Merge pull request #553 from radical-cybertools/devel

Release 1.6.0

.codecov.yml

@@ -6,4 +6,5 @@ coverage:
         threshold: 1%
         paths: 
           - "src"
+        base: "pr"
     patch: off

.github/workflows/python-app.yml

@@ -36,21 +36,28 @@ jobs:
         pip install hypothesis
         pip install coverage
         pip install codecov
+        pip install coveralls
         pip install pytest
         pip install pytest-xdist
         pip install pytest-timeout
-        pip install timeout_decorator
+        pip install timeout-decorator
     - name: Test with pytest
       env:
         RMQ_HOSTNAME: localhost
         RMQ_PORT: ${{ job.services.rabbitmq.ports[5672] }} # get randomly assigned published port
         RMQ_USERNAME: guest
         RMQ_PASSWORD: guest
+        LOC: /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages
       run: |
-        LOC=/opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages
-        coverage run --include=$LOC/radical/entk/* -m pytest -ra --timeout=600 -vvv --showlocals tests/test_component tests/test_utils/ tests/test_integration
+        coverage run --include=$LOC/radical/entk/* -m pytest -ra --timeout=600 -vvv --showlocals tests/test_component tests/test_utils/ tests/test_integration        
     - name: Codecov
-      uses: codecov/codecov-action@v1.0.15
+      env: 
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      run: |
+        coverage combine; \
+        coverage xml; \
+        coverage report; \
+        curl -s https://codecov.io/bash | bash
 
   flake8:
     runs-on: ubuntu-latest

.github/workflows/python-publish.yml

@@ -19,7 +19,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.x'
+        python-version: '3.6'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -29,5 +29,5 @@ jobs:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
+        python setup.py sdist
         twine upload dist/*

VERSION

@@ -1 +1 @@
-1.5.12
+1.6.0

examples/misc/lfs_tagging_dd.py

@@ -1,102 +1,105 @@
 #!/usr/bin/env python
 
 from radical.entk import Pipeline, Stage, Task, AppManager
-from radical.entk.exceptions import *
 import os
-import sys
-import argparse
 
-hostname = os.environ.get('RMQ_HOSTNAME','localhost')
-port = int(os.environ.get('RMQ_PORT',5672))
-
-
-def get_pipeline(shared_fs=False, size=1):
-
-    p = Pipeline()
-    p.name = 'p'
-
-    n = 4
-
-    s1 = Stage()
-    s1.name = 's1'
-    for x in range(n):
-        t = Task()
-        t.name = 't%s'%x
-
-        # dd if=/dev/random bs=<byte size of a chunk> count=<number of chunks> of=<output file name>
-
-        t.executable = 'dd'
-
-        if not shared_fs:
-            t.arguments = ['if=/dev/urandom','bs=%sM'%size, 'count=1', 'of=$NODE_LFS_PATH/s1_t%s.txt'%x]
-        else:
-            t.arguments = ['if=/dev/urandom','bs=%sM'%size, 'count=1', 'of=/home/vivek91/s1_t%s.txt'%x]
-
-        t.cpu_reqs['processes'] = 1
-        t.cpu_reqs['threads_per_process'] = 24
-        t.cpu_reqs['thread_type'] = ''
-        t.cpu_reqs['process_type'] = ''
-        t.lfs_per_process = 1024
-
-        s1.add_tasks(t)
-
-    p.add_stages(s1)
-
-    s2 = Stage()
-    s2.name = 's2'
+if os.environ.get('RADICAL_ENTK_VERBOSE') is None:
+    os.environ['RADICAL_ENTK_REPORT'] = 'True'
+
+# No need to change/set any variables if you installed RabbitMQ has a system
+# process. If you are running RabbitMQ in a Docker container or on a dedicated
+# virtual machine, set the variables "RMQ_HOSTNAME" and "RMQ_PORT" in the shell
+# environment in which you are running this script.
+hostname = os.environ.get('RMQ_HOSTNAME', 'localhost')
+port = int(os.environ.get('RMQ_PORT', '5672'))
+username = os.environ.get('RMQ_USERNAME')
+password = os.environ.get('RMQ_PASSWORD')
+
+
+# Each task of this example prints the hostname of the node on which it is
+# executed. Tagged tasks should print the same hostname.
+def get_pipeline(n=2):
+    '''
+    We create a pipeline with three stages, each with 1 task. The tasks of the
+    second and third stages are tagged to execute on the same compute node on
+    which the first stage's task executed.
+    '''
+
+    pipelines = list()
     for x in range(n):
-        t = Task()
-        t.executable = 'dd'
-
-        if not shared_fs:
-            t.arguments = ['if=$NODE_LFS_PATH/s1_t%s.txt'%x,'bs=%sM'%size, 'count=1', 'of=$NODE_LFS_PATH/s2_t%s.txt'%x]
-        else:
-            t.arguments = ['if=/home/vivek91/s1_t%s.txt'%x,'bs=%sM'%size, 'count=1', 'of=/home/vivek91/s2_t%s.txt'%x]
-
-        t.cpu_reqs['processes'] = 1
-        t.cpu_reqs['threads_per_process'] = 24
-        t.cpu_reqs['thread_type'] = ''
-        t.cpu_reqs['process_type'] = ''
-        t.tag = 't%s'%x
-
-        s2.add_tasks(t)
-
-
-    p.add_stages(s2)
-
-    return p
-
+        pipeline = Pipeline()
+        pipeline.name = 'p.%04d' % x
+
+        stage1 = Stage()
+        stage1.name = 'stage1'
+        # task1 of stage1 will execute on the first available and suitable node.
+        task1 = Task()
+        task1.name = 'task1.%04d' % x
+        task1.executable = 'hostname'
+        # Set enough threads for task1 to get a whole compute node
+        task1.cpu_reqs = {'cpu_processes': 1,
+                          'cpu_threads': 1,
+                          'cpu_process_type': None,
+                          'cpu_thread_type': None}
+        task1.lfs_per_process = 10
+        stage1.add_tasks(task1)
+
+        pipeline.add_stages(stage1)
+
+        stage2 = Stage()
+        stage2.name = 'stage2'
+
+        task2 = Task()
+        task2.name = 'task2.%04d' % x
+        task2.executable = 'hostname'
+        task2.cpu_reqs = {'cpu_processes': 1,
+                          'cpu_threads': 1,
+                          'cpu_process_type': None,
+                          'cpu_thread_type': None}
+        # We use the ID of task1 as the tag of task2. In this way, task2 will
+        # execute on the same node on which task1 executed.
+        task2.tags = {'colocate': task1.uid}
+        task2.lfs_per_process = 10
+        stage2.add_tasks(task2)
+
+
+        pipeline.add_stages(stage2)
+
+        stage3 = Stage()
+        stage3.name = 'stage3'
+
+        task3 = Task()
+        task3.name = 'task3.%04d' % x
+        task3.executable = 'hostname'
+        task3.cpu_reqs = {'cpu_processes': 1,
+                          'cpu_threads': 1,
+                          'cpu_process_type': None,
+                          'cpu_thread_type': None}
+        task3.lfs_per_process = 10
+        # We use the ID of task1 as the tag of task3. In this way, task3 will
+        # execute on the same node on which task1 and task2 executed.
+        task3.tag = {'colocate': task1.uid}
+        stage3.add_tasks(task3)
+
+        pipeline.add_stages(stage3)
+        pipelines.append(pipeline)
+
+    return pipelines
 
