Python Stage.name方法代码示例

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
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'
    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

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def generate_pipeline(name, stages):

    # Create a Pipeline object
    p = Pipeline()
    p.name = name


    for s_cnt in range(stages):

        # Create a Stage object
        s = Stage()
        s.name = 'Stage %s'%s_cnt

        for t_cnt in range(5):

            # Create a Task object
            t = Task()
            t.name = 'my-task'        # Assign a name to the task (optional)
            t.executable = '/bin/echo'   # Assign executable to the task
            # Assign arguments for the task executable
            t.arguments = ['I am task %s in %s in %s'%(t_cnt, s_cnt, name)]

            # Add the Task to the Stage
            s.add_tasks(t)

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

    return p

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def test_stage_post_exec():

    global p1
    
    p1.name = 'p1'

    s = Stage()
    s.name = 's1'

    for t in range(NUM_TASKS):
        s.add_tasks(create_single_task())

    s.post_exec = condition

    p1.add_stages(s)

    res_dict = {

            'resource': 'local.localhost',
            'walltime': 30,
            'cpus': 1,
    }

    os.environ['RADICAL_PILOT_DBURL'] = MLAB
    appman = AppManager(rts='radical.pilot', hostname=hostname, port=port)
    appman.resource_desc = res_dict
    appman.workflow = [p1]
    appman.run()

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def test_state_order():

    """
    **Purpose**: Test if the Pipeline, Stage and Task are assigned their states in the correct order
    """

    def create_single_task():

        t1 = Task()
        t1.name = 'simulation'
        t1.executable = ['/bin/date']
        t1.copy_input_data = []
        t1.copy_output_data = []

        return t1

    p1 = Pipeline()
    p1.name = 'p1'

    s = Stage()
    s.name = 's1'
    s.tasks = create_single_task()
    s.add_tasks(create_single_task())

    p1.add_stages(s)

    res_dict = {

            'resource': 'local.localhost',
            'walltime': 5,
            'cpus': 1,
            'project': ''

    }

    os.environ['RADICAL_PILOT_DBURL'] = MLAB
    os.environ['RP_ENABLE_OLD_DEFINES'] = 'True'
    
    appman = Amgr(hostname=hostname, port=port)
    appman.resource_desc = res_dict

    appman.workflow = [p1]
    appman.run()

    p_state_hist = p1.state_history
    assert p_state_hist == ['DESCRIBED', 'SCHEDULING', 'DONE']

    s_state_hist = p1.stages[0].state_history
    assert s_state_hist == ['DESCRIBED', 'SCHEDULING', 'SCHEDULED', 'DONE']

    tasks = p1.stages[0].tasks

    for t in tasks:

        t_state_hist = t.state_history
        assert t_state_hist == ['DESCRIBED', 'SCHEDULING', 'SCHEDULED', 'SUBMITTING', 'SUBMITTED',
                            'EXECUTED', 'DEQUEUEING', 'DEQUEUED', 'DONE']

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def on_true():

    global NUM_TASKS, CUR_STAGE

    NUM_TASKS *= 2

    s = Stage()
    s.name = 's%s'%CUR_STAGE

    for t in range(NUM_TASKS):
        s.add_tasks(create_single_task())

    s.post_exec = condition

    p1.add_stages(s)

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def test_integration_local():

    """
    **Purpose**: Run an EnTK application on localhost
    """

    def create_single_task():

        t1 = Task()
        t1.name = 'simulation'
        t1.executable = ['/bin/echo']
        t1.arguments = ['hello']
        t1.copy_input_data = []
        t1.copy_output_data = []

        return t1

    p1 = Pipeline()
    p1.name = 'p1'

    s = Stage()
    s.name = 's1'
    s.tasks = create_single_task()
    s.add_tasks(create_single_task())

    p1.add_stages(s)

    res_dict = {

            'resource': 'local.localhost',
            'walltime': 5,
            'cpus': 1,
            'project': ''

    }

    os.environ['RADICAL_PILOT_DBURL'] = MLAB

    appman = AppManager(hostname=hostname, port=port)
    appman.resource_desc = res_dict
    appman.workflow = [p1]
    appman.run()

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def generate_pipeline():

    # Create a Pipeline object
    p = Pipeline()
    p.name = 'p1'

    # Create a Stage object
    s1 = Stage()
    s1.name = 's1'

    # Create 4K tasks to ensure we don't hit any RMQ connection drops
    for _ in range(4096):
        t1 = Task()
        t1.executable = ['/bin/echo']
        t1.arguments = ['"Hello World"']

