Keisuke-kamata's workspace
Runs
14
Name
14 visualized
State
Notes
User
Tags
Created
Runtime
Sweep
cfg
do_testing
do_training
exp_manager.checkpoint_callback_params.always_save_nemo
exp_manager.checkpoint_callback_params.filename
exp_manager.checkpoint_callback_params.mode
exp_manager.checkpoint_callback_params.model_parallel_size
exp_manager.checkpoint_callback_params.monitor
exp_manager.checkpoint_callback_params.save_top_k
exp_manager.create_checkpoint_callback
exp_manager.create_tensorboard_logger
exp_manager.create_wandb_logger
exp_manager.exp_dir
exp_manager.explicit_log_dir
exp_manager.name
exp_manager.resume_if_exists
exp_manager.resume_ignore_no_checkpoint
exp_manager.wandb_logger_kwargs.group
exp_manager.wandb_logger_kwargs.job_type
exp_manager.wandb_logger_kwargs.log_model
exp_manager.wandb_logger_kwargs.name
exp_manager.wandb_logger_kwargs.offline
exp_manager.wandb_logger_kwargs.project
exp_manager.wandb_logger_kwargs.tags
model.activations_checkpoint_num_layers
model.apply_query_key_layer_scaling
model.attention_dropout
model.bert_binary_head
model.bias_gelu_fusion
model.data.cluster_mapping_tsv
model.data.data_prefix
model.data.dataloader_type
model.data.dataset_path
model.data.drop_last
model.data.dynamic_padding
model.data.eod_mask_loss
model.data.force_regen_sample_mapping
model.data.index_mapping_dir
model.data.masked_lm_prob
model.data.modify_percent
model.data.ngc_registry_target
model.data.ngc_registry_version
model.data.num_workers
Finished
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keisuke-kamata
4s
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Finished
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keisuke-kamata
esm2-650M
32m 34s
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{'drop_last': True, 'micro_batch_size': 8, 'seq_length': 1024, 'num_layers': 33, 'hidden_size': 1280, 'ffn_hidden_size': '${multiply:${model.hidden_size}, 4}', 'num_attention_heads': 20, 'megatron_legacy': False, 'position_embedding_type': 'rope', 'hidden_dropout': 0, 'embedding_use_attention_mask': True, 'embedding_token_dropout': True, 'mask_token_id': '${.tokenizer.mask_id}', 'attention_dropout': 0.0, 'normalize_attention_scores': False, 'tensor_model_parallel_size': 1, 'pipeline_model_parallel_size': 1, 'bias_gelu_fusion': False, 'use_esm_attention': True, 'esm_gelu': True, 'use_pt_layernorm': False, 'use_pt_mlp_out': False, 'max_position_embeddings': '${.seq_length}', 'encoder_seq_length': '${.seq_length}', 'optim': {'name': 'fused_adam', 'lr': 0.0004, 'weight_decay': 0.01, 'betas': [0.9, 0.98], 'sched': {'name': 'WarmupAnnealDecayHold', 'warmup_steps': 2000, 'min_lr': 4e-05, 'max_lr': 0.0004, 'max_steps': 500000, 'anneal_percentage': 0.1}}, 'init_method_std': 0.02, 'kv_channels': None, 'apply_query_key_layer_scaling': True, 'layernorm_epsilon': 1e-05, 'make_vocab_size_divisible_by': 128, 'pre_process': True, 'post_process': True, 'bert_binary_head': False, 'resume_from_checkpoint': None, 'masked_softmax_fusion': True, 'tokenizer': {'library': 'huggingface', 'type': 'BertWordPieceLowerCase', 'model_name': 'facebook/esm2_t33_650M_UR50D', 'mask_id': 32, 'model': None, 'vocab_file': None, 'merge_file': None}, 'native_amp_init_scale': 4294967296, 'native_amp_growth_interval': 1000, 'fp32_residual_connection': False, 'fp16_lm_cross_entropy': False, 'seed': 1234, 'use_cpu_initialization': False, 'onnx_safe': False, 'activations_checkpoint_method': None, 'activations_checkpoint_num_layers': 1, 'data': {'ngc_registry_target': 'uniref50_2022_05', 'ngc_registry_version': 'v23.06', 'data_prefix': '', 'num_workers': 8, 'dataloader_type': 'single', 'reset_position_ids': False, 'reset_attention_mask': False, 'eod_mask_loss': False, 'masked_lm_prob': 0.15, 'short_seq_prob': 0.1, 'skip_lines': 0, 'drop_last': False, 'pin_memory': False, 'dynamic_padding': False, 'force_regen_sample_mapping': False, 'dataset_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/', 'index_mapping_dir': '${model.data.dataset_path}', 'preprocessing': {'num_preprocess_workers': 