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olgabot/kill_aws_batch_jobs.ipynb

Last active November 5, 2019 13:00
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kill_aws_batch_jobs.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import boto3\n",
"\n",
"client = boto3.client('batch')\n"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true,
"jupyter": {
"outputs_hidden": true
}
},
"outputs": [
{
"data": {
"text/plain": [
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" 'jobName': 'sourmash_compute_sketch_2816_sc109ex944CCA_sc109etouchinghalf_IL46053_TTAGGC_moleculedna_ksize51_log2sketchsize16',\n",
" 'createdAt': 1563983723027,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'a7f4a53b-49da-4da4-b174-ef9340875fcb',\n",
" 'jobName': 'sourmash_compute_sketch_2815_944xsc109eCCA_944touchinghalf_IL46042_CGATGT_moleculedayhoff_ksize21_log2sketchsize14',\n",
" 'createdAt': 1563983723929,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '9438d86a-7915-490a-9866-a9189f47dfc4',\n",
" 'jobName': 'sourmash_compute_sketch_2815_944xsc109eCCA_944touchinghalf_IL46042_CGATGT_moleculedna_ksize51_log2sketchsize16',\n",
" 'createdAt': 1563983724208,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'e57131d9-bb34-43cf-a116-460241f51e75',\n",
" 'jobName': 'sourmash_compute_sketch_2816_sc109ex944CCA_sc109etouchinghalf_IL46053_TTAGGC_moleculeprotein_ksize27_log2sketchsize10',\n",
" 'createdAt': 1563983725196,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'c2be1a35-18d3-4e0d-8653-95354ca46d77',\n",
" 'jobName': 'sourmash_compute_sketch_2815_944xsc109eCCA_944touchinghalf_IL46042_CGATGT_moleculeprotein_ksize51_log2sketchsize10',\n",
" 'createdAt': 1563983725480,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '82cdfdf9-3fd8-4596-8efd-e218e6b76d93',\n",
" 'jobName': 'sourmash_compute_sketch_2814_944xsc109eCCA_944nontouchinghalf_IL46031_ATCACG_moleculedayhoff_ksize27_log2sketchsize14',\n",
" 'createdAt': 1563983725828,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '50aab81b-fabb-4ec4-923c-f832ecad0dd1',\n",
" 'jobName': 'sourmash_compute_sketch_2816_sc109ex944CCA_sc109etouchinghalf_IL46053_TTAGGC_moleculedayhoff_ksize21_log2sketchsize10',\n",
" 'createdAt': 1563983726456,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '033ac634-30f3-4700-8a40-3423dc4f88a8',\n",
" 'jobName': 'sourmash_compute_sketch_2627chimera5432bvs5423bzooidStageA2IL5953_S19_moleculeprotein_ksize51_log2sketchsize10',\n",
" 'createdAt': 1563983726971,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '5e5eba94-90f2-4862-ba98-b584dbc153d8',\n",
" 'jobName': 'sourmash_compute_sketch_2817_sc109ex944CCA_sc109enontouchinghalf_IL46064_TGACCA_moleculedayhoff_ksize21_log2sketchsize16',\n",
" 'createdAt': 1563983727669,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '85dece1c-2ef0-4e72-a7c3-a36fca44aeb5',\n",
" 'jobName': 'sourmash_compute_sketch_2816_sc109ex944CCA_sc109etouchinghalf_IL46053_TTAGGC_moleculedayhoff_ksize27_log2sketchsize16',\n",
" 'createdAt': 1563983727886,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '076b76d9-065b-4fac-b6b8-433d8afde2ed',\n",
" 'jobName': 'sourmash_compute_sketch_2815_944xsc109eCCA_944touchinghalf_IL46042_CGATGT_moleculedna_ksize21_log2sketchsize14',\n",
" 'createdAt': 1563983728569,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '2d816da0-dbbc-4e08-bc52-2472c704f1e0',\n",
