dpdispatcher package
Subpackages
Submodules
dpdispatcher.JobStatus module
dpdispatcher.base_context module
- class dpdispatcher.base_context.BaseContext(*args, **kwargs)[source]
Bases:
object
Methods
Generate the machine arginfo.
Generate the machine subfields.
bind_submission
check_finish
clean
download
kill
load_from_dict
read_file
upload
write_file
- classmethod machine_arginfo() dargs.dargs.Argument [source]
Generate the machine arginfo.
- Returns
- Argument
machine arginfo
- classmethod machine_subfields() List[dargs.dargs.Argument] [source]
Generate the machine subfields.
- Returns
- list[Argument]
machine subfields
- options = {'DpCloudServerContext', 'HDFSContext', 'LazyLocalContext', 'LebesgueContext', 'LocalContext', 'SSHContext'}
- subclasses_dict = {'DpCloudServer': <class 'dpdispatcher.dp_cloud_server_context.DpCloudServerContext'>, 'DpCloudServerContext': <class 'dpdispatcher.dp_cloud_server_context.DpCloudServerContext'>, 'HDFS': <class 'dpdispatcher.hdfs_context.HDFSContext'>, 'HDFSContext': <class 'dpdispatcher.hdfs_context.HDFSContext'>, 'LazyLocal': <class 'dpdispatcher.lazy_local_context.LazyLocalContext'>, 'LazyLocalContext': <class 'dpdispatcher.lazy_local_context.LazyLocalContext'>, 'Lebesgue': <class 'dpdispatcher.dp_cloud_server_context.LebesgueContext'>, 'LebesgueContext': <class 'dpdispatcher.dp_cloud_server_context.LebesgueContext'>, 'Local': <class 'dpdispatcher.local_context.LocalContext'>, 'LocalContext': <class 'dpdispatcher.local_context.LocalContext'>, 'SSH': <class 'dpdispatcher.ssh_context.SSHContext'>, 'SSHContext': <class 'dpdispatcher.ssh_context.SSHContext'>, 'dpcloudserver': <class 'dpdispatcher.dp_cloud_server_context.DpCloudServerContext'>, 'dpcloudservercontext': <class 'dpdispatcher.dp_cloud_server_context.DpCloudServerContext'>, 'hdfs': <class 'dpdispatcher.hdfs_context.HDFSContext'>, 'hdfscontext': <class 'dpdispatcher.hdfs_context.HDFSContext'>, 'lazylocal': <class 'dpdispatcher.lazy_local_context.LazyLocalContext'>, 'lazylocalcontext': <class 'dpdispatcher.lazy_local_context.LazyLocalContext'>, 'lebesgue': <class 'dpdispatcher.dp_cloud_server_context.LebesgueContext'>, 'lebesguecontext': <class 'dpdispatcher.dp_cloud_server_context.LebesgueContext'>, 'local': <class 'dpdispatcher.local_context.LocalContext'>, 'localcontext': <class 'dpdispatcher.local_context.LocalContext'>, 'ssh': <class 'dpdispatcher.ssh_context.SSHContext'>, 'sshcontext': <class 'dpdispatcher.ssh_context.SSHContext'>}
dpdispatcher.distributed_shell module
- class dpdispatcher.distributed_shell.DistributedShell(*args, **kwargs)[source]
Bases:
dpdispatcher.machine.Machine
Methods
do_submit
(job)submit th job to yarn using distributed shell
resources_arginfo
()Generate the resources arginfo.
resources_subfields
()Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
default_resources
deserialize
gen_command_env_cuda_devices
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
serialize
sub_script_cmd
sub_script_head
dpdispatcher.dp_cloud_server module
- class dpdispatcher.dp_cloud_server.DpCloudServer(*args, **kwargs)[source]
Bases:
dpdispatcher.machine.Machine
Methods
do_submit
(job)submit a single job, assuming that no job is running there.
resources_arginfo
()Generate the resources arginfo.
resources_subfields
()Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
default_resources
deserialize
gen_command_env_cuda_devices
gen_local_script
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
map_dp_job_state
serialize
sub_script_cmd
sub_script_head
- class dpdispatcher.dp_cloud_server.Lebesgue(*args, **kwargs)[source]
Bases:
dpdispatcher.dp_cloud_server.DpCloudServer
Methods
do_submit
(job)submit a single job, assuming that no job is running there.
resources_arginfo
()Generate the resources arginfo.
resources_subfields
()Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
default_resources
deserialize
gen_command_env_cuda_devices
gen_local_script
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
map_dp_job_state
serialize
sub_script_cmd
sub_script_head
dpdispatcher.dp_cloud_server_context module
- class dpdispatcher.dp_cloud_server_context.DpCloudServerContext(*args, **kwargs)[source]
Bases:
dpdispatcher.base_context.BaseContext
Methods
machine_arginfo
()Generate the machine arginfo.