16}, 'train': {'custom_pretraining_fasta_path': None, 'data_impl': 'csv_mmap', 'data_impl_kwargs': {'csv_mmap': {'data_col': 1, 'header_lines': 1}}, 'use_upsampling': True, 'range': 'x[000..049]', 'sample_from_map': True, 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'uf90_datapath': '${model.data.dataset_path}/uniref90membersandreps_ur50trainfiltreps.fasta', 'cluster_mapping_tsv': '${model.data.dataset_path}/uniref50_mapper_to_uniref90clustermembers_andselfuniref50.tsv', 'dataset_path': '${model.data.dataset_path}/uf50', 'sort_fastas': True, 'num_workers': '${model.data.num_workers}', 'uf90': {'uniref90_path': '${model.data.dataset_path}/uf90', 'dataset': {'uf90_csvs': 'x[000..049]'}, 'data_impl': 'csv_fields_mmap', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.train.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}'}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'val': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.val.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'test': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.test.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'modify_percent': 0.1, 'perturb_percent': 0.5, 'uf90': {'uniref90_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/uf90'}}, 'dwnstr_task_validation': {'enabled': False, 'dataset': {'class': 'bionemo.model.core.dwnstr_task_callbacks.PerTokenPredictionCallback', 'task_type': 'token-level-classification', 'infer_target': 'bionemo.model.protein.esm1nv.infer.ESM1nvInference', 'max_seq_length': '${model.seq_length}', 'emb_batch_size': 128, 'batch_size': 128, 'num_epochs': 10, 'shuffle': True, 'num_workers': 8, 'task_name': 'secondary_structure', 'dataset_path': '${oc.env:BIONEMO_HOME}/data/FLIP/${model.dwnstr_task_validation.dataset.task_name}', 'dataset': {'train': 'x000', 'test': 'x000'}, 'sequence_column': 'sequence', 'target_column': ['3state'], 'target_sizes': [3], 'mask_column': ['resolved'], 'random_seed': 1234, 'optim': {'name': 'adam', 'lr': 0.0001, 'betas': [0.9, 0.999], 'eps': 1e-08, 'weight_decay': 0.01, 'sched': {'name': 'WarmupAnnealing', 'min_lr': 1e-05, 'last_epoch': -1, 'warmup_ratio': 0.01, 'max_steps': 1000}}}}, 'global_batch_size': 8, 'precision': 32}
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Finished
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keisuke-kamata
esm2-650M
37m 5s
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keisuke-kamata
esm2-650M
44m
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Finished
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keisuke-kamata
esm2-650M
47m
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Finished
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keisuke-kamata
13s
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false
false
false
megatron_bert--{val_loss:.2f}-{step}-{consumed_samples}
min
${multiply:${model.tensor_model_parallel_size}, ${model.pipeline_model_parallel_size}}
val_loss
10
true
false
true
${oc.env:BIONEMO_HOME}/results/nemo_experiments/${.name}/${.wandb_logger_kwargs.name}
${.exp_dir}
${name}
true
true
${name}
data_upload
all
preproceed_data_upload
false
${oc.env:WANDB_PROJECT}
["${name}"]
1
true
0
false
false
/mapping.tsv
single
/workspace/bionemo/examples/tests/test_data/uniref202104_esm2_qc_test200_val200/uf50
false
false
false
false
${model.data.dataset_path}
0.15
0.1
uniref50_2022_05
v23.06
8
Finished
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keisuke-kamata
6s
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Finished
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keisuke-kamata
esm2-650M
2h 15m 27s
