Note

Go to the end to download the full example code.

Basic example on how to use the PBS cluster

Basic example

When you’re running hundreds or thousands of jobs, automation is a necessity. This is where hopla can help you.

A simple example of how to use hopla on a PBS cluster. Please check the user guide for a more in depth presentation of all functionalities.

Imports

import hopla
from pprint import pprint

Executor Context

executor = hopla.Executor(
    cluster="pbs",
    folder="/tmp/hopla",
    queue="Nspin_short",
    image="/tmp/hopla/my-apptainer-img.simg",
    walltime=1
)

Submit Jobs

jobs = [
    executor.submit("sleep", k) for k in range(1, 11)
]
pprint(jobs)
print(jobs[0].delayed_submission)

[DelayedPbsJob(
  job_id=1,
  submission_id=None,
),
 DelayedPbsJob(
  job_id=2,
  submission_id=None,
),
 DelayedPbsJob(
  job_id=3,
  submission_id=None,
),
 DelayedPbsJob(
  job_id=4,
  submission_id=None,
),
 DelayedPbsJob(
  job_id=5,
  submission_id=None,
),
 DelayedPbsJob(
  job_id=6,
  submission_id=None,
),
 DelayedPbsJob(
  job_id=7,
  submission_id=None,
),
 DelayedPbsJob(
  job_id=8,
  submission_id=None,
),
 DelayedPbsJob(
  job_id=9,
  submission_id=None,
),
 DelayedPbsJob(
  job_id=10,
  submission_id=None,
)]
DelayedSubmission(
  command=sleep 1,
  execution_parameters=,
)

Generate a batch

jobs[0].generate_batch()
print(jobs[0].paths)
batch = jobs[0].paths.submission_file
with open(batch) as of:
    print(of.read())

JobPaths(
  flux_dir=/tmp/hopla/logs/1_flux,
  job_id=1,
  joblib_file=/tmp/hopla/submissions/1_joblib_script.py,
  log_folder=/tmp/hopla/logs,
  oneshot_dir=/tmp/hopla/logs/1_oneshot,
  oneshot_file=/tmp/hopla/submissions/1_oneshot_script.sh,
  stderr=/tmp/hopla/logs/1_log.err,
  stdout=/tmp/hopla/logs/1_log.out,
  submission_file=/tmp/hopla/submissions/1_submission.sh,
  submission_folder=/tmp/hopla/submissions,
  task_file=/tmp/hopla/submissions/1_tasks.txt,
  worker_file=/tmp/hopla/submissions/worker.sh,
)
#!/bin/bash

# Parameters
#PBS -q Nspin_short
#PBS -l mem=2gb,ncpus=1,ngpus=0,walltime=1:00:00
#PBS -N hopla
#PBS -e /tmp/hopla/logs/1_log.err
#PBS -o /tmp/hopla/logs/1_log.out

# Environment
echo $PBS_JOBID
echo $HOSTNAME

# Command
apptainer run  /tmp/hopla/my-apptainer-img.simg sleep 1
echo "HOPLASAY-DONE"

Start Jobs

We can’t execute the code on the CI since the PBS infrastructure is not available.

from hopla.config import Config

with Config(dryrun=True, delay_s=3):
    executor(max_jobs=2)
    print(executor.report)

QSUB:   0%|          | 0/10 [00:00<?, ?it/s][command] qsub /tmp/hopla/submissions/1_submission.sh

QSUB:  10%|█         | 1/10 [00:00<00:00, 1718.98it/s][command] qsub /tmp/hopla/submissions/2_submission.sh

QSUB:  20%|██        | 2/10 [00:00<00:00, 1741.82it/s][command] qsub /tmp/hopla/submissions/3_submission.sh

QSUB:  30%|███       | 3/10 [00:03<00:07,  1.00s/it]
QSUB:  30%|███       | 3/10 [00:03<00:07,  1.00s/it][command] qsub /tmp/hopla/submissions/4_submission.sh

QSUB:  40%|████      | 4/10 [00:03<00:06,  1.00s/it][command] qsub /tmp/hopla/submissions/5_submission.sh

