@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.
- package/bin/synsc +0 -0
- package/package.json +1 -1
- package/bin/skills/accelerate/SKILL.md +0 -332
- package/bin/skills/accelerate/references/custom-plugins.md +0 -453
- package/bin/skills/accelerate/references/megatron-integration.md +0 -489
- package/bin/skills/accelerate/references/performance.md +0 -525
- package/bin/skills/adaptyv/SKILL.md +0 -114
- package/bin/skills/adaptyv/reference/api_reference.md +0 -308
- package/bin/skills/adaptyv/reference/examples.md +0 -913
- package/bin/skills/adaptyv/reference/experiments.md +0 -360
- package/bin/skills/adaptyv/reference/protein_optimization.md +0 -637
- package/bin/skills/aeon/SKILL.md +0 -374
- package/bin/skills/aeon/references/anomaly_detection.md +0 -154
- package/bin/skills/aeon/references/classification.md +0 -144
- package/bin/skills/aeon/references/clustering.md +0 -123
- package/bin/skills/aeon/references/datasets_benchmarking.md +0 -387
- package/bin/skills/aeon/references/distances.md +0 -256
- package/bin/skills/aeon/references/forecasting.md +0 -140
- package/bin/skills/aeon/references/networks.md +0 -289
- package/bin/skills/aeon/references/regression.md +0 -118
- package/bin/skills/aeon/references/segmentation.md +0 -163
- package/bin/skills/aeon/references/similarity_search.md +0 -187
- package/bin/skills/aeon/references/transformations.md +0 -246
- package/bin/skills/alphafold-database/SKILL.md +0 -513
- package/bin/skills/alphafold-database/references/api_reference.md +0 -423
- package/bin/skills/anndata/SKILL.md +0 -400
- package/bin/skills/anndata/references/best_practices.md +0 -525
- package/bin/skills/anndata/references/concatenation.md +0 -396
- package/bin/skills/anndata/references/data_structure.md +0 -314
- package/bin/skills/anndata/references/io_operations.md +0 -404
- package/bin/skills/anndata/references/manipulation.md +0 -516
- package/bin/skills/arboreto/SKILL.md +0 -243
- package/bin/skills/arboreto/references/algorithms.md +0 -138
- package/bin/skills/arboreto/references/basic_inference.md +0 -151
- package/bin/skills/arboreto/references/distributed_computing.md +0 -242
- package/bin/skills/arboreto/scripts/basic_grn_inference.py +0 -97
- package/bin/skills/astropy/SKILL.md +0 -331
- package/bin/skills/astropy/references/coordinates.md +0 -273
- package/bin/skills/astropy/references/cosmology.md +0 -307
- package/bin/skills/astropy/references/fits.md +0 -396
- package/bin/skills/astropy/references/tables.md +0 -489
- package/bin/skills/astropy/references/time.md +0 -404
- package/bin/skills/astropy/references/units.md +0 -178
- package/bin/skills/astropy/references/wcs_and_other_modules.md +0 -373
- package/bin/skills/audiocraft/SKILL.md +0 -564
- package/bin/skills/audiocraft/references/advanced-usage.md +0 -666
- package/bin/skills/audiocraft/references/troubleshooting.md +0 -504
- package/bin/skills/autogpt/SKILL.md +0 -403
- package/bin/skills/autogpt/references/advanced-usage.md +0 -535
- package/bin/skills/autogpt/references/troubleshooting.md +0 -420
- package/bin/skills/awq/SKILL.md +0 -310
- package/bin/skills/awq/references/advanced-usage.md +0 -324
- package/bin/skills/awq/references/troubleshooting.md +0 -344
- package/bin/skills/axolotl/SKILL.md +0 -158
- package/bin/skills/axolotl/references/api.md +0 -5548
- package/bin/skills/axolotl/references/dataset-formats.md +0 -1029
- package/bin/skills/axolotl/references/index.md +0 -15
- package/bin/skills/axolotl/references/other.md +0 -3563
- package/bin/skills/benchling-integration/SKILL.md +0 -480
- package/bin/skills/benchling-integration/references/api_endpoints.md +0 -883
- package/bin/skills/benchling-integration/references/authentication.md +0 -379
- package/bin/skills/benchling-integration/references/sdk_reference.md +0 -774
- package/bin/skills/bigcode-evaluation-harness/SKILL.md +0 -405
- package/bin/skills/bigcode-evaluation-harness/references/benchmarks.md +0 -393
- package/bin/skills/bigcode-evaluation-harness/references/custom-tasks.md +0 -424
- package/bin/skills/bigcode-evaluation-harness/references/issues.md +0 -394
- package/bin/skills/biopython/SKILL.md +0 -443
- package/bin/skills/biopython/references/advanced.md +0 -577
- package/bin/skills/biopython/references/alignment.md +0 -362
- package/bin/skills/biopython/references/blast.md +0 -455
- package/bin/skills/biopython/references/databases.md +0 -484
- package/bin/skills/biopython/references/phylogenetics.md +0 -566
- package/bin/skills/biopython/references/sequence_io.md +0 -285
- package/bin/skills/biopython/references/structure.md +0 -564
- package/bin/skills/biorxiv-database/SKILL.md +0 -483
- package/bin/skills/biorxiv-database/references/api_reference.md +0 -280
- package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +0 -445
- package/bin/skills/bioservices/SKILL.md +0 -361
- package/bin/skills/bioservices/references/identifier_mapping.md +0 -685
- package/bin/skills/bioservices/references/services_reference.md +0 -636
- package/bin/skills/bioservices/references/workflow_patterns.md +0 -811
- package/bin/skills/bioservices/scripts/batch_id_converter.py +0 -347
- package/bin/skills/bioservices/scripts/compound_cross_reference.py +0 -378
- package/bin/skills/bioservices/scripts/pathway_analysis.py +0 -309
- package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +0 -408
- package/bin/skills/bitsandbytes/SKILL.md +0 -411
- package/bin/skills/bitsandbytes/references/memory-optimization.md +0 -521