Generate the machine subfields.
bind_submission
check_file_exists
check_finish
check_home_file_exits
clean
download
kill
load_from_dict
read_file
read_home_file
upload
write_file
write_home_file
write_local_file
- class dpdispatcher.dp_cloud_server_context.LebesgueContext(*args, **kwargs)[source]
Bases:
dpdispatcher.dp_cloud_server_context.DpCloudServerContext
Methods
machine_arginfo
()Generate the machine arginfo.
machine_subfields
()Generate the machine subfields.
bind_submission
check_file_exists
check_finish
check_home_file_exits
clean
download
kill
load_from_dict
read_file
read_home_file
upload
write_file
write_home_file
write_local_file
dpdispatcher.dpdisp module
dpdispatcher.hdfs_cli module
- class dpdispatcher.hdfs_cli.HDFS[source]
Bases:
object
Fundamental class for HDFS basic manipulation
Methods
copy_from_local
(local_path, to_uri)Returns: True on success Raises: on unexpected error
exists
(uri)Check existence of hdfs uri Returns: True on exists Raises: RuntimeError
mkdir
(uri)Make new hdfs directory Returns: True on success Raises: RuntimeError
remove
(uri)Check existence of hdfs uri Returns: True on exists Raises: RuntimeError
copy_to_local
move
read_hdfs_file
- static copy_from_local(local_path, to_uri)[source]
Returns: True on success Raises: on unexpected error
dpdispatcher.hdfs_context module
- class dpdispatcher.hdfs_context.HDFSContext(*args, **kwargs)[source]
Bases:
dpdispatcher.base_context.BaseContext
Methods
download
(submission[, check_exists, ...])download backward files from HDFS root dir
machine_arginfo
()Generate the machine arginfo.
machine_subfields
()Generate the machine subfields.
upload
(submission[, dereference])upload forward files and forward command files to HDFS root dir
bind_submission
check_file_exists
check_finish
clean
get_job_root
kill
load_from_dict
read_file
write_file
- download(submission, check_exists=False, mark_failure=True, back_error=False)[source]
download backward files from HDFS root dir
- Parameters
- submissionSubmission class instance
represents a collection of tasks, such as backward file names
- Returns
- none
dpdispatcher.lazy_local_context module
- class dpdispatcher.lazy_local_context.LazyLocalContext(*args, **kwargs)[source]
Bases:
dpdispatcher.base_context.BaseContext
Methods
machine_arginfo
()Generate the machine arginfo.
machine_subfields
()Generate the machine subfields.
bind_submission
block_call
block_checkcall
call
check_file_exists
check_finish
clean
download
get_job_root
get_return
kill
load_from_dict
read_file
upload
write_file
dpdispatcher.local_context module
- class dpdispatcher.local_context.LocalContext(*args, **kwargs)[source]
Bases:
dpdispatcher.base_context.BaseContext
Methods
machine_arginfo
()Generate the machine arginfo.
machine_subfields
()Generate the machine subfields.
bind_submission
block_call
block_checkcall
call
check_file_exists
check_finish
clean
download
download_
get_job_root
get_return
kill
load_from_dict
read_file
upload
upload_
write_file
dpdispatcher.lsf module
- class dpdispatcher.lsf.LSF(*args, **kwargs)[source]
Bases:
dpdispatcher.machine.Machine
LSF batch
Methods
default_resources
(resources)do_submit
(job)submit a single job, assuming that no job is running there.
resources_arginfo
()Generate the resources arginfo.
Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
deserialize
gen_command_env_cuda_devices
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
serialize
sub_script_cmd
sub_script_head
dpdispatcher.machine module
- class dpdispatcher.machine.Machine(*args, **kwargs)[source]
Bases:
object
A machine is used to handle the connection with remote machines.
- Parameters
- contextSubClass derived from BaseContext
The context is used to mainatin the connection with remote machine.
Methods
do_submit
(job)submit a single job, assuming that no job is running there.
Generate the resources arginfo.
Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
default_resources
deserialize
gen_command_env_cuda_devices
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
serialize
sub_script_cmd
sub_script_head
- options = {'DistributedShell', 'DpCloudServer', 'LSF', 'Lebesgue', 'PBS', 'Shell', 'Slurm', 'SlurmJobArray', 'Torque'}
- classmethod resources_arginfo() dargs.dargs.Argument [source]
Generate the resources arginfo.
- Returns
- Argument
resources arginfo
- classmethod resources_subfields() List[dargs.dargs.Argument] [source]
Generate the resources subfields.
- Returns
- list[Argument]
resources subfields
- subclasses_dict = {'DistributedShell': <class 'dpdispatcher.distributed_shell.DistributedShell'>, 'DpCloudServer': <class 'dpdispatcher.dp_cloud_server.DpCloudServer'>, 'LSF': <class 'dpdispatcher.lsf.LSF'>, 'Lebesgue': <class 'dpdispatcher.dp_cloud_server.Lebesgue'>, 'PBS': <class 'dpdispatcher.pbs.PBS'>, 'Shell': <class 'dpdispatcher.shell.Shell'>, 'Slurm': <class 'dpdispatcher.slurm.Slurm'>, 'SlurmJobArray': <class 'dpdispatcher.slurm.SlurmJobArray'>, 'Torque': <class 'dpdispatcher.pbs.Torque'>, 'distributedshell': <class 'dpdispatcher.distributed_shell.DistributedShell'>, 'dpcloudserver': <class 'dpdispatcher.dp_cloud_server.DpCloudServer'>, 'lebesgue': <class 'dpdispatcher.dp_cloud_server.Lebesgue'>, 'lsf': <class 'dpdispatcher.lsf.LSF'>, 'pbs': <class 'dpdispatcher.pbs.PBS'>, 'shell': <class 'dpdispatcher.shell.Shell'>, 'slurm': <class 'dpdispatcher.slurm.Slurm'>, 'slurmjobarray': <class 'dpdispatcher.slurm.SlurmJobArray'>, 'torque': <class 'dpdispatcher.pbs.Torque'>}
dpdispatcher.pbs module
- class dpdispatcher.pbs.PBS(*args, **kwargs)[source]
Bases:
dpdispatcher.machine.Machine
Methods
do_submit
(job)submit a single job, assuming that no job is running there.
resources_arginfo
()Generate the resources arginfo.
resources_subfields
()Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
default_resources
deserialize
gen_command_env_cuda_devices
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
serialize
sub_script_cmd
sub_script_head
- class dpdispatcher.pbs.Torque(*args, **kwargs)[source]
Bases:
dpdispatcher.pbs.PBS
Methods
do_submit
(job)submit a single job, assuming that no job is running there.
resources_arginfo
()Generate the resources arginfo.
resources_subfields
()Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
default_resources
deserialize
gen_command_env_cuda_devices
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
serialize
sub_script_cmd
sub_script_head
dpdispatcher.shell module
- class dpdispatcher.shell.Shell(*args, **kwargs)[source]
Bases:
dpdispatcher.machine.Machine
Methods
do_submit
(job)submit a single job, assuming that no job is running there.
resources_arginfo
()Generate the resources arginfo.
resources_subfields
()Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
default_resources
deserialize
gen_command_env_cuda_devices
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
serialize
sub_script_cmd
sub_script_head
dpdispatcher.slurm module
- class dpdispatcher.slurm.Slurm(*args, **kwargs)[source]
Bases:
dpdispatcher.machine.Machine
Methods
do_submit
(job[, retry, max_retry])submit a single job, assuming that no job is running there.
resources_arginfo
()Generate the resources arginfo.
Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
default_resources
deserialize
gen_command_env_cuda_devices
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
serialize
sub_script_cmd
sub_script_head
- class dpdispatcher.slurm.SlurmJobArray(*args, **kwargs)[source]
Bases:
dpdispatcher.slurm.Slurm
Slurm with job array enabled for multiple tasks in a job
Methods
do_submit
(job[, retry, max_retry])submit a single job, assuming that no job is running there.
resources_arginfo
()Generate the resources arginfo.
resources_subfields
()Generate the resources subfields.
arginfo
bind_context
check_finish_tag
check_if_recover
check_status
default_resources
deserialize
gen_command_env_cuda_devices
gen_script
gen_script_command
gen_script_custom_flags_lines
gen_script_end
gen_script_env
gen_script_header
gen_script_wait
load_from_dict
load_from_json
serialize
sub_script_cmd
sub_script_head
dpdispatcher.ssh_context module
- class dpdispatcher.ssh_context.SSHContext(*args, **kwargs)[source]
Bases:
dpdispatcher.base_context.BaseContext
- Attributes
- sftp
- ssh
Methods
block_checkcall
(cmd[, asynchronously, ...])Run command with arguments.
machine_arginfo
()Generate the machine arginfo.