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{'drop_last': True, 'micro_batch_size': 8, 'seq_length': 1024, 'num_layers': 33, 'hidden_size': 1280, 'ffn_hidden_size': '${multiply:${model.hidden_size}, 4}', 'num_attention_heads': 20, 'megatron_legacy': False, 'position_embedding_type': 'rope', 'hidden_dropout': 0, 'embedding_use_attention_mask': True, 'embedding_token_dropout': True, 'mask_token_id': '${.tokenizer.mask_id}', 'attention_dropout': 0.0, 'normalize_attention_scores': False, 'tensor_model_parallel_size': 1, 'pipeline_model_parallel_size': 1, 'bias_gelu_fusion': False, 'use_esm_attention': True, 'esm_gelu': True, 'use_pt_layernorm': False, 'use_pt_mlp_out': False, 'max_position_embeddings': '${.seq_length}', 'encoder_seq_length': '${.seq_length}', 'optim': {'name': 'fused_adam', 'lr': 0.0004, 'weight_decay': 0.01, 'betas': [0.9, 0.98], 'sched': {'name': 'WarmupAnnealDecayHold', 'warmup_steps': 2000, 'min_lr': 4e-05, 'max_lr': 0.0004, 'max_steps': 500000, 'anneal_percentage': 0.1}}, 'init_method_std': 0.02, 'kv_channels': None, 'apply_query_key_layer_scaling': True, 'layernorm_epsilon': 1e-05, 'make_vocab_size_divisible_by': 128, 'pre_process': True, 'post_process': True, 'bert_binary_head': False, 'resume_from_checkpoint': None, 'masked_softmax_fusion': True, 'tokenizer': {'library': 'huggingface', 'type': 'BertWordPieceLowerCase', 'model_name': 'facebook/esm2_t33_650M_UR50D', 'mask_id': 32, 'model': None, 'vocab_file': None, 'merge_file': None}, 'native_amp_init_scale': 4294967296, 'native_amp_growth_interval': 1000, 'fp32_residual_connection': False, 'fp16_lm_cross_entropy': False, 'seed': 1234, 'use_cpu_initialization': False, 'onnx_safe': False, 'activations_checkpoint_method': None, 'activations_checkpoint_num_layers': 1, 'data': {'ngc_registry_target': 'uniref50_2022_05', 'ngc_registry_version': 'v23.06', 'data_prefix': '', 'num_workers': 8, 'dataloader_type': 'single', 'reset_position_ids': False, 'reset_attention_mask': False, 'eod_mask_loss': False, 'masked_lm_prob': 0.15, 'short_seq_prob': 0.1, 'skip_lines': 0, 'drop_last': False, 'pin_memory': False, 'dynamic_padding': False, 'force_regen_sample_mapping': False, 'dataset_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/', 'index_mapping_dir': '${model.data.dataset_path}', 'preprocessing': {'num_preprocess_workers': 16}, 'train': {'data_impl': 'csv_mmap', 'data_impl_kwargs': {'csv_mmap': {'data_col': 1, 'header_lines': 1}}, 'use_upsampling': True, 'range': 'x[000..049]', 'sample_from_map': True, 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'uf90_datapath': '${model.data.dataset_path}/uniref90membersandreps_ur50trainfiltreps.fasta', 'cluster_mapping_tsv': '${model.data.dataset_path}/uniref50_mapper_to_uniref90clustermembers_andselfuniref50.tsv', 'dataset_path': '${model.data.dataset_path}/uf50', 'sort_fastas': True, 'num_workers': '${model.data.num_workers}', 'uf90': {'uniref90_path': '${model.data.dataset_path}/uf90', 'dataset': {'uf90_csvs': 'x[000..049]'}, 'data_impl': 'csv_fields_mmap', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.train.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}'}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'val': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.val.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'test': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.test.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'modify_percent': 0.1, 'perturb_percent': 0.5, 'uf90': {'uniref90_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/uf90'}}, 'dwnstr_task_validation': {'enabled': False, 'dataset': {'class': 'bionemo.model.core.dwnstr_task_callbacks.PerTokenPredictionCallback', 'task_type': 'token-level-classification', 'infer_target': 'bionemo.model.protein.esm1nv.infer.ESM1nvInference', 'max_seq_length': '${model.seq_length}', 'emb_batch_size': 128, 'batch_size': 128, 'num_epochs': 10, 'shuffle': True, 'num_workers': 8, 'task_name': 'secondary_structure', 'dataset_path': '${oc.env:BIONEMO_HOME}/data/FLIP/${model.dwnstr_task_validation.dataset.task_name}', 'dataset': {'train': 'x000', 'test': 'x000'}, 'sequence_column': 'sequence', 'target_column': ['3state'], 'target_sizes': [3], 'mask_column': ['resolved'], 'random_seed': 1234, 'optim': {'name': 'adam', 'lr': 0.0001, 'betas': [0.9, 0.999], 'eps': 1e-08, 'weight_decay': 0.01, 'sched': {'name': 'WarmupAnnealing', 'min_lr': 1e-05, 'last_epoch': -1, 'warmup_ratio': 0.01, 'max_steps': 1000}}}}, 'global_batch_size': 8, 'precision': 32}
