...

• allows to express the workflow

• allows a way to map tasks to resources (i.e. number of cores for each task, etc .. )

• gives monitoring capability to keep track of e.g. progress of task farm, CPU load, memory consumption etc.

As a by-product, we get the benefit of:

• packing thin tasks (e.g. 1 core task) on a single Shaheen node, maximizing the node utilization

• introducing a hook to dynamically allocate more worker nodes as SLURM jobs and extend the resources available to the scheduler to run the task farm

• possibility to resume the task farm as a new set of jobs (depending on if you have added some logic) , therefore allowing checkpoint-restart.

Implementation

We are leveraging Dask’s execution engine on Shaheen’s compute nodes for this purpose.

...

• A user_workflow.py script to express the steps in a workflow. It also allows expressing the parameters and passes a task and its corresponding parameter to the Dask cluster via the client API.

• A wrapper.sh is an executable bash script which does steps common to each task, e.g. setting the environment. The command line (including the options/arguments) are passes as an argument when invoking the wrapper script

• Two jobscripts to interact with SLURM

  • sched.slurm is a jobscript which invokes Dask scheduler and invokes the user_workflow.py when worker nodes are ready. It also submits the worker.slurm script to SLURM depending on the value of NUM_WORKERS set in the script

  • worker.slurm allocates resources for a worker node which is a Shaheen compute node as a SLURM job, where Dask workers will start and will connect to an existing Dask scheduler . This jobscript also allows tuning the configuration of resources available for each Dask worker, i.e CPUs or memory

User workflow script

The script below

#!/usr/bin/env python

from dask.distributed import Client,as_completed
import os,time, subprocess as sb
import numpy as np
#client = Client(scheduler_file='scheduler_%s.json'%jobid,direct_to_workers=True)  # start local workers as processes
client = Client(scheduler_file='scheduler.json')  # start local workers as processes


def params(filename='foo.txt'):
    f = open(filename,'r+')
    files = f.read().splitlines() # List with stripped line-breaks 
    f.close()
    return files

def func(x,out_dir):
    fo=open(os.path.join(out_dir,'out.log'),'w+')
    fe=open(os.path.join(out_dir,'err.log'),'w+')
    
    srcdir='/scratch/shaima0d/tickets/39404/user_case'
    EXE='FreeFem++-nw'

    # Pre-processing steps --  before launching the application
    o = sb.run(['rsync','-r','%s'%(os.path.join(srcdir,'pv_LIR_etau_IVCurve_SF.edp')),
        'pv_LIR_etau_IVCurve_SF.edp']
        ,cwd=out_dir)
    o = sb.run(['rsync','-r','%s'%(os.path.join(srcdir,'BF_RefMeshLIR_100x100x95x100.msh')),
        'BF_RefMeshLIR_100x100x95x100.msh']
        ,cwd=out_dir)
    o = sb.run(['rsync','-r','%s'%(os.path.join(os.environ['PWD'],'wrapper.sh')),
        'wrapper.sh']
        ,cwd=out_dir)

    # Launch the application along with its optinos as command line arugument to wrapper script 
    o = sb.run(['./wrapper.sh','%s'%(EXE),'pv_LIR_etau_IVCurve_SF.edp','%s'%(x)],
                stdout=fo,stderr=fe,
                shell=False,cwd=out_dir)
    # Post-processing steps
        # - Copy the output file and rename it to index according to the task
        # - Delete the task directory if the processing was successful
    
    return True

base_dir=os.environ['EXP_NAME']
os.makedirs(base_dir,exist_ok=True)

# the logic of parameter setting is encapsulated in params function:
x = params()

outdirs=list()
for i in range(len(x)):
    sample_dir=os.path.join(base_dir,'%s'%(str(i+1)))
    os.makedirs(sample_dir,exist_ok=True)
    outdirs.append(sample_dir)
print('outdirs[%d]:: '%(len(outdirs)),outdirs)


futures=client.map(func,x,outdirs)

for future in as_completed(futures):
    print('result: ',future.result())

client.close()

Wrapper script

Here you can set the environment to run the target application and invoke it via the arguments passed in from the user_workflow.py script where the wrapper.sh was invoked.

