| """Test libhpc.""" |
| import os |
| import pytest |
| import pytest_mock |
|
|
| from pathlib import Path |
| from subprocess import CompletedProcess |
|
|
| from haddock.libs.libhpc import ( |
| HPCWorker, |
| extract_slurm_status, |
| JOB_STATUS_DIC, |
| to_torque_time, |
| ) |
|
|
| from haddock.libs.libsubprocess import CNSJob |
|
|
|
|
| def test_to_torque_time(): |
| """Test minutes to HH:MM:SS cast.""" |
| assert to_torque_time(10) == '00:10:00' |
| assert to_torque_time(60) == '01:00:00' |
| assert to_torque_time(70) == '01:10:00' |
| assert to_torque_time(1510) == '25:10:00' |
| assert to_torque_time(6070) == '101:10:00' |
|
|
|
|
| @pytest.fixture |
| def slurm_scontrol_terminated_jobid(): |
| return """JobId=42909924 JobName=proabc2.job |
| UserId=enmr(1095) GroupId=users(100) MCS_label=N/A |
| Priority=1 Nice=0 Account=(null) QOS=normal |
| JobState=RUNNING Reason=None Dependency=(null) |
| Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0 |
| DerivedExitCode=0:0 |
| RunTime=00:00:01 TimeLimit=04:00:00 TimeMin=N/A |
| SubmitTime=2023-10-17T10:03:01 EligibleTime=2023-10-17T10:03:01 |
| AccrueTime=2023-10-17T10:03:01 |
| StartTime=2023-10-17T10:03:02 EndTime=2023-10-17T14:03:02 Deadline=N/A |
| PreemptTime=None SuspendTime=None SecsPreSuspend=0 |
| LastSchedEval=2023-10-17T10:03:02 |
| Partition=short AllocNode:Sid=bianca:124111 |
| ReqNodeList=(null) ExcNodeList=(null) |
| NodeList=node011 |
| BatchHost=node011 |
| NumNodes=1 NumCPUs=1 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:*:* |
| TRES=cpu=1,node=1,billing=1 |
| Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=* |
| Nodes=node011 CPU_IDs=4 Mem=0 GRES_IDX= |
| MinCPUsNode=1 MinMemoryNode=0 MinTmpDiskNode=0 |
| Features=(null) DelayBoot=00:00:00 |
| OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null) |
| Command=/trinity/home/enmr/csb_webserver/data/runs/proabc2/nAO_3OnarD4a/proabc2.job |
| WorkDir=/trinity/home/enmr/csb_webserver/data/runs/proabc2 |
| StdErr=/trinity/home/enmr/csb_webserver/data/runs/proabc2/nAO_3OnarD4a/proabc2.err |
| StdIn=/dev/null |
| StdOut=/trinity/home/enmr/csb_webserver/data/runs/proabc2/nAO_3OnarD4a/proabc2.out |
| Power= |
| """ |
|
|
|
|
| def test_slurm_status(slurm_scontrol_terminated_jobid): |
| status = extract_slurm_status(slurm_scontrol_terminated_jobid) |
| assert status == 'RUNNING' |
| assert JOB_STATUS_DIC[status] == 'running' |
|
|
|
|
| @pytest.fixture |
| def slurm_scontrol_wrongjobid(): |
| return 'slurm_load_jobs error: Invalid job id specified' |
|
|
|
|
| def test_slurm_nojobid(slurm_scontrol_wrongjobid): |
| status = extract_slurm_status(slurm_scontrol_wrongjobid) |
| assert status == 'FAILED' |
|
|
|
|
| @pytest.fixture |
| def hpcworker(mocker): |
| """Instanciate a HPCWorker object.""" |
| mocker.patch( |
| "haddock.libs.libsubprocess.CNSJob.cns_exec", |
| return_value=None, |
| ) |
| return HPCWorker( |
| tasks=[ |
| CNSJob( |
| Path('rigidbody.inp'), |
| Path('rigidbody.out'), |
| envvars={ |
| 'MODDIR': '.', |
| 'TOPPAR': 'topology_params', |
| 'MODULE': 'rigidbody', |
| }, |
| cns_exec=None, |
| ), |
| ], |
| num=1, |
| job_id=123456789, |
| workfload_manager='slurm', |
| queue=10, |
| ) |
|
|
|
|
| def test_hpcworker_run(hpcworker, mocker): |
| """Test the `run` function of a HPCWorker object.""" |
| mocker.patch( |
| "subprocess.run", |
| return_value=CompletedProcess( |
| args=['sbatch', str(hpcworker.job_fname)], |
| returncode=0, |
| stdout=b'Submitted batch job 42914957', |
| stderr=b'', |
| ) |
| ) |
| hpcworker.run() |
| assert os.path.exists(hpcworker.job_fname) |
| os.remove(hpcworker.job_fname) |
| assert hpcworker.job_id == 42914957 |
| assert hpcworker.job_status == 'submitted' |
|
|
|
|
| def test_hpcworker_update_status( |
| hpcworker, |
| slurm_scontrol_terminated_jobid, |
| mocker, |
| ): |
| """Test `update_status` function.""" |
| mocker.patch( |
| "subprocess.run", |
| return_value=CompletedProcess( |
| args=['scontrol', 'show', 'jobid', '-dd', '42909924'], |
| returncode=0, |
| stdout=bytes(slurm_scontrol_terminated_jobid, 'utf-8'), |
| stderr=b'', |
| ) |
| ) |
| status = hpcworker.update_status() |
| assert status == hpcworker.job_status |
| assert status == 'running' |
|
|
