@synsci/cli-darwin-x64 1.1.97 → 1.1.99

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1549) hide show
  1. package/bin/synsc +0 -0
  2. package/package.json +1 -1
  3. package/bin/skills/accelerate/SKILL.md +0 -332
  4. package/bin/skills/accelerate/references/custom-plugins.md +0 -453
  5. package/bin/skills/accelerate/references/megatron-integration.md +0 -489
  6. package/bin/skills/accelerate/references/performance.md +0 -525
  7. package/bin/skills/adaptyv/SKILL.md +0 -114
  8. package/bin/skills/adaptyv/reference/api_reference.md +0 -308
  9. package/bin/skills/adaptyv/reference/examples.md +0 -913
  10. package/bin/skills/adaptyv/reference/experiments.md +0 -360
  11. package/bin/skills/adaptyv/reference/protein_optimization.md +0 -637
  12. package/bin/skills/aeon/SKILL.md +0 -374
  13. package/bin/skills/aeon/references/anomaly_detection.md +0 -154
  14. package/bin/skills/aeon/references/classification.md +0 -144
  15. package/bin/skills/aeon/references/clustering.md +0 -123
  16. package/bin/skills/aeon/references/datasets_benchmarking.md +0 -387
  17. package/bin/skills/aeon/references/distances.md +0 -256
  18. package/bin/skills/aeon/references/forecasting.md +0 -140
  19. package/bin/skills/aeon/references/networks.md +0 -289
  20. package/bin/skills/aeon/references/regression.md +0 -118
  21. package/bin/skills/aeon/references/segmentation.md +0 -163
  22. package/bin/skills/aeon/references/similarity_search.md +0 -187
  23. package/bin/skills/aeon/references/transformations.md +0 -246
  24. package/bin/skills/alphafold-database/SKILL.md +0 -513
  25. package/bin/skills/alphafold-database/references/api_reference.md +0 -423
  26. package/bin/skills/anndata/SKILL.md +0 -400
  27. package/bin/skills/anndata/references/best_practices.md +0 -525
  28. package/bin/skills/anndata/references/concatenation.md +0 -396
  29. package/bin/skills/anndata/references/data_structure.md +0 -314
  30. package/bin/skills/anndata/references/io_operations.md +0 -404
  31. package/bin/skills/anndata/references/manipulation.md +0 -516
  32. package/bin/skills/arboreto/SKILL.md +0 -243
  33. package/bin/skills/arboreto/references/algorithms.md +0 -138
  34. package/bin/skills/arboreto/references/basic_inference.md +0 -151
  35. package/bin/skills/arboreto/references/distributed_computing.md +0 -242
  36. package/bin/skills/arboreto/scripts/basic_grn_inference.py +0 -97
  37. package/bin/skills/astropy/SKILL.md +0 -331
  38. package/bin/skills/astropy/references/coordinates.md +0 -273
  39. package/bin/skills/astropy/references/cosmology.md +0 -307
  40. package/bin/skills/astropy/references/fits.md +0 -396
  41. package/bin/skills/astropy/references/tables.md +0 -489
  42. package/bin/skills/astropy/references/time.md +0 -404
  43. package/bin/skills/astropy/references/units.md +0 -178
  44. package/bin/skills/astropy/references/wcs_and_other_modules.md +0 -373
  45. package/bin/skills/audiocraft/SKILL.md +0 -564
  46. package/bin/skills/audiocraft/references/advanced-usage.md +0 -666
  47. package/bin/skills/audiocraft/references/troubleshooting.md +0 -504
  48. package/bin/skills/autogpt/SKILL.md +0 -403
  49. package/bin/skills/autogpt/references/advanced-usage.md +0 -535
  50. package/bin/skills/autogpt/references/troubleshooting.md +0 -420
  51. package/bin/skills/awq/SKILL.md +0 -310
  52. package/bin/skills/awq/references/advanced-usage.md +0 -324
  53. package/bin/skills/awq/references/troubleshooting.md +0 -344
  54. package/bin/skills/axolotl/SKILL.md +0 -158
  55. package/bin/skills/axolotl/references/api.md +0 -5548
  56. package/bin/skills/axolotl/references/dataset-formats.md +0 -1029
  57. package/bin/skills/axolotl/references/index.md +0 -15
  58. package/bin/skills/axolotl/references/other.md +0 -3563
  59. package/bin/skills/benchling-integration/SKILL.md +0 -480
  60. package/bin/skills/benchling-integration/references/api_endpoints.md +0 -883
  61. package/bin/skills/benchling-integration/references/authentication.md +0 -379
  62. package/bin/skills/benchling-integration/references/sdk_reference.md +0 -774
  63. package/bin/skills/bigcode-evaluation-harness/SKILL.md +0 -405
  64. package/bin/skills/bigcode-evaluation-harness/references/benchmarks.md +0 -393
  65. package/bin/skills/bigcode-evaluation-harness/references/custom-tasks.md +0 -424
  66. package/bin/skills/bigcode-evaluation-harness/references/issues.md +0 -394
  67. package/bin/skills/biopython/SKILL.md +0 -443
  68. package/bin/skills/biopython/references/advanced.md +0 -577
  69. package/bin/skills/biopython/references/alignment.md +0 -362
  70. package/bin/skills/biopython/references/blast.md +0 -455
  71. package/bin/skills/biopython/references/databases.md +0 -484
  72. package/bin/skills/biopython/references/phylogenetics.md +0 -566
  73. package/bin/skills/biopython/references/sequence_io.md +0 -285
  74. package/bin/skills/biopython/references/structure.md +0 -564
  75. package/bin/skills/biorxiv-database/SKILL.md +0 -483
  76. package/bin/skills/biorxiv-database/references/api_reference.md +0 -280
  77. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +0 -445
  78. package/bin/skills/bioservices/SKILL.md +0 -361
  79. package/bin/skills/bioservices/references/identifier_mapping.md +0 -685
  80. package/bin/skills/bioservices/references/services_reference.md +0 -636
  81. package/bin/skills/bioservices/references/workflow_patterns.md +0 -811
  82. package/bin/skills/bioservices/scripts/batch_id_converter.py +0 -347
  83. package/bin/skills/bioservices/scripts/compound_cross_reference.py +0 -378
  84. package/bin/skills/bioservices/scripts/pathway_analysis.py +0 -309
  85. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +0 -408
  86. package/bin/skills/bitsandbytes/SKILL.md +0 -411
  87. package/bin/skills/bitsandbytes/references/memory-optimization.md +0 -521
  88. package/bin/skills/bitsandbytes/references/qlora-training.md +0 -521
  89. package/bin/skills/bitsandbytes/references/quantization-formats.md +0 -447
  90. package/bin/skills/blip-2/SKILL.md +0 -564
  91. package/bin/skills/blip-2/references/advanced-usage.md +0 -680
  92. package/bin/skills/blip-2/references/troubleshooting.md +0 -526
  93. package/bin/skills/brenda-database/SKILL.md +0 -719
  94. package/bin/skills/brenda-database/references/api_reference.md +0 -537
  95. package/bin/skills/brenda-database/scripts/brenda_queries.py +0 -844
  96. package/bin/skills/brenda-database/scripts/brenda_visualization.py +0 -772
  97. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +0 -1053
  98. package/bin/skills/cellxgene-census/SKILL.md +0 -511
  99. package/bin/skills/cellxgene-census/references/census_schema.md +0 -182
  100. package/bin/skills/cellxgene-census/references/common_patterns.md +0 -351
  101. package/bin/skills/chembl-database/SKILL.md +0 -389
  102. package/bin/skills/chembl-database/references/api_reference.md +0 -272
  103. package/bin/skills/chembl-database/scripts/example_queries.py +0 -278
  104. package/bin/skills/chroma/SKILL.md +0 -406
  105. package/bin/skills/chroma/references/integration.md +0 -38
  106. package/bin/skills/cirq/SKILL.md +0 -346
  107. package/bin/skills/cirq/references/building.md +0 -307
  108. package/bin/skills/cirq/references/experiments.md +0 -572
  109. package/bin/skills/cirq/references/hardware.md +0 -515
  110. package/bin/skills/cirq/references/noise.md +0 -515
  111. package/bin/skills/cirq/references/simulation.md +0 -350
  112. package/bin/skills/cirq/references/transformation.md +0 -416
  113. package/bin/skills/citation-management/SKILL.md +0 -1109
  114. package/bin/skills/citation-management/assets/bibtex_template.bib +0 -264
  115. package/bin/skills/citation-management/assets/citation_checklist.md +0 -386
  116. package/bin/skills/citation-management/references/bibtex_formatting.md +0 -908
  117. package/bin/skills/citation-management/references/citation_validation.md +0 -794
  118. package/bin/skills/citation-management/references/google_scholar_search.md +0 -725
  119. package/bin/skills/citation-management/references/metadata_extraction.md +0 -870
  120. package/bin/skills/citation-management/references/pubmed_search.md +0 -839
  121. package/bin/skills/citation-management/scripts/doi_to_bibtex.py +0 -182
  122. package/bin/skills/citation-management/scripts/extract_metadata.py +0 -570
  123. package/bin/skills/citation-management/scripts/format_bibtex.py +0 -349
  124. package/bin/skills/citation-management/scripts/search_google_scholar.py +0 -251
  125. package/bin/skills/citation-management/scripts/search_pubmed.py +0 -348
  126. package/bin/skills/citation-management/scripts/validate_citations.py +0 -494
  127. package/bin/skills/clinical-decision-support/README.md +0 -129
  128. package/bin/skills/clinical-decision-support/SKILL.md +0 -506
  129. package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +0 -380
  130. package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +0 -222
  131. package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +0 -359
  132. package/bin/skills/clinical-decision-support/assets/color_schemes.tex +0 -149
  133. package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +0 -208
  134. package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +0 -328
  135. package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +0 -529