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Finished
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keisuke-kamata
esm2-650M
21m 12s
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{'drop_last': True, 'micro_batch_size': 4, 'seq_length': 1024, 'num_layers': 33, 'hidden_size': 1280, 'ffn_hidden_size': '${multiply:${model.hidden_size}, 4}', 'num_attention_heads': 20, 'megatron_legacy': False, 'position_embedding_type': 'rope', 'hidden_dropout': 0, 'embedding_use_attention_mask': True, 'embedding_token_dropout': True, 'mask_token_id': '${.tokenizer.mask_id}', 'attention_dropout': 0.0, 'normalize_attention_scores': False, 'tensor_model_parallel_size': 1, 'pipeline_model_parallel_size': 1, 'bias_gelu_fusion': False, 'use_esm_attention': True, 'esm_gelu': True, 'use_pt_layernorm': False, 'use_pt_mlp_out': False, 'max_position_embeddings': '${.seq_length}', 'encoder_seq_length': '${.seq_length}', 'optim': {'name': 'fused_adam', 'lr': 0.0004, 'weight_decay': 0.01, 'betas': [0.9, 0.98], 'sched': {'name': 'WarmupAnnealDecayHold', 'warmup_steps': 2000, 'min_lr': 4e-05, 'max_lr': 0.0004, 'max_steps': 500000, 'anneal_percentage': 0.1}}, 'init_method_std': 0.02, 'kv_channels': None, 'apply_query_key_layer_scaling': True, 'layernorm_epsilon': 1e-05, 'make_vocab_size_divisible_by': 128, 'pre_process': True, 'post_process': True, 'bert_binary_head': False, 'resume_from_checkpoint': None, 'masked_softmax_fusion': True, 'tokenizer': {'library': 'huggingface', 'type': 'BertWordPieceLowerCase', 'model_name': 'facebook/esm2_t33_650M_UR50D', 'mask_id': 32, 'model': None, 'vocab_file': None, 'merge_file': None}, 'native_amp_init_scale': 4294967296, 'native_amp_growth_interval': 1000, 'fp32_residual_connection': False, 'fp16_lm_cross_entropy': False, 'seed': 1234, 'use_cpu_initialization': False, 'onnx_safe': False, 'activations_checkpoint_method': None, 'activations_checkpoint_num_layers': 1, 'data': {'ngc_registry_target': 'uniref50_2022_05', 'ngc_registry_version': 'v23.06', 'data_prefix': '', 'num_workers': 8, 'dataloader_type': 'single', 'reset_position_ids': False, 'reset_attention_mask': False, 'eod_mask_loss': False, 'masked_lm_prob': 0.15, 'short_seq_prob': 0.1, 'skip_lines': 0, 'drop_last': False, 'pin_memory': False, 'dynamic_padding': False, 'force_regen_sample_mapping': False, 'dataset_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/', 'index_mapping_dir': '${model.data.dataset_path}', 'preprocessing': {'num_preprocess_workers': 16}, 'train': {'data_impl': 'csv_mmap', 'data_impl_kwargs': {'csv_mmap': {'data_col': 1, 'header_lines': 1}}, 'use_upsampling': True, 'range': 'x[000..049]', 'sample_from_map': True, 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'uf90_datapath': '${model.data.dataset_path}/uniref90membersandreps_ur50trainfiltreps.fasta', 'cluster_mapping_tsv': '${model.data.dataset_path}/uniref50_mapper_to_uniref90clustermembers_andselfuniref50.tsv', 'dataset_path': '${model.data.dataset_path}/uf50', 'sort_fastas': True, 'num_workers': '${model.data.num_workers}', 'uf90': {'uniref90_path': '${model.data.dataset_path}/uf90', 'dataset': {'uf90_csvs': 'x[000..049]'}, 'data_impl': 'csv_fields_mmap', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.train.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}'}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'val': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.val.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'test': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.test.