- package/bin/skills/bitsandbytes/references/qlora-training.md +0 -521
- package/bin/skills/bitsandbytes/references/quantization-formats.md +0 -447
- package/bin/skills/blip-2/SKILL.md +0 -564
- package/bin/skills/blip-2/references/advanced-usage.md +0 -680
- package/bin/skills/blip-2/references/troubleshooting.md +0 -526
- package/bin/skills/brenda-database/SKILL.md +0 -719
- package/bin/skills/brenda-database/references/api_reference.md +0 -537
- package/bin/skills/brenda-database/scripts/brenda_queries.py +0 -844
- package/bin/skills/brenda-database/scripts/brenda_visualization.py +0 -772
- package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +0 -1053
- package/bin/skills/cellxgene-census/SKILL.md +0 -511
- package/bin/skills/cellxgene-census/references/census_schema.md +0 -182
- package/bin/skills/cellxgene-census/references/common_patterns.md +0 -351
- package/bin/skills/chembl-database/SKILL.md +0 -389
- package/bin/skills/chembl-database/references/api_reference.md +0 -272
- package/bin/skills/chembl-database/scripts/example_queries.py +0 -278
- package/bin/skills/chroma/SKILL.md +0 -406
- package/bin/skills/chroma/references/integration.md +0 -38
- package/bin/skills/cirq/SKILL.md +0 -346
- package/bin/skills/cirq/references/building.md +0 -307
- package/bin/skills/cirq/references/experiments.md +0 -572
- package/bin/skills/cirq/references/hardware.md +0 -515
- package/bin/skills/cirq/references/noise.md +0 -515
- package/bin/skills/cirq/references/simulation.md +0 -350
- package/bin/skills/cirq/references/transformation.md +0 -416
- package/bin/skills/citation-management/SKILL.md +0 -1109
- package/bin/skills/citation-management/assets/bibtex_template.bib +0 -264
- package/bin/skills/citation-management/assets/citation_checklist.md +0 -386
- package/bin/skills/citation-management/references/bibtex_formatting.md +0 -908
- package/bin/skills/citation-management/references/citation_validation.md +0 -794
- package/bin/skills/citation-management/references/google_scholar_search.md +0 -725
- package/bin/skills/citation-management/references/metadata_extraction.md +0 -870
- package/bin/skills/citation-management/references/pubmed_search.md +0 -839
- package/bin/skills/citation-management/scripts/doi_to_bibtex.py +0 -182
- package/bin/skills/citation-management/scripts/extract_metadata.py +0 -570
- package/bin/skills/citation-management/scripts/format_bibtex.py +0 -349
- package/bin/skills/citation-management/scripts/search_google_scholar.py +0 -251
- package/bin/skills/citation-management/scripts/search_pubmed.py +0 -348
- package/bin/skills/citation-management/scripts/validate_citations.py +0 -494
- package/bin/skills/clinical-decision-support/README.md +0 -129
- package/bin/skills/clinical-decision-support/SKILL.md +0 -506
- package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +0 -380
- package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +0 -222
- package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +0 -359
- package/bin/skills/clinical-decision-support/assets/color_schemes.tex +0 -149
- package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +0 -208
- package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +0 -328
- package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +0 -529
- package/bin/skills/clinical-decision-support/references/biomarker_classification.md +0 -719
- package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +0 -604
- package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +0 -840
- package/bin/skills/clinical-decision-support/references/outcome_analysis.md +0 -640
- package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +0 -427
- package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +0 -521
- package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +0 -383
- package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +0 -417
- package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +0 -509
- package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +0 -441
- package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +0 -326
- package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +0 -641
- package/bin/skills/clinical-reports/README.md +0 -236
- package/bin/skills/clinical-reports/SKILL.md +0 -1127
- package/bin/skills/clinical-reports/assets/case_report_template.md +0 -352
- package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +0 -353
- package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +0 -359
- package/bin/skills/clinical-reports/assets/consult_note_template.md +0 -305
- package/bin/skills/clinical-reports/assets/discharge_summary_template.md +0 -453
- package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +0 -395
- package/bin/skills/clinical-reports/assets/history_physical_template.md +0 -305
- package/bin/skills/clinical-reports/assets/lab_report_template.md +0 -309
- package/bin/skills/clinical-reports/assets/pathology_report_template.md +0 -249
- package/bin/skills/clinical-reports/assets/quality_checklist.md +0 -338
- package/bin/skills/clinical-reports/assets/radiology_report_template.md +0 -318
- package/bin/skills/clinical-reports/assets/soap_note_template.md +0 -253
- package/bin/skills/clinical-reports/references/case_report_guidelines.md +0 -570
- package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +0 -693
- package/bin/skills/clinical-reports/references/data_presentation.md +0 -530
- package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -629
