kemal
3291609577
scripts/p8/prepare.py lays out the 360 GEO IDATs under their header barcode/position; scripts/p8/validate_p8.py computes concordance, NRD, no-call rate, per-class and per-MAF sensitivity/specificity/precision/F1 vs NYGC 30x and GIAB HG001, replicate concordance, systematic/allele-swap site errors, per-chip batch table and duplicate detection. Cloud userdata can skip the Omni2.5 archive (OMNI=0).
131 lines
8.3 KiB
Bash
Executable File
131 lines
8.3 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Self-destructing, budget-guarded AWS validation run for SimurgArray.
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#
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# bash scripts/cloud/trial.sh setup <alert-email> # one-time: budget alert, results bucket, instance role
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# bash scripts/cloud/trial.sh launch # start one spot run (terminates itself when done)
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# bash scripts/cloud/trial.sh status # instance state + last lines of the remote log
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# bash scripts/cloud/trial.sh results # download log/summary of the latest run
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# bash scripts/cloud/trial.sh kill # emergency: terminate every trial instance now
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# bash scripts/cloud/trial.sh audit # list anything still costing money
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#
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# Cost guards: spot price cap, hard time cap (shutdown = terminate), EXIT trap shutdown, CloudWatch idle alarm
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# that terminates from outside, disk deleted with the instance, monthly budget e-mail alert.
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set -euo pipefail
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cd "$(dirname "$0")/../.."
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REGION=${REGION:-us-east-1}
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TYPE=${TYPE:-m7g.4xlarge}
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MAX_PRICE=${MAX_PRICE:-0.30} # USD/hour spot cap (on-demand is 0.6528)
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MAX_MINUTES=${MAX_MINUTES:-360} # hard cap: 6 hours
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DISK_GB=${DISK_GB:-250}
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DISK_MBPS=${DISK_MBPS:-125} # gp3 throughput (125 = free baseline; each extra MB/s ~ $0.00005/h)
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DISK_IOPS=${DISK_IOPS:-3000} # gp3 IOPS (3000 = free baseline)
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BUDGET_USD=${BUDGET_USD:-10}
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TASK=${TASK:-p3} # scripts/cloud/tasks/<TASK>.sh
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TAG=simurg-trial
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ACCOUNT=$(aws sts get-caller-identity --query Account --output text)
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BUCKET=simurg-trial-$ACCOUNT
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ROLE=simurg-trial-role
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AWS="aws --region $REGION"
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cmd=${1:-help}
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case "$cmd" in
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setup)
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EMAIL=${2:?usage: trial.sh setup <alert-email>}
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echo "-> budget alert: \$$BUDGET_USD/month, e-mail $EMAIL at 50%, 100% actual and 100% forecast"
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cat > /tmp/simurg-budget.json <<EOF
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{"BudgetName":"$TAG-monthly","BudgetLimit":{"Amount":"$BUDGET_USD","Unit":"USD"},"TimeUnit":"MONTHLY","BudgetType":"COST"}
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EOF
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notif() { echo "{\"Notification\":{\"NotificationType\":\"$1\",\"ComparisonOperator\":\"GREATER_THAN\",\"Threshold\":$2,\"ThresholdType\":\"PERCENTAGE\"},\"Subscribers\":[{\"SubscriptionType\":\"EMAIL\",\"Address\":\"$EMAIL\"}]}"; }
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echo "[$(notif ACTUAL 50),$(notif ACTUAL 100),$(notif FORECASTED 100)]" > /tmp/simurg-notif.json
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aws budgets create-budget --account-id "$ACCOUNT" --budget file:///tmp/simurg-budget.json \
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--notifications-with-subscribers file:///tmp/simurg-notif.json 2>/dev/null || echo " (budget already exists)"
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echo "-> results bucket s3://$BUCKET (objects expire after 30 days)"
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$AWS s3api create-bucket --bucket "$BUCKET" >/dev/null 2>&1 || true
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$AWS s3api put-public-access-block --bucket "$BUCKET" --public-access-block-configuration \
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BlockPublicAcls=true,IgnorePublicAcls=true,BlockPublicPolicy=true,RestrictPublicBuckets=true
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$AWS s3api put-bucket-lifecycle-configuration --bucket "$BUCKET" --lifecycle-configuration \
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'{"Rules":[{"ID":"expire","Status":"Enabled","Filter":{},"Expiration":{"Days":30}}]}'
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echo "-> instance role $ROLE (read/write only this bucket)"
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aws iam create-role --role-name $ROLE --assume-role-policy-document \
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'{"Version":"2012-10-17","Statement":[{"Effect":"Allow","Principal":{"Service":"ec2.amazonaws.com"},"Action":"sts:AssumeRole"}]}' \
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>/dev/null 2>&1 || true
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aws iam put-role-policy --role-name $ROLE --policy-name bucket-only --policy-document \
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"{\"Version\":\"2012-10-17\",\"Statement\":[{\"Effect\":\"Allow\",\"Action\":[\"s3:GetObject\",\"s3:PutObject\"],\"Resource\":\"arn:aws:s3:::$BUCKET/*\"}]}"
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aws iam create-instance-profile --instance-profile-name $ROLE >/dev/null 2>&1 || true
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aws iam add-role-to-instance-profile --instance-profile-name $ROLE --role-name $ROLE 2>/dev/null || true
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echo "setup done (budget alerts need you to confirm nothing; AWS e-mails $EMAIL when thresholds are crossed)"
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;;
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launch)
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running=$($AWS ec2 describe-instances --filters Name=tag:Project,Values=$TAG \
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Name=instance-state-name,Values=pending,running --query 'length(Reservations[].Instances[])')
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[[ "$running" == "0" ]] || { echo "a trial instance is already running; refusing to start another"; exit 1; }
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RUN=run-$(date -u +%Y%m%dT%H%M%SZ)
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echo "-> packing repository at $(git rev-parse --short HEAD) -> s3://$BUCKET/$RUN/"
