def __init__(self,
tok_func: Callable = BaseProteinTokenizer,
lang: str = 'prot',
n_cpus: int = None):
self.tok_func = tok_func
self.lang = lang
self.n_cpus = n_cpus or num_cpus() // 2
def test_num_cpus_without_sched_getaffinity(os_mock):
os_mock.sched_getaffinity = Mock(side_effect=AttributeError)
os_mock.cpu_count = Mock(return_value=3)
assert core.num_cpus() == 3
def test_num_cpus_with_sched_getaffinity(os_mock):
os_mock.sched_getaffinity = Mock(return_value=["foo", "bar"])
assert core.num_cpus() == 2
def main(gpu: Param("GPU to run on", str)=None,
max_cpu_per_dataloader: Param("Max CPU", int, opt=True)=8,
bs: Param("batch size", int)=256,
fp16: Param("mixed precision", int, opt=True)=0,
use_sp_processor: Param("use sentence piece as processor", int) = 0,
sp_model: Param("sentence piece trained model file", str)=None,
sp_vocab: Param("sentence piece trained model file", str)=None,
):
datetime_str = f'{datetime.now():%Y-%m-%d_%H-%M-%S%z}'
random_seed = 0
max_vocab = 30000
print('max_cpu_per_dataloader', max_cpu_per_dataloader, 'bs', bs,
'fp16', fp16, 'sp_processor', use_sp_processor, 'sp_model', sp_model, 'sp_vocab', sp_vocab)
"""## Prepare Dataset"""
local_project_path = './data/sprot_lm/'
#### Distributed
print('gpu', gpu)
gpu = setup_distrib(gpu)
n_gpus = num_distrib()
if n_gpus > 0:
workers = min(max_cpu_per_dataloader, num_cpus()//n_gpus)
else:
workers = min(max_cpu_per_dataloader, num_cpus())
print(gpu, 'n_gpus', n_gpus)
print(gpu, 'workers', workers)
"""## Prepare fastai"""
np.random.seed(random_seed)
if not os.path.exists(local_project_path):
os.makedirs(local_project_path)
print('local_project_path:', local_project_path)
"""## Tokenization"""
tokenizer = Tokenizer(tok_func=dna_tokenizer, pre_rules=[],
post_rules=[], special_cases=[])
processor = [TokenizeProcessor(tokenizer=tokenizer, include_bos=True,
include_eos=True), NumericalizeProcessor(max_vocab=max_vocab)]
df = pickle.load(
open('./data/sprot_lm/sprot_sequence_taxon_anc.pickle', 'rb'))
if use_sp_processor: # './data/sprot_lm/tmp/spm.model', './data/sprot_lm/tmp/spm.vocab'
processor = [OpenFileProcessor(), SPProcessor(sp_model=sp_model, sp_vocab=sp_vocab, max_sentence_len=35826, max_vocab_sz=max_vocab)]
data_lm = (TextList.from_df(df, path=local_project_path, cols='seq_anc_tax', processor=processor)
.split_by_rand_pct(0.1, seed = random_seed)
.label_for_lm()
.databunch(bs=bs, num_workers=workers))
data_lm.vocab.save(local_project_path +
'vocab_lm_sprot_seq_anc_tax-' + datetime_str + '.pickle')
print('data_cls Training set size', len(data_lm.train_ds))
print('data_cls Validation set size', len(data_lm.valid_ds))
print('vocab size ', len(data_lm.vocab.itos))
learn_lm = language_model_learner(
data_lm, AWD_LSTM, drop_mult=0.1, pretrained=False)
if gpu is None:
print(gpu, 'DataParallel')
learn_lm.model = nn.DataParallel(learn_lm.model)
else:
print(gpu, 'to_distributed')
learn_lm.to_distributed(gpu)
if fp16:
learn_lm.to_fp16()
lr = 3e-3
print(gpu, 'freeze')
learn_lm.freeze()
learn_lm.fit_one_cycle(1, lr, moms=(0.8, 0.7)) # I don't know why multigpu doesn't work without first freezing
print(gpu, 'unfreeze')
learn_lm.unfreeze()
learn_lm.fit_one_cycle(10, lr*10, moms=(0.8, 0.7))
learn_lm.save('lm-sp-anc-v1-1-' + datetime_str)
learn_lm.save_encoder('lm-sp-ans-v1-1-enc-' + datetime_str)
learn_lm.fit_one_cycle(10, lr, moms=(0.8, 0.7))
learn_lm.save('lm-sp-anc-v1-2-' + datetime_str)
learn_lm.save_encoder('lm-sp-ans-v1-2-enc-' + datetime_str)
learn_lm.fit_one_cycle(10, lr/10, moms=(0.8, 0.7))
learn_lm.save('lm-sp-anc-v1-3' + datetime_str)
learn_lm.save_encoder('lm-sp-ans-v1-3-enc-' + datetime_str)
learn_lm.export(file = 'export-lm-sp-ans-v1-3' + datetime_str+ '.pkl')
print('Done')
def test_num_cpus_without_sched_getaffinity(os_mock): os_mock.sched_getaffinity = Mock(side_effect=AttributeError) os_mock.cpu_count = Mock(return_value=3) assert core.num_cpus() == 3
def test_num_cpus_with_sched_getaffinity(os_mock): os_mock.sched_getaffinity = Mock(return_value=["foo", "bar"]) assert core.num_cpus() == 2