  136. package/bin/skills/clinical-decision-support/references/biomarker_classification.md +0 -719
  137. package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +0 -604
  138. package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +0 -840
  139. package/bin/skills/clinical-decision-support/references/outcome_analysis.md +0 -640
  140. package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +0 -427
  141. package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +0 -521
  142. package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +0 -383
  143. package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +0 -417
  144. package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +0 -509
  145. package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +0 -441
  146. package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +0 -326
  147. package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +0 -641
  148. package/bin/skills/clinical-reports/README.md +0 -236
  149. package/bin/skills/clinical-reports/SKILL.md +0 -1127
  150. package/bin/skills/clinical-reports/assets/case_report_template.md +0 -352
  151. package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +0 -353
  152. package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +0 -359
  153. package/bin/skills/clinical-reports/assets/consult_note_template.md +0 -305
  154. package/bin/skills/clinical-reports/assets/discharge_summary_template.md +0 -453
  155. package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +0 -395
  156. package/bin/skills/clinical-reports/assets/history_physical_template.md +0 -305
  157. package/bin/skills/clinical-reports/assets/lab_report_template.md +0 -309
  158. package/bin/skills/clinical-reports/assets/pathology_report_template.md +0 -249
  159. package/bin/skills/clinical-reports/assets/quality_checklist.md +0 -338
  160. package/bin/skills/clinical-reports/assets/radiology_report_template.md +0 -318
  161. package/bin/skills/clinical-reports/assets/soap_note_template.md +0 -253
  162. package/bin/skills/clinical-reports/references/case_report_guidelines.md +0 -570
  163. package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +0 -693
  164. package/bin/skills/clinical-reports/references/data_presentation.md +0 -530
  165. package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -629
  166. package/bin/skills/clinical-reports/references/medical_terminology.md +0 -588
  167. package/bin/skills/clinical-reports/references/patient_documentation.md +0 -744
  168. package/bin/skills/clinical-reports/references/peer_review_standards.md +0 -585
  169. package/bin/skills/clinical-reports/references/regulatory_compliance.md +0 -577
  170. package/bin/skills/clinical-reports/scripts/check_deidentification.py +0 -332
  171. package/bin/skills/clinical-reports/scripts/compliance_checker.py +0 -78
  172. package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +0 -97
  173. package/bin/skills/clinical-reports/scripts/format_adverse_events.py +0 -97
  174. package/bin/skills/clinical-reports/scripts/generate_report_template.py +0 -149
  175. package/bin/skills/clinical-reports/scripts/terminology_validator.py +0 -126
  176. package/bin/skills/clinical-reports/scripts/validate_case_report.py +0 -323
  177. package/bin/skills/clinical-reports/scripts/validate_trial_report.py +0 -88
  178. package/bin/skills/clinicaltrials-database/SKILL.md +0 -507
  179. package/bin/skills/clinicaltrials-database/references/api_reference.md +0 -358
  180. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +0 -215
  181. package/bin/skills/clinpgx-database/SKILL.md +0 -638
  182. package/bin/skills/clinpgx-database/references/api_reference.md +0 -757
  183. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +0 -518
  184. package/bin/skills/clinvar-database/SKILL.md +0 -362
  185. package/bin/skills/clinvar-database/references/api_reference.md +0 -227
  186. package/bin/skills/clinvar-database/references/clinical_significance.md +0 -218
  187. package/bin/skills/clinvar-database/references/data_formats.md +0 -358
  188. package/bin/skills/clip/SKILL.md +0 -253
  189. package/bin/skills/clip/references/applications.md +0 -207
  190. package/bin/skills/cobrapy/SKILL.md +0 -463
  191. package/bin/skills/cobrapy/references/api_quick_reference.md +0 -655
  192. package/bin/skills/cobrapy/references/workflows.md +0 -593
  193. package/bin/skills/colab-finetuning/SKILL.md +0 -153
  194. package/bin/skills/colab-finetuning/references/bridge-setup.md +0 -68
  195. package/bin/skills/colab-finetuning/references/gpu-tiers.md +0 -54
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  197. package/bin/skills/constitutional-ai/SKILL.md +0 -290
  198. package/bin/skills/cosmic-database/SKILL.md +0 -336
  199. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +0 -220
  200. package/bin/skills/cosmic-database/scripts/download_cosmic.py +0 -231
  201. package/bin/skills/crewai/SKILL.md +0 -498
  202. package/bin/skills/crewai/references/flows.md +0 -438
  203. package/bin/skills/crewai/references/tools.md +0 -429
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  205. package/bin/skills/dask/SKILL.md +0 -456
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  209. package/bin/skills/dask/references/dataframes.md +0 -368
  210. package/bin/skills/dask/references/futures.md +0 -541
  211. package/bin/skills/dask/references/schedulers.md +0 -504
  212. package/bin/skills/datacommons-client/SKILL.md +0 -255
  213. package/bin/skills/datacommons-client/references/getting_started.md +0 -417
  214. package/bin/skills/datacommons-client/references/node.md +0 -250
  215. package/bin/skills/datacommons-client/references/observation.md +0 -185
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  217. package/bin/skills/datamol/SKILL.md +0 -706
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  224. package/bin/skills/deepchem/SKILL.md +0 -597
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  227. package/bin/skills/deepchem/scripts/graph_neural_network.py +0 -338
  228. package/bin/skills/deepchem/scripts/predict_solubility.py +0 -224
  229. package/bin/skills/deepchem/scripts/transfer_learning.py +0 -375
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- ## DeepSpeed-MoE for NLG: Reducing the training cost of language models by 5 times
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- **URL:** https://www.deepspeed.ai/2021/12/09/deepspeed-moe-nlg.html
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- **Contents:**
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- - DeepSpeed-MoE for NLG: Reducing the training cost of language models by 5 times
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- - Contents
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- - MoE based NLG model architecture
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- - MoE training infrastructure and dataset
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- - MoE leads to better quality for NLG models
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- - Same quality with 5x less training cost
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- - MoE for Inference
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- - Conclusion and Release
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- - Acknowledgement
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- Autoregressive transformer-based natural language generation (referred to as NLG in the rest of the blog) models can offer convincing solutions to a broad range of language tasks from document summarization, headline generation, question and answering to even generating code in a wide variety of programming languages. Due to the general applicability of these models, improving their quality has been of great interest for both academia and industry alike.
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- The quality of NLG improves with the increase in model size. However, today we are getting close to the limit of what the current generation of hardware can do. The Megatron-Turing NLG 530B model took 3 months to train on over 2K A100 GPUs on the NVIDIA Selene Supercomputer, consuming over 3 million GPU hours. Another 3 to 5 times of increase in model size would be infeasible within a reasonable timeframe. Given the exorbitant compute resources required to train the state-of-art NLG models, a natural question to ask is: “Is it possible to make non-trivial improvement to model quality without increasing the compute cost?” Or equivalently, “Is it possible to produce model with similar quality using 3 to 5 times less resources?”
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- Recent works like GShard and Switch Transformers have shown that Mixture of Experts (MoE) model structure reduces large model training cost significantly for transformer-based encoder-decoder models. An MoE model contains a set of sparsely gated experts. During training and inference, only a subset of these experts is activated for each input token. Therefore, the model could scale to billions of parameters without a proportional increase in the computation. Despite showing promising results, the effectiveness of MoE for the much more computation intensive NLG family models remains mostly unknown.
