is 803897
2024-11-27 12:02:13,551 - INFO : job: a9b29add52b7c29d91b5b26b2c3aae99ff2d27d7 submit; job_id is 803898
2024-11-27 12:02:13,568 - INFO : job: d3de077e16150b4b84e7186904477af4be382f7c submit; job_id is 803899
2024-11-27 12:16:16,845 - INFO : job: 26dad25f1e072c05c7b3c041933108bd8515ec3c 803896 terminated;fail_cout is 1; resubmitting job
2024-11-27 12:16:16,864 - INFO : job:26dad25f1e072c05c7b3c041933108bd8515ec3c re-submit after terminated; new job_id is 803913
2024-11-27 12:16:17,079 - INFO : job:26dad25f1e072c05c7b3c041933108bd8515ec3c job_id:803913 after re-submitting; the state now is <JobStatus.waiting: 2>
2024-11-27 12:16:17,079 - INFO : job: bc817200d66825111065f773a821b7170a88bf87 803897 terminated;fail_cout is 1; resubmitting job
2024-11-27 12:16:17,097 - INFO : job:bc817200d66825111065f773a821b7170a88bf87 re-submit after terminated; new job_id is 803914
2024-11-27 12:16:17,310 - INFO : job:bc817200d66825111065f773a821b7170a88bf87 job_id:803914 after re-submitting; the state now is <JobStatus.waiting: 2>
2024-11-27 12:16:17,310 - INFO : job: a9b29add52b7c29d91b5b26b2c3aae99ff2d27d7 803898 terminated;fail_cout is 1; resubmitting job
2024-11-27 12:16:17,338 - INFO : job:a9b29add52b7c29d91b5b26b2c3aae99ff2d27d7 re-submit after terminated; new job_id is 803915
2024-11-27 12:16:17,550 - INFO : job:a9b29add52b7c29d91b5b26b2c3aae99ff2d27d7 job_id:803915 after re-submitting; the state now is <JobStatus.running: 3>
2024-11-27 12:16:17,550 - INFO : job: d3de077e16150b4b84e7186904477af4be382f7c 803899 terminated;fail_cout is 1; resubmitting job
2024-11-27 12:16:17,572 - INFO : job:d3de077e16150b4b84e7186904477af4be382f7c re-submit after terminated; new job_id is 803916
2024-11-27 12:16:17,783 - INFO : job:d3de077e16150b4b84e7186904477af4be382f7c job_id:803916 after re-submitting; the state now is <JobStatus.waiting: 2>
2024-11-27 12:47:54,102 - INFO : job: 26dad25f1e072c05c7b3c041933108bd8515ec3c 803913 terminated;fail_cout is 2; resubmitting job
2024-11-27 12:47:54,144 - INFO : job:26dad25f1e072c05c7b3c041933108bd8515ec3c re-submit after terminated; new job_id is 803970
2024-11-27 12:47:54,427 - INFO : job:26dad25f1e072c05c7b3c041933108bd8515ec3c job_id:803970 after re-submitting; the state now is <JobStatus.running: 3>
2024-11-27 12:47:54,428 - INFO : job: bc817200d66825111065f773a821b7170a88bf87 803914 terminated;fail_cout is 2; resubmitting job
2024-11-27 12:47:54,447 - INFO : job:bc817200d66825111065f773a821b7170a88bf87 re-submit after terminated; new job_id is 803971
2024-11-27 12:47:54,659 - INFO : job:bc817200d66825111065f773a821b7170a88bf87 job_id:803971 after re-submitting; the state now is <JobStatus.waiting: 2>
2024-11-27 12:47:54,659 - INFO : job: a9b29add52b7c29d91b5b26b2c3aae99ff2d27d7 803915 terminated;fail_cout is 2; resubmitting job
2024-11-27 12:47:54,680 - INFO : job:a9b29add52b7c29d91b5b26b2c3aae99ff2d27d7 re-submit after terminated; new job_id is 803972
2024-11-27 12:47:54,892 - INFO : job:a9b29add52b7c29d91b5b26b2c3aae99ff2d27d7 job_id:803972 after re-submitting; the state now is <JobStatus.waiting: 2>
2024-11-27 12:47:54,892 - INFO : job: d3de077e16150b4b84e7186904477af4be382f7c 803916 terminated;fail_cout is 2; resubmitting job
2024-11-27 12:47:54,913 - INFO : job:d3de077e16150b4b84e7186904477af4be382f7c re-submit after terminated; new job_id is 803973
2024-11-27 12:47:55,125 - INFO : job:d3de077e16150b4b84e7186904477af4be382f7c job_id:803973 after re-submitting; the state now is <JobStatus.waiting: 2>
2024-11-27 12:52:55,888 - INFO : job: 26dad25f1e072c05c7b3c041933108bd8515ec3c 803970 terminated;fail_cout is 3; resubmitting job
Traceback (most recent call last):
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dpdispatcher/submission.py", line 353, in handle_unexpected_submission_state
    job.handle_unexpected_job_state()
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dpdispatcher/submission.py", line 851, in handle_unexpected_job_state
    raise RuntimeError(err_msg)
RuntimeError: job:26dad25f1e072c05c7b3c041933108bd8515ec3c 803970 failed 3 times. job_detail:{'26dad25f1e072c05c7b3c041933108bd8515ec3c': {'job_task_list': [{'command': 'sed -i "s#\\$(pwd)#$(pwd)#g" script2 && python3 script2', 'task_work_path': './', 'forward_files': ['script2', './/tmp/inputs/artifacts/topology', './/tmp/inputs/artifacts/conf', './/tmp/inputs/artifacts/dflow_python_packages'], 'backward_files': ['.//tmp/outputs/artifacts/task_path', './/tmp/outputs/parameters/cv_dim_2', 'log'], 'outlog': 'log', 'errlog': 'log'}], 'resources': {'number_node': 1, 'cpu_per_node': 8, 'gpu_per_node': 0, 'queue_name': 'cpu', 'group_size': 1, 'custom_flags': ['#SBATCH --time=120:00:00'], 'strategy': {'if_cuda_multi_devices': False, 'ratio_unfinished': 0.0}, 'para_deg': 1, 'module_purge': False, 'module_unload_list': [], 'module_list': [], 'source_list': ['export CONDA_PREFIX=/home/jygu/.conda/envs/rid-kit', 'conda activate /home/jygu/.conda/envs/rid-kit', 'export LIBRARY_PATH=/home/jygu/.conda/envs/rid-kit/lib:$LIBRARY_PATH', 'export LD_LIBRARY_PATH=/home/jygu/.conda/envs/rid-kit/lib:$LD_LIBRARY_PATH', 'export LD_LIBRARY_PATH=/opt/ohpc/pub/compiler/gcc/12.2.0/lib64:$LD_LIBRARY_PATH', 'export PYTHONPATH=/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages:$PYTHONPATH'], 'envs': {'DFLOW_WORKFLOW': 'ala-dipeptide-1', 'DFLOW_POD': 'iter-001-prep-exploration-0', 'PYTHONUNBUFFERED': 'true', 'ARGO_TEMPLATE': "''"}, 'prepend_script': [], 'append_script': [], 'wait_time': 0, 'kwargs': {}}, 'job_state': <JobStatus.terminated: 4>, 'job_id': '803970', 'fail_count': 3}}
Possible remote error message: ==> /home/jygu/wxy/rid_kit/rid-kit-master/ala-dipeptide-1/iter-001-prep-exploration-0/workdir/d158c24da9879e8890a921023117f9b33c496398/./log <==
d-kit/lib/python3.9/site-packages/rid/common/mol.py", line 5, in <module>
  File "/home/jygu/wxy/rid_kit/rid-kit-master/ala-dipeptide-1/iter-001-prep-exploration-0/workdir/d158c24da9879e8890a921023117f9b33c496398/tmp/inputs/artifacts/dflow_python_packages/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/rid/common/mol.py", line 5, in <module>
        import mdtraj as mdfrom rid.common.mol import get_distance_from_atomid,get_dihedral_value_from_resid