" 'jobName': 'sourmash_compute_sketch_2815_944xsc109eCCA_944touchinghalf_IL46042_CGATGT_moleculedna_ksize27_log2sketchsize10',\n",
" 'createdAt': 1563983729010,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '44fcba7a-c2ba-4f7f-947c-031f152b2f22',\n",
" 'jobName': 'sourmash_compute_sketch_2816_sc109ex944CCA_sc109etouchinghalf_IL46053_TTAGGC_moleculedna_ksize33_log2sketchsize10',\n",
" 'createdAt': 1563983729319,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'd517da8c-4d5a-452e-9f1a-9e7bfee8baec',\n",
" 'jobName': 'sourmash_compute_sketch_2816_sc109ex944CCA_sc109etouchinghalf_IL46053_TTAGGC_moleculedna_ksize51_log2sketchsize14',\n",
" 'createdAt': 1563983729847,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '4e7c589b-6b9e-435a-915d-ece1008f4705',\n",
" 'jobName': 'sourmash_compute_sketch_2815_944xsc109eCCA_944touchinghalf_IL46042_CGATGT_moleculeprotein_ksize33_log2sketchsize10',\n",
" 'createdAt': 1563983730247,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'cc8e019b-230c-47b1-bcd6-ec678042fc9a',\n",
" 'jobName': 'sourmash_compute_sketch_2817_sc109ex944CCA_sc109enontouchinghalf_IL46064_TGACCA_moleculedna_ksize21_log2sketchsize16',\n",
" 'createdAt': 1563983730869,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '0cc40102-e112-4d21-b285-e960823b4c8b',\n",
" 'jobName': 'sourmash_compute_sketch_2817_sc109ex944CCA_sc109enontouchinghalf_IL46064_TGACCA_moleculeprotein_ksize21_log2sketchsize14',\n",
" 'createdAt': 1563983731347,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '89b301ef-0459-4a08-ac20-8e1f4fe299d7',\n",
" 'jobName': 'sourmash_compute_sketch_2818_944axByd196_6_4_145_naive_IL46075_ACAGTG_moleculedna_ksize21_log2sketchsize10',\n",
" 'createdAt': 1563983731869,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '5c2dc3e1-c2c3-4c51-9ad0-79c73a95e95b',\n",
" 'jobName': 'sourmash_compute_sketch_2817_sc109ex944CCA_sc109enontouchinghalf_IL46064_TGACCA_moleculedayhoff_ksize51_log2sketchsize12',\n",
" 'createdAt': 1563983732427,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '574eec1a-50d8-461b-ae80-d86772a8ca19',\n",
" 'jobName': 'sourmash_compute_sketch_2817_sc109ex944CCA_sc109enontouchinghalf_IL46064_TGACCA_moleculedna_ksize51_log2sketchsize12',\n",
" 'createdAt': 1563983733051,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'bbd6fb37-c080-4d93-913a-8aae9c16248c',\n",
" 'jobName': 'sourmash_compute_sketch_2817_sc109ex944CCA_sc109enontouchinghalf_IL46064_TGACCA_moleculeprotein_ksize27_log2sketchsize14',\n",
" 'createdAt': 1563983733441,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'e465d5d6-26d5-43a1-b7dc-01962bd1179d',\n",
" 'jobName': 'sourmash_compute_sketch_2814_944xsc109eCCA_944nontouchinghalf_IL46031_ATCACG_moleculedna_ksize33_log2sketchsize10',\n",
" 'createdAt': 1563983733986,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'f7b905f7-56ef-4de3-aa7d-9dc338c05bd0',\n",
" 'jobName': 'sourmash_compute_sketch_2816_sc109ex944CCA_sc109etouchinghalf_IL46053_TTAGGC_moleculedayhoff_ksize33_log2sketchsize12',\n",
" 'createdAt': 1563983734506,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '298457f6-fd72-4baa-bbc6-380d4be39d45',\n",
" 'jobName': 'sourmash_compute_sketch_2816_sc109ex944CCA_sc109etouchinghalf_IL46053_TTAGGC_moleculeprotein_ksize33_log2sketchsize12',\n",