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- Given the tremendous compute and energy requirements for training NLG family of models, we explore the opportunities that MoE presents to reduce their training cost. We show that MoE can be applied to NLG family of models to significantly improve their model quality with the same training cost. Alternatively, it can achieve 5x reduction in training cost to achieve the same model quality of a dense NLG model. For example, by applying MoE we achieved the model quality of a 6.7B parameter dense NLG model at the cost of training a 1.3B parameter dense model, thanks to the sparse structure of MoE.
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- Assuming the scaling holds, the results have the potential to completely transform the large model training landscape in terms of cost. For example, a trillion-parameter dense model can be potentially trained at the cost of a 200B parameter (like GPT-3) sized dense model, translating to millions of dollars in training cost reduction and energy savings (Brown et al., 2020, Language models are few-shot learners).
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- To create an MoE based NLG model we studied the GPT like transformer-based NLG model. To complete training in a reasonable timeframe, the following models are selected: 350M (24 layers, 1024 hidden size, 16 attention heads), 1.3B (24 layers, 2048 hidden size, 16 attention heads), and 6.7B (32 layers, 4096 hidden size, 32 attention heads). We use “350M+MoE-128” to denote a MoE model that uses 350M dense model as the base model and adds 128 experts on every other feedforward layer. That is to say, there are in total 12 MoE layers for both 350M+MoE-128 and 1.3B+MoE-128.
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- We use a gating function to activate a subset of experts in the MoE layer for each token. Specifically, in our experiments, only the top-1 expert is selected. Therefore, during both training and inference, our MoE model will have the same number of parameters to be activated for each token as their dense part. For example, our 1.3B+MoE-128 will only activate 1.3B parameter per token, and the amount of training computation per token will be similar to a 1.3B dense model.
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- We pre-trained both the dense and MoE version of the above models using DeepSpeed on 128 A100 GPUs. DeepSpeed uses a combination of data parallel and expert parallel training to effectively scale the MoE model training.
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- We used the same training data as described in the MT-NLG blog. For a fair comparison, we use 300B tokens to train both the dense model and the MoE model.
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- Figure 1 shows that the validation loss for the MoE versions of the model is significantly better than their dense counter parts. Furthermore, notice that the validation loss of the MoE model, 350M+MoE-128, is on par with the validation loss of the 1.3B dense model with 4x larger base. This is also true for 1.3B+MoE-128 in comparison with 6.7B dense model with 5x larger base. Furthermore, the model quality is on par not only for the validation loss but also for a wide variety of 6 ZeRO-shot evaluation tasks as shown in Table 1, demonstrating that these models in fact have very similar model quality.
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- Figure 1: Token-wise validation loss curves for dense and MoE NLG models with different model sizes.
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- Table 1: ZeRO-shot evaluation results (last six columns) for different dense and MoE NLG models. All ZeRO-shot evaluation results use the accuracy metric.
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- As we saw from the results above, adding MoE with 128 experts to the NLG model significantly improves the quality of the NLG model. However, these experts do not change the compute requirements of the model as each token is only processed by a single expert. Therefore, the compute requirements for dense model and its corresponding MoE models with the same base are similar.
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- More concretely, a 1.3B+MoE-128 model training requires roughly the same amount of compute operations as 1.3B dense, while offering much better model quality. Furthermore, our results show that by applying MoE we can achieve the model quality of a 6.7B parameter dense model at the training cost of 1.3B parameter dense model, resulting in an effective training compute reduction of 5x.
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- This compute cost reduction can directly be translated into throughput gain, training time and training cost reduction by leveraging the efficient DeepSpeed MoE training system. Table 2 shows the training throughput of the 1.3B+MoE-128 model in comparison to the 6.7B dense model on 128 NVIDIA A100 GPUs.
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- The training cost reduction of MoE is not free and comes at the expense of increasing the total number of parameters required to achieve the same model quality compared to dense models. The 1.3B+MoE-128 have roughly 8x the number of parameters (52B) compared to the 6.7B dense model. So, does this mean inference will be 8x slower than the dense model, since inference is generally limited by the time taken to read all the model parameters, especially for small batch sizes?
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- Not quite. Note that in the 1.3B+MoE-128 model, each token is processed by a unique expert per MoE layer, and the total number of parameters used in processing the token is just 1.3B. This can in theory result in even faster inference than the quality-equivalent dense 6.7B model because of 5x less compute and parameter read. In reality though, the number of tokens in a batch during inference is generally larger than 1. Inferencing, a long sequence length or a non-unit batch size may require loading all the experts, increasing the total number of parameters loaded by 8x compared to the quality-equivalent dense model. Therefore, achieving good inference performance with MoE is still challenging even though the parameters used and the computation incurred per token is small compared to the quality-equivalent dense model.
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- Nonetheless, we believe that it is possible to use different forms of parallelism to leverage massive memory bandwidth by scaling across a large number of devices to speed up MoE inference, making it comparable or faster than quality-equivalent dense models for extended inference scenarios and creating opportunities to make MoE based models cost efficient for inference in addition to training.
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- We demonstrate that MoE based models can be applied to NLG task, reducing the training cost by 5x compared to dense, autoregressive transformer-based models like GPT-3 and MT-NLG 530B. Through MoE based low-cost training we hope to make high quality language models accessible to a broad audience, even with limited compute resources.
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- To this end we are releasing our end-to-end pipeline for training MoE based NLG models, along with specific example scripts and tutorial to help get started with our pipeline. We look forward to the application and the innovations that this may bring to the deep learning community.
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- This work was done in collaboration with Brandon Norick, Zhun Liu, Xia Song from the Turing Team, and Young Jin Kim, Alex Muzio, Hany Hassan Awadalla from Z-Code Team. We also thank Luis Vargas, Umesh Madan, Gopi Kumar, Andrey Proskurin and Mikhail Parakhin for their continuous support and guidance.
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- ## ZeRO-Inference: Democratizing massive model inference
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- **URL:** https://www.deepspeed.ai/2022/09/09/zero-inference.html
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- **Contents:**
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- - ZeRO-Inference: Democratizing massive model inference
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- - Contents
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- - Introduction
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- - How ZeRO-Inference works
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- - Offload all model weights
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- - Optimizations
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- - Alternative approach: Host some model weights in GPU memory
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- - Model Scaling on 1 GPU
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- - Token Generation Performance
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- - Models
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- The current trends in artificial intelligence (AI) domains such as image, speech, and natural language, demonstrate that model quality can be improved by increasing model size. In natural language processing, for example, the state-of-the-art (SOTA) model has grown from 300 million parameters (Bert-Large) to 500 billion parameters (Megatron-Turing-530B) in less than four years. However, this dramatic growth in model sizes has significantly increased the GPU cost to train, finetune or inference these models, making them unaffordable to most users. To democratize access to AI innovations, large organizations, such as Hugging Face (BigScience), Meta, and Yandex have recently publicly released pre-trained massive models. Unfortunately, even these publicly available models are not broadly usable because many users cannot afford the dozens of GPUs required to fit them for inference computation. For example, half-precision inference computation on Megatron-Turing-530B (SOTA model for natural language) requires at least 40 A100-40GB GPUs, which is unaffordable to many students, model scientists, hobbyists, and small businesses that could benefit from using these powerful models. And so, a real concern is that if the dramatic increase in model sizes continues, then a growing fraction of users could be excluded from the benefits of these AI innovations.
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- DeepSpeed, a part of Microsoft’s AI at Scale Initiative, has developed the ZeRO-Inference technology to address these obstacles to AI democratization. ZeRO-Inference comes from the family of ZeRO technologies, which are a collection of powerful memory and parallelism optimizations for efficient large scale model training and inference on modern GPU clusters. DeepSpeed had previously developed ZeRO-Infinity, a technology that leverages heterogeneous memory (GPU, CPU, and NVMe) to efficiently scale model training to extreme levels. ZeRO-Inference adapts and optimizes ZeRO-Infinity techniques for model inference on GPUs by hosting the model weights in CPU or NVMe memory, thus hosting no (zero) weights in GPU. This approach is inspired by the observation that the aggregate capacity of CPU and NVMe memories in most commodity computing devices (e.g., laptops, desktops, workstations, etc.) is on the order of terabytes and sufficient to host the largest known models for inference computation. By leveraging this non-GPU memory, ZeRO-Inference enables inference computation of massive models (with hundreds of billions of parameters) on as few as a single GPU, thereby making massive model inference accessible to almost everyone. Moreover, by dramatically reducing GPU memory requirements with CPU or NVMe memory which are significantly cheaper, it significantly reduces the cost of massive model inference, offering an affordable inference path to SOTA models.
