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upgrade all tasks to dpdispatcher #749

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merged 4 commits into from
Jun 9, 2022
Merged

upgrade all tasks to dpdispatcher #749

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53f65c6
upgrade all tasks to dpdispatcher
njzjz Jun 8, 2022
204de44
fix method args
njzjz Jun 8, 2022
e644b0e
fix typo
njzjz Jun 8, 2022
a7385c3
change the variable name from `work_dir` to `work_path`
njzjz Jun 8, 2022
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38 changes: 21 additions & 17 deletions dpgen/data/reaction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,16 @@
output: data
"""

import argparse
import warnings
import glob
import json
import os
import random

import dpdata
from dpgen import dlog
from dpgen.dispatcher.Dispatcher import make_dispatcher
from dpgen.dispatcher.Dispatcher import make_submission_compat
from dpgen.remote.decide_machine import convert_mdata
from dpgen.generator.run import create_path, make_fp_task_name
from dpgen.util import sepline

Expand Down Expand Up @@ -73,14 +74,15 @@ def make_lmp(jdata):
return lmp_string


def run_reaxff(jdata, mdata, dispatcher, log_file="reaxff_log"):
def run_reaxff(jdata, mdata, log_file="reaxff_log"):
work_path = reaxff_path
reaxff_command = "{} -in {}".format(mdata["reaxff_command"], lmp_path)
run_tasks = glob.glob(os.path.join(work_path, 'task.*'))
run_tasks.sort()
run_tasks = [os.path.basename(ii) for ii in run_tasks]

dispatcher.run_jobs(mdata['reaxff_resources'],
make_submission_compat(mdata['reaxff_machine'],
mdata['reaxff_resources'],
[reaxff_command],
work_path,
run_tasks,
Expand All @@ -89,7 +91,8 @@ def run_reaxff(jdata, mdata, dispatcher, log_file="reaxff_log"):
[ff_path, data_init_path, control_path, lmp_path],
[trj_path],
outlog=log_file,
errlog=log_file)
errlog=log_file,
api_version=mdata.get("api_version", "0.9"))


def link_trj(jdata):
Expand All @@ -102,7 +105,7 @@ def link_trj(jdata):
os.path.join(task_path, trj_path)))


def run_build_dataset(jdata, mdata, dispatcher, log_file="build_log"):
def run_build_dataset(jdata, mdata, log_file="build_log"):
work_path = build_path
build_command = "{cmd} -n {dataset_name} -a {type_map} -d {lammpstrj} -c {cutoff} -s {dataset_size} -k \"{qmkeywords}\" --nprocjob {nprocjob} --nproc {nproc}".format(
cmd=mdata["build_command"],
Expand All @@ -119,7 +122,8 @@ def run_build_dataset(jdata, mdata, dispatcher, log_file="build_log"):
run_tasks.sort()
run_tasks = [os.path.basename(ii) for ii in run_tasks]

dispatcher.run_jobs(mdata['build_resources'],
make_submission_compat(mdata['build_machine'],
mdata['build_resources'],
[build_command],
work_path,
run_tasks,
Expand All @@ -128,7 +132,8 @@ def run_build_dataset(jdata, mdata, dispatcher, log_file="build_log"):
[trj_path],
[f"dataset_{dataset_name}_gjf"],
outlog=log_file,
errlog=log_file)
errlog=log_file,
api_version=mdata.get("api_version", "0.9"))


def link_fp_input():
Expand All @@ -146,7 +151,6 @@ def link_fp_input():

def run_fp(jdata,
mdata,
dispatcher,
log_file="output",
forward_common_files=[]):
fp_command = mdata['fp_command']
Expand All @@ -162,7 +166,8 @@ def run_fp(jdata,

run_tasks = [os.path.basename(ii) for ii in fp_run_tasks]

dispatcher.run_jobs(mdata['fp_resources'],
make_submission_compat(mdata['fp_machine'],
mdata['fp_resources'],
[fp_command],
work_path,
run_tasks,
Expand All @@ -171,7 +176,8 @@ def run_fp(jdata,
["input"],
[log_file],
outlog=log_file,
errlog=log_file)
errlog=log_file,
api_version=mdata.get("api_version", "0.9"))


def convert_data(jdata):
Expand All @@ -198,6 +204,7 @@ def gen_init_reaction(args):
with open(args.MACHINE, "r") as fp:
mdata = json.load(fp)

