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Merge pull request #128 from ReactionMechanismGenerator/local2
Run ARC on a server
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| import job | ||
| import ssh | ||
| import local | ||
| import inputs | ||
| import submit | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,115 @@ | ||
| #!/usr/bin/env python | ||
| # encoding: utf-8 | ||
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| """ | ||
| A module for running jobs on the local machine | ||
| When transitioning to Python 3, use subprocess.run(), https://docs.python.org/3/library/subprocess.html#subprocess.run | ||
| """ | ||
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| from __future__ import (absolute_import, division, print_function, unicode_literals) | ||
| import subprocess | ||
| import os | ||
| import shutil | ||
| import datetime | ||
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| from arc.job.ssh import check_job_status_in_stdout | ||
| from arc.settings import servers, check_status_command, submit_command, submit_filename, delete_command, output_filename | ||
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| ################################################################## | ||
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| def execute_command(command, shell=True): | ||
| """ | ||
| Execute a command. `command` is an array of string commands to send. | ||
| If path is not an empty string, the command will be executed in the directory path it points to. | ||
| Returns lists of stdin, stdout, stderr corresponding to the commands sent. | ||
| `shell` specifies whether the command should be executed using bash instead of Python | ||
| """ | ||
| if not isinstance(command, list) and not shell: | ||
| command = [command] | ||
| stdout = subprocess.check_output(command, shell=shell) | ||
| return stdout.splitlines(), '' | ||
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| def check_job_status(job_id): | ||
| """ | ||
| Possible statuses: `before_submission`, `running`, `errored on node xx`, `done` | ||
| Status line formats: | ||
| pharos: '540420 0.45326 xq1340b user_name r 10/26/2018 11:08:30 long1@node18.cluster' | ||
| rmg: '14428 debug xq1371m2 user_name R 50-04:04:46 1 node06' | ||
| """ | ||
| server = 'local' | ||
| cmd = check_status_command[servers[server]['cluster_soft']] + ' -u ' + servers[server]['un'] | ||
| stdout = execute_command(cmd)[0] | ||
| return check_job_status_in_stdout(job_id=job_id, stdout=stdout, server=server) | ||
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| def delete_job(job_id): | ||
| """ | ||
| Deletes a running job | ||
| """ | ||
| cmd = delete_command[servers['local']['cluster_soft']] + ' ' + str(job_id) | ||
| execute_command(cmd) | ||
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| def check_running_jobs_ids(): | ||
| """ | ||
| Return a list of ``int`` representing job IDs of all jobs submitted by the user on a server | ||
| """ | ||
| running_jobs_ids = list() | ||
| cmd = check_status_command[servers['local']['cluster_soft']] + ' -u ' + servers['local']['un'] | ||
| stdout = execute_command(cmd)[0] | ||
| for i, status_line in enumerate(stdout): | ||
| if (servers['local']['cluster_soft'].lower() == 'slurm' and i > 0)\ | ||
| or (servers['local']['cluster_soft'].lower() == 'oge' and i > 1): | ||
| running_jobs_ids.append(int(status_line.split()[0])) | ||
| return running_jobs_ids | ||
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| def submit_job(path): | ||
| """ | ||
| Submit a job | ||
| `path` is the job's folder path, where the submit script is located (without the submit script file name) | ||
| """ | ||
| job_status = '' | ||
| job_id = 0 | ||
| cmd = 'cd ' + path + '; ' + submit_command[servers['local']['cluster_soft']] + ' '\ | ||
| + submit_filename[servers['local']['cluster_soft']] | ||
| stdout = execute_command(cmd)[0] | ||
| if 'submitted' in stdout[0].lower(): | ||
| job_status = 'running' | ||
| if servers['local']['cluster_soft'].lower() == 'oge': | ||
| job_id = int(stdout[0].split()[2]) | ||
| elif servers['local']['cluster_soft'].lower() == 'slurm': | ||
| job_id = int(stdout[0].split()[3]) | ||
| else: | ||
| raise ValueError('Unrecognized cluster software {0}'.format(servers['local']['cluster_soft'])) | ||
| return job_status, job_id | ||
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| def get_last_modified_time(file_path): | ||
| """returns the last modified time of `file_path` in a datetime format""" | ||
| try: | ||
| timestamp = os.stat(file_path).st_mtime | ||
| except (IOError, OSError): | ||
| return None | ||
| return datetime.datetime.fromtimestamp(timestamp) | ||
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| def write_file(file_path, file_string): | ||
| """ | ||
| Write `file_string` as the file's content in `file_path` | ||
| """ | ||
| with open(file_path, 'w') as f: | ||
| f.write(file_string) | ||
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| def rename_output(local_file_path, software): | ||
| """ | ||
| Rename the output file to "output.out" for consistency between software | ||
