Docker SGE (Son of Grid Engine)

Kubernetes All-in-One Usage

1. Setup Kubernetes cluster, DNS service, and SGE cluster

Set KUBE_SERVER, DNS_DOMAIN, and DNS_SERVER_IP currectly. And run ./kubernetes/setup_all.sh with number of SGE workers.

export KUBE_SERVER=xxx.xxx.xxx.xxx
export DNS_DOMAIN=xxxx.xxxx
export DNS_SERVER_IP=xxx.xxx.xxx.xxx
./kubernetes/setup_all.sh 20

2. Submit Job

kubectl exec sgemaster -- sudo su sgeuser bash -c '. /etc/profile.d/sge.sh; echo "/bin/hostname" | qsub'
kubectl exec sgemaster -- sudo su sgeuser bash -c 'cat /home/sgeuser/STDIN.o1'

3. Add SGE workers

./kubernetes/add_sge_workers.sh 10

Kubernetes Step-by-Step Usage

1. Setup Kubernetes cluster

./kubernetes/setup_k8s.sh

2. Setup DNS service

Set KUBE_SERVER, DNS_DOMAIN, and DNS_SERVER_IP currectly

export KUBE_SERVER=xxx.xxx.xxx.xxx
export DNS_DOMAIN=xxxx.xxxx
export DNS_SERVER_IP=xxx.xxx.xxx.xxx
./kubernetes/setup_dns.sh

3. Check DNS service

• Boot test client

kubectl create -f ./kubernetes/skydns/busybox.yaml

• Check normal lookup

kubectl exec busybox -- nslookup kubernetes

• Check reverse lookup

kubectl exec busybox -- nslookup 10.0.0.1

• Check pod name lookup

kubectl exec busybox -- nslookup busybox.default

4. Setup SGE cluster

Run ./kubernetes/setup_sge.sh with number of SGE workers.

./kubernetes/setup_sge.sh 10

5. Submit job

kubectl exec sgemaster -- sudo su sgeuser bash -c '. /etc/profile.d/sge.sh; echo "/bin/hostname" | qsub'
kubectl exec sgemaster -- sudo su sgeuser bash -c 'cat /home/sgeuser/STDIN.o1'

6. Add SGE workers

./kubernetes/add_sge_workers.sh 10

Simple Docker Command Usage

1. Load nfsd module

modprobe nfsd

2. Boot DNS server

docker run -d --hostname resolvable -v /var/run/docker.sock:/tmp/docker.sock -v /etc/resolv.conf:/tmp/resolv.conf mgood/resolvable

3. Boot NFS servers

docker run -d --name nfshome --privileged cpuguy83/nfs-server /exports
docker run -d --name nfsopt --privileged cpuguy83/nfs-server /exports

4. Boot SGE master

docker run -d -h sgemaster --name sgemaster --privileged --link nfshome:nfshome --link nfsopt:nfsopt wtakase/sge-master

5. Boot SGE workers

docker run -d -h sgeworker01 --name sgeworker01 --privileged --link sgemaster:sgemaster --link nfshome:nfshome --link nfsopt:nfsopt wtakase/sge-worker
docker run -d -h sgeworker02 --name sgeworker02 --privileged --link sgemaster:sgemaster --link nfshome:nfshome --link nfsopt:nfsopt wtakase/sge-worker

6. Submit job

docker exec -u sgeuser -it sgemaster bash -c '. /etc/profile.d/sge.sh; echo "/bin/hostname" | qsub'
docker exec -u sgeuser -it sgemaster cat /home/sgeuser/STDIN.o1