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$ sudo yum remove partekflow[~] openssl genrsa -out flow.key 2048[~] openssl ecparam -genkey -name secp384r1 -out flow.key[~] openssl req -new -x509 -sha256 -key flow.key -out flow.crt -days 3650[~] keytool -import -file /home/flow/.partekflow/keys/flow.key -alias someName -keystore /usr/lib/jvm/java-11-openjdk-amd64/lib/security/cacerts -storepass changeit -nopromptexport CATALINA_OPTS="$CATALINA_OPTS -Djavax.net.ssl.trustStore=${HOME}/keys"
docker psdocker execservices:
flowheadnode:
restart: unless-stopped
image: public.ecr.aws/partek-flow/rtw:latest
hostname: flowheadnode
environment:
# Set license location. Can be a server ex. @lic-test.example.com or /home/flow/.partekflow/license/Partek.lic
- PARTEKLM_LICENSE_FILE=/home/flow/.partekflow/license/Partek.lic
ports:
- "8080:8080"
# The MAC must match what is in the license file or defined on the license server. Please change this.
networks:
flexlm:
mac_address: aa:bb:cc:dd:ee:ff
# The internal path must be /home/flow
volumes:
# This uses an external path for the Flow data. The 'flow' user inside the container must be able to read and write to this directory.
- /home/flow:/home/flow
networks:
flexlm:
cd home/flowwget --content-disposition http://packages.partek.com/linux/flowwget --content-disposition http://packages.partek.com/linux/flow-workerexport CATALINA_OPTS="$CATALINA_OPTS -Djava.awt.headless=true
-DflowDispatcher.flow.command.hostname=head-node.local
-DflowDispatcher.akka.remote.netty.tcp.hostname=head-node.local"~/partek_flow/start_flow.shnetstat -tulpn~/partek_flow/stop_flow.sh~/partek_flow/start_flow.sh~/partek_flow/stop_flow.sh~/partek_flow/start_flow.sh./partekFlowRemoteWorker.sh head-node.local compute-0/home/flow/PartekFlowRemoteWorker/partekFlowRemoteWorker.sh head-node.local compute-0$(hostname -s)/home/flow/PartekFlowRemoteWorker/partekFlowRemoteWorker.sh head-node.local compute-0./partek_flow/stop_flow.shwget --content-disposition http://packages.partek.com/linux/flow-releasewget --content-disposition http://packages.partek.com/linux/flow-worker-releaseps aux | grep flowmv partek_flow partek_flow_prevmv PartekFlowRemoteWorker PartekFlowRemoteWorker_prevtar -czvf partek-db-bkp-date.tgz ~/.partekflow./partek_flow/start_flow.shtail -f partek_flow/logs/catalina.out~/.partekflow/logs/flow.logapiVersion: v1
kind: Pod
metadata:
name: flowheadnode
namespace: partek-flow
labels:
app.kubernetes.io/name: flowheadnode
deployment: dev
spec:
securityContext:
fsGroup: 1000
containers:
- name: flowheadnode
image: xxxxxxxxxxxx.dkr.ecr.us-west-2.amazonaws.com/partek-flow:current-23.0809.22
resources:
requests:
memory: "16Gi"
cpu: 8
env:
- name: PARTEKLM_LICENSE_FILE
value: "@flexlmserver"
- name: PARTEK_COMMON_NO_TOTAL_LIMITS
value: "1"
- name: CATALINA_OPTS
value: "-DFLOW_WORKER_MEMORY_MB=1024 -DFLOW_WORKER_CORES=2 -Djavax.net.ssl.trustStore=/etc/flowconfig/cacerts -Xmx14g"
volumeMounts:
- name: home-flow
mountPath: /home/flow
- name: flowconfig
readOnly: true
mountPath: "/etc/flowconfig"
volumes:
- name: home-flow
persistentVolumeClaim:
claimName: partek-flow-pvc
- name: flowconfig
secret:
secretName: flowconfigspec:
securityContext:
fsGroup: 1000# This allows us to create pods with only a request set, but not a limit set. Further tuning is recommended.
