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Add tests and testdata for S3 backend

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This commit is contained in:
Jan Eitzinger
2024-02-19 09:14:53 +01:00
parent 03a496d477
commit 256d1b85f6
8 changed files with 916 additions and 27 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
pkg/archive/fsBackend.go
View File

@@ -509,5 +509,6 @@ func (fsa *FsArchive) ImportJob(
if err := f.Close(); err != nil {
log.Warn("Error while closing data.json file")
}
return err
return nil
}

140
pkg/archive/s3Backend.go
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@@ -227,6 +227,94 @@ func (s3a *S3Archive) LoadClusterCfg(name string) (*schema.Cluster, error) {
return DecodeCluster(r)
}
func (s3a *S3Archive) Iter(loadMetricData bool) <-chan JobContainer {
ch := make(chan JobContainer)
go func() {
clusterDirs := s3a.client.ListObjects(context.Background(), s3a.bucket, minio.ListObjectsOptions{Recursive: false})
for clusterDir := range clusterDirs {
if clusterDir.Err != nil {
fmt.Println(clusterDir.Err)
return
}
fmt.Println(clusterDir.Key)
if clusterDir.Size != 0 {
continue
}
key := filepath.Join("", clusterDir.Key)
fmt.Println(key)
lvl1Dirs := s3a.client.ListObjects(context.Background(), s3a.bucket, minio.ListObjectsOptions{Recursive: false, Prefix: key})
for lvl1Dir := range lvl1Dirs {
fmt.Println(lvl1Dir.Key)
ch <- JobContainer{Meta: nil, Data: nil}
}
//
// for _, lvl1Dir := range lvl1Dirs {
// if !lvl1Dir.IsDir() {
// // Could be the cluster.json file
// continue
// }
//
// lvl2Dirs, err := os.ReadDir(filepath.Join(fsa.path, clusterDir.Name(), lvl1Dir.Name()))
// if err != nil {
// log.Fatalf("Reading jobs failed @ lvl2 dirs: %s", err.Error())
// }
//
// for _, lvl2Dir := range lvl2Dirs {
// dirpath := filepath.Join(fsa.path, clusterDir.Name(), lvl1Dir.Name(), lvl2Dir.Name())
// startTimeDirs, err := os.ReadDir(dirpath)
// if err != nil {
// log.Fatalf("Reading jobs failed @ starttime dirs: %s", err.Error())
// }
//
// for _, startTimeDir := range startTimeDirs {
// if startTimeDir.IsDir() {
// b, err := os.ReadFile(filepath.Join(dirpath, startTimeDir.Name(), "meta.json"))
// if err != nil {
// log.Errorf("loadJobMeta() > open file error: %v", err)
// }
// job, err := loadJobMeta(b)
// if err != nil && !errors.Is(err, &jsonschema.ValidationError{}) {
// log.Errorf("in %s: %s", filepath.Join(dirpath, startTimeDir.Name()), err.Error())
// }
//
// if loadMetricData {
// var isCompressed bool = true
// filename := filepath.Join(dirpath, startTimeDir.Name(), "data.json.gz")
//
// if !util.CheckFileExists(filename) {
// filename = filepath.Join(dirpath, startTimeDir.Name(), "data.json")
// isCompressed = false
// }
//
// f, err := os.Open(filename)
// if err != nil {
// log.Errorf("fsBackend LoadJobData()- %v", err)
// }
// defer f.Close()
//
// data, err := loadJobData(f, filename, isCompressed)
// if err != nil && !errors.Is(err, &jsonschema.ValidationError{}) {