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'modify_percent': 0.1, 'perturb_percent': 0.5, 'uf90': {'uniref90_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/uf90'}}, 'dwnstr_task_validation': {'enabled': False, 'dataset': {'class': 'bionemo.model.core.dwnstr_task_callbacks.PerTokenPredictionCallback', 'task_type': 'token-level-classification', 'infer_target': 'bionemo.model.protein.esm1nv.infer.ESM1nvInference', 'max_seq_length': '${model.seq_length}', 'emb_batch_size': 128, 'batch_size': 128, 'num_epochs': 10, 'shuffle': True, 'num_workers': 8, 'task_name': 'secondary_structure', 'dataset_path': '${oc.env:BIONEMO_HOME}/data/FLIP/${model.dwnstr_task_validation.dataset.task_name}', 'dataset': {'train': 'x000', 'test': 'x000'}, 'sequence_column': 'sequence', 'target_column': ['3state'], 'target_sizes': [3], 'mask_column': ['resolved'], 'random_seed': 1234, 'optim': {'name': 'adam', 'lr': 0.0001, 'betas': [0.9, 0.999], 'eps': 1e-08, 'weight_decay': 0.01, 'sched': {'name': 'WarmupAnnealing', 'min_lr': 1e-05, 'last_epoch': -1, 'warmup_ratio': 0.01, 'max_steps': 1000}}}}, 'global_batch_size': 4, 'precision': 32}
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Finished
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keisuke-kamata
esm2-650M
49m 40s
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{'drop_last': True, 'micro_batch_size': 4, 'seq_length': 1024, 'num_layers': 33, 'hidden_size': 1280, 'ffn_hidden_size': '${multiply:${model.hidden_size}, 4}', 'num_attention_heads': 20, 'megatron_legacy': False, 'position_embedding_type': 'rope', 'hidden_dropout': 0, 'embedding_use_attention_mask': True, 'embedding_token_dropout': True, 'mask_token_id': '${.tokenizer.mask_id}', 'attention_dropout': 0.0, 'normalize_attention_scores': False, 'tensor_model_parallel_size': 1, 'pipeline_model_parallel_size': 1, 'bias_gelu_fusion': False, 'use_esm_attention': True, 'esm_gelu': True, 'use_pt_layernorm': False, 'use_pt_mlp_out': False, 'max_position_embeddings': '${.seq_length}', 'encoder_seq_length': '${.seq_length}', 'optim': {'name': 'fused_adam', 'lr': 0.0004, 'weight_decay': 0.01, 'betas': [0.9, 0.98], 'sched': {'name': 'WarmupAnnealDecayHold', 'warmup_steps': 2000, 'min_lr': 4e-05, 'max_lr': 0.0004, 'max_steps': 500000, 'anneal_percentage': 0.1}}, 'init_method_std': 0.02, 'kv_channels': None, 'apply_query_key_layer_scaling': True, 'layernorm_epsilon': 1e-05, 'make_vocab_size_divisible_by': 128, 'pre_process': True, 'post_process': True, 'bert_binary_head': False, 'resume_from_checkpoint': None, 'masked_softmax_fusion': True, 'tokenizer': {'library': 'huggingface', 'type': 'BertWordPieceLowerCase', 'model_name': 'facebook/esm2_t33_650M_UR50D', 'mask_id': 32, 'model': None, 'vocab_file': None, 'merge_file': None}, 'native_amp_init_scale': 4294967296, 'native_amp_growth_interval': 1000, 'fp32_residual_connection': False, 'fp16_lm_cross_entropy': False, 'seed': 1234, 'use_cpu_initialization': False, 'onnx_safe': False, 'activations_checkpoint_method': None, 'activations_checkpoint_num_layers': 1, 'data': {'ngc_registry_target': 'uniref50_2022_05', 'ngc_registry_version': 'v23.06', 'data_prefix': '', 'num_workers': 8, 'dataloader_type': 'single', 'reset_position_ids': False, 'reset_attention_mask': False, 'eod_mask_loss': False, 'masked_lm_prob': 0.15, 'short_seq_prob': 0.1, 'skip_lines': 0, 'drop_last': False, 'pin_memory': False, 'dynamic_padding': False, 'force_regen_sample_mapping': False, 'dataset_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/', 'index_mapping_dir': '${model.data.dataset_path}', 'preprocessing': {'num_preprocess_workers': 16}, 'train': {'data_impl': 'csv_mmap', 'data_impl_kwargs': {'csv_mmap': {'data_col': 1, 'header_lines': 1}}, 'use_upsampling': True, 'range': 'x[000..049]', 'sample_from_map': True, 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'uf90_datapath': '${model.data.dataset_path}/uniref90membersandreps_ur50trainfiltreps.fasta', 'cluster_mapping_tsv': '${model.data.dataset_path}/uniref50_mapper_to_uniref90clustermembers_andselfuniref50.tsv', 'dataset_path': '${model.data.dataset_path}/uf50', 'sort_fastas': True, 'num_workers': '${model.data.num_workers}', 'uf90': {'uniref90_path': '${model.data.dataset_path}/uf90', 'dataset': {'uf90_csvs': 'x[000..049]'}, 'data_impl': 'csv_fields_mmap', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.train.