apiVersion: v1
kind: LimitRange
metadata:
name: partek-flow-limit-range
spec:
limits:
- max:
memory: 512Gi
cpu: 64
default:
memory: 512Gi
cpu: 64
defaultRequest:
memory: 4Gi
cpu: 2
type: Container-DFLOW_WORKER_MEMORY_MB=1024 -DFLOW_WORKER_CORES=2-Djavax.net.ssl.trustStore=/etc/flowconfig/cacerts-Xmx14gapiVersion: v1
kind: Service
metadata:
name: flowheadnode
spec:
type: ClusterIP
ports:
- port: 80
targetPort: 8080
protocol: TCP
name: http
- port: 2552
targetPort: 2552
protocol: TCP
name: akka
- port: 8443
targetPort: 8443
protocol: TCP
name: licensing
selector:
app.kubernetes.io/name: flowheadnodeapiVersion: networking.k8s.io/v1
kind: Ingress
metadata:
name: flowheadnode
annotations:
kubernetes.io/ingress.class: "nginx"
nginx.ingress.kubernetes.io/force-ssl-redirect: "true"
spec:
rules:
- host: flow.dev-devsvc.domain.com
http:
paths:
- path: /
pathType: Prefix
backend:
service:
name: flowheadnode
port:
number: 80# On a NEW deployment, you need to exec into this pod and add the license file
# to /usr/local/flexlm/licenses
# After a license file is present, the flexlm daemon will start automatically
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: flexlmserver-pvc
spec:
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 10Gi # flex.log is the only thing that slowly grows here
storageClassName: gp2-ebs-sc
volumeMode: Filesystem
---
apiVersion: v1
kind: Service
metadata:
name: flexlmserver
spec:
type: ClusterIP
ports:
- port: 27000
targetPort: 27000
protocol: TCP
name: flexmain
- port: 27001
targetPort: 27001
protocol: TCP
name: flexvendor
selector:
app.kubernetes.io/name: flexlmserver
---
apiVersion: v1
kind: Pod
metadata:
name: flexlmserver
namespace: partek-flow
labels:
app.kubernetes.io/name: flexlmserver
spec:
containers:
- name: flexlmserver
image: public.ecr.aws/partek-flow/kube-flexlm-server
ports:
- containerPort: 27000
- containerPort: 27001
resources:
limits:
memory: "256Mi"
cpu: 1
securityContext:
capabilities:
add: ["NET_ADMIN"]
volumeMounts:
- name: flexlmserver-pvc
mountPath: /usr/local/flexlm/licenses
volumes:
- name: flexlmserver-pvc
persistentVolumeClaim:
claimName: flexlmserver-pvc$ chmod 600 Flow-Key.pem$ ssh -i Flow-Testing.pem [email protected]$ sudo su$ mkfs -t ext4 /dev/xvdb$ mount -t ext4 /dev/xvdb /mnt/$ rsync -avr /home/ /mnt/$ umount /mnt/$ mount -a$ sudo apt-get update$ sudo apt-get install software-properties-common$ sudo add-apt-repository -y ppa:openjdk-r/ppa$ sudo apt-get install openjdk-8-jdk python python-pip python-dev zlib1g-dev python-matplotlib r-base python-htseq libxml2-dev perl make gcc g++ zlib1g libbz2-1.0 libstdc++6 libgcc1 libncurses5 libsqlite3-0 libfreetype6 libpng12-0 zip unzip libgomp1 libxrender1 libxtst6 libxi6 debconf $ sudo pip install --upgrade pip && pip install --upgrade --upgrade-strategy eager --force-reinstall virtualenv numpy pysam cnvkit$ cd (we will install Partek Flow to ubuntu's home directory)$ wget --content-disposition packages.partek.com/linux/flow-release$ unzip PartekFlow*.zip$ ./partek_flow/start_flow.sh$ curl -F "[email protected]" https://installfeedback.partek.com/fuploadpip install --user cnvkit==0.9.5pip install --user numpy==1.19.5 Cython==0.29.30 cykhash==2.0.0 macs3==3.0.0a7pip install virtualenvvirtualenv ~/.partekflow/.localsource ~/.partekflow/.local/bin/activatepip install HTSeq==0.11.0pip install cnvkit==0.9.5wget customer.partek.com/python-dependencies.zipunizp -d ~/.partekflow/ python-dependencies.zipexport R_LIBS_USER=$HOME/.R.libPaths("~/.R")(.packages())packageVersion("packageName")R_HOME=/path/to/Rwget http://cran.wustl.edu/src/base/R-3/R-3.1.2.tar.gztar xfz R-3.1.2.tar.gz cd R-3.1.2./configure --with-x=no && makesymlink.system.packages: TRUE