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- The massive computational requirements of large model inference means that accelerators like GPUs are required for efficient execution. Therefore, an important design decision for large model inference on limited GPU budget is how to apportion GPU memory among model weights, inference inputs, and intermediate results.
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- ZeRO-Inference pins the entire model weights in CPU or NVMe (whichever is sufficient to accommodate the full model) and streams the weights layer-by-layer into the GPU for inference computation. After computing a layer, the outputs are retained in GPU memory as inputs for the next layer, while memory consumed by the layer weights is released for use by the next layer. Thus, model inference time is composed of the time to compute the layers on GPU, and the time to fetch the layers over PCIe. For large model inference, this approach provides scaling and efficiency benefits, as explained below.
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- ZeRO-Inference offers scaling benefits in two ways. First, by keeping just one (or a few) model layers in GPU memory at any time, ZeRO-Inference significantly reduces the amount of GPU memory required to inference massive models. For current SOTA models which have about a hundred layers (e.g., 96 and 105 layers in GPT3-175B and Megatron-Turing-530B respectively), ZeRO-Inference reduces the GPU memory requirements by up to two orders of magnitude. For example, with ZeRO-Inference, GPU memory consumption of Megaton-Turing-530B for half-precision inference drops from 1TB to 10GB. Second, by fitting the model into CPU or NVMe memory which are orders of magnitude cheaper than GPU memory, ZeRO-Inference makes scaling to future SOTA models (e.g., with trillions or tens-of-trillions of parameters) more affordable compared to approaches that fit the entire model into GPU memory.
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- ZeRO-Inference delivers efficient computation for throughput-oriented inference applications despite the latency of fetching model weights from CPU or NVMe over PCIe interconnect. The primary reason for this is that by limiting GPU memory usage of the model to one or a few layers of weights, ZeRO-Inference can use the majority of GPU memory to support a large amount of input tokens in the form of long sequences or large batch sizes. A large model layer requires a significant amount of computation, especially when processing inputs with many input tokens. For example, one GPT3-175B layer requires about 7 TFlops to process an input of batch size 1 and sequence length of 2048. Therefore, for inference scenarios with long sequence length and large batch sizes, the computation time dominates the latency of fetching model weights, which ultimately improves efficiency. In summary, ZeRO-Inference’s strategy to utilize GPU memory to support large number of input tokens results in high performance inference for large models.
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- To further improve system efficiency, ZeRO-Inference leverages two additional optimizations to reduce the latency of fetching layer weights from CPU or NVMe memory into GPU memory.
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- The first optimization involves overlapping the fetch of a layer with the computation of an earlier layer, a.k.a., layer prefetching. Layer prefetching allows ZeRO-Inference to hide portions of the transfer latency of the prefetched layers. This is especially useful when computation time is not large enough or cannot be sufficiently increased (e.g., with larger batch size) to dominate the latency of fetching layer weights.
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- The second optimization, which is applicable for inference on multiple GPUs, involves parallelizing the fetch of each layer across multiple GPUs by using each GPU to fetch only a portion of the layer. Employing the aggregate PCIe links of the GPUs in this manner essentially increases the transfer bandwidth linearly, thus reducing the latency. With this approach, fetching layers into GPU memory occurs in two phases. First, each GPU independently fetches a partition of the layer over PCIe into its memory. At this point, only a partition of the layer will be resident on each GPU. Next, each GPU assembles the full layer for computation by fetching the missing layer pieces from other GPUs over the high-bandwidth GPU-GPU interconnect (e.g., NVLink, xGMI, etc.). Since GPU-GPU interconnect bandwidth is typically over an order of magnitude higher than PCIe bandwidth, efficient multi-GPU or multi-node communication primitives, such as NCCL or RCCL all-gather, can be used to efficiently assemble the full layer on all GPUs with negligible latency compared to the PCIe latency.
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- An alternative approach to ZeRO-Inference is to pin as many of the model weights as possible into GPU memory and fetch the remainder (from CPU or NVMe) when needed for computation. A benefit of this approach is avoidance of the latency of fetching weights that are already pinned in GPU memory. However, this approach has two downsides: (i) the latency savings for hundred-billion parameter models are negligible since only a small fraction of the weights can fit in GPU memory, and (ii) even when a decent portion of the model weights can fit (e.g., > 50% for ~10B models), the remaining GPU memory can only fit small batch sizes which hurts inference throughput. We later show evaluation results to demonstrate that this approach is sub-optimal.
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- ZeRO-Inference enables significant model scaling for inference on a single GPU compared to a baseline that hosts the model in GPU memory (i.e., HBM). As an example, we consider half-precision model inference using a single NVIDIA Tesla V100 GPU in a NVIDIA DGX2 system. While the V100 GPU has 32GB of memory, the system is equipped with 1.5TB of CPU DRAM and 30TB of NVMe storage. The maximum model size supported for inference computation on GPU depends on the memory in which the model is hosted. Figure 1 below shows the achievable model scales in this system for GPU inference with ZeRO-Inference. In comparison, the baseline cannot support models larger than 16 billion parameters for GPU inference1. In contrast, ZeRO-Inference has the flexibility to host the model in a different memory (DRAM or NVMe) than HBM. This flexibility allows ZeRO-Inference to support much larger models than baseline. For example, by hosting a model on NVMe memory, Zero-Inference can support models with up to 15 trillion parameters for GPU inference, which is almost a thousand times larger compared to baseline. A practical takeaway from Figure 1 is that ZeRO-Inference enables single GPU inference computation of current SOTA models, since they are smaller than 15 trillion parameters.
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- An important inference workload is token generation based on an input prompt. In this workload the model is provided a text sequence as input prompt, and based on this prompt, the model generates output text of configurable length. We use this workload to demonstrate the performance of ZeRO-Inference. This workload consists of two phases: (1) the prompt processing phase where the model processes the input prompt, and (2) the generation phase where the model generates the output tokens.
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- ZeRO-Inference is targeted for throughput-oriented inference applications, and so the performance metric that we use for this workload is the number of tokens generated per second in the generation phase. We use the Hugging Face token generation pipeline in our experiments to measure the performance of using a greedy search algorithm to generate ten output tokens given an input prompt of four tokens. The generation pipeline in our experiments uses KV-caching optimization to improve performance by caching generated tokens to avoid re-computation. We consider the performance impact of three aspects of ZeRO-Inference design choices and optimizations: (1) full offloading model weights as opposed to partial offloading, (2) prefetching layer weights ahead of use, and (3) using multiple GPUs to parallelize layer fetching over PCIe. Additionally, we measure the performance impact of varying the number of output tokens.
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- For our experiments, we use the three publicly available massive language models listed in Table 1. We configure these models for half-precision inference computations. ZeRO-Inference is required to inference these models on a single V100-32GB since they are bigger than GPU memory.
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- A key design choice in ZeRO-Offload is to offload all the weights of models larger than GPU memory rather than host a subset of the weights in GPU memory. Our intuition for this approach is that for throughput-oriented inference applications, the larger batch sizes enabled by full offload yields better performance than partial offload. In Table 2, we present results for OPT-30B token generation on a single V100-32GB that compare fully offloading the model weights versus hosting a portion (i.e., 10 and 12 billion parameters2) in GPU memory. The results show that full offload delivers the best performance for both CPU memory (43 tokens per second) and NVMe memory (30 tokens per second). With both CPU and NVMe memory, full offload is over 1.3x and 2.4x faster than partial offload of 18 and 20 billion parameters respectively. The performance advantage of full offload comes from the larger batch sizes compared to the partial offload options. Thus when a model does not fit in GPU, using GPU memory to increase batch size rather than to partially fit the model leads to faster token generation.
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- ZeRO-Inference fetches layers ahead of use, overlapping with current layer computation, to hide layer transfer latency. We measure the impact of prefetching on token generation performance on a single V100-32GB and summarize the results in Table 3. We observe that prefetching did not improve CPU offload. This is because the relatively short sequences in token generation (i.e., less than 50 tokens) resulted in layer computation time that is insufficient to hide a significant portion of layer fetch time from CPU. In contrast, prefetching improves NVMe offloading performance by 1.13x, 1.14x and 1.21x for OPT-30B, OPT-175B, and BLOOM-176B respectively. This is because transferring weights from NVMe through CPU memory allows prefetching to overlap transfers from CPU to GPU memory with transfers from NVMe to CPU boosting the effective transfer bandwidth.
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- ZeRO-Inference leverages the four PCIe interconnects between GPUs and CPU memory to parallelize layer fetching for faster inference computations on multiple GPUs. In Table 4, we report the throughput improvements for token generation on two and four GPUs compared to a single GPU3 . These results were collected with layer prefetching enabled. The reported throughput numbers are per GPU showing that token generation becomes faster on each GPU as the aggregated PCIe links reduce the layer fetch latencies. The improved per GPU throughput translates to super-linear scaling performance. Additionally, these results suggest improved bandwidths of future PCIe generations could help to improve ZeRO-Inference performance.