ModuleNotFoundError  File "/home/jygu/wxy/rid_kit/rid-kit-master/ala-dipeptide-1/iter-001-prep-exploration-0/workdir/d158c24da9879e8890a921023117f9b33c496398/tmp/inputs/artifacts/dflow_python_packages/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/rid/common/mol.py", line 5, in <module>
: No module named 'mdtraj'
        import mdtraj as mdimport mdtraj as md

ModuleNotFoundErrorModuleNotFoundError: : No module named 'mdtraj'No module named 'mdtraj'

    import mdtraj as md
ModuleNotFoundError: No module named 'mdtraj'


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/jygu/wxy/rid_kit/rid-kit-master/ala-dipeptide-1/iter-001-prep-exploration-0/script", line 105, in <module>
    submission.run_submission(clean=True)
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dpdispatcher/submission.py", line 258, in run_submission
    self.handle_unexpected_submission_state()
  File "/home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages/dpdispatcher/submission.py", line 356, in handle_unexpected_submission_state
    raise RuntimeError(
RuntimeError: Meet errors will handle unexpected submission state.
Debug information: remote_root==/home/jygu/wxy/rid_kit/rid-kit-master/ala-dipeptide-1/iter-001-prep-exploration-0/workdir/d158c24da9879e8890a921023117f9b33c496398.
Debug information: submission_hash==d158c24da9879e8890a921023117f9b33c496398.
Please check the dirs and scripts in remote_root. The job information mentioned above may help.
2024-11-27 12:52:55 | INFO | rid.entrypoint.main | The task is displayed on "https://127.0.0.1:2746".
2024-11-27 12:52:55 | INFO | rid.entrypoint.main | Artifacts (Files) are listed on "https://127.0.0.1:9001".

After I enter the command pip show mdtraj

Name: mdtraj
Version: 1.9.9
Summary: MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
Home-page: http://mdtraj.org
Author: Robert McGibbon
Author-email: [email protected]
License: LGPLv2.1+
Location: /home/jygu/.conda/envs/rid-kit/lib/python3.9/site-packages
Requires: astunparse, numpy, pyparsing, scipy
Required-by: rid-kit
Lingua principale
Python
Stelle
53
Fork
26
Nessuna PR unita negli ultimi 30g

Preparare l'ambiente

Questo progetto non fornisce container di sviluppo, Dockerfile né guida per i contributori, quindi l'ambiente è a tuo carico: parti dal suo README e consulta la nostra guida al primo contributo per i passaggi generali.

Come iniziare

  1. Leggi tutta la issue e poi la guida ai contributi del progetto.
  2. Commenta sulla issue per dire che te ne occupi tu — evita che due persone facciano lo stesso lavoro.
  3. Fai un fork del repository e lavora su un branch.
  4. Apri una pull request che faccia riferimento al numero della issue.

Altre issue di deepmodeling/rid-kit

Tutte le issue di deepmodeling/rid-kit

Issue simili

Altre issue su Python

Ricevi le nuove issue nella tua casella

Un breve riepilogo di issue GitHub adatte ai principianti.