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Merge pull request #61 from Cloudac7/lsf
Update LSF module to keep consistent with DPDispatcher
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,80 +1,49 @@ | ||
| import os | ||
| import sys | ||
| import json | ||
| from dpdispatcher.submission import Submission, Job, Task, Resources | ||
| from dpdispatcher.machine import Machine | ||
|
|
||
| sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) | ||
|
|
||
| from dpdispatcher.ssh_context import SSHSession, SSHContext | ||
| from dpdispatcher.submission import Submission, Task, Resources | ||
| from dpdispatcher.lsf import LSF | ||
|
|
||
| # edit ssh parameters | ||
| ssh_session = SSHSession( | ||
| hostname='127.0.0.1', | ||
| port=22, | ||
| remote_root='/home/dp/dpdispatcher/tests', | ||
| username='debug' | ||
| ) | ||
| # local_root is the relevant path that containing tasks to be submit | ||
| ssh_context = SSHContext(local_root='test_lsf_dir', ssh_session=ssh_session) | ||
| lsf = LSF(context=ssh_context) | ||
|
|
||
| prepend_text = ''' | ||
| module load cuda/9.2 | ||
| module load gcc/4.9.4 | ||
| module load deepmd/1.0 | ||
| source /home/dp/scripts/avail_gpu.sh | ||
| ''' | ||
| # task_need_resources has no effect | ||
| with open("jsons/machine_lsf.json", 'r') as f: | ||
| mdata = json.load(f) | ||
|
|
||
| lsf_bsub_dict = { | ||
| 'R': "'select[hname != g005]'" | ||
| } | ||
| resources = Resources( | ||
| number_node=1, | ||
| cpu_per_node=4, | ||
| gpu_per_node=0, | ||
| queue_name="gpu", | ||
| walltime="24:00:00", | ||
| prepend_text=prepend_text, | ||
| append_text="", | ||
| gpu_usage=False, | ||
| gpu_new_syntax=False, | ||
| extra_specification=lsf_bsub_dict, | ||
| group_size=1 | ||
| ) | ||
| machine = Machine.load_from_dict(mdata['machine']) | ||
| resources = Resources.load_from_dict(mdata['resources']) | ||
|
|
||
| # task_need_resources has no effect | ||
| submission = Submission( | ||
| work_base='0_md', # the dir containing all of task_work_path | ||
| resources=resources, # resources above | ||
| forward_common_files=['graph.pb'], # file to be upload | ||
| backward_common_files=['*.json'] # file to be downloaded | ||
| work_base='0_md/', | ||
| machine=machine, | ||
| resources=resources, | ||
| forward_common_files=['graph.pb'], | ||
| backward_common_files=[] | ||
| ) | ||
|
|
||
| task1 = Task( | ||
| command='lmp_mpi_20201029 -i input.lammps', | ||
| task_work_path='bct-1', | ||
| command='lmp -i input.lammps', | ||
| task_work_path='bct-1/', | ||
| forward_files=['conf.lmp', 'input.lammps'], | ||
| backward_files=['log.lammps'], | ||
| backward_files=['log.lammps'] | ||
| ) | ||
| task2 = Task( | ||
| command='lmp_mpi_20201029 -i input.lammps', | ||
| task_work_path='bct-2', | ||
| command='lmp -i input.lammps', | ||
| task_work_path='bct-2/', | ||
| forward_files=['conf.lmp', 'input.lammps'], | ||
| backward_files=['log.lammps'], | ||
| backward_files=['log.lammps'] | ||
| ) | ||
| task3 = Task( | ||
| command='lmp_mpi_20201029 -i input.lammps', | ||
| task_work_path='bct-3', | ||
| command='lmp -i input.lammps', | ||
| task_work_path='bct-3/', | ||
| forward_files=['conf.lmp', 'input.lammps'], | ||
| backward_files=['log.lammps'], | ||
| backward_files=['log.lammps'] | ||
| ) | ||
| task4 = Task( | ||
| command='lmp_mpi_20201029 -i input.lammps', | ||
| task_work_path='bct-4', | ||
| command='lmp -i input.lammps', | ||
| task_work_path='bct-4/', | ||
| forward_files=['conf.lmp', 'input.lammps'], | ||
| backward_files=['log.lammps'], | ||
| backward_files=['log.lammps'] | ||
| ) | ||
| submission.register_task_list([task1, task2, task3, task4, ]) | ||
| submission.generate_jobs() | ||
| submission.bind_batch(batch=lsf) | ||
|
|
||
| submission.run_submission() | ||
| submission.run_submission(clean=True) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| { | ||
| "machine":{ | ||
| "batch_type": "LSF", | ||
| "context_type": "SSHContext", | ||
| "local_root": "./test_lsf_dir", | ||
| "remote_root": "/data/home/ypliu/dptasks", | ||
| "remote_profile": { | ||
| "hostname": "123.45.78.99", | ||
| "port": 56789, | ||
| "username": "ypliu" | ||
| } | ||
| }, | ||
| "resources":{ | ||
| "number_node": 1, | ||
| "cpu_per_node": 4, | ||
| "gpu_per_node": 1, | ||
| "queue_name": "gpu", | ||
| "group_size": 4, | ||
| "custom_flags": [ | ||
| "#BSUB -R \"select[hname != g005]\"", | ||
| "#BSUB -W 24:00" | ||
| ], | ||
| "strategy": { | ||
| "if_cuda_multi_devices": false | ||
| }, | ||
| "para_deg": 1, | ||
| "module_unload_list": [], | ||
| "module_list": [ | ||
| "use.own", | ||
| "deepmd/1.3" | ||
| ], | ||
| "source_list": [ | ||
| "/data/home/ypliu/scripts/avail_gpu.sh", | ||
| "/data/home/ypliu/dprun/tf_envs.sh" | ||
| ], | ||
| "envs": {"DP_DISPATCHER_EXPORT": "test_foo_bar_baz"}, | ||
| "kwargs": { | ||
| "gpu_usage": false, | ||
| "gpu_new_syntax": false | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| ../../graph.pb |