        # Add the Task to the Stage
        s1.add_tasks(t1)

    # Add Stage to the Pipeline
    p.add_stages(s1)

    return p

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def generate_pipeline():

    # Create a Pipeline object
    p = Pipeline()
    p.name = 'p1'

    # Create a Stage object
    s1 = Stage()
    s1.name = 's1'

    # Create a Task object which creates a file named 'output.txt' of size 1 MB
    t1 = Task()
    t1.name = 't1'
    t1.executable = ['/bin/false']
    # t1.arguments = ['"Hello World"','>>','temp.txt']

    # Add the Task to the Stage
    s1.add_tasks(t1)

    # Add Stage to the Pipeline
    p.add_stages(s1)

    return p

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def test_stage_exceptions(t, l, i, b, se):
    """
    ***Purpose***: Test if correct exceptions are raised when attributes are
    assigned unacceptable values.
    """

    s = Stage()

    data_type = [t, l, i, b, se]

    for data in data_type:

        print 'Using: %s, %s' % (data, type(data))

        if not isinstance(data, str):
            with pytest.raises(TypeError):
                s.name = data

        with pytest.raises(TypeError):
            s.tasks = data

        with pytest.raises(TypeError):
            s.add_tasks(data)

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def test_stage_pass_uid():

    s = Stage()
    s._uid = 's'
    s.name = 's1'
    s.parent_pipeline['uid'] = 'p'
    s.parent_pipeline['name'] = 'p1'

    t1 = Task()
    t2 = Task()
    s.add_tasks([t1,t2])

    s._pass_uid()

    assert t1.parent_stage['uid'] == s.uid
    assert t1.parent_stage['name'] == s.name
    assert t1.parent_pipeline['uid'] == s.parent_pipeline['uid']
    assert t1.parent_pipeline['name'] == s.parent_pipeline['name']

    assert t2.parent_stage['uid'] == s.uid
    assert t2.parent_stage['name'] == s.name
    assert t2.parent_pipeline['uid'] == s.parent_pipeline['uid']
    assert t2.parent_pipeline['name'] == s.parent_pipeline['name']

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
    def InitCycle(self, Replicas, Replica_Cores, md_executable, ExchangeMethod, timesteps): # "Cycle" = 1 MD stage plus the subsequent exchange computation

        """ 
        Initial cycle consists of:
        1) Create tarball of MD input data 
        2) Transfer the tarball to pilot sandbox
        3) Untar the tarball
        4) Run first Cycle
        """    
        
        #Initialize Pipeline
        #self._prof.prof('InitTar', uid=self._uid)
        p = Pipeline()
        p.name = 'initpipeline'

        md_dict    = dict() #Bookkeeping
        tar_dict   = dict() #Bookkeeping

        ##Write the input files

        self._prof.prof('InitWriteInputs', uid=self._uid)

                             

        writeInputs.writeInputs(max_temp=350,min_temp=250,replicas=Replicas,timesteps=timesteps)

        self._prof.prof('EndWriteInputs', uid=self._uid)

        
        self._prof.prof('InitTar', uid=self._uid)
        #Create Tarball of input data

        tar = tarfile.open("Input_Files.tar","w")
        for name in ["prmtop", "inpcrd", "mdin"]:
            tar.add(name)
        for r in range (Replicas):
            tar.add('mdin_{0}'.format(r))
        tar.close()

        #delete all input files outside the tarball

        for r in range (Replicas):
            os.remove('mdin_{0}'.format(r))

        self._prof.prof('EndTar', uid=self._uid)

                
        #Create Untar Stage

        untar_stg = Stage()
        untar_stg.name = 'untarStg'
    
        #Untar Task

        untar_tsk                   = Task()
        untar_tsk.name              = 'untartsk'
        untar_tsk.executable        = ['python']
        
        untar_tsk.upload_input_data = ['untar_input_files.py','Input_Files.tar']
        untar_tsk.arguments         = ['untar_input_files.py','Input_Files.tar']
        untar_tsk.cores             = 1

        untar_stg.add_tasks(untar_tsk)
        p.add_stages(untar_stg)

             
        tar_dict[0] = '$Pipeline_%s_Stage_%s_Task_%s'%(p.name,
                                                       untar_stg.name,
                                                       untar_tsk.name)
                 


        # First MD stage: needs to be defined separately since workflow is not built from a predetermined order

        md_stg = Stage()
        md_stg.name = 'mdstg0'
        self._prof.prof('InitMD_0', uid=self._uid)
        