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- We measure the performance impact of the number of output tokens since the memory overhead of KV-caching optimization increases with longer output tokens and could limit batch size. First, we consider the impact of token lengths 10, 20, 50, and 100 on batch size that can fit one V100-32GB GPU. The results in Table 5 show a 2X reduction in batch size for a 5X increase in token count (compared to baseline count of 10).
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- Next, we measure the impact on generation throughput using four V100-32GB GPUs. The results are presented in Table 6 for CPU offload, and Table 7 for NVMe-Offload. We observe an impact that is consistent across models and offload memory, which is that increasing the number of output tokens reduces throughput proportionally to batch size reduction. These results also demonstrate the importance of large batch sizes to the performance of ZeRO-Inference.
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- We briefly discuss how users can determine when ZeRO-Inference is suitable for their application and how to enable ZeRO-Inference in DeepSpeed.
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- ZeRO-Inference is designed for inference applications that require GPU acceleration but lack sufficient GPU memory to host the model. Also, ZeRO-Inference is optimized for inference applications that are throughput-oriented and allow large batch sizes. Alternative techniques, such as Accelerate, DeepSpeed-Inference, and DeepSpeed-MII that fit the entire model into GPU memory, possibly using multiple GPUs, are more suitable for inference applications that are latency sensitive or have small batch sizes.
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- ZeRO-Inference is available in the DeepSpeed library versions >= 0.6.6. Integrating ZeRO-Inference into token generation pipelines, such as Hugging Face generate, requires updating the DeepSpeed configuration to set ZeRO optimization to stage 3 and parameter offloading to CPU or NVMe.
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- Below is a configuration snippet for enabling ZeRO-Inference with offloading to CPU memory.
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- Below is a configuration snippet for offloading to a NVMe device mounted on “/local_nvme”.
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- Recent advances in AI technology have primarily come from extreme scaling of model sizes. However, extreme model scaling has also made the hardware cost of training and inferencing prohibitive for all but the largest organizations, severely restricting access to AI innovations. To help democratize AI, we developed ZeRO-Inference, a technology that enables inference computations of massive models on as few as a single GPU. ZeRO-Inference reduces the GPU cost of SOTA model inference by hosting the model on CPU or NVMe memory and streaming the model layers into GPU memory for inference computation. ZeRO-Inference complements the democratization efforts of large organizations that publicly release pre-trained SOTA models by ensuring that inference computation of these models is affordable for most users (e.g., students, hobbyists, model scientists, etc.).
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- The DeepSpeed team would like to acknowledge Stas Bekman for previewing this blog and providing valuable feedback.
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- 16 billion parameters model won’t fit in V100-32GB for half-precision inference since no memory will be left for inputs and intermediate results. ↩
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- Pinning more parameters in GPU memory resulted in out of memory errors for small batch sizes. ↩
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- For multiple GPU runs, we select GPUs with independent PCIe interconnects to CPU memory. ↩
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- Updated: September 9, 2022
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- **Examples:**
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- ...
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- ```
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- # Deepspeed - 2020
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- ## DeepSpeed Microsoft Research Webinar is now on-demand
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- **URL:** https://www.deepspeed.ai/2020/08/06/webinar-on-demand.html
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- **Contents:**
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- - DeepSpeed Microsoft Research Webinar is now on-demand
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- - Contents
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- Updated: August 6, 2020
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- ## An Order-of-Magnitude Larger and Faster Training with ZeRO-2
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- **URL:** https://www.deepspeed.ai/2020/05/18/zero-stage2.html
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- **Contents:**
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- - An Order-of-Magnitude Larger and Faster Training with ZeRO-2
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- ZeRO-2 expands the scope of memory optimizations in the original ZeRO by tackling the full spectrum of memory consumption during training. More specifically, ZeRO-2 introduces new technology to reduce the memory footprint of gradients, activation memory, and fragmented memory, in addition to optimizer state memory optimization in the original ZeRO. Altogether, the memory savings empower DeepSpeed to improve the scale and speed of deep learning training by an order of magnitude. More concretely, ZeRO-2 allows training models as large as 170 billion parameters up to 10x faster compared to state of the art.
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- For more information on ZeRO-2, see our blog post.
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- For more information on how to use ZeRO-2, see an example of training GPT family of models in this tutorial.
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- For a technical overview, see our technical report.
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- Updated: May 18, 2020
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- ## 10x bigger model training on a single GPU with ZeRO-Offload
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- **URL:** https://www.deepspeed.ai/2020/09/08/ZeRO-Offload.html
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- - 10x bigger model training on a single GPU with ZeRO-Offload
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- We introduce a new technology called ZeRO-Offload to enable 10X bigger model training on a single GPU. ZeRO-Offload extends ZeRO-2 to leverage both CPU and GPU memory for training large models. Using a machine with a single GPU, our users now can run models of up to 13 billion parameters without running out of memory, 10x bigger than the existing approaches, while obtaining competitive throughput. This feature democratizes multi-billion-parameter model training and opens the window for many deep learning practitioners to explore bigger and better models.
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- ## Progressive Layer Dropping
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- **URL:** https://www.deepspeed.ai/2020/10/28/progressive-layer-dropping-news.html
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- - Progressive Layer Dropping
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- We introduce a new technology called progressive layer dropping (PLD) to speedup the pre-training of Transformer-based networks through efficient and robust compressed training. The pre-training step of Transformer networks often suffer from unbearable overall computational expenses. We analyze the training dynamics and stability of Transformer networks and propose PLD to sparsely update Transformer blocks following a progressive dropping schedule, which smoothly increases the layer dropping rate for each mini-batch as training evolves along both the temporal and the model depth dimension. PLD is able to allow the pre-training to be 2.5X faster to get similar accuracy on downstream tasks and allows the training to be 24% faster when training the same number of samples, not at the cost of excessive hardware resources.
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- ## ZeRO-2 & DeepSpeed: Shattering Barriers of Deep Learning Speed & Scale
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- **URL:** https://www.deepspeed.ai/2020/05/18/press-release.html
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- - ZeRO-2 & DeepSpeed: Shattering Barriers of Deep Learning Speed & Scale
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- Updated: May 18, 2020
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- ## ZeRO stage 1 with reduced communication
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- **URL:** https://www.deepspeed.ai/2020/03/17/reduce-scatter.html
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- - ZeRO stage 1 with reduced communication
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- - Further updates coming soon!
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- Updated: March 17, 2020
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- ## Powering 10x longer sequences and 6x faster execution through DeepSpeed Sparse Attention
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- **URL:** https://www.deepspeed.ai/2020/09/08/sparse-attention-news.html
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- - Powering 10x longer sequences and 6x faster execution through DeepSpeed Sparse Attention
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- DeepSpeed offers sparse attention kernels, an instrumental technology to support long sequences of model inputs, whether for text, image, or sound. Compared with the classic dense Transformers, it powers an order-of-magnitude longer input sequence and obtains up to 6x faster execution with comparable accuracy. It also outperforms state-of-the-art sparse implementations with 1.5-3x faster execution. Furthermore, our sparse kernels support efficient execution of flexible sparse format and empower users to innovate on their custom sparse structures.
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- ## ZeRO & DeepSpeed: New system optimizations enable training models with over 100 billion parameters
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- **URL:** https://www.deepspeed.ai/2020/02/13/release.html
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- - ZeRO & DeepSpeed: New system optimizations enable training models with over 100 billion parameters
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- ## Microsoft DeepSpeed achieves the fastest BERT training time
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- **URL:** https://www.deepspeed.ai/2020/05/27/fastest-bert-training.html
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- - Microsoft DeepSpeed achieves the fastest BERT training time
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- - Performance Results for BERT Pretraining
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- - Performance Results for Fine-Tuning Tasks
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- - BERT Highly Optimized Transformer Kernels
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- - (a) Advanced fused kernels to reduce data movement
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- - (b) Invertible operators to save memory and run large batches
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- - Overlapping I/O with Computation through Asynchronous Prefetching Queue
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- - Exploiting Sparsity of BERT’s Output Processing
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- - Pre-LayerNorm vs Post-LayerNorm Architecture
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- Good news! DeepSpeed obtains the fastest BERT training record: 44 minutes on 1024 NVIDIA V100 GPU. This is a 30% improvement over the best published result of 67 mins in end-to-end training time to achieve the same accuracy on the same number and generation of GPUs. This improvement does not come at the cost of excessive hardware resources but comes from improved software efficiency. For example, DeepSpeed can attain a staggering 64 teraflops of single GPU performance on a NVIDIA V100 GPU which is over 50% of the hardware peak.