Generate the machine subfields.
bind_submission
block_call
call
check_file_exists
check_finish
clean
close
download
get_job_root
get_return
kill
load_from_dict
read_file
upload
write_file
- block_checkcall(cmd, asynchronously=False, stderr_whitelist=None)[source]
Run command with arguments. Wait for command to complete. If the return code was zero then return, otherwise raise RuntimeError.
- Parameters
- cmd: str
The command to run.
- asynchronously: bool, optional, default=False
Run command asynchronously. If True, nohup will be used to run the command.
- classmethod machine_subfields() List[dargs.dargs.Argument] [source]
Generate the machine subfields.
- Returns
- list[Argument]
machine subfields
- property sftp
- property ssh
- class dpdispatcher.ssh_context.SSHSession(hostname, username, password=None, port=22, key_filename=None, passphrase=None, timeout=10, totp_secret=None)[source]
Bases:
object
- Attributes
sftp
Returns sftp.
Methods
exec_command
(cmd[, retry])Calling self.ssh.exec_command but has an exception check.
arginfo
close
ensure_alive
get_ssh_client
- property sftp
Returns sftp. Open a new one if not existing.
dpdispatcher.submission module
- class dpdispatcher.submission.Job(job_task_list, *, resources, machine=None)[source]
Bases:
object
Job is generated by Submission automatically. A job ususally has many tasks and it may request computing resources from job scheduler systems. Each Job can generate a script file to be submitted to the job scheduler system or executed locally.
- Parameters
- job_task_listlist of Task
the tasks belonging to the job
- resourcesResources
the machine resources. Passed from Submission when it constructs jobs.
- machinemachine
machine object to execute the job. Passed from Submission when it constructs jobs.
Methods
deserialize
(job_dict[, machine])convert the job_dict to a Submission class object
get the jobs.
serialize
([if_static])convert the Task class instance to a dictionary.
get_hash
handle_unexpected_job_state
job_to_json
register_job_id
submit_job
- classmethod deserialize(job_dict, machine=None)[source]
convert the job_dict to a Submission class object
- Parameters
- submission_dictdict
path-like, the base directory of the local tasks
- Returns
- submissionJob
the Job class instance converted from the job_dict
- get_job_state()[source]
get the jobs. Usually, this method will query the database of slurm or pbs job scheduler system and get the results.
Notes
this method will not submit or resubmit the jobs if the job is unsubmitted.
- class dpdispatcher.submission.Resources(number_node, cpu_per_node, gpu_per_node, queue_name, group_size, *, custom_flags=[], strategy={'if_cuda_multi_devices': False}, para_deg=1, module_unload_list=[], module_purge=False, module_list=[], source_list=[], envs={}, wait_time=0, **kwargs)[source]
Bases:
object
Resources is used to describe the machine resources we need to do calculations.
- Parameters
- number_nodeint
The number of node need for each job.
- cpu_per_nodeint
cpu numbers of each node.
- gpu_per_nodeint
gpu numbers of each node.
- queue_namestr
The queue name of batch job scheduler system.
- group_sizeint
The number of tasks in a job.
- custom_flagslist of Str
The extra lines pass to job submitting script header
- strategydict
strategies we use to generation job submitting scripts. if_cuda_multi_devices : bool
If there are multiple nvidia GPUS on the node, and we want to assign the tasks to different GPUS. If true, dpdispatcher will manually export environment variable CUDA_VISIBLE_DEVICES to different task. Usually, this option will be used with Task.task_need_resources variable simultaneously.
- para_degint
Decide how many tasks will be run in parallel. Usually run with strategy[‘if_cuda_multi_devices’]
- source_listlist of Path
The env file to be sourced before the command execution.
- wait_timeint
The waitting time in second after a single task submitted. Default: 0.
