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BraCa
Asked: 2011-10-09 04:32:02 +0800 CST

PBS Jobs - serial vs parallel job which one is better for my scenario

  • 772

I have access to a cluster that uses 'torque' (I think) and we use PBS scripts to submit jobs. I need to run more then 200 instances of an app that I've developed in java. The app acts as a peer forming a P2P network, which means that those instances communicate with each other through sockets.

I was able to do my tests with 100 instances running on a single node on the cluster, but when running 200 instances on a single node it doesn't work, and I can't ask for more resources (mem, cores, etc.)

My question is: should I do this the way I'm doing it? With a serial script in which I start all my instances one by one sending them to the background and then wait for them?

Could this be accomplished with a parallel script in which I could ask for 2 nodes and instantiate 100 instances of my app in each node? In this case, I have some other questions: How can I do it? and is there any guarantee that both jobs run at the same time? All 200 instances must be running at the same time.

  • To form the P2P network at least one peer IP address must be known in a serial job, I can get the node IP address in the script and pass it as a parameter to the app, but in a parallel job with 2 nodes how can I do this?

This is part of the script that I'm currently using...

#PBS -l nodes=1:ppn=4
#PBS -l pmem=6GB
#PBS -l walltime=00:20:00
IP=`/sbin/ifconfig eth0 | grep 'inet ' | awk '{print $2}' | sed 's/addr://'`
PORT_PEER=3000
java -jar $JAR $JAR_PARAMS -ip=$IP -port=$PORT_PEER & # first peer, others connect to this one..
  for i in {1..99}
  do
   PORT_PEER=`expr $PORT_PEER + 2`;
   java -jar $JAR $JAR_PARAMS -ip=$IP -port=$PORT_PEER -bootstrap=$IP:3000 &
   sleep 1s
  done
 wait # wait here until all instances terminates
linux cluster pbs

1 Answers

  1. Best Answer

    If you change the script to something like:

    #PBS -l nodes=2:ppn=4

    you'll get 2 nodes, each with at least 4 available cores. You may already know that.

    Your TORQUE admin may have also enabled pbsdsh. With the proper arguments, you can use that to run commands on each node reserved by your job. Without pbsdsh, if they've at least enabled rsh access among systems in one queue, you can parse through the contents of the file given by the environment variable $PBS_NODEFILE and rsh to each one that's not the main host, running a shell script on each.

    So, untested, but something like:

    # main-script.sh (runs on primary node, spawns off java processes on all
# nodes in job)
#PBS -l nodes=2:ppn=4
MASTER_IP=`/sbin/ifconfig eth0 | grep 'inet ' | awk '{print $2}' \
    | sed 's/addr://'`
PORT_PEER=3000
# first peer, others connect to this one..
java -jar ${JAR} ${JAR_PARAMS} -ip=${MASTER_IP} -port=${PORT_PEER} &
# run 2 copies of smaller-script.sh on unique hostnames in this job
pbsdsh -u -c 2 /path/to/smaller-script.sh ${MASTER_IP}

    and

    # smaller-script.sh (runs on each node in job)
MASTER_IP=$1
PORT_PEER=3000
IP=`/sbin/ifconfig eth0 | grep 'inet ' | awk '{print $2}' | sed 's/addr://'`
# other peers, connecting back to first peer from other script
for i in {1..99}
do
    PORT_PEER=`expr $PORT_PEER + 2`;
    java -jar ${JAR} ${JAR_PARAMS} -ip=${IP} -port=${PORT_PEER} \
        -bootstrap=${MASTER_IP}:3000 &
    sleep 1s
done
wait # wait here until all instances terminates

    should get you started.

    • 1