// log.Errorf("in %s: %s", filepath.Join(dirpath, startTimeDir.Name()), err.Error())
// }
// ch <- JobContainer{Meta: job, Data: &data}
// log.Errorf("in %s: %s", filepath.Join(dirpath, startTimeDir.Name()), err.Error())
// } else {
// ch <- JobContainer{Meta: job, Data: nil}
// }
// }
// }
// }
// }
}
close(ch)
}()
return ch
}
func (s3a *S3Archive) ImportJob(
jobMeta *schema.JobMeta,
jobData *schema.JobData,
@@ -239,36 +327,37 @@ func (s3a *S3Archive) ImportJob(
r, w := io.Pipe()
if err := EncodeJobMeta(w, jobMeta); err != nil {
log.Error("Error while encoding job metadata to meta.json file")
return err
}
go func() {
defer w.Close()
if err := EncodeJobMeta(w, jobMeta); err != nil {
log.Error("Error while encoding job metadata to meta.json object")
}
}()
key := getPath(&job, "./", "meta.json")
s3a.client.PutObject(context.Background(),
s3a.bucket, key, r,
int64(unsafe.Sizeof(job)), minio.PutObjectOptions{})
_, e := s3a.client.PutObject(context.Background(),
s3a.bucket, key, r, -1, minio.PutObjectOptions{})
if err := w.Close(); err != nil {
log.Warn("Error while closing meta.json file")
return err
if e != nil {
log.Errorf("Put error %#v", e)
return e
}
r, w = io.Pipe()
//
// f, err = os.Create(path.Join(dir, "data.json"))
// if err != nil {
// log.Error("Error while creating filepath for data.json")
// return err
// }
// if err := EncodeJobData(f, jobData); err != nil {
// log.Error("Error while encoding job metricdata to data.json file")
// return err
// }
// if err := f.Close(); err != nil {
// log.Warn("Error while closing data.json file")
// }
// return err
//
go func() {
defer w.Close()
if err := EncodeJobData(w, jobData); err != nil {
log.Error("Error while encoding job metricdata to data.json object")
}
}()
key = getPath(&job, "./", "data.json")
_, e = s3a.client.PutObject(context.Background(),
s3a.bucket, key, r, -1, minio.PutObjectOptions{})
if e != nil {
log.Errorf("Put error %#v", e)
return e
}
return nil
}
@@ -315,4 +404,3 @@ func (s3a *S3Archive) GetClusters() []string {
//
// func (s3a *S3Archive) CompressLast(starttime int64) int64
//
// func (s3a *S3Archive) Iter(loadMetricData bool) <-chan JobContainer

51
pkg/archive/s3Backend_test.go
View File

@@ -5,7 +5,10 @@
package archive
import (
"bytes"
"encoding/json"
"fmt"
"os"
"testing"
"time"
@@ -100,3 +103,51 @@ func TestS3LoadCluster(t *testing.T) {
t.Fail()
}
}
func TestS3JobImport(t *testing.T) {
var s3a S3Archive
_, err := s3a.Init(json.RawMessage("{\"endpoint\":\"192.168.1.10:9100\",\"accessKeyID\":\"uACSaCN2Chiotpnr4bBS\",\"secretAccessKey\":\"MkEbBsFvMii1K5GreUriTJZxH359B1n28Au9Kaml\",\"bucket\":\"cc-archive\",\"useSSL\":false}"))
if err != nil {
t.Fatal(err)
}
raw, err := os.ReadFile("./testdata/archive/fritz/398/759/1675954289/meta.json")
if err != nil {
t.Fatal("Error while reading metadata file for import")
}
dec := json.NewDecoder(bytes.NewReader(raw))
dec.DisallowUnknownFields()
jobMeta := schema.JobMeta{BaseJob: schema.JobDefaults}