#!/bin/bash

module swap PrgEnv-cray PrgEnv-gnu
module load freefem/4.7
module list
echo "running $@"
$@

SLURM jobscripts

There are two scripts needed in this workflow

Scheduler script

The scheduler script will, e.g. look as below. Until line 59, its a boiler plate code, which remains pretty much same for any workload. You can control and modify the ports dask_dashboard port and the job’s wall time if you like. Lines 59-64 invoke the user_workflow.py script on the head node which will spawn work on the available worker nodes. There is a sleep command to wait until all worker nodes are up and running.

#!/bin/bash -l
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --partition=workq
#SBATCH --hint=nomultithread
#SBATCH --time=01:00:00

module load dask

NUM_WORKERS=4
WORKER_JOB_PREFIX=test_workers
export EXP_NAME=experiment_${SLURM_JOBID}

export LC_ALL=C.UTF-8
export LANG=C.UTF-8

# get tunneling info 
export XDG_RUNTIME_DIR="" 
node=$(hostname -s) 
user=$(whoami) 
gateway=${EPROXY_LOGIN} 
submit_host=${SLURM_SUBMIT_HOST} 
port=8889
dask_dashboard=9000

if [ -f 'scheduler.json' ]; then
	rm scheduler.json
fi

srun -u --hint=nomultithread dask-scheduler --scheduler-file=scheduler.json --dashboard-address=${node}:${dask_dashboard} --port=6192 --interface=ipogif0 &


echo $node on $gateway pinned to port $port
# print tunneling instructions jupyter-log
echo -e "
To connect to the compute node ${node} on Shaheen running your jupyter notebook server,
you need to run following two commands in a terminal

1. Command to create ssh tunnel from you workstation/laptop to cdlX:
ssh -L ${dask_dashboard}:localhost:${dask_dashboard} ${user}@${submit_host}.hpc.kaust.edu.sa

2. Command to create ssh tunnel to run on cdlX:
ssh -L ${dask_dashboard}:${node}:${dask_dashboard} ${user}@${gateway}

Copy the link provided below by jupyter-server and replace the nid0XXXX with localhost before pasting it in your browser on your workstation/laptop
"

while [ ! -f 'scheduler.json' ] ; 
do
	sleep 2
	echo "Waiting for dask scheduler to start"
done

for ((i=1; i< $((NUM_WORKERS + 1)); i++))
	do
		sbatch -J ${WORKER_JOB_PREFIX}  worker.slurm
done

sleep 180
echo "Starting workload"
python -u user_workflow.py
scancel -n ${WORKER_JOB_PREFIX} 
exit 0
wait

Worker script

The worker.slurm script is submitted automatically by the sched.slurm script. However, if you feel that the task farm requires more resource, you can submit additional worker jobs manually to extend the compute resources

#!/bin/bash -l
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --partition=workq
#SBATCH --hint=nomultithread
#SBATCH --time=01:00:00

module load dask

export LC_ALL=C.UTF-8
export LANG=C.UTF-8
mkdir workers${SLURM_JOBID}


srun -n 1 -c ${SLURM_CPUS_PER_TASK} -u --hint=nomultithread --cpu-bind=cores dask-worker --scheduler-file=scheduler.json --interface=ipogif0 --nprocs=${SLURM_CPUS_PER_TASK}

Execution

When all scripts are ready, you can simply submit the sched.slurm job to start the workflow:

sbatch sched.slurm

As on optional step, for additional workers more than that set in the sched.slurm script as parameter NUM_WORKERS a job can manually be submitted to SLURM queue to extend the compute resource.

sbatch worker.slurm

For instructions on how to connect to the Dask Dashboard and monitor the progress, please following:

Using Dask on Shaheen