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Fix/atera update #161

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Merged
dariarom94 merged 2 commits into from
Jul 6, 2026
Merged

Fix/atera update #161

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8985867
adjust mem
dariarom94 Jul 2, 2026
7633523
Publish atera loader output to local raw/ folder; update nebius labels
dariarom94 Jul 2, 2026
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4 changes: 3 additions & 1 deletion scripts/create_resources/spatial/process_10x_atera_nebius.sh
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Expand Up @@ -8,7 +8,9 @@ cd "$REPO_ROOT"

set -e

publish_dir="s3://openproblems-data/resources/datasets"
# store the loader output locally, mirroring the process_datasets layout ($id/)
# but under a sibling raw/ folder
publish_dir="/scratch/task_ist_preprocessing/raw"

cat > /tmp/params_atera.yaml << HERE
param_list:
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12 changes: 9 additions & 3 deletions src/base/labels_nebius.config
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Expand Up @@ -47,20 +47,26 @@ process {
withLabel: midcpu { cpus = 15 }
withLabel: highcpu { cpus = 30 }
withLabel: lowmem {
memory = { get_memory( 20.GB * task.attempt ) }
// Nebius 48vcpu-192gb nodes: 188 GB allocatable
memory = { get_memory( 25.GB * task.attempt ) }
disk = { 50.GB * task.attempt }
pod = [[nodeSelector: 'nebius.com/node-group-id=mk8snodegroup-e00p5wjvb7bc55b2js']]
}
withLabel: midmem {
// Nebius 64vcpu-256gb nodes: 251 GB allocatable
memory = { get_memory( 50.GB * task.attempt ) }
disk = { 100.GB * task.attempt }
pod = [[nodeSelector: 'nebius.com/node-group-id=mk8snodegroup-e00wvqfyde1nfwezs0']]
}
withLabel: highmem {
memory = { task.attempt == 1 ? 200.GB : 500.GB }
// Nebius 128vcpu-512gb nodes: 503 GB allocatable — cap well below node max
memory = { task.attempt == 1 ? 200.GB : 450.GB }
disk = 200.GB
pod = [[nodeSelector: 'nebius.com/node-group-id=mk8snodegroup-e00hnqhyfdcsy9m09n']]
}
withLabel: veryhighmem {
memory = { get_memory( 200.GB * task.attempt ) }
// Nebius 128vcpu-512gb nodes: 503 GB allocatable — cap at 450 GB to leave headroom
memory = { [ 200.GB * task.attempt, 450.GB ].min() }
disk = { 400.GB * task.attempt }
pod = [[nodeSelector: 'nebius.com/node-group-id=mk8snodegroup-e00hnqhyfdcsy9m09n']]
}
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2 changes: 1 addition & 1 deletion src/datasets/loaders/tenx_atera/config.vsh.yaml
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Expand Up @@ -68,4 +68,4 @@ runners:
- type: executable
- type: nextflow
directives:
label: [midmem, midcpu, midtime]
label: [highmem, midcpu, midtime]
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