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}'}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'val': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.val.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'test': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.test.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'modify_percent': 0.1, 'perturb_percent': 0.5, 'uf90': {'uniref90_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/uf90'}}, 'dwnstr_task_validation': {'enabled': False, 'dataset': {'class': 'bionemo.model.core.dwnstr_task_callbacks.PerTokenPredictionCallback', 'task_type': 'token-level-classification', 'infer_target': 'bionemo.model.protein.esm1nv.infer.ESM1nvInference', 'max_seq_length': '${model.seq_length}', 'emb_batch_size': 128, 'batch_size': 128, 'num_epochs': 10, 'shuffle': True, 'num_workers': 8, 'task_name': 'secondary_structure', 'dataset_path': '${oc.env:BIONEMO_HOME}/data/FLIP/${model.dwnstr_task_validation.dataset.task_name}', 'dataset': {'train': 'x000', 'test': 'x000'}, 'sequence_column': 'sequence', 'target_column': ['3state'], 'target_sizes': [3], 'mask_column': ['resolved'], 'random_seed': 1234, 'optim': {'name': 'adam', 'lr': 0.0001, 'betas': [0.9, 0.999], 'eps': 1e-08, 'weight_decay': 0.01, 'sched': {'name': 'WarmupAnnealing', 'min_lr': 1e-05, 'last_epoch': -1, 'warmup_ratio': 0.01, 'max_steps': 1000}}}}, 'global_batch_size': 4, 'precision': 32}
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Finished
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keisuke-kamata
esm2-650M
2h 46m 57s
-
{'drop_last': True, 'micro_batch_size': 4, 'seq_length': 1024, 'num_layers': 33, 'hidden_size': 1280, 'ffn_hidden_size': '${multiply:${model.hidden_size}, 4}', 'num_attention_heads': 20, 'megatron_legacy': False, 'position_embedding_type': 'rope', 'hidden_dropout': 0, 'embedding_use_attention_mask': True, 'embedding_token_dropout': True, 'mask_token_id': '${.tokenizer.mask_id}', 'attention_dropout': 0.0, 'normalize_attention_scores': False, 'tensor_model_parallel_size': 1, 'pipeline_model_parallel_size': 1, 'bias_gelu_fusion': False, 'use_esm_attention': True, 'esm_gelu': True, 'use_pt_layernorm': False, 'use_pt_mlp_out': False, 'max_position_embeddings': '${.seq_length}', 'encoder_seq_length': '${.seq_length}', 'optim': {'name': 'fused_adam', 'lr': 0.0004, 'weight_decay': 0.01, 'betas': [0.9, 0.98], 'sched': {'name': 'WarmupAnnealDecayHold', 'warmup_steps': 2000, 'min_lr': 4e-05, 'max_lr': 0.0004, 'max_steps': 500000, 'anneal_percentage': 0.1}}, 'init_method_std': 0.02, 'kv_channels': None, 'apply_query_key_layer_scaling': True, 'layernorm_epsilon': 1e-05, 'make_vocab_size_divisible_by': 128, 'pre_process': True, 'post_process': True, 'bert_binary_head': False, 'resume_from_checkpoint': None, 'masked_softmax_fusion': True, 'tokenizer': {'library': 'huggingface', 'type': 'BertWordPieceLowerCase', 'model_name': 'facebook/esm2_t33_650M_UR50D', 'mask_id': 32, 'model': None, 'vocab_file': None, 'merge_file': None}, 'native_amp_init_scale': 4294967296, 'native_amp_growth_interval': 1000, 'fp32_residual_connection': False, 'fp16_lm_cross_entropy': False, 'seed': 1234, 'use_cpu_initialization': False, 'onnx_safe': False, 'activations_checkpoint_method': None, 'activations_checkpoint_num_layers': 1, 'data': {'ngc_registry_target': 'uniref50_2022_05', 'ngc_registry_version': 'v23.06', 'data_prefix': '', 'num_workers': 8, 'dataloader_type': 'single', 'reset_position_ids': False, 'reset_attention_mask': False, 'eod_mask_loss': False, 'masked_lm_prob': 0.15, 'short_seq_prob': 0.1, 'skip_lines': 0, 'drop_last': False, 'pin_memory': False, 'dynamic_padding': False, 'force_regen_sample_mapping': False, 'dataset_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/', 'index_mapping_dir': '${model.data.dataset_path}', 'preprocessing': {'num_preprocess_workers': 16}, 'train': {'data_impl': 'csv_mmap', 'data_impl_kwargs': {'csv_mmap': {'data_col': 1, 'header_lines': 1}}, 'use_upsampling': True, 'range': 'x[000..049]', 'sample_from_map': True, 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'uf90_datapath': '${model.data.dataset_path}/uniref90membersandreps_ur50trainfiltreps.fasta', 'cluster_mapping_tsv': '${model.data.dataset_path}/uniref50_mapper_to_uniref90clustermembers_andselfuniref50.tsv', 'dataset_path': '${model.data.dataset_path}/uf50', 'sort_fastas': True, 'num_workers': '${model.data.num_workers}', 'uf90': {'uniref90_path': '${model.data.dataset_path}/uf90', 'dataset': {'uf90_csvs': 'x[000..049]'}, 'data_impl': 'csv_fields_mmap', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.train.