- package/bin/skills/clinical-reports/references/medical_terminology.md +0 -588
- package/bin/skills/clinical-reports/references/patient_documentation.md +0 -744
- package/bin/skills/clinical-reports/references/peer_review_standards.md +0 -585
- package/bin/skills/clinical-reports/references/regulatory_compliance.md +0 -577
- package/bin/skills/clinical-reports/scripts/check_deidentification.py +0 -332
- package/bin/skills/clinical-reports/scripts/compliance_checker.py +0 -78
- package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +0 -97
- package/bin/skills/clinical-reports/scripts/format_adverse_events.py +0 -97
- package/bin/skills/clinical-reports/scripts/generate_report_template.py +0 -149
- package/bin/skills/clinical-reports/scripts/terminology_validator.py +0 -126
- package/bin/skills/clinical-reports/scripts/validate_case_report.py +0 -323
- package/bin/skills/clinical-reports/scripts/validate_trial_report.py +0 -88
- package/bin/skills/clinicaltrials-database/SKILL.md +0 -507
- package/bin/skills/clinicaltrials-database/references/api_reference.md +0 -358
- package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +0 -215
- package/bin/skills/clinpgx-database/SKILL.md +0 -638
- package/bin/skills/clinpgx-database/references/api_reference.md +0 -757
- package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +0 -518
- package/bin/skills/clinvar-database/SKILL.md +0 -362
- package/bin/skills/clinvar-database/references/api_reference.md +0 -227
- package/bin/skills/clinvar-database/references/clinical_significance.md +0 -218
- package/bin/skills/clinvar-database/references/data_formats.md +0 -358
- package/bin/skills/clip/SKILL.md +0 -253
- package/bin/skills/clip/references/applications.md +0 -207
- package/bin/skills/cobrapy/SKILL.md +0 -463
- package/bin/skills/cobrapy/references/api_quick_reference.md +0 -655
- package/bin/skills/cobrapy/references/workflows.md +0 -593
- package/bin/skills/colab-finetuning/SKILL.md +0 -153
- package/bin/skills/colab-finetuning/references/bridge-setup.md +0 -68
- package/bin/skills/colab-finetuning/references/gpu-tiers.md +0 -54
- package/bin/skills/colab-finetuning/references/troubleshooting.md +0 -79
- package/bin/skills/constitutional-ai/SKILL.md +0 -290
- package/bin/skills/cosmic-database/SKILL.md +0 -336
- package/bin/skills/cosmic-database/references/cosmic_data_reference.md +0 -220
- package/bin/skills/cosmic-database/scripts/download_cosmic.py +0 -231
- package/bin/skills/crewai/SKILL.md +0 -498
- package/bin/skills/crewai/references/flows.md +0 -438
- package/bin/skills/crewai/references/tools.md +0 -429
- package/bin/skills/crewai/references/troubleshooting.md +0 -480
- package/bin/skills/dask/SKILL.md +0 -456
- package/bin/skills/dask/references/arrays.md +0 -497
- package/bin/skills/dask/references/bags.md +0 -468
- package/bin/skills/dask/references/best-practices.md +0 -277
- package/bin/skills/dask/references/dataframes.md +0 -368
- package/bin/skills/dask/references/futures.md +0 -541
- package/bin/skills/dask/references/schedulers.md +0 -504
- package/bin/skills/datacommons-client/SKILL.md +0 -255
- package/bin/skills/datacommons-client/references/getting_started.md +0 -417
- package/bin/skills/datacommons-client/references/node.md +0 -250
- package/bin/skills/datacommons-client/references/observation.md +0 -185
- package/bin/skills/datacommons-client/references/resolve.md +0 -246
- package/bin/skills/datamol/SKILL.md +0 -706
- package/bin/skills/datamol/references/conformers_module.md +0 -131
- package/bin/skills/datamol/references/core_api.md +0 -130
- package/bin/skills/datamol/references/descriptors_viz.md +0 -195
- package/bin/skills/datamol/references/fragments_scaffolds.md +0 -174
- package/bin/skills/datamol/references/io_module.md +0 -109
- package/bin/skills/datamol/references/reactions_data.md +0 -218
- package/bin/skills/deepchem/SKILL.md +0 -597
- package/bin/skills/deepchem/references/api_reference.md +0 -303
- package/bin/skills/deepchem/references/workflows.md +0 -491
- package/bin/skills/deepchem/scripts/graph_neural_network.py +0 -338
- package/bin/skills/deepchem/scripts/predict_solubility.py +0 -224
- package/bin/skills/deepchem/scripts/transfer_learning.py +0 -375
- package/bin/skills/deepspeed/SKILL.md +0 -141
- package/bin/skills/deepspeed/references/08.md +0 -17
- package/bin/skills/deepspeed/references/09.md +0 -173
- package/bin/skills/deepspeed/references/2020.md +0 -378
- package/bin/skills/deepspeed/references/2023.md +0 -279
- package/bin/skills/deepspeed/references/assets.md +0 -179
- package/bin/skills/deepspeed/references/index.md +0 -35
- package/bin/skills/deepspeed/references/mii.md +0 -118
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- package/bin/skills/deepspeed/references/tutorials.md +0 -6554
- package/bin/skills/deeptools/SKILL.md +0 -531
- package/bin/skills/deeptools/assets/quick_reference.md +0 -58
- package/bin/skills/deeptools/references/effective_genome_sizes.md +0 -116
- package/bin/skills/deeptools/references/normalization_methods.md +0 -410
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- package/bin/skills/deeptools/references/workflows.md +0 -474
- package/bin/skills/deeptools/scripts/validate_files.py +0 -195
- package/bin/skills/deeptools/scripts/workflow_generator.py +0 -454
- package/bin/skills/denario/SKILL.md +0 -215
- package/bin/skills/denario/references/examples.md +0 -494