if err = dec.Decode(&jobMeta); err != nil {
t.Fatal("Error while decoding raw json metadata for import")
}
raw, err = os.ReadFile("./testdata/archive/fritz/398/759/1675954289/data.json")
if err != nil {
t.Fatal("Error while reading jobdata file for import")
}
dec = json.NewDecoder(bytes.NewReader(raw))
dec.DisallowUnknownFields()
jobData := schema.JobData{}
if err = dec.Decode(&jobData); err != nil {
t.Fatal("Error while decoding raw json jobdata for import")
}
s3a.ImportJob(&jobMeta, &jobData)
}
func TestS3Iter(t *testing.T) {
var s3a S3Archive
_, err := s3a.Init(json.RawMessage("{\"endpoint\":\"192.168.1.10:9100\",\"accessKeyID\":\"uACSaCN2Chiotpnr4bBS\",\"secretAccessKey\":\"MkEbBsFvMii1K5GreUriTJZxH359B1n28Au9Kaml\",\"bucket\":\"cc-archive\",\"useSSL\":false}"))
if err != nil {
t.Fatal(err)
}
for jobContainer := range s3a.Iter(false) {
if jobContainer.Meta == nil {
fmt.Println("Is nil")
}
}
}

1
pkg/archive/testdata/archive/fritz/398/759/1675954289/data.json vendored Normal file
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1
pkg/archive/testdata/archive/fritz/398/759/1675954289/meta.json vendored Normal file
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@@ -0,0 +1 @@
{"jobId":398759,"user":"k106eb10","project":"k106eb","cluster":"fritz","subCluster":"main","partition":"singlenode","arrayJobId":0,"numNodes":1,"numHwthreads":72,"numAcc":0,"exclusive":1,"monitoringStatus":1,"smt":0,"jobState":"completed","duration":456,"walltime":86340,"resources":[{"hostname":"f1039"}],"metaData":{"jobName":"ams_pipeline","jobScript":"#!/bin/bash -l\n#SBATCH --job-name=ams_pipeline\n#SBATCH --time=23:59:00\n#SBATCH --partition=singlenode\n#SBATCH --ntasks=72\n#SBATCH --hint=multithread\n#SBATCH --chdir=/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_9_D1_3_Al4Ba/cfg/AlNi4\n#SBATCH --export=NONE\nunset SLURM_EXPORT_ENV\nuss=$(whoami)\nfind /dev/shm/ -user $uss -type f -mmin +30 -delete\ncd \"/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_9_D1_3_Al4Ba/cfg/AlNi4\"\nams_pipeline pipeline.json \u003e \"/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_9_D1_3_Al4Ba/cfg/AlNi4/ams_pipeline_job.sh.out\" 2\u003e \"/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_9_D1_3_Al4Ba/cfg/AlNi4/ams_pipeline_job.sh.err\"\n","slurmInfo":"\nJobId=398759 JobName=ams_pipeline\n UserId=k106eb10(210387) GroupId=80111\n Account=k106eb QOS=normal \n Requeue=False Restarts=0 BatchFlag=True \n TimeLimit=1439\n SubmitTime=2023-02-09T14:10:18\n Partition=singlenode \n NodeList=f1039\n NumNodes=1 NumCPUs=72 NumTasks=72 CPUs/Task=1\n NTasksPerNode:Socket:Core=0:None:None\n TRES_req=cpu=72,mem=250000M,node=1,billing=72\n TRES_alloc=cpu=72,node=1,billing=72\n Command=/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_9_D1_3_Al4Ba/cfg/AlNi4/ams_pipeline_job.sh\n WorkDir=/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_9_D1_3_Al4Ba/cfg/AlNi4\n StdErr=\n