dpgen init_bulk machine parameters

init_bulk_mdata:
type: dict
argument path: init_bulk_mdata

machine.json file

api_version:
type: str
argument path: init_bulk_mdata/api_version

Please set to 1.0

deepmd_version:
type: str, optional, default: 2
argument path: init_bulk_mdata/deepmd_version

DeePMD-kit version, e.g. 2.1.3

fp:
type: dict
argument path: init_bulk_mdata/fp

Parameters of command, machine, and resources for fp

command:
type: str
argument path: init_bulk_mdata/fp/command

Command of a program.

machine:
type: dict
argument path: init_bulk_mdata/fp/machine
batch_type:
type: str
argument path: init_bulk_mdata/fp/machine/batch_type

The batch job system type. Option: SlurmJobArray, PBS, Lebesgue, LSF, DpCloudServer, Slurm, DistributedShell, Shell, Torque

local_root:
type: NoneType | str
argument path: init_bulk_mdata/fp/machine/local_root

The dir where the tasks and relating files locate. Typically the project dir.

remote_root:
type: NoneType | str, optional
argument path: init_bulk_mdata/fp/machine/remote_root

The dir where the tasks are executed on the remote machine. Only needed when context is not lazy-local.

clean_asynchronously:
type: bool, optional, default: False
argument path: init_bulk_mdata/fp/machine/clean_asynchronously

Clean the remote directory asynchronously after the job finishes.

Depending on the value of context_type, different sub args are accepted.

context_type:
type: str (flag key)
argument path: init_bulk_mdata/fp/machine/context_type
possible choices: LocalContext, LebesgueContext, HDFSContext, DpCloudServerContext, LazyLocalContext, SSHContext

The connection used to remote machine. Option: SSHContext, LocalContext, LebesgueContext, DpCloudServerContext, HDFSContext, LazyLocalContext

When context_type is set to LocalContext (or its aliases localcontext, Local, local):

remote_profile:
type: dict, optional
argument path: init_bulk_mdata/fp/machine[LocalContext]/remote_profile

The information used to maintain the connection with remote machine. This field is empty for this context.

When context_type is set to LebesgueContext (or its aliases lebesguecontext, Lebesgue, lebesgue):

remote_profile:
type: dict
argument path: init_bulk_mdata/fp/machine[LebesgueContext]/remote_profile

The information used to maintain the connection with remote machine.

email:
type: str
argument path: init_bulk_mdata/fp/machine[LebesgueContext]/remote_profile/email

Email

password:
type: str
argument path: init_bulk_mdata/fp/machine[LebesgueContext]/remote_profile/password

Password

program_id:
type: int, alias: project_id
argument path: init_bulk_mdata/fp/machine[LebesgueContext]/remote_profile/program_id

Program ID

keep_backup:
type: bool, optional
argument path: init_bulk_mdata/fp/machine[LebesgueContext]/remote_profile/keep_backup

keep download and upload zip

input_data:
type: dict
argument path: init_bulk_mdata/fp/machine[LebesgueContext]/remote_profile/input_data

Configuration of job

When context_type is set to HDFSContext (or its aliases hdfscontext, HDFS, hdfs):

remote_profile:
type: dict, optional
argument path: init_bulk_mdata/fp/machine[HDFSContext]/remote_profile

The information used to maintain the connection with remote machine. This field is empty for this context.

When context_type is set to DpCloudServerContext (or its aliases dpcloudservercontext, DpCloudServer, dpcloudserver):

remote_profile:
type: dict
argument path: init_bulk_mdata/fp/machine[DpCloudServerContext]/remote_profile

The information used to maintain the connection with remote machine.

email:
type: str
argument path: init_bulk_mdata/fp/machine[DpCloudServerContext]/remote_profile/email

Email

password:
type: str
argument path: init_bulk_mdata/fp/machine[DpCloudServerContext]/remote_profile/password

Password

program_id:
type: int, alias: project_id
argument path: init_bulk_mdata/fp/machine[DpCloudServerContext]/remote_profile/program_id

Program ID

keep_backup:
type: bool, optional
argument path: init_bulk_mdata/fp/machine[DpCloudServerContext]/remote_profile/keep_backup

keep download and upload zip

input_data:
type: dict
argument path: init_bulk_mdata/fp/machine[DpCloudServerContext]/remote_profile/input_data

Configuration of job

When context_type is set to LazyLocalContext (or its aliases lazylocalcontext, LazyLocal, lazylocal):

remote_profile:
type: dict, optional
argument path: init_bulk_mdata/fp/machine[LazyLocalContext]/remote_profile

The information used to maintain the connection with remote machine. This field is empty for this context.