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- In this blog post, we will discuss four technological improvements that enable DeepSpeed to achieve this record-breaking BERT training time.
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- These optimizations not only benefit BERT; they are also applicable to many other transformer-based models such as RoBERTa, XLNet, and UniLM. Furthermore, besides the improvements mentioned for pre-training, DeepSpeed achieves up to 1.5x speedups for the downstream tasks, such as the fine-tuning for Bing-BERT SQuAD.
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- Compared to SOTA, DeepSpeed significantly improves single GPU performance for transformer-based model like BERT. Figure 1 shows the single GPU throughput of training BERT-Large optimized through DeepSpeed, comparing with the two well-known PyTorch implementations from NVIDIA BERT and Hugging Face BERT. DeepSpeed reaches as high as 64 and 53 teraflops throughputs (corresponding to 272 and 52 samples/second) for sequence lengths 128 and 512, respectively, exhibiting up to 28% throughput improvements over NVIDIA BERT and up to 62% over HuggingFace BERT. We also support up to 1.8x larger batch size without running out of memory.
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- To achieve this performance, DeepSpeed implements a stochastic transformer which exhibits some level of non-deterministic noise without affecting overall convergence. In addition, DeepSpeed also implements a deterministic transformer kernel that is completely reproducible at the expense of a small performance regression of approximately 2% on average. Users can easily choose and switch between the two versions depending on their usage scenarios: Stochastic version pursues ultimate training performance goal, and deterministic version may save development time by better facilitating experimentation and debugging. We report performance numbers for both these kernels in Figure 1. The performance numbers were collected with a gradient accumulation step of 10 for all batch sizes and configurations, since on average an overall batch size used in practical scenarios range from a few hundred to a few thousand.
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- Figure 1: Performance evaluation of BERT-Large on a single V100 GPU, comparing DeepSpeed with NVIDIA and HuggingFace versions of BERT in mixed-sequence length training. The labeled points show the highest throughput of each implementation in teraflops (Tflops). DeepSpeed boosts throughput and allows for higher batch sizes without running out-of-memory.
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- Looking at distributed training across GPUs, Table 1 shows our end-to-end BERT-Large pre-training time (F1 score of 90.5 for SQUAD) using 16 to 1024 GPUs. We complete BERT pre-training in 44 minutes using 1024 V100 GPUs (64 NVIDIA DGX-2 nodes). In comparison, the previous SOTA from NVIDIA takes 47 mins using 1472 V100 GPUs. DeepSpeed is not only faster but also uses 30% less resources. Using the same 1024 GPUS,NVIDIA BERT takes 67 minutes using the same 1024 GPUs [1] BERT, whereas DeepSpeed takes 44 minutes, reducing training time by 30%. Similarly, on 256 GPUs, NVIDIA BERT takes 236 minutes while DeepSpeed takes 144 minutes (39% faster).
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- Table 1: BERT-Large training time using 1 to 64 DGX-2’s with DeepSpeed.
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- At the recent GTC 2020, NVIDIA announced the next generation hardware A100, which now offers 2.5X hardware peak performance over the V100 GPU. Assuming the A100 GPU allows us to obtain the same percentage of hardware peak performance (50%) as we obtained on V100 GPUs, we expect to obtain even higher throughput by combining our software optimizations with the new hardware. We project it would reduce BERT training time further to less than 25 minutes on a cluster of 1024 A100 GPUs.
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- In addition to the performance benefits we show for the pre-training, we have evaluated the performance of our customized kernel for fine-tuning the downstream tasks. Tables 2 and 3 show the samples-per-second achieved when running Bing-BERT SQuAD on NVIDIA V100 using 16 and 32 GB of memory, using PyTorch and DeepSpeed transformer kernels. For the 16-GB V100, we can achieve up to 1.5x speedup while supporting 2x larger batch size per GPU. On the other hand, we can support as large as 32 batch size (2.6x more than Pytorch) using 32GB of memory, while providing 1.3x speedup for the end-to-end fine-tune training. Note, that we use the best samples-per-second to compute speedup for the cases that PyTorch runs out-of-memory (OOM).
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- Table 2. Samples/second for running SQuAD fine-tuning on NVIDIA V100 (16-GB) using PyTorch and DeepSpeed transformer kernels.
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- Table 3: Samples/second for running SQuAD fine-tuning on NVIDIA V100 (32-GB) using PyTorch and DeepSpeed transformer kernels.
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- GPUs have very high peak floating-point throughput, but the default Transformer blocks in most framework implementations are far from reaching this peak. Figure 2 shows the structure of a Transformer block with the LayerNorm placed on the input stream of the two sublayers: Attention and Feed-Forward. To approach the GPU peak performance, we employ two lines of optimizations in our own Transformer kernel implementation: advanced fusion, and invertible operators.
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- Figure 2: Transformer Layer with Pre-LayerNorm Architecture
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- We observe that transformer-based networks trigger many invocations of CUDA kernels operating in a producer-consumer fashion, adding a lot of cost for transferring data to and from global memory and overhead from kernel launching. Existing compiler-based approaches perform fine-grained fusion (e.g., fusion of element-wise operations), leading to missed fusion opportunities. In contrast, we fully exploit both fine-grain and coarse-grained fusion, tailored for Transformer blocks.
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- QKV and various fusions. We merge the three Query (Q), Key (K), and Value (V) weight matrices to dispatch a larger QKV GEMM to expose more parallelism and improve data locality on GPU’s shared memory and register files, as shown in Figure 3. Next, we combine the data-layout transformation of the QKV’s output matrix with the bias addition. We then partition the large QKV matrix into three transformed ones, used for the following self-attention computation.
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- As Figure 3 illustrates, we read the QKV matrix in consecutive rows (shown by red box), and write them in the three transformed Q, K, and V matrices. Since each matrix starts from a different offset, we may have uncoalesced access to the main memory. Thus, we use the shared memory as an intermediate buffer, in order to rearrange the data in a way that we can put the data in consecutive parts of memory. Even though we produce an uncoalesced pattern when accessing shared memory, we reduce the cost of uncoalesced access to main memory to better exploit memory bandwidth, resulting in 3% to 5% performance improvement in the end-to-end training.
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- Figure 3: QKV’s GEMM and transform Kernel-Fusion
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- We perform additional fusions such as merging the addition of bias from the attention-output GEMM with the addition from the residual connection and also dropout, which allows accesses to happen in the register files and shared memory, which are orders of magnitude faster than the expensive write-back to the global memory.
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- Warp-level communication. To alleviate the synchronization overhead among parallel GPU cores and further increase the resource utilization of the fused kernels, we use the warp-level (data shuffle instructions) instead of the default inter-warp communication. Take the layer-normalization and SoftMax kernel as examples, we perform each reduction operation inside a warp, while distributing different reductions across different warps. This way, we alleviate the synchronization among the parallel threads and further increase the GPU resource utilization.
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- Stochastic vs deterministic kernels. DL training is generally robust to some level of stochasticity, and in some cases, controlled noises such as dropouts act as regularizer which improve generalization. In designing our transformer kernel, we embrace some level of stochasticity to improve throughput by allowing for limited data race conditions to exist in the kernel: We leverage implicit warp synchronous programming to achieve higher performance for the warp-level cooperative operations [3]. The lack of explicit warp level synchronization act as non-deterministic noise without affecting the overall convergence behavior of the transformer kernels while giving a decent throughput boost.
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- In addition, DeepSpeed also implements a non-stochastic transformer kernel with explicit warp synchronization that produces deterministic results at the expense of a small performance regression. Users can easily choose and switch between the two versions depending on their usage scenarios: Stochastic version pursues ultimate training performance goal, and deterministic version may save development time by better facilitating experimentation and debugging.
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- In our experiments, we use stochastic kernels for the pre-training BERT, while using non-stochastic kernels for fine-tuning to achieve fully reproducible results. We recommend using stochastic kernels for training tasks involving massive amounts of data such as pre-training, while using non-stochastic version when training with limited data such as in the case of fine-tuning for more consistent results.
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- Cost-effective rematerialization. When fusing kernels of the different operations, we observe that some operators are inexpressive to compute but incur expensive data movement cost, such as addition of bias and dropout. For these operations, we avoid saving their results in the forward pass, but instead recompute them during the backward pass, which turns out to be much faster than having their results written and reloaded from the main memory.