StdOut=ams_pipeline.o%j\n"},"startTime":1675954289,"statistics":{"clock":{"unit":{"base":"Hz","prefix":"M"},"avg":2353.432,"min":948.182,"max":2788.083},"cpu_load":{"unit":{"base":""},"avg":51.549,"min":11.01,"max":69.65},"cpu_power":{"unit":{"base":"W"},"avg":341.035,"min":97.175,"max":504.194},"cpu_user":{"unit":{"base":""},"avg":67.956,"min":0.07,"max":96.219},"flops_any":{"unit":{"base":"F/s","prefix":"G"},"avg":232.513,"min":0,"max":410.287},"flops_dp":{"unit":{"base":"F/s","prefix":"G"},"avg":116.255,"min":0,"max":205.143},"flops_sp":{"unit":{"base":"F/s","prefix":"G"},"avg":0.003,"min":0,"max":0.009},"ib_recv":{"unit":{"base":"B/s"},"avg":22674.825,"min":39.601,"max":47259.522},"ib_recv_pkts":{"unit":{"base":"packets/s"},"avg":321.484,"min":0.2,"max":680.887},"ib_xmit":{"unit":{"base":"B/s"},"avg":140.208,"min":39.601,"max":576.666},"ib_xmit_pkts":{"unit":{"base":"packets/s"},"avg":0.685,"min":0.2,"max":1.984},"ipc":{"unit":{"base":"IPC"},"avg":0.944,"min":0.21,"max":1.424},"mem_bw":{"unit":{"base":"B/s","prefix":"G"},"avg":39.231,"min":0.023,"max":86.676},"mem_power":{"unit":{"base":"W"},"avg":18.049,"min":7.256,"max":26.926},"mem_used":{"unit":{"base":"B","prefix":"G"},"avg":19.107,"min":3.866,"max":24.729},"nfs4_read":{"unit":{"base":"B/s","prefix":"M"},"avg":389.875,"min":0,"max":1390},"nfs4_total":{"unit":{"base":"B/s","prefix":"M"},"avg":5032.75,"min":956,"max":10098},"nfs4_write":{"unit":{"base":"B/s","prefix":"M"},"avg":21.125,"min":0,"max":41},"vectorization_ratio":{"unit":{"base":"%"},"avg":60.12,"min":0.028,"max":99.133}}}

BIN
pkg/archive/testdata/archive/fritz/398/760/1675954305/data.json.gz vendored Normal file
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Binary file not shown.

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pkg/archive/testdata/archive/fritz/398/760/1675954305/meta.json vendored Normal file
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@@ -0,0 +1 @@
{"jobId":398760,"user":"k106eb10","project":"k106eb","cluster":"fritz","subCluster":"main","partition":"singlenode","arrayJobId":0,"numNodes":1,"numHwthreads":72,"numAcc":0,"exclusive":1,"monitoringStatus":1,"smt":0,"jobState":"completed","duration":424,"walltime":86340,"resources":[{"hostname":"f0726"}],"metaData":{"jobName":"ams_pipeline","jobScript":"#!/bin/bash -l\n#SBATCH --job-name=ams_pipeline\n#SBATCH --time=23:59:00\n#SBATCH --partition=singlenode\n#SBATCH --ntasks=72\n#SBATCH --hint=multithread\n#SBATCH --chdir=/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_58_D2_e_BaHg11/cfg/Ni3Al33\n#SBATCH --export=NONE\nunset SLURM_EXPORT_ENV\nuss=$(whoami)\nfind /dev/shm/ -user $uss -type f -mmin +30 -delete\ncd \"/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_58_D2_e_BaHg11/cfg/Ni3Al33\"\nams_pipeline pipeline.json \u003e \"/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_58_D2_e_BaHg11/cfg/Ni3Al33/ams_pipeline_job.sh.out\" 2\u003e \"/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_58_D2_e_BaHg11/cfg/Ni3Al33/ams_pipeline_job.sh.err\"\n","slurmInfo":"\nJobId=398760 