When context_type is set to SSHContext (or its aliases sshcontext, SSH, ssh):

remote_profile:
type: dict
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile

The information used to maintain the connection with remote machine.

hostname:
type: str
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile/hostname

hostname or ip of ssh connection.

username:
type: str
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile/username

username of target linux system

password:
type: str, optional
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile/password

(deprecated) password of linux system. Please use SSH keys instead to improve security.

port:
type: int, optional, default: 22
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile/port

ssh connection port.

key_filename:
type: NoneType | str, optional, default: None
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile/key_filename

key filename used by ssh connection. If left None, find key in ~/.ssh or use password for login

passphrase:
type: NoneType | str, optional, default: None
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile/passphrase

passphrase of key used by ssh connection

timeout:
type: int, optional, default: 10
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile/timeout

timeout of ssh connection

totp_secret:
type: NoneType | str, optional, default: None
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile/totp_secret

Time-based one time password secret. It should be a base32-encoded string extracted from the 2D code.

tar_compress:
type: bool, optional, default: True
argument path: init_bulk_mdata/fp/machine[SSHContext]/remote_profile/tar_compress

The archive will be compressed in upload and download if it is True. If not, compression will be skipped.

resources:
type: dict
argument path: init_bulk_mdata/fp/resources
number_node:
type: int, optional, default: 1
argument path: init_bulk_mdata/fp/resources/number_node

The number of node need for each job

cpu_per_node:
type: int, optional, default: 1
argument path: init_bulk_mdata/fp/resources/cpu_per_node

cpu numbers of each node assigned to each job.

gpu_per_node:
type: int, optional, default: 0
argument path: init_bulk_mdata/fp/resources/gpu_per_node

gpu numbers of each node assigned to each job.

queue_name:
type: str, optional, default: ````
argument path: init_bulk_mdata/fp/resources/queue_name

The queue name of batch job scheduler system.

group_size:
type: int
argument path: init_bulk_mdata/fp/resources/group_size

The number of tasks in a job. 0 means infinity.

custom_flags:
type: list, optional
argument path: init_bulk_mdata/fp/resources/custom_flags

The extra lines pass to job submitting script header

strategy:
type: dict, optional
argument path: init_bulk_mdata/fp/resources/strategy

strategies we use to generation job submitting scripts.

if_cuda_multi_devices:
type: bool, optional, default: False
argument path: init_bulk_mdata/fp/resources/strategy/if_cuda_multi_devices

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.

ratio_unfinished:
type: float, optional, default: 0.0
argument path: init_bulk_mdata/fp/resources/strategy/ratio_unfinished

The ratio of jobs that can be unfinished.

para_deg:
type: int, optional, default: 1
argument path: init_bulk_mdata/fp/resources/para_deg

Decide how many tasks will be run in parallel.

source_list:
type: list, optional, default: []
argument path: init_bulk_mdata/fp/resources/source_list

The env file to be sourced before the command execution.

module_purge:
type: bool, optional, default: False
argument path: init_bulk_mdata/fp/resources/module_purge

Remove all modules on HPC system before module load (module_list)

module_unload_list:
type: list, optional, default: []
argument path: init_bulk_mdata/fp/resources/module_unload_list

The modules to be unloaded on HPC system before submitting jobs

module_list:
type: list, optional, default: []
argument path: init_bulk_mdata/fp/resources/module_list

