iwp_entk.py

import os
import radical.pilot as rp
from radical.entk import Pipeline, Stage, Task, AppManager


crop_size = int(360)              #covnvert this to argument later
worker_root = r"/pylon5/mc3bggp/aymen/local_dir/datasets/polygon/"                                                                 #convert this to argument later
weights_path = r"/pylon5/mc3bggp/aymen/local_dir/datasets/logs/ice_wedge_polygon20180823T1403/mask_rcnn_ice_wedge_polygon_0008.h5" #convert this to argument later
imgs_path = r"/pylon5/mc3bggp/aymen/local_dir/datasets/polygon/input_img/"                                                         #convert this to argument later

# ------------------------------------------------------------------------------
# Set default verbosity

if os.environ.get('RADICAL_ENTK_VERBOSE') == None:
    os.environ['RADICAL_ENTK_REPORT'] = 'True'

hostname = os.environ.get('RMQ_HOSTNAME', 'two.radical-project.org')
port = int(os.environ.get('RMQ_PORT', 33235))

if __name__ == '__main__':

    # Create a Pipeline object
    p = Pipeline()

#---------------------------------------------------------
# Build Preprocessing level

    # Create a Stage object
    s = Stage()

    # Create a Task object
    t = Task()
    t.pre_exec = ['module unload intel/19.5',
                  'module load intel/18.4',
                  'module list',
                  'mpirun -info',
                  'mpirun -x',
                  'mpirun -envlist',
                  'source activate polygons',
                  'export PYTHONPATH=/pylon5/mc3bggp/aymen/anaconda3/envs/polygons/lib/python3.6/site-packages:$PYTHONPATH',
                  'export PYTHONPATH=/pylon5/mc3bggp/aymen/local_dir/utils:$PYTHONPATH']

    t.name = 'Preprocessing'        # Assign a name to the task (optional, do not use ',' or '_')
    t.executable = 'python'         # Assign executable to the task
    t.arguments = ['/pylon5/mc3bggp/aymen/local_dir/iwp_mpi_preprocessing.py', '%s' % imgs_path, '%s' % worker_root, '%s' % crop_size]
    #t.arguments = ['/home/aymen/SummerRadical/which_mpi/contrsact_cmd.py']
    t.cpu_reqs = {'processes': 28,
                  'process_type': 'MPI',
                  'thread_type': 'OpenMP',
                  'threads_per_process': 1}
    # Add Task to the Stage
    s.add_tasks(t)

    # Add Stage to the Pipeline
    p.add_stages(s)

    # Create Application Manager
    appman = AppManager(hostname=hostname, port=port, autoterminate=True, write_workflow=True)

    # Create a dictionary describe four mandatory keys:
    # resource, walltime, and cpus
    # resource is 'local.localhost' to execute locally
    res_dict = {

        'resource' : 'xsede.bridges',
        'walltime' : 60,
        'cpus'     : 28,
        'project'  : 'mc3bggp',
        'queue'    : 'RM',
        'schema'   :'gsissh',
    }

    # Assign resource request description to the Application Manager
    appman.resource_desc = res_dict
    # Assign the workflow as a set or list of Pipelines to the Application Manager
    # Note: The list order is not guaranteed to be preserved
    appman.workflow = set([p])

    # Run the Application Manager
    appman.run()