JobName=ams_pipeline\n UserId=k106eb10(210387) GroupId=80111\n Account=k106eb QOS=normal \n Requeue=False Restarts=0 BatchFlag=True \n TimeLimit=1439\n SubmitTime=2023-02-09T14:10:18\n Partition=singlenode \n NodeList=f0726\n NumNodes=1 NumCPUs=72 NumTasks=72 CPUs/Task=1\n NTasksPerNode:Socket:Core=0:None:None\n TRES_req=cpu=72,mem=250000M,node=1,billing=72\n TRES_alloc=cpu=72,node=1,billing=72\n Command=/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_58_D2_e_BaHg11/cfg/Ni3Al33/ams_pipeline_job.sh\n WorkDir=/home/atuin/k106eb/k106eb10/ACE/Ni-Al/DFT/VASP_PBE_500_0.125_0.1_NM/AlNi/binaries/bulk/moreprototypesYury/gen_58_D2_e_BaHg11/cfg/Ni3Al33\n StdErr=\n StdOut=ams_pipeline.o%j\n"},"startTime":1675954305,"statistics":{"clock":{"unit":{"base":"Hz","prefix":"M"},"avg":2080.276,"min":177.875,"max":2999.808},"cpu_load":{"unit":{"base":""},"avg":51.85,"min":17.55,"max":70.19},"cpu_power":{"unit":{"base":"W"},"avg":895207.403,"min":99.623,"max":5813238.184},"cpu_user":{"unit":{"base":""},"avg":69.514,"min":0.141,"max":95.954},"flops_any":{"unit":{"base":"F/s","prefix":"G"},"avg":449583.761,"min":0,"max":3594180.285},"flops_dp":{"unit":{"base":"F/s","prefix":"G"},"avg":224791.879,"min":0,"max":1797090.142},"flops_sp":{"unit":{"base":"F/s","prefix":"G"},"avg":0.004,"min":0,"max":0.009},"ib_recv":{"unit":{"base":"B/s"},"avg":22280.656,"min":39.602,"max":48063.992},"ib_recv_pkts":{"unit":{"base":"packets/s"},"avg":315.311,"min":0.2,"max":685.046},"ib_xmit":{"unit":{"base":"B/s"},"avg":139.722,"min":39.131,"max":568.239},"ib_xmit_pkts":{"unit":{"base":"packets/s"},"avg":0.685,"min":0.183,"max":2.167},"ipc":{"unit":{"base":"IPC"},"avg":0.693,"min":0.169,"max":0.871},"mem_bw":{"unit":{"base":"B/s","prefix":"G"},"avg":277555.465,"min":0.023,"max":2219018.206},"mem_power":{"unit":{"base":"W"},"avg":73514.92,"min":7.599,"max":485466.144},"mem_used":{"unit":{"base":"B","prefix":"G"},"avg":12.971,"min":3.973,"max":21.517},"nfs4_read":{"unit":{"base":"B/s","prefix":"M"},"avg":413.25,"min":0,"max":1730},"nfs4_total":{"unit":{"base":"B/s","prefix":"M"},"avg":5063.875,"min":1102,"max":10701},"nfs4_write":{"unit":{"base":"B/s","prefix":"M"},"avg":17.875,"min":1,"max":45},"vectorization_ratio":{"unit":{"base":"%"},"avg":54.299,"min":0,"max":98.808}}}

746
pkg/archive/testdata/archive/fritz/cluster.json vendored Normal file
View File

@@ -0,0 +1,746 @@
{
"name": "fritz",
"metricConfig": [
{
"name": "cpu_load",
"unit": {
"base": ""
},
"scope": "node",
"aggregation": "avg",
"timestep": 60,
"peak": 72,
"normal": 72,
"caution": 36,
"alert": 20
},
{
"name": "cpu_user",
"unit": {
"base": ""
},
"scope": "hwthread",
"aggregation": "avg",
"timestep": 60,
"peak": 100,
"normal": 50,
"caution": 20,
"alert": 10
},
{
"name": "mem_used",
"unit": {
"base": "B",
"prefix": "G"
},
"scope": "node",
"aggregation": "sum",
"timestep": 60,
"peak": 256,
"normal": 128,
"caution": 200,
"alert": 240
},
{
"name": "flops_any",
"unit": {
"base": "F/s",
"prefix": "G"
},
