For Openshift jobs, one way is to use the oc run command to execute a command against an image, this will run the command inside a pod. Is there way to apply configuration such as a config map or secret to this mechanism (oc run).
Please advise.
B
Create a deployment config for these requirement. In which you can declare environment variables, commands, declare secrets etc. It will be easy to maintain too.
see this example pod in kind. in this you can also add command and env variables. it will not restart the container itself. not complete but you will get the idea.
apiVersion: v1
kind: Pod
metadata:
name: pod-elasticsearch-1
namespace: common-data
labels:
elasticsearch-name: pod-elasticsearch-1
node: elasticsearch
type: elasticsearch-logs
spec:
containers:
- resources:
limits:
memory: "24Gi"
cpu: "2"
requests:
memory: "16Gi"
cpu: "1"
ulimits:
memlock:
soft: -1
hard: -1
nofile:
soft: 65536
hard: 65536
image: docker.elastic.co/elasticsearch/elasticsearch:5.5.2
name: elasticsearch-custom
command: [ "elasticsearch"]
args: ["-E" , "cluster.name=es-ocp-app-cluster",
"-E" , "node.name=master-es-node-1",
"-E" , "node.master=true",
"-E" , "node.data=true",
"-E" , "network.publish_host= svc-elasticsearch-1 ",
#"-E" , "network.host=_site_",
"-E" , "http.host=0.0.0.0",
Related
We are running jmx through Tauras using 2 containers in Kubernetes.
We are seeing only 50 users in results instead of 100(50*2 containers).
Can anyone please through some light if we are missing something here.
We get two jtl and checking them individual or combined the total users are same 50 only. Is it related to same Thread name being generated and logged in jtl file or something else.
Here is the yml details:
apiVersion: v1
kind: ConfigMap
metadata:
name: joba
namespace: AAA
data:
protocol: "https"
serverUrl: “testurl”
users: "50”
duration: "1m"
nodeName: "Nodename"
---
apiVersion: /v1
kind: Job
metadata:
name: perftest
namespace: dev
spec:
template:
spec:
containers:
- args: ["split -l ${users} --numeric-suffixes Test.csv Test-; /bin/bash ./Shellscripttoread_assignvariables.sh;"]
command: ["/bin/bash", "-c"]
env:
- name: JobNumber
value: "00"
envFrom:
- configMapRef:
name: job-multi
image: imagepath
name: ubuntu-00
resources:
limits:
memory: “8000Mi"
cpu: "2880m"
- args: ["split -l ${users} --numeric-suffixes Test.csv Test-; /bin/bash ./Shellscripttoread_assignvariables.sh;"]
command: ["/bin/bash", "-c"]
env:
- name: JobNumber
value: "01”
envFrom:
- configMapRef:
name: job-multi
image: imagepath
name: ubuntu-01
resources:
limits:
memory: “8000Mi"
cpu: "2880m"
Your YAML is very nice but it doesn't tell anything about how do you launch JMeter or what these shell scripts you invoke are doing.
If you just kick off 2 separate JMeter instances by means of k8s - JMeter will look at the number of active threads from the .jtl file and given the Sampler/Transaction names are the same JMeter "thinks" that the tests were executed on one engine.
The workaround is to add i.e. machineName() or __machineIP() function to sampler/transaction labels, this way JMeter will distinguish the results coming from different instances and you will see real number of active threads.
The solution would be running your JMeter test in Distributed Mode so master will run in one pod, slaves in their own pods and the master will be responsible for transferring .jmx script to the slaves and collecting results from them
New to kubernetes i´m trying to move a current pipeline we have using a queing system without k8s.
I have a perl script that generates a list of batch jobs (yml files) for each of the samples that i have to process.
Then i run kubectl apply --recursive -f 16S_jobscripts/
For example each sample needs to be treated sequentially and go through different processing
Exemple:
SampleA -> clean -> quality -> some_calculation
SampleB -> clean -> quality -> some_calculation
and so on for 300 samples.
So the idea is to prepare all the yml files and run them sequentially. This is working.
BUT, with this approach i need to wait that all samples are processed (let´s say that all the clean jobs need to completed before i run the next jobs quality).
what would be the best approach in such case, run each sample independently ?? how ?
The yml below describe one Sample for one job. You can see that i´m using a counter (mergereads-1 for sample1(A))
apiVersion: batch/v1
kind: Job
metadata:
name: merge-reads-1
namespace: namespace-id-16s
labels:
jobgroup: mergereads
spec:
template:
metadata:
name: mergereads-1
labels:
jobgroup: mergereads
spec:
containers:
- name: mergereads-$idx
image: .../bbmap:latest
command: ['sh', '-c']
args: ['
cd workdir &&
bbmerge.sh -Xmx1200m in1=files/trimmed/1.R1.trimmed.fq.gz in2=files/trimmed/1.R2.trimmed.fq.gz out=files/mergedpairs/1.merged.fq.gz merge=t mininsert=300 qtrim2=t minq=27 ratiomode=t &&
ls files/mergedpairs/
']
resources:
limits:
cpu: 1
memory: 2000Mi
requests:
cpu: 0.8
memory: 1500Mi
volumeMounts:
- mountPath: '/workdir'
name: db
volumes:
- name: db
persistentVolumeClaim:
claimName: workdir
restartPolicy: Never
If i understand you correctly you can use parallel-jobs with a use of Job Patterns.