The modules to be loaded on HPC system before submitting jobs

envs:
type: dict, optional, default: {}
argument path: init_bulk_mdata/fp/resources/envs

The environment variables to be exported on before submitting jobs

wait_time:
type: int | float, optional, default: 0
argument path: init_bulk_mdata/fp/resources/wait_time

The waitting time in second after a single task submitted

Depending on the value of batch_type, different sub args are accepted.

batch_type:
type: str (flag key)
argument path: init_bulk_mdata/fp/resources/batch_type
possible choices: LSF, DpCloudServer, DistributedShell, Slurm, PBS, Shell, Lebesgue, Torque, SlurmJobArray

The batch job system type loaded from machine/batch_type.

When batch_type is set to LSF (or its alias lsf):

kwargs:
type: dict
argument path: init_bulk_mdata/fp/resources[LSF]/kwargs

Extra arguments.

gpu_usage:
type: bool, optional, default: False
argument path: init_bulk_mdata/fp/resources[LSF]/kwargs/gpu_usage

Choosing if GPU is used in the calculation step.

gpu_new_syntax:
type: bool, optional, default: False
argument path: init_bulk_mdata/fp/resources[LSF]/kwargs/gpu_new_syntax

For LFS >= 10.1.0.3, new option -gpu for #BSUB could be used. If False, and old syntax would be used.

gpu_exclusive:
type: bool, optional, default: True
argument path: init_bulk_mdata/fp/resources[LSF]/kwargs/gpu_exclusive

Only take effect when new syntax enabled. Control whether submit tasks in exclusive way for GPU.

custom_gpu_line:
type: NoneType | str, optional, default: None
argument path: init_bulk_mdata/fp/resources[LSF]/kwargs/custom_gpu_line

Custom GPU configuration, starting with #BSUB

When batch_type is set to DpCloudServer (or its alias dpcloudserver):

kwargs:
type: dict, optional
argument path: init_bulk_mdata/fp/resources[DpCloudServer]/kwargs

This field is empty for this batch.

When batch_type is set to DistributedShell (or its alias distributedshell):

kwargs:
type: dict, optional
argument path: init_bulk_mdata/fp/resources[DistributedShell]/kwargs

This field is empty for this batch.

When batch_type is set to Slurm (or its alias slurm):

kwargs:
type: dict, optional
argument path: init_bulk_mdata/fp/resources[Slurm]/kwargs

Extra arguments.

custom_gpu_line:
type: NoneType | str, optional, default: None
argument path: init_bulk_mdata/fp/resources[Slurm]/kwargs/custom_gpu_line

Custom GPU configuration, starting with #SBATCH

When batch_type is set to PBS (or its alias pbs):

kwargs:
type: dict, optional
argument path: init_bulk_mdata/fp/resources[PBS]/kwargs

This field is empty for this batch.

When batch_type is set to Shell (or its alias shell):

kwargs:
type: dict, optional
argument path: init_bulk_mdata/fp/resources[Shell]/kwargs

This field is empty for this batch.

When batch_type is set to Lebesgue (or its alias lebesgue):

kwargs:
type: dict, optional
argument path: init_bulk_mdata/fp/resources[Lebesgue]/kwargs

This field is empty for this batch.

When batch_type is set to Torque (or its alias torque):

kwargs:
type: dict, optional
argument path: init_bulk_mdata/fp/resources[Torque]/kwargs

This field is empty for this batch.

When batch_type is set to SlurmJobArray (or its alias slurmjobarray):

kwargs:
type: dict, optional
argument path: init_bulk_mdata/fp/resources[SlurmJobArray]/kwargs

Extra arguments.

custom_gpu_line:
type: NoneType | str, optional, default: None
argument path: init_bulk_mdata/fp/resources[SlurmJobArray]/kwargs/custom_gpu_line

Custom GPU configuration, starting with #SBATCH

user_forward_files:
type: list, optional
argument path: init_bulk_mdata/fp/user_forward_files

Files to be forwarded to the remote machine.

user_backward_files:
type: list, optional
argument path: init_bulk_mdata/fp/user_backward_files

Files to be backwarded from the remote machine.