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}'}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'val': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.val.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'test': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.test.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'modify_percent': 0.1, 'perturb_percent': 0.5, 'uf90': {'uniref90_path': './artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/uf90'}}, 'dwnstr_task_validation': {'enabled': False, 'dataset': {'class': 'bionemo.model.core.dwnstr_task_callbacks.PerTokenPredictionCallback', 'task_type': 'token-level-classification', 'infer_target': 'bionemo.model.protein.esm1nv.infer.ESM1nvInference', 'max_seq_length': '${model.seq_length}', 'emb_batch_size': 128, 'batch_size': 128, 'num_epochs': 10, 'shuffle': True, 'num_workers': 8, 'task_name': 'secondary_structure', 'dataset_path': '${oc.env:BIONEMO_HOME}/data/FLIP/${model.dwnstr_task_validation.dataset.task_name}', 'dataset': {'train': 'x000', 'test': 'x000'}, 'sequence_column': 'sequence', 'target_column': ['3state'], 'target_sizes': [3], 'mask_column': ['resolved'], 'random_seed': 1234, 'optim': {'name': 'adam', 'lr': 0.0001, 'betas': [0.9, 0.999], 'eps': 1e-08, 'weight_decay': 0.01, 'sched': {'name': 'WarmupAnnealing', 'min_lr': 1e-05, 'last_epoch': -1, 'warmup_ratio': 0.01, 'max_steps': 1000}}}}, 'global_batch_size': 4, 'precision': 32}
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Finished
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keisuke-kamata
esm2-650M
3h 30m 11s
-
{'drop_last': True, 'micro_batch_size': 4, 'seq_length': 1024, 'num_layers': 33, 'hidden_size': 1280, 'ffn_hidden_size': '${multiply:${model.hidden_size}, 4}', 'num_attention_heads': 20, 'megatron_legacy': False, 'position_embedding_type': 'rope', 'hidden_dropout': 0, 'embedding_use_attention_mask': True, 'embedding_token_dropout': True, 'mask_token_id': '${.tokenizer.mask_id}', 'attention_dropout': 0.0, 'normalize_attention_scores': False, 'tensor_model_parallel_size': 1, 'pipeline_model_parallel_size': 1, 'bias_gelu_fusion': False, 'use_esm_attention': True, 'esm_gelu': True, 'use_pt_layernorm': False, 'use_pt_mlp_out': False, 'max_position_embeddings': '${.seq_length}', 'encoder_seq_length': '${.seq_length}', 'optim': {'name': 'fused_adam', 'lr': 0.0004, 'weight_decay': 0.01, 'betas': [0.9, 0.98], 'sched': {'name': 'WarmupAnnealDecayHold', 'warmup_steps': 2000, 'min_lr': 4e-05, 'max_lr': 0.0004, 'max_steps': 500000, 'anneal_percentage': 0.1}}, 'init_method_std': 0.02, 'kv_channels': None, 'apply_query_key_layer_scaling': True, 'layernorm_epsilon': 1e-05, 'make_vocab_size_divisible_by': 128, 'pre_process': True, 'post_process': True, 'bert_binary_head': False, 'resume_from_checkpoint': None, 'masked_softmax_fusion': True, 'tokenizer': {'library': 'huggingface', 'type': 'BertWordPieceLowerCase', 'model_name': 'facebook/esm2_t33_650M_UR50D', 'mask_id': 32, 'model': None, 'vocab_file': None, 'merge_file': None}, 'native_amp_init_scale': 4294967296, 'native_amp_growth_interval': 1000, 'fp32_residual_connection': False, 'fp16_lm_cross_entropy': False, 'seed': 1234, 'use_cpu_initialization': False, 'onnx_safe': False, 'activations_checkpoint_method': None, 'activations_checkpoint_num_layers': 1, 'data': {'ngc_registry_target': 'uniref50_2022_05', 'ngc_registry_version': 'v23.06', 'data_prefix': '', 'num_workers': 8, 'dataloader_type': 'single', 'reset_position_ids': False, 'reset_attention_mask': False, 