" 'createdAt': 1563983735116,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'd56251af-8f8d-46b5-b661-d55e22ba73fa',\n",
" 'jobName': 'sourmash_compute_sketch_2816_sc109ex944CCA_sc109etouchinghalf_IL46053_TTAGGC_moleculedna_ksize33_log2sketchsize14',\n",
" 'createdAt': 1563983735572,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '68489a37-fb42-4d3e-ad58-0af5c08dadca',\n",
" 'jobName': 'sourmash_compute_sketch_2817_sc109ex944CCA_sc109enontouchinghalf_IL46064_TGACCA_moleculedayhoff_ksize27_log2sketchsize10',\n",
" 'createdAt': 1563983736141,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '3d33087c-35ea-4205-ba3c-8526941e028e',\n",
" 'jobName': 'sourmash_compute_sketch_2818_944axByd196_6_4_145_naive_IL46075_ACAGTG_moleculedayhoff_ksize51_log2sketchsize10',\n",
" 'createdAt': 1563983736666,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'e2ca0769-e057-40fc-8c99-e8cd1609faa2',\n",
" 'jobName': 'sourmash_compute_sketch_2815_944xsc109eCCA_944touchinghalf_IL46042_CGATGT_moleculeprotein_ksize27_log2sketchsize14',\n",
" 'createdAt': 1563983737178,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '731b7250-1ad0-4b98-bf28-312d79169639',\n",
" 'jobName': 'sourmash_compute_sketch_2818_944axByd196_6_4_145_naive_IL46075_ACAGTG_moleculeprotein_ksize51_log2sketchsize10',\n",
" 'createdAt': 1563983737715,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': 'c6658710-8e89-40bf-aad8-f969f44c547d',\n",
" 'jobName': 'sourmash_compute_sketch_2815_944xsc109eCCA_944touchinghalf_IL46042_CGATGT_moleculedna_ksize21_log2sketchsize12',\n",
" 'createdAt': 1563983738235,\n",
" 'status': 'RUNNABLE'},\n",
" {'jobId': '4d54f2c0-bf0f-4331-b931-0a422903748d',\n",
" 'jobName': 'sourmash_compute_sketch_2814_944xsc109eCCA_944nontouchinghalf_IL46031_ATCACG_moleculedayhoff_ksize51_log2sketchsize16',\n",
" 'createdAt': 1563983738813,\n",
" 'status': 'RUNNABLE'}],\n",
" 'nextToken': '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'}"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"default = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036'\n",
"response = client.list_jobs(jobQueue=default, jobStatus='RUNNABLE')\n",
"response\n",
" "
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'jobId': '01c7da3a-4bcb-41e0-9a5c-23033c7de0d2',\n",
" 'jobName': 'sourmash_compare_sketches_moleculedayhoff_ksize27_log2sketchsize10',\n",
" 'createdAt': 1563980998453,\n",
" 'status': 'RUNNABLE'}"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"response['jobSummaryList'][0]"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"for job in response['jobSummaryList']:\n",
" client.terminate_job(jobId=job['jobId'], reason='Too many resources - olga killing')"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"highpriority = 'highpriority-971039e0-830c-11e9-9e0b-02c5b84a8036'\n",
"response = client.list_jobs(jobQueue=highpriority, jobStatus='RUNNABLE')\n",
"for job in response['jobSummaryList']:\n",
" if 'sourmash' in job['jobName']:\n",
" client.terminate_job(jobId=job['jobId'], reason='Too many resources - olga killing')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python [conda env:kmer-hashing]",
"language": "python",
"name": "conda-env-kmer-hashing-py"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.8"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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