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- We also observe that the intermediate activations from several operators in the Transformer blocks incur a large memory consumption, such as SoftMax and Layer Norm. For these operators, we drop the inputs to these layers to reduce the footprint of activation memory, by leveraging the fact that they are invertible functions, which are functions whose backward pass is independent of the inputs and can be formulated based only on the outputs [2]. Figure 4 and Figure 5 show the examples of the original implementation of SoftMax and Layer-Norm in PyTorch versus the invertible SoftMax implementation in DeepSpeed. Through this optimization, we are able to reduce the activation memory of the operator by half, and the reduced memory allows us to train with larger batch sizes, which once again improves GPU efficiency.
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- Figure 4: DeepSpeed invertible SoftMax operation versus Default PyTorch SoftMax operation
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- Figure 5: DeepSpeed invertible LayerNorm operation versus Default PyTorch LayerNorm operation
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- Beyond highly optimized transformer kernels, the BERT training has other performance limiting factors, e.g., data loading. We develop our own asynchronous worker which prefetches batches of data into a queue only at “safe points” – points when the CPUs are idle (e.g., right after asynchronously launching the forward pass). In this way, we make sure that there is no dequeuing and copying data from CPU to GPU when there is computation on the CPU side. This is different from the default PyTorch data loader, which can prefetch data at any points and cause performance interference. By using this method, we hide almost all I/O overhead, which accounts for 4% of the original training time.
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- We improve the end-to-end training time by 5.4% by recognizing and exploiting sparsity in BERT’s output processing. The output processing involves two steps: i) BERT projection from the hidden output dimension of the final transformer layer to the language vocabulary, using a matrix-matrix multiplication, and ii) a cross-entropy of the masked output tokens to the get each sequence’s prediction error. The cost of the first step is proportional to the vocabulary size, hidden output dimension and the sequence length, and can be as expensive as a transformer layer computation or more. However, only about 15% of the tokens are masked, and we only need the cross-entropy for the masked tokens. Therefore, the projection can be done as an efficient sparse computation. To do so, we discard the rows of the final transformer layer that corresponding to the non-masked tokens before doing the projection, reducing the computation cost of output processing by 85%.
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- We observe that with large batch size (e.g., 64K) the default BERT pre-training suffers from training instability, which can result in model divergence or convergence to bad/suspicious local optima. Further investigation shows that the default BERT has vanishing gradients issue. To mitigate the issue, we changed the placement of LayerNorm (Post-LayerNorm) by placing it only on the input stream of the sublayers in the Transformer block (called Pre-LayerNorm), a modification described by several recent works for neural machine translation. The Pre-LayerNorm results in several useful characteristics such as avoiding vanishing gradient, stable optimization, and performance gain. It allows us to train at aggregated batch size of 64K with increased learning rate and faster convergence.
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- To try out these optimizations and training recipe, please check out our BERT training tutorial and source code at the DeepSpeed GitHub repo.
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- [1] “NVIDIA Clocks World’s Fastest BERT Training Time and Largest Transformer Based Model, Paving Path For Advanced Conversational AI” https://devblogs.nvidia.com/training-bert-with-gpus/.
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- [2] S. R. Bulo, L. Porzi, and P. Kontschieder, “In-place activated batch norm for memory-optimized training of dnns” 2017. http://arxiv.org/abs/1712.02616.
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- [3] Mark Harris and Kyrylo Perelygin, “Cooperative Groups: Flexible CUDA Thread Programming”, https://devblogs.nvidia.com/cooperative-groups/.
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- ## Training a Trillion Parameters with Pipeline Parallelism
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- **URL:** https://www.deepspeed.ai/2020/09/08/pipeline-parallelism.html
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- **Contents:**
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- DeepSpeed includes new support for pipeline parallelism! DeepSpeed’s training engine provides hybrid 3D parallelism for training models with over a trillion parameters. In addition to scaling to the extreme, we have demonstrated that hybrid parallelism accelerates training on clusters with low-bandwidth network by up to 7x.
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- ## Turing-NLG: A 17-billion-parameter language model by Microsoft
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- **URL:** https://www.deepspeed.ai/2020/02/13/turing-nlg.html
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- **Contents:**
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- - Turing-NLG: A 17-billion-parameter language model by Microsoft
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- - Contents
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- Updated: February 13, 2020
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- ## Up to 5x less communication and 3.4x faster training through 1-bit Adam
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- **URL:** https://www.deepspeed.ai/2020/09/08/onebit-adam-news.html
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- **Contents:**
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- - Up to 5x less communication and 3.4x faster training through 1-bit Adam
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- Adam is an effective and probably the most well-utilized optimizer for training many large-scale deep learning models. However, Adam is generally not compatible with communication-efficient optimization algorithms, and therefore the communication cost could become a bottleneck while scaling across distributed devices. We introduce a new algorithm - 1-bit Adam - and its efficient implementation in DeepSpeed. 1-bit Adam offers the same convergence as Adam, incurs up to 5x less communication that enables up to 3.5x higher throughput for BERT-Large pretraining and up to 2.7x higher throughput for SQuAD fine-tuning on bandwidth-limited clusters.
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- ## DeepSpeed Sparse Attention
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- **URL:** https://www.deepspeed.ai/2020/09/08/sparse-attention.html
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- **Contents:**
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- - DeepSpeed Sparse Attention
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- - Contents
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- - Performance Results
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- Attention-based deep learning models such as the transformers are highly effective in capturing the relationship between tokens in an input sequence, even across long distances. As a result, they are used with text, image, and sound-based inputs, where the sequence length can be in thousands of tokens. However, despite the effectiveness of attention modules to capture long term dependencies, in practice, their application to long sequence input is limited by compute and memory requirements of the attention computation that grow quadratically, O(n^2), with the sequence length n.
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- To address this limitation, DeepSpeed offers a suite of sparse attention kernels –an instrumental technology that can reduce the compute and memory requirement of attention computation by orders-of-magnitude via block-sparse computation. The suite not only alleviates the memory bottleneck of attention calculation, but also performs sparse computation efficiently. Its APIs allow convenient integration with any transformer-based models. Along with providing a wide spectrum of sparsity structures, it has the flexibility of handling any user-defined block-sparse structures. More specifically, sparse attention (SA) can be designed to compute local attention between nearby tokens, or global attention via summary tokens computed with local attention. Moreover, SA can also allow random attention, or any combination of local, global, and random attention as shown in the following figure with blue, orange, and green blocks, respectively. As a result, SA decreases the memory footprint to O(wn), in which 1 < w < n is a parameter, whose value depends on the attention structure.
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- This library is PyTorch based and develops required kernels through Triton platform; kernels are not written in CUDA, which leaves the door open for CPU/OpenCL/Vulkan support in the future. The library is an extension to DeepSpeed and can be used through DeepSpeed as well as stand alone. Block-sparse computations handled by DeepSpeed Sparse Attention kernels are illustrated in following figures for forward and backward passes respectively. In the figures, S stands for a block-sparse matrix and D a dense matrix.
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- To learn more about Sparsity Config, and also how to use this library, please check our tutorial that provides detailed information about it.
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- We also define a template to have variable structure (top figure), which can be used to simply customize any block-sparse random/local/global attention pattern. In addition to this list, user can add any other sparsity structure as described in tutorial section.
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- ## The Fastest and Most Efficient BERT Training through Optimized Transformer Kernels
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- **URL:** https://www.deepspeed.ai/2020/05/18/bert-record.html
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- **Contents:**
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- - The Fastest and Most Efficient BERT Training through Optimized Transformer Kernels
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- We introduce new technology to accelerate single GPU performance via kernel optimizations. These optimizations not only create a strong foundation for scaling out large models, but also improve the single GPU performance of highly tuned and moderately sized models like BERT by more than 30%, reaching a staggering performance of 66 teraflops per V100 GPU, which is 52% of the hardware peak. Using optimized transformer kernels as the building block, DeepSpeed achieves the fastest BERT training record: 44 minutes on 1,024 NVIDIA V100 GPUs, compared with the best published result of 67 minutes on the same number and generation of GPUs.