| `local_file_path` is the full path to the output.out file, | ||
| `software` is the software used for the job by which the original output file name is determined | ||
| """ | ||
| software = software.lower() | ||
| if os.path.isfile(os.path.join(os.path.dirname(local_file_path), output_filename[software])): | ||
| shutil.move(src=os.path.join(os.path.dirname(local_file_path), output_filename[software]), dst=local_file_path) |
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| @@ -0,0 +1,59 @@ | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
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| """ | ||
| This module contains unit tests of the arc.job.local module | ||
| """ | ||
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| from __future__ import (absolute_import, division, print_function, unicode_literals) | ||
| import unittest | ||
| import os | ||
| import shutil | ||
| import datetime | ||
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| import arc.job.local as local | ||
| from arc.settings import arc_path | ||
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| ################################################################################ | ||
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| class TestLocal(unittest.TestCase): | ||
| """ | ||
| Contains unit tests for the local module | ||
| """ | ||
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| def test_execute_command(self): | ||
| """Test executing a local command""" | ||
| command1 = 'ls' | ||
| out1 = local.execute_command(command1) | ||
| self.assertIsInstance(out1, tuple) | ||
| self.assertIsInstance(out1[0], list) | ||
| self.assertEqual(out1[1], '') | ||
| self.assertIn('arc', out1[0]) | ||
| self.assertIn('ARC.py', out1[0]) | ||
| self.assertIn('environment.yml', out1[0]) | ||
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| def test_get_last_modified_time(self): | ||
| """Test the get_last_modified_time() function""" | ||
| path = os.path.join(arc_path, 'ARC.py') | ||
| t = local.get_last_modified_time(path) | ||
| self.assertIsInstance(t, datetime.datetime) | ||
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| def test_rename_output(self): | ||
| """Test the rename_output() function""" | ||
| path1 = os.path.join(arc_path, 'scratch', 'input.log') | ||
| path2 = os.path.join(arc_path, 'scratch', 'output.out') | ||
| if not os.path.exists(os.path.join(arc_path, 'scratch')): | ||
| os.makedirs(os.path.join(arc_path, 'scratch')) | ||
| with open(path1, 'w'): | ||
| pass | ||
| local.rename_output(local_file_path=path2, software='gaussian') | ||
| self.assertFalse(os.path.isfile(path1)) | ||
| self.assertTrue(os.path.isfile(path2)) | ||
| shutil.rmtree(os.path.join(arc_path, 'scratch')) | ||
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| ################################################################################ | ||
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| if __name__ == '__main__': | ||
| unittest.main(testRunner=unittest.TextTestRunner(verbosity=2)) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
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| """ | ||
| This module contains unit tests of the arc.job.ssh module | ||
| """ | ||
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| from __future__ import (absolute_import, division, print_function, unicode_literals) | ||
| import unittest | ||
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| import arc.job.ssh as ssh | ||
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| ################################################################################ | ||
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| class TestSSH(unittest.TestCase): | ||
| """ | ||
| Contains unit tests for the SSH module | ||
| """ | ||
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| def test_check_job_status_in_stdout(self): | ||
| """Test checking the job status in stdout""" | ||
| stdout = """job-ID prior name user state submit/start at queue slots ja-task-ID | ||
| ----------------------------------------------------------------------------------------------------------------- | ||
| 582682 0.45451 a9654 alongd e 04/17/2019 16:22:14 long5@node93.cluster 48 | ||
| 588334 0.45451 pf1005a alongd r 05/07/2019 16:24:31 long3@node67.cluster 48 | ||
| 588345 0.45451 a14121 alongd r 05/08/2019 02:11:42 long3@node69.cluster 48 """ | ||
| status1 = ssh.check_job_status_in_stdout(job_id=588345, stdout=stdout, server='server1') | ||
| self.assertEqual(status1, 'running') | ||
| status2 = ssh.check_job_status_in_stdout(job_id=582682, stdout=stdout, server='server1') | ||
| self.assertEqual(status2, 'errored') | ||
| status3 = ssh.check_job_status_in_stdout(job_id=582600, stdout=stdout, server='server1') | ||
| self.assertEqual(status3, 'done') | ||
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| ################################################################################ | ||
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| if __name__ == '__main__': | ||
| unittest.main(testRunner=unittest.TextTestRunner(verbosity=2)) |
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