It does support parallel processing of a set of independent but
related work items.
Also you can consider using Argo.
https://github.com/argoproj/argo
Argo Workflows is an open source container-native workflow engine for
orchestrating parallel jobs on Kubernetes. Argo Workflows is
implemented as a Kubernetes CRD (Custom Resource Definition).
Please let me know if that helps.
I’m having some trouble limiting my Pods access to the GPUs available on my cluster.
Here is my .yaml:
kind: Pod
metadata:
name: train-gpu
spec:
containers:
- name: train-gpu
image: index.docker.io/myprivaterepository/train:latest
command: ["sleep"]
args: ["100000"]
resources:
limits:
nvidia.com/gpu: 1 # requesting 1 GPU
When I run the nvidia-smi command inside of this pod all of the GPUs show up, rather than just 1.
Any advice would be much appreciated.
Some information that may be useful:
Kubernetes version:
Client Version: version.Info{Major:“1”, Minor:“16”, GitVersion:“v1.16.1”, GitCommit:“d647ddbd755faf07169599a625faf302ffc34458”, GitTreeState:“clean”, BuildDate:“2019-10-07T14:30:40Z”, GoVersion:“go1.12.10”, Compiler:“gc”, Platform:“linux/amd64”}
Server Version: version.Info{Major:“1”, Minor:“15”, GitVersion:“v1.15.3”, GitCommit:“2d3c76f9091b6bec110a5e63777c332469e0cba2”, GitTreeState:“clean”, BuildDate:“2019-08-19T11:05:50Z”, GoVersion:“go1.12.9”, Compiler:“gc”, Platform:“linux/amd64”}
Docker base image:
FROM nvidia/cuda:10.1-base-ubuntu18.04
For logs, I mount a volume from host on to the pod. This is written in the deployment yaml.
But, if my 2 pods run on the same host, there will be conflict as both pods will produce log files with same name.
Can I use some dynamic variables in deployment file so that mount on host is created with different name for different pods?
you can use subPathExpr to achieve the uniqueness in the absolute path, this is one of the use case of the this feature. As of now its is alpha in k1.14.
In this example, a Pod uses subPathExpr to create a directory pod1 within the hostPath volume /var/log/pods, using the pod name from the Downward API. The host directory /var/log/pods/pod1 is mounted at /logs in the container.
apiVersion: v1
kind: Pod
metadata:
name: pod1
spec:
containers:
- name: container1
env:
- name: POD_NAME
valueFrom:
fieldRef:
apiVersion: v1
fieldPath: metadata.name
image: busybox
command: [ "sh", "-c", "while [ true ]; do echo 'Hello'; sleep 10; done | tee -a /logs/hello.txt" ]
volumeMounts:
- name: workdir1
mountPath: /logs
subPathExpr: $(POD_NAME)
restartPolicy: Never
volumes:
- name: workdir1
hostPath:
path: /var/log/pods
look at pod affinity/anti affinity to not to schedule the replica on the same node. that way each replica of a specific deployment gets deployed on separate node. you will not have to bother about same folder being used by multiple pods.
I had to spend hours for this, your solution worked like a charm!
Had tried with, none worked despite being given in multiple documents.
subPathExpr: "$POD_NAME"
subPathExpr: $POD_NAME
subPathExpr: ${POD_NAME}
Finally this worked, subPathExpr: $(POD_NAME)
I am working on a new scheduler's stress test in Kubernetes. I need to open a lot of CPU and memory pods to analyze performance.
I am using image: polinux/stress in my pods.
I would like to ask if there is any instruction, or when I write the yaml file, I can set this successfully generated pod to delete itself within the time set by me.
The following yaml file is the pod I am writing for stress testing. I would like to ask if I can write it from here to let him delete it after a period of time.
apiVersion: v1
kind: Pod
metadata:
name: alltest12
namespace: test
spec:
containers:
- name: alltest
image: polinux/stress
resources:
requests:
memory: "1000Mi"
cpu: "1"
limits:
memory: "1000Mi"
cpu: "1"
command: ["stress"]
args: ["--vm", "1", "--vm-bytes", "500M", "--vm-hang", "1"]
If polinux/stress contains a shell, I believe you can have the thing kill itself:
- containers:
image: polinux/stress
command:
- sh
- -c
- |
sh -c "sleep 300; kill -9 1" &
stress --vm 1 --vm-bytes 500M --vm-hang 1
Or even slightly opposite:
- |
stress --vm etc etc &
child_pid=$!
sleep 300
kill -9 $child_pid
And you can parameterize that setup using env::
env:
- name: LIVE_SECONDS
value: "300"
command:
- sh
- -c
- |
sleep ${LIVE_SECONDS}
kill -9 $child_pid