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- ## DeepSpeed Microsoft Research Webinar on August 6th, 2020
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- **URL:** https://www.deepspeed.ai/2020/07/23/deepspeed-webinar.html
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- - DeepSpeed Microsoft Research Webinar on August 6th, 2020
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- ## DeepSpeed with 1-bit Adam: 5x less communication and 3.4x faster training
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- **URL:** https://www.deepspeed.ai/2020/09/08/onebit-adam-blog-post.html
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- **Contents:**
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- - DeepSpeed with 1-bit Adam: 5x less communication and 3.4x faster training
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- - Contents
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- - 1. Introduction
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- - 1.1 Background: Classic compression techniques
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- - 1.2 Challenges in applying error-compensation to Adam
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- - 2. Compressing communication with 1-bit Adam
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- - 2.1 How 1-bit Adam works under the hood
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- - 2.2 Addressing system challenges for 1-bit Adam
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- - 3. Benefits of 1-bit Adam on communication-constrained systems
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- - 4. Dive deeper into 1-bit Adam evaluation results
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- Scalable training of large models (like BERT and GPT-3) requires careful optimization rooted in model design, architecture, and system capabilities. From a system standpoint, communication has become a major bottleneck, especially on commodity systems with standard TCP interconnects that offer limited network bandwidth. Communication compression is an important technique to reduce training time on such systems. One of the most effective ways to compress communication is via error compensation compression, which offers robust convergence speed, even under 1-bit compression. However, state-of-the-art error compensation techniques only work with basic optimizers like Stochastic Gradient Descent (SGD) and momentum SGD, which are linearly dependent on the gradients. They do not work with non-linear gradient-based optimizers like Adam, which offers state-of-the-art convergence efficiency and accuracy for many tasks, including training of BERT-like models. For a powerful optimizer like ADAM, the non-linear dependency on gradient (in the variance term) makes it challenging to develop error compensation-based compression techniques, limiting the practical value of the state-of-the-art communication compression techniques.
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- One way of communication compression is 1-bit compression, which can be expressed as:
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- With this compression, we could achieve a 32x reduction of memory size by representing each number using one bit. The problem is that using this straightforward method would significantly degrade the convergence speed, which makes this method inapplicable. To solve this problem, recent studies show that by using error compensation compression, we could expect almost the same convergence rate with communication compression. The idea of error compensation can be summarized as: 1) doing compression, 2) memorizing the compression error, and then 3) adding the compression error back in during the next iteration. For SGD, doing error compression leads to:
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- Where C(⋅) is the 1-bit compression operator. The good thing about doing this error compensation is that the history compression error (e_t and e_(t-1)) would be canceled by itself eventually, which can be seen by:
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- This strategy has been proven to work for optimization algorithms that are linearly dependent on the gradient, such as SGD and Momentum SGD.
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- We provide an overview of the Adam algorithm below. The update rules are as follows.
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- As shown in the equations above, the variance term v_t is nonlinearly dependent on the gradient g_t. If we apply basic error compensation compression to Adam, we observe that Adam will not converge as shown in Figure 1.
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- Figure 1: Inapplicability of Error-compensation Compression for Adam due to non-linear dependence on the gradient
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- To compress communication while using the Adam optimizer, we develop 1-bit Adam, which addresses the non-linearity in gradients via preconditioning. We observe that the magnitude of changes on the non-linear term, variance ( v_t), decrease significantly after a few epochs of training and setting v_t constant afterwards will not change the convergence speed. The proposed 1-bit Adam optimizer, as shown in Figure 2, consists of two parts: the warmup stage, which is essentially the vanilla Adam algorithm; and the compression stage, which keeps the variance term constant and compresses the remaining linear term, that is the momentum, into 1-bit representation.
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- The compression stage of the algorithm is controlled by a threshold parameter (as shown in Figure 2). When we detect that the change in “variance” falls below a certain threshold, we switch to the compression stage. Our study shows that only 15-20% of the overall training steps are needed for the warmup stage.
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- Figure 2: Comparison of distributed training steps in classic Adam and the proposed 1-bit compressed Adam algorithm
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- The weight update rule for 1-bit Adam is governed by the following equations.
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- For the i-th worker, in the compression stage:
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- Where x_t is the model after iteration (t-1), m_t^(i), e_t^(i) are the momentum and compression error on worker i after iteration (t-1), and v_warmup is the variance term after the warmup stage.
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- Besides the algorithmic challenge, there are two system challenges in applying 1-bit Adam in training systems. First, we need efficient kernels that convert the momentum to 1-bit representations. Second, we need efficient communication schemes to exchange this compressed momentum across different GPUs. The goal of compression is to reduce the overall training time so that commodity systems with bandwidth-limited interconnects can be used to train large models. We address these challenges in DeepSpeed and introduce a fully optimized 1-bit Adam implementation for training on communication-constrained systems.
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- 1-bit Adam offers the same convergence as Adam, incurs up to 5x less communication that enables up to 3.5x higher throughput for BERT-Large pretraining and up to 2.7x higher throughput for SQuAD fine-tuning. This end-to-end throughput improvement is enabled by the 6.6x (Figure 3) and 6.2x (Figure 4) speedup observed during the compression stage. It is worth mentioning that our 1-bit Adam optimizer scales so well on a 40 Gigabit Ethernet system that its performance is comparable to Adam’s scalability on a 40 Gigabit InfiniBand QDR system. We note that the effective bandwidth on 40 Gigabit Ethernet is 4.1 Gbps based on iperf benchmarks whereas InfiniBand provides near-peak bandwidth of 32Gbps based on InfiniBand perftest microbenchmarks.
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- Figure 3: Scalability of 1-bit Adam for BERT-Large Pretraining on V100 GPUs with batch size of 16/GPU.
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- Figure 4: Scalability of 1-bit Adam for SQuAD Finetuning on V100 GPUs with batch size of 3/GPU.
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- One major question for using 1-bit Adam is the convergence speed, and we find that 1-bit Adam can achieve the same convergence speed and comparable testing performance using the same number of training samples as shown in Figure 5.
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- Figure 5: 1-bit Adam converges like Adam using the same number of training samples.
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- Detailed BERT-Base and BERT-Large results are shown in Table 1. We see that the scores are on par with or better than the original model for both the uncompressed and compressed cases.
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- Table 1: Verifying correctness of 1-bit Adam on various testing tasks
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- Up to 5x less communication: 1-bit Adam provides the same convergence as Adam and reduces the communication volume by 16x during the compression stage for 16-bit (FP16) training. For BERT pretraining, this leads to an overall communication reduction of 5x as we observed the warmup stage to be just 15% of the end-to-end training time.
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- The formula to calculate the communication volume ratio of the original versus 1-bit Adam is as follows:
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- In the case of warmup equaling 15%, original Adam incurs 5x of the communication as 1-bit Adam.
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- We present two main results for training BERT-Large on systems with two different bandwidth-limited interconnects: 1) 40 gigabit Ethernet (Figure 5) and 2) 40 gbps InfiniBand QDR (Figure 6). During the compression phase, we observe up to 6.6x higher throughput on the system with Ethernet and up to 2x higher throughput on the system with InfiniBand, resulting in end-to-end speed up (including both warmup and compression stages) of 3.5x and 2.7x, respectively. The major benefit of 1-bit Adam comes from the communication volume reduction—enabled by our compressed momentum exchange—and from our custom allreduce operation that implements efficient 1-bit communication using non-blocking gather operations followed by an allgather operation.
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- It is important to note that one can also increase total batch size to reduce communication using optimizers like LAMB instead of Adam for BERT pretraining. However, 1-bit Adam avoids the need for rigorous hyperparameter tuning, which is often more difficult for large batches from our experience. Furthermore, 1-bit Adam also works very well for workloads that have small critical batch size (cannot converge well with large batch size) like many fine-tuning tasks.
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- Figure 5: Performance of 1-bit Adam for BERT-Large training on 40 Gbps Ethernet interconnect during the compression stage.
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- Figure 6: Performance of 1-bit Adam for BERT-Large training on 40 Gbps InfiniBand interconnect during the compression stage.
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- 1-bit Adam offers scalability not only on large-scale training tasks but also on tasks like SQuAD fine-tuning. As shown in Figures 7 and 8, 1-bit Adam scales well on both Ethernet- and InfiniBand-based systems and offers up to 6.2x higher throughput (during the compression stage) on the Ethernet-based system, resulting in 2.7x end-to-end speedup (25% warmup plus 75% compression stage). For SQuAD fine-tuning, we observed that a total batch size of 96 offers the best F1 score. Batch sizes larger than this value lower the convergence rate and require additional hyperparameter tuning. Therefore, in order to scale to 32 GPUs, we can only apply a small batch size of 3-4 per GPU. This makes fine-tuning tasks communication intensive and hard to scale. 1-bit Adam addresses the scaling challenge well, obtaining 3.4x communication reduction without enlarging batch size, and it results in a 2.7x end-to-end speedup.
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- Figure 7: Performance of 1-bit Adam for SQuAD fine-tuning on 40 gbps Ethernet during the compression stage.
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- Figure 8: Performance of 1-bit Adam for SQuAD fine-tuning on 40 gbps InfiniBand interconnect during the compression stage.
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- **Examples:**
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- Example 1 (unknown):
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- ```unknown
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- 1 / (warmup + (1 – warmup)/16)
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- ```
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