- package/bin/skills/denario/references/installation.md +0 -213
- package/bin/skills/denario/references/llm_configuration.md +0 -265
- package/bin/skills/denario/references/research_pipeline.md +0 -471
- package/bin/skills/diffdock/SKILL.md +0 -483
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- package/bin/skills/diffdock/scripts/analyze_results.py +0 -334
- package/bin/skills/diffdock/scripts/prepare_batch_csv.py +0 -254
- package/bin/skills/diffdock/scripts/setup_check.py +0 -278
- package/bin/skills/dnanexus-integration/SKILL.md +0 -383
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- package/bin/skills/uspto-database/scripts/trademark_client.py +0 -311
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# Lambda Labs Advanced Usage Guide
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## Multi-Node Distributed Training
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### PyTorch DDP across nodes
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```python
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# train_multi_node.py
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import os
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import torch
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import torch.distributed as dist
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def setup_distributed():
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# Environment variables set by launcher
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dist.init_process_group(
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def main():
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model = MyModel().cuda(local_rank)
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model = DDP(model, device_ids=[local_rank])
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# Training loop with synchronized gradients
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train_one_epoch(model, dataloader)
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# Save checkpoint on rank 0 only
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dist.destroy_process_group()
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main()
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### Launch on multiple instances
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```bash
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# On Node 0 (master)
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export MASTER_ADDR=<NODE0_PRIVATE_IP>
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export MASTER_PORT=29500
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torchrun \
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--nnodes=2 \
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--nproc_per_node=8 \
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--master_addr=$MASTER_ADDR \
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train_multi_node.py
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torchrun \
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--nnodes=2 \
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--nproc_per_node=8 \
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--node_rank=1 \
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--master_addr=$MASTER_ADDR \
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--master_port=$MASTER_PORT \
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train_multi_node.py
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### FSDP for large models
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### DeepSpeed ZeRO
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```bash
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# Launch with DeepSpeed
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deepspeed --num_nodes=2 \
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## API Automation
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### Auto-launch training jobs
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```python
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class LambdaJobManager:
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response = api.launch_instance(request)
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raise TimeoutError(f"Instance {instance_id} not ready after {timeout}s")
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def terminate(self, instance_ids: list[str]):
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["gpu_8x_h100_sxm5", "gpu_8x_a100_80gb_sxm4"],
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if gpu_type:
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instance = manager.launch_and_wait(
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gpu_type, region,
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filesystem="training-data"
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)
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print(f"Ready: ssh ubuntu@{instance['ip']}")
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### Batch job submission
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```python
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import subprocess
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import paramiko
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def run_remote_job(ip: str, ssh_key_path: str, commands: list[str]):
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"""Execute commands on remote instance."""