mdata = convert_mdata(mdata, ["reaxff", "build", "fp"])
record = "record.reaction"
iter_rec = -1
numb_task = 7
Expand All @@ -213,18 +220,15 @@ def gen_init_reaction(args):
elif ii == 0:
link_reaxff(jdata)
elif ii == 1:
dispatcher = make_dispatcher(mdata["reaxff_machine"])
run_reaxff(jdata, mdata, dispatcher)
run_reaxff(jdata, mdata)
elif ii == 2:
link_trj(jdata)
elif ii == 3:
dispatcher = make_dispatcher(mdata["build_machine"])
run_build_dataset(jdata, mdata, dispatcher)
run_build_dataset(jdata, mdata)
elif ii == 4:
link_fp_input()
elif ii == 5:
dispatcher = make_dispatcher(mdata["fp_machine"])
run_fp(jdata, mdata, dispatcher)
run_fp(jdata, mdata)
elif ii == 6:
convert_data(jdata)
with open(record, "a") as frec:
Expand Down
11 changes: 6 additions & 5 deletions dpgen/data/surf.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python3

import time
import warnings
import os,json,shutil,re,glob,argparse
import numpy as np
import subprocess as sp
Expand All @@ -12,7 +12,7 @@
from dpgen import dlog
from dpgen import ROOT_PATH
from dpgen.remote.decide_machine import convert_mdata
from dpgen.dispatcher.Dispatcher import Dispatcher, make_dispatcher
from dpgen.dispatcher.Dispatcher import make_submission_compat
#-----PMG---------
from pymatgen.io.vasp import Poscar
from pymatgen.core import Structure, Element
Expand Down Expand Up @@ -565,15 +565,16 @@ def run_vasp_relax(jdata, mdata):
run_tasks = [ii.replace(work_dir+"/", "") for ii in relax_run_tasks]

#dlog.info(run_tasks)
dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size)
dispatcher.run_jobs(fp_resources,
make_submission_compat(mdata['fp_machine'],
fp_resources,
[fp_command],
work_dir,
run_tasks,
fp_group_size,
forward_common_files,
forward_files,
backward_files)
backward_files,
api_version=mdata.get("api_version", "0.9"))

def gen_init_surf(args):
try:
Expand Down
79 changes: 79 additions & 0 deletions dpgen/dispatcher/Dispatcher.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from distutils.version import LooseVersion
import os,sys,time,random,json,glob
import warnings
from typing import List
from dpdispatcher import Task, Submission, Resources, Machine
from dpgen.dispatcher.LocalContext import LocalSession
Expand Down Expand Up @@ -406,3 +407,81 @@ def mdata_arginfo() -> List[Argument]:
return [
command_arginfo, machine_arginfo, resources_arginfo,
]


def make_submission_compat(
machine: dict,
resources: dict,
commands: List[str],
work_path: str,
run_tasks: List[str],
group_size: int,
forward_common_files: List[str],
forward_files: List[str],
backward_files: List[str],
outlog: str="log",
errlog: str="err",
api_version: str="0.9",
) -> None:
"""Make submission with compatibility of both dispatcher API v0 and v1.
If `api_version` is less than 1.0, use `make_dispatcher`. If
`api_version` is large than 1.0, use `make_submission`.
Parameters
----------
machine : dict
machine dict
resources : dict
resource dict
commands : list[str]
list of commands
work_path : str
working directory
run_tasks : list[str]
list of paths to running tasks
group_size : int
group size
forward_common_files : list[str]
forwarded common files shared for all tasks
forward_files : list[str]
forwarded files for each task
backward_files : list[str]
backwarded files for each task
outlog : str, default=log
path to log from stdout
errlog : str, default=err
path to log from stderr
api_version : str, default=0.9
API version. 1.0 is recommended
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Do you think that we should upgrade the default to 1.0 ?

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Upgrading to 1.0 is a breaking change, so we should do it only before the release of DP-GEN 1.0.0.

"""
if LooseVersion(api_version) < LooseVersion('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
dispatcher = make_dispatcher(machine, resources, work_dir, run_tasks, group_size)
dispatcher.run_jobs(resources,
commands,
work_path,
run_tasks,
group_size,
forward_common_files,
forward_files,
backward_files,
outlog=outlog,
errlog=errlog)

elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
machine,
resources,
commands=commands,
work_path=work_path,
run_tasks=run_tasks,
group_size=group_size,
forward_common_files=forward_common_files,
forward_files=forward_files,
backward_files=backward_files,
outlog=outlog,
errlog=errlog)
submission.run_submission()