"scope": "hwthread",
"aggregation": "sum",
"timestep": 60,
"peak": 5600,
"normal": 1000,
"caution": 200,
"alert": 50
},
{
"name": "flops_sp",
"unit": {
"base": "F/s",
"prefix": "G"
},
"scope": "hwthread",
"aggregation": "sum",
"timestep": 60,
"peak": 5600,
"normal": 1000,
"caution": 200,
"alert": 50
},
{
"name": "flops_dp",
"unit": {
"base": "F/s",
"prefix": "G"
},
"scope": "hwthread",
"aggregation": "sum",
"timestep": 60,
"peak": 2300,
"normal": 500,
"caution": 100,
"alert": 50
},
{
"name": "mem_bw",
"unit": {
"base": "B/s",
"prefix": "G"
},
"scope": "socket",
"aggregation": "sum",
"timestep": 60,
"peak": 350,
"normal": 100,
"caution": 50,
"alert": 10
},
{
"name": "clock",
"unit": {
"base": "Hz",
"prefix": "M"
},
"scope": "hwthread",
"aggregation": "avg",
"timestep": 60,
"peak": 3000,
"normal": 2400,
"caution": 1800,
"alert": 1200
},
{
"name": "cpu_power",
"unit": {
"base": "W"
},
"scope": "socket",
"aggregation": "sum",
"timestep": 60,
"peak": 500,
"normal": 250,
"caution": 100,
"alert": 50
},
{
"name": "mem_power",
"unit": {
"base": "W"
},
"scope": "socket",
"aggregation": "sum",
"timestep": 60,
"peak": 100,
"normal": 50,
"caution": 20,
"alert": 10
},
{
"name": "ipc",
"unit": {
"base": "IPC"
},
"scope": "hwthread",
"aggregation": "avg",
"timestep": 60,
"peak": 4,
"normal": 2,
"caution": 1,
"alert": 0.5
},
{
"name": "vectorization_ratio",
"unit": {
"base": ""
},
"scope": "hwthread",
"aggregation": "avg",
"timestep": 60,
"peak": 100,
"normal": 60,
"caution": 40,
"alert": 10
},
{
"name": "ib_recv",
"unit": {
"base": "B/s"
},
"scope": "node",
"aggregation": "sum",
"timestep": 60,
"peak": 1250000,
"normal": 6000000,
"caution": 200,
"alert": 1
},
{
"name": "ib_xmit",
"unit": {
"base": "B/s"
},
"scope": "node",
"aggregation": "sum",
"timestep": 60,
"peak": 1250000,
"normal": 6000000,
"caution": 200,
"alert": 1
},
{
"name": "ib_recv_pkts",
"unit": {
"base": ""
},
"scope": "node",
"aggregation": "sum",
"timestep": 60,
"peak": 6,
"normal": 4,
"caution": 2,
"alert": 1
},
{
"name": "ib_xmit_pkts",
"unit": {
"base": ""
},
"scope": "node",
"aggregation": "sum",
"timestep": 60,
"peak": 6,
"normal": 4,
"caution": 2,
"alert": 1
},
{
"name": "nfs4_read",
"unit": {
"base": "B/s",
"prefix": "M"
},
"scope": "node",
"aggregation": "sum",
"timestep": 60,
"peak": 6,
"normal": 4,
"caution": 2,
"alert": 1
},
{
"name": "nfs4_write",
"unit": {
"base": "B/s",
"prefix": "M"
},
"scope": "node",
"aggregation": "sum",
"timestep": 60,
"peak": 6,
"normal": 4,
"caution": 2,
"alert": 1
},
{
"name": "nfs4_total",
"unit": {
"base": "B/s",
"prefix": "M"
},
"scope": "node",
"aggregation": "sum",
"timestep": 60,
"peak": 6,
"normal": 4,
"caution": 2,
"alert": 1
}
],
"subClusters": [
{
"name": "main",
"nodes": "f01[01-88],f02[01-88],f03[01-88],f03[01-88],f04[01-88],f05[01-88],f06[01-88],f07[01-88],f08[01-88],f09[01-88],f10[01-88],f11[01-56],f12[01-56]",
"processorType": "Intel Icelake",
"socketsPerNode": 2,
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