{ "cells": [ { "cell_type": "code", "execution_count": null, "id": "64b666af-def5-4acf-99f1-b1f04c28c22b", "metadata": { "tags": [] }, "outputs": [], "source": [ "import boto3\n", "import sagemaker\n", "client = boto3.client(\"sagemaker\")\n", "sess=sagemaker.Session()\n", "default_bucket= sess.default_bucket()" ] }, { "cell_type": "code", "execution_count": null, "id": "42cb9479-473c-4f03-a40a-24bc1ac6b19a", "metadata": { "tags": [] }, "outputs": [], "source": [ "#User inputs for pipeline run \n", "fasta_file = 'T1030.fasta' #Default pipeline execution name will drop .fasta\n", "!mkdir ./sequence_input/\n", "!curl 'https://www.predictioncenter.org/casp14/target.cgi?target=T1030&view=sequence' > ./sequence_input/T1030.fasta " ] }, { "cell_type": "code", "execution_count": null, "id": "db04f78a-e59f-472c-9738-b2efa4c4662c", "metadata": { "tags": [] }, "outputs": [], "source": [ "#Upload to S3\n", "AminoAcidSeq = open('./sequence_input/T1030.fasta', 'rb')\n", "s3 = boto3.resource('s3')\n", "fastaKey = f'sequence_input/{fasta_file}'\n", "response = s3.Bucket(default_bucket).put_object(Key=fastaKey, Body=AminoAcidSeq)\n", "fasta_s3_uri = f's3://{default_bucket}/{fastaKey}'\n", "experiment_name = fasta_file[:fasta_file.find(\".\")] " ] }, { "cell_type": "code", "execution_count": null, "id": "23db383c-8218-4a2f-b9d7-729ba9e05c4a", "metadata": { "tags": [] }, "outputs": [], "source": [ "response = client.start_pipeline_execution(\n", " PipelineName='ProteinFoldWorkflow',\n", " PipelineExecutionDisplayName= experiment_name,\n", " PipelineExecutionDescription=f'This pipeline was executed via boto3 and is running an inference for {experiment_name}',\n", " PipelineParameters=[\n", " {\n", " 'Name':'FastaFileName',\n", " 'Value':fasta_file,\n", " },\n", " {\n", " 'Name':'FastaInputS3URI',\n", " 'Value':fasta_s3_uri,\n", " },\n", " {\n", " 'Name':'db_preset',\n", " 'Value':'full_dbs',\n", " }, \n", " {\n", " 'Name':'MaxTemplateDate',\n", " 'Value':'2020-05-1',\n", " }, \n", " {\n", " 'Name':'ModelPreset',\n", " 'Value':'monomer',\n", " }, \n", " {\n", " 'Name':'NumMultimerPredictionsPerModel',\n", " 'Value':'5',\n", " }, \n", " {\n", " 'Name':'InferenceInstanceType',\n", " 'Value':'ml.g5.4xlarge',\n", " }, \n", " {\n", " 'Name':'MSAInstanceType',\n", " 'Value':'ml.m5.4xlarge',\n", " }, \n", " ],\n", " ParallelismConfiguration={\n", " 'MaxParallelExecutionSteps': 2\n", " }\n", ")\n", "print(response)" ] } ], "metadata": { "availableInstances": [ { "_defaultOrder": 0, "_isFastLaunch": true, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 4, "name": "ml.t3.medium", "vcpuNum": 2 }, { "_defaultOrder": 1, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 8, "name": "ml.t3.large", "vcpuNum": 2 }, { "_defaultOrder": 2, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 16, "name": "ml.t3.xlarge", "vcpuNum": 4 }, { "_defaultOrder": 3, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 32, "name": "ml.t3.2xlarge", "vcpuNum": 8 }, { "_defaultOrder": 4, "_isFastLaunch": true, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 8, "name": "ml.m5.large", "vcpuNum": 2 }, { "_defaultOrder": 5, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 16, "name": "ml.m5.xlarge", "vcpuNum": 4 }, { "_defaultOrder": 6, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 32, "name": "ml.m5.2xlarge", "vcpuNum": 8 }, { "_defaultOrder": 7, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 64, "name": "ml.m5.4xlarge", "vcpuNum": 16 }, { "_defaultOrder": 8, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 128, "name": "ml.m5.8xlarge", "vcpuNum": 32 }, { "_defaultOrder": 9, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 192, "name": "ml.m5.12xlarge", "vcpuNum": 48 }, { "_defaultOrder": 10, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 256, "name": "ml.m5.16xlarge", "vcpuNum": 64 }, { "_defaultOrder": 11, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 384, "name": "ml.m5.24xlarge", "vcpuNum": 96 }, { "_defaultOrder": 12, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 8, "name": "ml.m5d.large", "vcpuNum": 2 }, { "_defaultOrder": 13, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 16, "name": "ml.m5d.xlarge", "vcpuNum": 4 }, { "_defaultOrder": 14, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 32, "name": "ml.m5d.2xlarge", "vcpuNum": 8 }, { "_defaultOrder": 15, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 64, "name": "ml.m5d.4xlarge", "vcpuNum": 16 }, { "_defaultOrder": 16, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 128, "name": "ml.m5d.8xlarge", "vcpuNum": 32 }, { "_defaultOrder": 17, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 192, "name": "ml.m5d.12xlarge", "vcpuNum": 48 }, { "_defaultOrder": 18, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 256, "name": "ml.m5d.16xlarge", "vcpuNum": 64 }, { "_defaultOrder": 19, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 384, "name": "ml.m5d.24xlarge", "vcpuNum": 96 }, { "_defaultOrder": 