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client = paramiko.SSHClient()
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client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
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client.connect(ip, username="ubuntu", key_filename=ssh_key_path)
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for cmd in commands:
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stdin, stdout, stderr = client.exec_command(cmd)
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print(stdout.read().decode())
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if stderr.read():
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print(f"Error: {stderr.read().decode()}")
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client.close()
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# Submit training job
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commands = [
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"cd /lambda/nfs/storage/project",
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"git pull",
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249
|
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"pip install -r requirements.txt",
|
|
250
|
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"nohup torchrun --nproc_per_node=8 train.py > train.log 2>&1 &"
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251
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]
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252
|
-
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253
|
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run_remote_job(instance["ip"], "~/.ssh/lambda_key", commands)
|
|
254
|
-
```
|
|
255
|
-
|
|
256
|
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### Monitor training progress
|
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257
|
-
|
|
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|
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```python
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|
259
|
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def monitor_job(ip: str, ssh_key_path: str, log_file: str = "train.log"):
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"""Stream training logs from remote instance."""
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|
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import time
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262
|
-
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|
263
|
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client = paramiko.SSHClient()
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|
264
|
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client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
|
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265
|
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client.connect(ip, username="ubuntu", key_filename=ssh_key_path)
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266
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-
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267
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# Tail log file
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stdin, stdout, stderr = client.exec_command(f"tail -f {log_file}")
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269
|
-
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270
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try:
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for line in stdout:
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print(line.strip())
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273
|
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except KeyboardInterrupt:
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pass
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finally:
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276
|
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client.close()
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|
277
|
-
```
|
|
278
|
-
|
|
279
|
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## 1-Click Cluster Workflows
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280
|
-
|
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281