Methods
arginfo
deserialize
load_from_dict
load_from_json
serialize
- class dpdispatcher.submission.Submission(work_base, machine=None, resources=None, forward_common_files=[], backward_common_files=[], *, task_list=[])[source]
Bases:
object
A submission represents a collection of tasks. These tasks usually locate at a common directory. And these Tasks may share common files to be uploaded and downloaded.
- Parameters
- work_basePath
the base directory of the local tasks. It is usually the dir name of project .
- machineMachine
machine class object (for example, PBS, Slurm, Shell) to execute the jobs. The machine can still be bound after the instantiation with the bind_submission method.
- resourcesResources
the machine resources (cpu or gpu) used to generate the slurm/pbs script
- forward_common_fileslist
the common files to be uploaded to other computers before the jobs begin
- backward_common_fileslist
the common files to be downloaded from other computers after the jobs finish
- task_listlist of Task
a list of tasks to be run.
Methods
bind_machine
(machine)bind this submission to a machine.
check whether all the jobs in the submission.
deserialize
(submission_dict[, machine])convert the submission_dict to a Submission class object
After tasks register to the self.belonging_tasks, This method generate the jobs and add these jobs to self.belonging_jobs.
handle unexpected job state of the submission.
run_submission
(*[, exit_on_submit, clean])main method to execute the submission.
serialize
([if_static])convert the Submission class instance to a dictionary.
check whether all the jobs in the submission.
clean_jobs
download_jobs
get_hash
register_task
register_task_list
submission_from_json
submission_to_json
try_recover_from_json
upload_jobs
- bind_machine(machine)[source]
bind this submission to a machine. update the machine’s context remote_root and local_root.
- Parameters
- machineMachine
the machine to bind with
- check_all_finished()[source]
check whether all the jobs in the submission.
Notes
This method will not handle unexpected job state in the submission.
- classmethod deserialize(submission_dict, machine=None)[source]
convert the submission_dict to a Submission class object
- Parameters
- submission_dictdict
path-like, the base directory of the local tasks
- Returns
- submissionSubmission
the Submission class instance converted from the submission_dict
- generate_jobs()[source]
After tasks register to the self.belonging_tasks, This method generate the jobs and add these jobs to self.belonging_jobs. The jobs are generated by the tasks randomly, and there are self.resources.group_size tasks in a task. Why we randomly shuffle the tasks is under the consideration of load balance. The random seed is a constant (to be concrete, 42). And this insures that the jobs are equal when we re-run the program.
- handle_unexpected_submission_state()[source]
handle unexpected job state of the submission. If the job state is unsubmitted, submit the job. If the job state is terminated (killed unexpectly), resubmit the job. If the job state is unknown, raise an error.
- run_submission(*, exit_on_submit=False, clean=True)[source]
main method to execute the submission. First, check whether old Submission exists on the remote machine, and try to recover from it. Second, upload the local files to the remote machine where the tasks to be executed. Third, run the submission defined previously. Forth, wait until the tasks in the submission finished and download the result file to local directory. if exit_on_submit is True, submission will exit.
- serialize(if_static=False)[source]
convert the Submission class instance to a dictionary.
- Parameters
- if_staticbool
whether dump the job runtime infomation (like job_id, job_state, fail_count) to the dictionary.
- Returns
- submission_dictdict
the dictionary converted from the Submission class instance
- class dpdispatcher.submission.Task(command, task_work_path, forward_files=[], backward_files=[], outlog='log', errlog='err')[source]
Bases:
object
A task is a sequential command to be executed, as well as the files it depends on to transmit forward and backward.
- Parameters
- commandStr
the command to be executed.
- task_work_pathPath
the directory of each file where the files are dependent on.
- forward_fileslist of Path
the files to be transmitted to remote machine before the command execute.
- backward_fileslist of Path
the files to be transmitted from remote machine after the comand finished.
- outlogStr
the filename to which command redirect stdout
- errlogStr
the filename to which command redirect stderr
Methods
deserialize
(task_dict)convert the task_dict to a Task class object
arginfo
get_hash
load_from_json
serialize
dpdispatcher.utils module
- dpdispatcher.utils.generate_totp(secret: str, period: int = 30, token_length: int = 6) int [source]
Generate time-based one time password (TOTP) from the secret.
Some HPCs use TOTP for two-factor authentication for safety.
- Parameters
- secret: str
The encoded secret provided by the HPC. It’s usually extracted from a 2D code and base32 encoded.
- period: int, default=30
Time period where the code is valid in seconds.
- token_length: int, default=6
The token length.
- Returns
- token: int
The generated token.
References