 
 if __name__ == '__main__':
 
-    args = argparse.ArgumentParser()
-    args.add_argument('sharedfs')
-    args.add_argument('size')
-
-    args = args.parse_args()
-    if args.sharedfs == 'shared':
-        shared_fs = True
-    else:
-        shared_fs = False
-    size = args.size
-
-    print('SharedFS: ', shared_fs, size)
-
-    os.environ['RADICAL_PILOT_DBURL'] = 'mongodb://entk:entk123@ds159631.mlab.com:59631/da-lfs-test'
-
+    # Request at least two compute nodes
     res_dict = {
-                'resource'      : 'xsede.comet',
-                'walltime'      : 30,
-                'cpus'          : 120,
-                'project'       : 'unc100'
-                # 'project'       : 'gk4',
-                # 'queue'         : 'high'
+                'resource'      : 'local.localhost',
+                'walltime'      : 20,
+                'cpus'          : 2,
             }
 
-    appman = AppManager(hostname=hostname, port=port)
+    appman = AppManager(hostname=hostname, port=port, username=username, password=password)
     appman.resource_desc = res_dict
 
-    p = get_pipeline(shared_fs=shared_fs, size=size)
-    appman.workflow = [p]
+    # Select n to be >= to the number of available compute nodes.
+    p = get_pipeline(n=2)
+    appman.workflow = set(p)
     appman.run()

src/radical/entk/__init__.py

@@ -1,4 +1,4 @@
-
+# pylint: disable=unused-argument
 # ------------------------------------------------------------------------------
 #
 from .pipeline import Pipeline
@@ -17,10 +17,12 @@
 import requests                     as req
 from packaging.version import parse as parse_version
 
+
 def custom_formatwarning(msg, *args, **kwargs):
     # ignore everything except the message
     return str(msg) + '\n'
 
+
 warnings.formatwarning = custom_formatwarning
 
 version_short, version_detail, version_base, version_branch, \

src/radical/entk/execman/mock/task_manager.py

@@ -244,13 +244,15 @@ def _process_tasks(self, task_queue, rmgr, rmq_conn_params):
                     bulk_tasks.append(task)
 
                     self._advance(task, 'Task', states.SUBMITTING,
-                                  mq_channel, '%s-tmgr-to-sync' % self._sid)
+                                  mq_channel, rmq_conn_params,
+                                  '%s-tmgr-to-sync' % self._sid)
 
                 # this mock RTS immmedialtely completes all tasks
                 for task in bulk_tasks:
 
                     self._advance(task, 'Task', states.COMPLETED,
-                                  mq_channel, '%s-cb-to-sync' % self._sid)
+                                  mq_channel, rmq_conn_params,
+                                  '%s-cb-to-sync' % self._sid)
 
                     task_as_dict = json.dumps(task.to_dict())
                     mq_channel.basic_publish(

src/radical/entk/execman/rp/resource_manager.py

@@ -162,8 +162,8 @@ def _pilot_state_cb(pilot, state):
                        'job_name'      : self._job_name
                        }
 
-            # Create Compute Pilot with validated resource description
-            pdesc = rp.ComputePilotDescription(pd_init)
+            # Create Pilot with validated resource description
+            pdesc = rp.PilotDescription(pd_init)
             self._prof.prof('rreq created', uid=self._uid)
 
             # Launch the pilot