|
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### Slurm job submission
|
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282
|
-
|
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283
|
-
```bash
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284
|
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#!/bin/bash
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285
|
-
#SBATCH --job-name=llm-training
|
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286
|
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#SBATCH --nodes=4
|
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287
|
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#SBATCH --ntasks-per-node=8
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288
|
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#SBATCH --gpus-per-node=8
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289
|
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#SBATCH --time=24:00:00
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290
|
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#SBATCH --output=logs/%j.out
|
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291
|
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#SBATCH --error=logs/%j.err
|
|
292
|
-
|
|
293
|
-
# Set up distributed environment
|
|
294
|
-
export MASTER_ADDR=$(scontrol show hostnames $SLURM_JOB_NODELIST | head -n 1)
|
|
295
|
-
export MASTER_PORT=29500
|
|
296
|
-
|
|
297
|
-
# Launch training
|
|
298
|
-
srun torchrun \
|
|
299
|
-
--nnodes=$SLURM_NNODES \
|
|
300
|
-
--nproc_per_node=$SLURM_GPUS_PER_NODE \
|
|
301
|
-
--rdzv_backend=c10d \
|
|
302
|
-
--rdzv_endpoint=$MASTER_ADDR:$MASTER_PORT \
|
|
303
|
-
train.py \
|
|
304
|
-
--config config.yaml
|
|
305
|
-
```
|
|
306
|
-
|
|
307
|
-
### Interactive cluster session
|
|
308
|
-
|
|
309
|
-
```bash
|
|
310
|
-
# Request interactive session
|
|
311
|
-
srun --nodes=1 --ntasks=1 --gpus=8 --time=4:00:00 --pty bash
|
|
312
|
-
|
|
313
|
-
# Now on compute node with 8 GPUs
|
|
314
|
-
nvidia-smi
|
|
315
|
-
python train.py
|
|
316
|
-
```
|
|
317
|
-
|
|
318
|
-
### Monitoring cluster jobs
|
|
319
|
-
|
|
320
|
-
```bash
|
|
321
|
-
# View job queue
|
|
322
|
-
squeue
|
|
323
|
-
|
|
324
|
-
# View job details
|
|
325
|
-
scontrol show job <JOB_ID>
|
|
326
|
-
|
|
327
|
-
# Cancel job
|
|
328
|
-
scancel <JOB_ID>
|
|
329
|
-
|
|
330
|
-
# View node status
|
|
331
|
-
sinfo
|
|
332
|
-
|
|
333
|
-
# View GPU usage across cluster
|
|
334
|
-
srun --nodes=4 nvidia-smi --query-gpu=name,utilization.gpu --format=csv
|
|
335
|
-
```
|
|
336
|
-
|
|
337
|
-
## Advanced Filesystem Usage
|
|
338
|
-
|
|
339
|
-
### Data staging workflow
|
|
340
|
-
|
|
341
|
-
```bash
|
|
342
|
-
# Stage data from S3 to filesystem (one-time)
|
|
343
|
-
aws s3 sync s3://my-bucket/dataset /lambda/nfs/storage/datasets/
|
|
344
|
-
|
|
345
|
-
# Or use rclone
|
|
346
|
-
rclone sync s3:my-bucket/dataset /lambda/nfs/storage/datasets/
|
|
347
|
-
```
|
|
348
|
-
|
|
349
|
-
### Shared filesystem across instances
|
|
350
|
-
|
|
351
|
-
```python
|
|
352
|
-
# Instance 1: Write checkpoints
|
|
353
|
-
checkpoint_path = "/lambda/nfs/shared/checkpoints/model_step_1000.pt"
|
|
354
|
-
torch.save(model.state_dict(), checkpoint_path)
|
|
355
|
-
|
|
356
|
-
# Instance 2: Read checkpoints
|
|
357
|
-
model.load_state_dict(torch.load(checkpoint_path))
|
|
358
|
-
```
|
|
359
|
-
|
|
360
|
-
### Filesystem best practices
|
|
361
|
-
|
|
362
|
-
```bash
|
|
363
|
-
# Organize for ML workflows
|
|
364
|
-
/lambda/nfs/storage/
|
|
365
|
-
├── datasets/
|
|
366
|
-
│ ├── raw/ # Original data
|
|
367
|
-
│ └── processed/ # Preprocessed data
|
|
368
|
-
├── models/
|
|
369
|
-
│ ├── pretrained/ # Base models
|
|
370
|
-
│ └── fine-tuned/ # Your trained models
|
|
371
|
-
├── checkpoints/
|
|
372
|
-
│ └── experiment_1/ # Per-experiment checkpoints
|
|
373
|
-
├── logs/
|
|
374
|
-
│ └── tensorboard/ # Training logs
|
|
375
|
-
└── outputs/
|
|
376
|
-
└── inference/ # Inference results
|
|
377
|
-
```
|
|
378
|
-
|
|
379
|
-
## Environment Management
|
|
380
|
-
|
|
381
|
-
### Custom Python environments
|
|
382
|
-
|
|
383
|
-
```bash
|
|
384
|
-
# Don't modify system Python, create venv
|
|
385
|
-
python -m venv ~/myenv
|
|
386
|
-
source ~/myenv/bin/activate