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git archive --format=tar.gz -o /tmp/simurg-repo.tar.gz HEAD
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$AWS s3 cp /tmp/simurg-repo.tar.gz "s3://$BUCKET/$RUN/repo.tar.gz" --only-show-errors
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[[ -f scripts/cloud/tasks/$TASK.sh ]] || { echo "unknown TASK $TASK"; exit 2; }
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OMNI=${OMNI:-1} # 0: the task does not need the 107 GB Omni2.5 archive
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sed -e "s/__BUCKET__/$BUCKET/" -e "s/__RUN__/$RUN/" -e "s/__MAX_MINUTES__/$MAX_MINUTES/" -e "s/__TASK__/$TASK/g" \
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-e "s/__OMNI__/$OMNI/" \
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scripts/cloud/userdata.sh > /tmp/simurg-userdata.sh
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AMI=$($AWS ssm get-parameter --name /aws/service/canonical/ubuntu/server/24.04/stable/current/arm64/hvm/ebs-gp3/ami-id \
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--query Parameter.Value --output text)
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echo "-> task: $TASK"
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echo "-> launching $TYPE spot (cap \$$MAX_PRICE/h, hard limit ${MAX_MINUTES} min, ${DISK_GB} GB disk deleted on exit)"
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ID=$($AWS ec2 run-instances --image-id "$AMI" --instance-type "$TYPE" --count 1 \
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--iam-instance-profile Name=$ROLE \
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--instance-initiated-shutdown-behavior terminate \
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--instance-market-options "MarketType=spot,SpotOptions={MaxPrice=$MAX_PRICE,SpotInstanceType=one-time,InstanceInterruptionBehavior=terminate}" \
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--block-device-mappings "DeviceName=/dev/sda1,Ebs={VolumeSize=$DISK_GB,VolumeType=gp3,Throughput=$DISK_MBPS,Iops=$DISK_IOPS,DeleteOnTermination=true}" \
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--metadata-options HttpTokens=required \
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--user-data file:///tmp/simurg-userdata.sh \
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--tag-specifications "ResourceType=instance,Tags=[{Key=Project,Value=$TAG},{Key=Run,Value=$RUN}]" \
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"ResourceType=volume,Tags=[{Key=Project,Value=$TAG},{Key=Run,Value=$RUN}]" \
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--query 'Instances[0].InstanceId' --output text)
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echo "$ID $RUN" > .trial-last
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echo "-> idle alarm: terminate if average CPU < 2% for 30 minutes"
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$AWS cloudwatch put-metric-alarm --alarm-name "$TAG-idle-$ID" --namespace AWS/EC2 --metric-name CPUUtilization \
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--dimensions Name=InstanceId,Value="$ID" --statistic Average --period 300 --evaluation-periods 6 \
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--threshold 2 --comparison-operator LessThanThreshold --treat-missing-data notBreaching \
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--alarm-actions "arn:aws:automate:$REGION:ec2:terminate"
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echo "launched $ID ($RUN). Check with: bash scripts/cloud/trial.sh status"
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;;
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status)
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read -r ID RUN < .trial-last
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$AWS ec2 describe-instances --instance-ids "$ID" \
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--query 'Reservations[0].Instances[0].[InstanceId,State.Name,InstanceType,LaunchTime]' --output text
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$AWS s3 cp "s3://$BUCKET/$RUN/log.txt" - 2>/dev/null | tail -n "${LINES_:-15}" || echo "(no log uploaded yet)"
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;;
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results)
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read -r ID RUN < .trial-last
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mkdir -p "results/$RUN"
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$AWS s3 cp "s3://$BUCKET/$RUN/" "results/$RUN/" --recursive --exclude repo.tar.gz --only-show-errors
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ls -la "results/$RUN"
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;;
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kill)
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ids=$($AWS ec2 describe-instances --filters Name=tag:Project,Values=$TAG \
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Name=instance-state-name,Values=pending,running,stopping,stopped --query 'Reservations[].Instances[].InstanceId' --output text)
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[[ -n "$ids" ]] && $AWS ec2 terminate-instances --instance-ids $ids --output text || echo "no trial instances"
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;&
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audit)
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echo "-- instances (any project) --"
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$AWS ec2 describe-instances --filters Name=instance-state-name,Values=pending,running,stopping,stopped \
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--query 'Reservations[].Instances[].[InstanceId,State.Name,InstanceType]' --output text
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echo "-- volumes --"
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$AWS ec2 describe-volumes --query 'Volumes[].[VolumeId,State,Size]' --output text
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echo "-- snapshots owned --"
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$AWS ec2 describe-snapshots --owner-ids self --query 'Snapshots[].[SnapshotId,VolumeSize]' --output text
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echo "-- elastic IPs --"
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$AWS ec2 describe-addresses --query 'Addresses[].PublicIp' --output text
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echo "-- trial alarms (deleting alarms of terminated instances) --"
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for a in $($AWS cloudwatch describe-alarms --alarm-name-prefix "$TAG-idle-" --query 'MetricAlarms[].AlarmName' --output text); do
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iid=${a#"$TAG-idle-"}
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st=$($AWS ec2 describe-instances --instance-ids "$iid" --query 'Reservations[0].Instances[0].State.Name' --output text 2>/dev/null || echo gone)
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if [[ "$st" == "terminated" || "$st" == "gone" ]]; then $AWS cloudwatch delete-alarms --alarm-names "$a"; echo "deleted $a"; else echo "$a ($st)"; fi
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done
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;;
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*)
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sed -n '2,15p' "$0"
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;;
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esac
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