QSUB:  50%|█████     | 5/10 [00:06<00:06,  1.24s/it]
QSUB:  50%|█████     | 5/10 [00:06<00:06,  1.24s/it][command] qsub /tmp/hopla/submissions/6_submission.sh

QSUB:  60%|██████    | 6/10 [00:06<00:04,  1.24s/it][command] qsub /tmp/hopla/submissions/7_submission.sh

QSUB:  70%|███████   | 7/10 [00:09<00:04,  1.35s/it]
QSUB:  70%|███████   | 7/10 [00:09<00:04,  1.35s/it][command] qsub /tmp/hopla/submissions/8_submission.sh

QSUB:  80%|████████  | 8/10 [00:09<00:02,  1.35s/it][command] qsub /tmp/hopla/submissions/9_submission.sh

QSUB:  90%|█████████ | 9/10 [00:12<00:01,  1.41s/it]
QSUB:  90%|█████████ | 9/10 [00:12<00:01,  1.41s/it][command] qsub /tmp/hopla/submissions/10_submission.sh

QSUB: 100%|██████████| 10/10 [00:12<00:00,  1.41s/it]
QSUB: 100%|██████████| 10/10 [00:15<00:00,  1.50s/it]
----------------------------------------
DelayedPbsJob<job_id=1>exitcode: failure
DelayedPbsJob<job_id=1>submission: /tmp/hopla/submissions/1_submission.sh
DelayedPbsJob<job_id=1>stdout: none
DelayedPbsJob<job_id=1>stderr: none
----------------------------------------
DelayedPbsJob<job_id=2>exitcode: failure
DelayedPbsJob<job_id=2>submission: /tmp/hopla/submissions/2_submission.sh
DelayedPbsJob<job_id=2>stdout: none
DelayedPbsJob<job_id=2>stderr: none
----------------------------------------
DelayedPbsJob<job_id=3>exitcode: failure
DelayedPbsJob<job_id=3>submission: /tmp/hopla/submissions/3_submission.sh
DelayedPbsJob<job_id=3>stdout: none
DelayedPbsJob<job_id=3>stderr: none
----------------------------------------
DelayedPbsJob<job_id=4>exitcode: failure
DelayedPbsJob<job_id=4>submission: /tmp/hopla/submissions/4_submission.sh
DelayedPbsJob<job_id=4>stdout: none
DelayedPbsJob<job_id=4>stderr: none
----------------------------------------
DelayedPbsJob<job_id=5>exitcode: failure
DelayedPbsJob<job_id=5>submission: /tmp/hopla/submissions/5_submission.sh
DelayedPbsJob<job_id=5>stdout: none
DelayedPbsJob<job_id=5>stderr: none
----------------------------------------
DelayedPbsJob<job_id=6>exitcode: failure
DelayedPbsJob<job_id=6>submission: /tmp/hopla/submissions/6_submission.sh
DelayedPbsJob<job_id=6>stdout: none
DelayedPbsJob<job_id=6>stderr: none
----------------------------------------
DelayedPbsJob<job_id=7>exitcode: failure
DelayedPbsJob<job_id=7>submission: /tmp/hopla/submissions/7_submission.sh
DelayedPbsJob<job_id=7>stdout: none
DelayedPbsJob<job_id=7>stderr: none
----------------------------------------
DelayedPbsJob<job_id=8>exitcode: failure
DelayedPbsJob<job_id=8>submission: /tmp/hopla/submissions/8_submission.sh
DelayedPbsJob<job_id=8>stdout: none
DelayedPbsJob<job_id=8>stderr: none
----------------------------------------
DelayedPbsJob<job_id=9>exitcode: failure
DelayedPbsJob<job_id=9>submission: /tmp/hopla/submissions/9_submission.sh
DelayedPbsJob<job_id=9>stdout: none
DelayedPbsJob<job_id=9>stderr: none
----------------------------------------
DelayedPbsJob<job_id=10>exitcode: failure
DelayedPbsJob<job_id=10>submission: /tmp/hopla/submissions/10_submission.sh
DelayedPbsJob<job_id=10>stdout: none
DelayedPbsJob<job_id=10>stderr: none

Total running time of the script: (0 minutes 15.236 seconds)

Estimated memory usage: 109 MB

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