|
|
387
|
-
|
|
388
|
-
# Install packages
|
|
389
|
-
pip install torch transformers accelerate
|
|
390
|
-
|
|
391
|
-
# Save to filesystem for reuse
|
|
392
|
-
cp -r ~/myenv /lambda/nfs/storage/envs/myenv
|
|
393
|
-
```
|
|
394
|
-
|
|
395
|
-
### Conda environments
|
|
396
|
-
|
|
397
|
-
```bash
|
|
398
|
-
# Install miniconda (if not present)
|
|
399
|
-
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
|
|
400
|
-
bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3
|
|
401
|
-
|
|
402
|
-
# Create environment
|
|
403
|
-
~/miniconda3/bin/conda create -n ml python=3.10 pytorch pytorch-cuda=12.1 -c pytorch -c nvidia -y
|
|
404
|
-
|
|
405
|
-
# Activate
|
|
406
|
-
source ~/miniconda3/bin/activate ml
|
|
407
|
-
```
|
|
408
|
-
|
|
409
|
-
### Docker containers
|
|
410
|
-
|
|
411
|
-
```bash
|
|
412
|
-
# Pull and run NVIDIA container
|
|
413
|
-
docker run --gpus all -it --rm \
|
|
414
|
-
-v /lambda/nfs/storage:/data \
|
|
415
|
-
nvcr.io/nvidia/pytorch:24.01-py3
|
|
416
|
-
|
|
417
|
-
# Run training in container
|
|
418
|
-
docker run --gpus all -d \
|
|
419
|
-
-v /lambda/nfs/storage:/data \
|
|
420
|
-
-v $(pwd):/workspace \
|
|
421
|
-
nvcr.io/nvidia/pytorch:24.01-py3 \
|
|
422
|
-
python /workspace/train.py
|
|
423
|
-
```
|
|
424
|
-
|
|
425
|
-
## Monitoring and Observability
|
|
426
|
-
|
|
427
|
-
### GPU monitoring
|
|
428
|
-
|
|
429
|
-
```bash
|
|
430
|
-
# Real-time GPU stats
|
|
431
|
-
watch -n 1 nvidia-smi
|
|
432
|
-
|
|
433
|
-
# GPU utilization over time
|
|
434
|
-
nvidia-smi dmon -s u -d 1
|
|
435
|
-
|
|
436
|
-
# Detailed GPU info
|
|
437
|
-
nvidia-smi -q
|
|
438
|
-
```
|
|
439
|
-
|
|
440
|
-
### System monitoring
|
|
441
|
-
|
|
442
|
-
```bash
|
|
443
|
-
# CPU and memory
|
|
444
|
-
htop
|
|
445
|
-
|
|
446
|
-
# Disk I/O
|
|
447
|
-
iostat -x 1
|
|
448
|
-
|
|
449
|
-
# Network
|
|
450
|
-
iftop
|
|
451
|
-
|
|
452
|
-
# All resources
|
|
453
|
-
glances
|
|
454
|
-
```
|
|
455
|
-
|
|
456
|
-
### TensorBoard integration
|
|
457
|
-
|
|
458
|
-
```bash
|
|
459
|
-
# Start TensorBoard
|
|
460
|
-
tensorboard --logdir /lambda/nfs/storage/logs --port 6006 --bind_all
|
|
461
|
-
|
|
462
|
-
# SSH tunnel from local machine
|
|
463
|
-
ssh -L 6006:localhost:6006 ubuntu@<IP>
|
|
464
|
-
|
|
465
|
-
# Access at http://localhost:6006
|
|
466
|
-
```
|
|
467
|
-
|
|
468
|
-
### Weights & Biases integration
|
|
469
|
-
|
|
470
|
-
```python
|
|
471
|
-
import wandb
|
|
472
|
-
|
|
473
|
-
# Initialize with API key
|
|
474
|
-
wandb.login(key=os.environ["WANDB_API_KEY"])
|
|
475
|
-
|
|
476
|
-
# Start run
|
|
477
|
-
wandb.init(
|
|
478
|
-
project="lambda-training",
|
|
479
|
-
config={"learning_rate": 1e-4, "epochs": 100}
|
|
480
|
-
)
|
|
481
|
-
|
|
482
|
-
# Log metrics
|
|
483
|
-
wandb.log({"loss": loss, "accuracy": acc})
|
|
484
|
-
|
|
485
|
-
# Save artifacts to filesystem + W&B
|
|
486
|
-
wandb.save("/lambda/nfs/storage/checkpoints/best_model.pt")
|
|
487
|
-
```
|
|
488
|
-
|
|
489
|
-
## Cost Optimization Strategies
|
|
490
|
-
|
|
491
|
-
### Checkpointing for interruption recovery
|
|
492
|
-
|
|
493
|
-
```python
|
|
494
|
-
import os
|
|
495
|
-
|
|
496
|
-
def save_checkpoint(model, optimizer, epoch, loss, path):
|
|
497
|
-
torch.save({
|
|
498
|
-
'epoch': epoch,
|
|
499
|
-
'model_state_dict': model.state_dict(),
|
|
500
|
-
'optimizer_state_dict': optimizer.state_dict(),
|
|
501
|
-
'loss': loss,
|
|
502
|
-
}, path)
|
|
503
|
-
|
|
504
|
-
def load_checkpoint(path, model, optimizer):
|
|
505
|
-
if os.path.exists(path):
|
|
506
|
-
checkpoint = torch.load(path)
|
|
507
|
-
model.load_state_dict(checkpoint['model_state_dict'])
|
|
508
|
-
optimizer.load_state_dict(checkpoint['optimizer_state_dict'])
|
|
509
|
-
return checkpoint['epoch'], checkpoint['loss']
|
|
510
|
-
return 0, float('inf')
|
|
511
|
-
|
|
512
|
-
# Save every N steps to filesystem
|
|
513
|
-
checkpoint_path = "/lambda/nfs/storage/checkpoints/latest.pt"
|
|
514
|
-
if step % 1000 == 0:
|
|
515
|
-
save_checkpoint(model, optimizer, epoch, loss, checkpoint_path)
|
|
516
|
-
```
|
|
517
|
-
|
|
518
|
-
### Instance selection by workload
|
|
519
|
-
|
|
520
|
-
```python
|
|
521
|
-
def recommend_instance(model_params: int, batch_size: int, task: str) -> str:
|
|
522
|
-
"""Recommend Lambda instance based on workload."""