'eod_mask_loss': False, 'masked_lm_prob': 0.15, 'short_seq_prob': 0.1, 'skip_lines': 0, 'drop_last': False, 'pin_memory': False, 'dynamic_padding': False, 'force_regen_sample_mapping': False, 'dataset_path': '/workspace/bionemo/artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/', 'index_mapping_dir': '${model.data.dataset_path}', 'preprocessing': {'num_preprocess_workers': 16}, 'train': {'data_impl': 'csv_mmap', 'data_impl_kwargs': {'csv_mmap': {'data_col': 1, 'header_lines': 1}}, 'use_upsampling': True, 'range': 'x[000..049]', 'sample_from_map': True, 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'uf90_datapath': '${model.data.dataset_path}/uniref90membersandreps_ur50trainfiltreps.fasta', 'cluster_mapping_tsv': '${model.data.dataset_path}/uniref50_mapper_to_uniref90clustermembers_andselfuniref50.tsv', 'dataset_path': '${model.data.dataset_path}/uf50', 'sort_fastas': True, 'num_workers': '${model.data.num_workers}', 'uf90': {'uniref90_path': '${model.data.dataset_path}/uf90', 'dataset': {'uf90_csvs': 'x[000..049]'}, 'data_impl': 'csv_fields_mmap', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.train.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}'}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'val': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.val.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'test': {'use_upsampling': False, 'range': 'x[000..049]', 'uf50_datapath': '${model.data.dataset_path}/uniref50_train_filt.fasta', 'dataset_path': '${model.data.dataset_path}/uf50', 'data_impl': 'csv_fields_mmap', 'num_workers': '${model.data.num_workers}', 'data_impl_kwargs': {'csv_fields_mmap': {'header_lines': 1, 'newline_int': 10, 'workers': '${model.data.test.num_workers}', 'sort_dataset_paths': True, 'data_sep': ',', 'data_fields': {'sequence': 3, 'sequence_id': 1}}}, 'index_mapping_dir': '${model.data.index_mapping_dir}', 'max_seq_length': '${model.seq_length}', 'seed': '${model.seed}'}, 'modify_percent': 0.1, 'perturb_percent': 0.5, 'uf90': {'uniref90_path': '/workspace/bionemo/artifacts/uniref202104_esm2_qc_test200_val200_preprocessed:v0/uf90'}}, 'dwnstr_task_validation': {'enabled': False, 'dataset': {'class': 'bionemo.model.core.dwnstr_task_callbacks.PerTokenPredictionCallback', 'task_type': 'token-level-classification', 'infer_target': 'bionemo.model.protein.esm1nv.infer.ESM1nvInference', 'max_seq_length': '${model.seq_length}', 'emb_batch_size': 128, 'batch_size': 128, 'num_epochs': 10, 'shuffle': True, 'num_workers': 8, 'task_name': 'secondary_structure', 'dataset_path': '${oc.env:BIONEMO_HOME}/data/FLIP/${model.dwnstr_task_validation.dataset.task_name}', 'dataset': {'train': 'x000', 'test': 'x000'}, 'sequence_column': 'sequence', 'target_column': ['3state'], 'target_sizes': [3], 'mask_column': ['resolved'], 'random_seed': 1234, 'optim': {'name': 'adam', 'lr': 0.0001, 'betas': [0.9, 0.999], 'eps': 1e-08, 'weight_decay': 0.01, 'sched': {'name': 'WarmupAnnealing', 'min_lr': 1e-05, 'last_epoch': -1, 'warmup_ratio': 0.01, 'max_steps': 1000}}}}, 'global_batch_size': 4, 'precision': 32}
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keisuke-kamata
15s
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false
false
false
megatron_bert--{val_loss:.2f}-{step}-{consumed_samples}
min
${multiply:${model.tensor_model_parallel_size}, ${model.pipeline_model_parallel_size}}
val_loss
10
true
false
true
${oc.env:BIONEMO_HOME}/results/nemo_experiments/${.name}/${.wandb_logger_kwargs.name}
${.exp_dir}
${name}
true
true
${name}
data_upload
all
preproceed_data_upload
false
${oc.env:WANDB_PROJECT}
["${name}"]
1
true
0
false
false
/mapping.tsv
single
/workspace/bionemo/artifacts/uniref202104_esm2_qc_test200_val200:v0/workspace/bionemo/examples/tests/test_data/uniref202104_esm2_qc_test200_val200/uf50
false
false
false
false
${model.data.dataset_path}
0.15
0.1
uniref50_2022_05
v23.06
8
Finished
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keisuke-kamata
16s
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