20, "_isFastLaunch": false, "category": "General purpose", "gpuNum": 0, "hideHardwareSpecs": true, "memoryGiB": 0, "name": "ml.geospatial.interactive", "supportedImageNames": [ "sagemaker-geospatial-v1-0" ], "vcpuNum": 0 }, { "_defaultOrder": 21, "_isFastLaunch": true, "category": "Compute optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 4, "name": "ml.c5.large", "vcpuNum": 2 }, { "_defaultOrder": 22, "_isFastLaunch": false, "category": "Compute optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 8, "name": "ml.c5.xlarge", "vcpuNum": 4 }, { "_defaultOrder": 23, "_isFastLaunch": false, "category": "Compute optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 16, "name": "ml.c5.2xlarge", "vcpuNum": 8 }, { "_defaultOrder": 24, "_isFastLaunch": false, "category": "Compute optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 32, "name": "ml.c5.4xlarge", "vcpuNum": 16 }, { "_defaultOrder": 25, "_isFastLaunch": false, "category": "Compute optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 72, "name": "ml.c5.9xlarge", "vcpuNum": 36 }, { "_defaultOrder": 26, "_isFastLaunch": false, "category": "Compute optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 96, "name": "ml.c5.12xlarge", "vcpuNum": 48 }, { "_defaultOrder": 27, "_isFastLaunch": false, "category": "Compute optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 144, "name": "ml.c5.18xlarge", "vcpuNum": 72 }, { "_defaultOrder": 28, "_isFastLaunch": false, "category": "Compute optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 192, "name": "ml.c5.24xlarge", "vcpuNum": 96 }, { "_defaultOrder": 29, "_isFastLaunch": true, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 16, "name": "ml.g4dn.xlarge", "vcpuNum": 4 }, { "_defaultOrder": 30, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 32, "name": "ml.g4dn.2xlarge", "vcpuNum": 8 }, { "_defaultOrder": 31, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 64, "name": "ml.g4dn.4xlarge", "vcpuNum": 16 }, { "_defaultOrder": 32, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 128, "name": "ml.g4dn.8xlarge", "vcpuNum": 32 }, { "_defaultOrder": 33, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 4, "hideHardwareSpecs": false, "memoryGiB": 192, "name": "ml.g4dn.12xlarge", "vcpuNum": 48 }, { "_defaultOrder": 34, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 256, "name": "ml.g4dn.16xlarge", "vcpuNum": 64 }, { "_defaultOrder": 35, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 61, "name": "ml.p3.2xlarge", "vcpuNum": 8 }, { "_defaultOrder": 36, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 4, "hideHardwareSpecs": false, "memoryGiB": 244, "name": "ml.p3.8xlarge", "vcpuNum": 32 }, { "_defaultOrder": 37, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 8, "hideHardwareSpecs": false, "memoryGiB": 488, "name": "ml.p3.16xlarge", "vcpuNum": 64 }, { "_defaultOrder": 38, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 8, "hideHardwareSpecs": false, "memoryGiB": 768, "name": "ml.p3dn.24xlarge", "vcpuNum": 96 }, { "_defaultOrder": 39, "_isFastLaunch": false, "category": "Memory Optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 16, "name": "ml.r5.large", "vcpuNum": 2 }, { "_defaultOrder": 40, "_isFastLaunch": false, "category": "Memory Optimized", "gpuNum": 0, "hideHardwareSpecs": false, "memoryGiB": 32, "name": "ml.r5.xlarge", "vcpuNum": 4 }, { 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"hideHardwareSpecs": false, "memoryGiB": 768, "name": "ml.r5.24xlarge", "vcpuNum": 96 }, { "_defaultOrder": 47, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 16, "name": "ml.g5.xlarge", "vcpuNum": 4 }, { "_defaultOrder": 48, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 32, "name": "ml.g5.2xlarge", "vcpuNum": 8 }, { "_defaultOrder": 49, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 64, "name": "ml.g5.4xlarge", "vcpuNum": 16 }, { "_defaultOrder": 50, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 128, "name": "ml.g5.8xlarge", "vcpuNum": 32 }, { "_defaultOrder": 51, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 1, "hideHardwareSpecs": false, "memoryGiB": 256, "name": "ml.g5.16xlarge", "vcpuNum": 64 }, { "_defaultOrder": 52, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 4, "hideHardwareSpecs": false, "memoryGiB": 192, "name": "ml.g5.12xlarge", "vcpuNum": 48 }, { "_defaultOrder": 53, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 4, "hideHardwareSpecs": false, "memoryGiB": 384, "name": "ml.g5.24xlarge", "vcpuNum": 96 }, { "_defaultOrder": 54, "_isFastLaunch": false, "category": "Accelerated computing", "gpuNum": 8, "hideHardwareSpecs": false, "memoryGiB": 768, "name": "ml.g5.48xlarge", "vcpuNum": 192 } ], "instance_type": "ml.t3.medium", "kernelspec": { "display_name": "Python 3 (Data Science)", "language": "python", "name": "python3__SAGEMAKER_INTERNAL__arn:aws:sagemaker:us-west-2:236514542706:image/datascience-1.0" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": 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