|
|
523
|
-
|
|
524
|
-
if task == "inference":
|
|
525
|
-
if model_params < 7e9:
|
|
526
|
-
return "gpu_1x_a10" # $0.75/hr
|
|
527
|
-
elif model_params < 13e9:
|
|
528
|
-
return "gpu_1x_a6000" # $0.80/hr
|
|
529
|
-
else:
|
|
530
|
-
return "gpu_1x_h100_pcie" # $2.49/hr
|
|
531
|
-
|
|
532
|
-
elif task == "fine-tuning":
|
|
533
|
-
if model_params < 7e9:
|
|
534
|
-
return "gpu_1x_a100" # $1.29/hr
|
|
535
|
-
elif model_params < 13e9:
|
|
536
|
-
return "gpu_4x_a100" # $5.16/hr
|
|
537
|
-
else:
|
|
538
|
-
return "gpu_8x_h100_sxm5" # $23.92/hr
|
|
539
|
-
|
|
540
|
-
elif task == "pretraining":
|
|
541
|
-
return "gpu_8x_h100_sxm5" # Maximum performance
|
|
542
|
-
|
|
543
|
-
return "gpu_1x_a100" # Default
|
|
544
|
-
```
|
|
545
|
-
|
|
546
|
-
### Auto-terminate idle instances
|
|
547
|
-
|
|
548
|
-
```python
|
|
549
|
-
import time
|
|
550
|
-
from datetime import datetime, timedelta
|
|
551
|
-
|
|
552
|
-
def auto_terminate_idle(api_key: str, idle_threshold_hours: float = 2):
|
|
553
|
-
"""Terminate instances idle for too long."""
|
|
554
|
-
manager = LambdaJobManager(api_key)
|
|
555
|
-
|
|
556
|
-
with lambda_cloud_client.ApiClient(manager.config) as client:
|
|
557
|
-
api = lambda_cloud_client.DefaultApi(client)
|
|
558
|
-
instances = api.list_instances()
|
|
559
|
-
|
|
560
|
-
for instance in instances.data:
|
|
561
|
-
# Check if instance has been running without activity
|
|
562
|
-
# (You'd need to track this separately)
|
|
563
|
-
launch_time = instance.launched_at
|
|
564
|
-
if datetime.now() - launch_time > timedelta(hours=idle_threshold_hours):
|
|
565
|
-
print(f"Terminating idle instance: {instance.id}")
|
|
566
|
-
manager.terminate([instance.id])
|
|
567
|
-
```
|
|
568
|
-
|
|
569
|
-
## Security Best Practices
|
|
570
|
-
|
|
571
|
-
### SSH key rotation
|
|
572
|
-
|
|
573
|
-
```bash
|
|
574
|
-
# Generate new key pair
|
|
575
|
-
ssh-keygen -t ed25519 -f ~/.ssh/lambda_key_new -C "lambda-$(date +%Y%m)"
|
|
576
|
-
|
|
577
|
-
# Add new key via Lambda console or API
|
|
578
|
-
# Update authorized_keys on running instances
|
|
579
|
-
ssh ubuntu@<IP> "echo '$(cat ~/.ssh/lambda_key_new.pub)' >> ~/.ssh/authorized_keys"
|
|
580
|
-
|
|
581
|
-
# Test new key
|
|
582
|
-
ssh -i ~/.ssh/lambda_key_new ubuntu@<IP>
|
|
583
|
-
|
|
584
|
-
# Remove old key from Lambda console
|
|
585
|
-
```
|
|
586
|
-
|
|
587
|
-
### Firewall configuration
|
|
588
|
-
|
|
589
|
-
```bash
|
|
590
|
-
# Lambda console: Only open necessary ports
|
|
591
|
-
# Recommended:
|
|
592
|
-
# - 22 (SSH) - Always needed
|
|
593
|
-
# - 6006 (TensorBoard) - If using
|
|
594
|
-
# - 8888 (Jupyter) - If using
|
|
595
|
-
# - 29500 (PyTorch distributed) - For multi-node only
|
|
596
|
-
```
|
|
597
|
-
|
|
598
|
-
### Secrets management
|
|
599
|
-
|
|
600
|
-
```bash
|
|
601
|
-
# Don't hardcode API keys in code
|
|
602
|
-
# Use environment variables
|
|
603
|
-
export HF_TOKEN="hf_..."
|
|
604
|
-
export WANDB_API_KEY="..."
|
|
605
|
-
|
|
606
|
-
# Or use .env file (add to .gitignore)
|
|
607
|
-
source .env
|
|
608
|
-
|
|
609
|
-
# On instance, store in ~/.bashrc
|
|
610
|
-
echo 'export HF_TOKEN="..."' >> ~/.bashrc
|
|
611
|
-
```
|