        # MD tasks
               
        for r in range (Replicas):

            
            md_tsk                  = AMBERTask(cores=Replica_Cores, MD_Executable=md_executable)
            md_tsk.name             = 'mdtsk-{replica}-{cycle}'.format(replica=r,cycle=0)
            md_tsk.link_input_data += [
                                       '%s/inpcrd'%tar_dict[0],
                                       '%s/prmtop'%tar_dict[0],
                                       '%s/mdin_{0}'.format(r)%tar_dict[0]  #Use for full temperature exchange
                                       #'%s/mdin'%tar_dict[0]  #Testing only
                                       ] 
            md_tsk.arguments        = ['-O','-p','prmtop', '-i', 'mdin_{0}'.format(r), # Use this for full Temperature Exchange
                                       '-c','inpcrd','-o','out_{0}'.format(r),
                                       '-inf','mdinfo_{0}'.format(r)]
            md_dict[r]              = '$Pipeline_%s_Stage_%s_Task_%s'%(p.name, md_stg.name, md_tsk.name)

            md_stg.add_tasks(md_tsk)
            self.md_task_list.append(md_tsk)
            #print md_tsk.uid
        p.add_stages(md_stg)
#.........这里部分代码省略.........

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def generate_pipeline():

    # Create a Pipeline object
    p = Pipeline()
    p.name = 'p1'

    # Create a Stage object
    s1 = Stage()
    s1.name = 's1'

    # Create a Task object which creates a file named 'output.txt' of size 1 MB
    t1 = Task()
    t1.name = 't1'
    t1.executable = '/bin/bash'
    t1.arguments = ['-l', '-c', 'base64 /dev/urandom | head -c 1000000 > output.txt']

    # Add the Task to the Stage
    s1.add_tasks(t1)

    # Add Stage to the Pipeline
    p.add_stages(s1)

    # Create another Stage object to hold character count tasks
    s2 = Stage()
    s2.name = 's2'
    s2_task_uids = []

    for cnt in range(30):

        # Create a Task object
        t2 = Task()
        t2.name = 't%s' % (cnt + 1)
        t2.executable = '/bin/bash'
        t2.arguments = ['-l', '-c', 'grep -o . output.txt | sort | uniq -c > ccount.txt']
        # Copy data from the task in the first stage to the current task's location
        t2.copy_input_data = ['$Pipeline_%s_Stage_%s_Task_%s/output.txt' % (p.name, s1.name, t1.name)]

        # Add the Task to the Stage
        s2.add_tasks(t2)
        s2_task_uids.append(t2.name)

    # Add Stage to the Pipeline
    p.add_stages(s2)

    # Create another Stage object to hold checksum tasks
    s3 = Stage()
    s3.name = 's3'

    for cnt in range(30):

        # Create a Task object
        t3 = Task()
        t3.name = 't%s' % (cnt + 1)
        t3.executable = '/bin/bash'
        t3.arguments = ['-l', '-c', 'sha1sum ccount.txt > chksum.txt']
        # Copy data from the task in the first stage to the current task's location
        t3.copy_input_data = ['$Pipeline_%s_Stage_%s_Task_%s/ccount.txt' % (p.name, s2.name, s2_task_uids[cnt])]
        # Download the output of the current task to the current location
        t3.download_output_data = ['chksum.txt > chksum_%s.txt' % cnt]

        # Add the Task to the Stage
        s3.add_tasks(t3)

    # Add Stage to the Pipeline
    p.add_stages(s3)

    return p

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
def test_rp_da_scheduler_bw():

    """
    **Purpose**: Run an EnTK application on localhost
    """

    p1 = Pipeline()
    p1.name = 'p1'

    n = 10

    s1 = Stage()
    s1.name = 's1'
    for x in range(n):
        t = Task()
        t.name = 't%s'%x
        t.executable = ['/bin/hostname']
        t.arguments = ['>','hostname.txt']
        t.cpu_reqs['processes'] = 1
        t.cpu_reqs['threads_per_process'] = 16
        t.cpu_reqs['thread_type'] = ''
        t.cpu_reqs['process_type'] = ''
        t.lfs_per_process = 10
        t.download_output_data = ['hostname.txt > s1_t%s_hostname.txt'%(x)]

        s1.add_tasks(t)

    p1.add_stages(s1)

    s2 = Stage()
    s2.name = 's2'
    for x in range(n):
        t = Task()
        t.executable = ['/bin/hostname']
        t.arguments = ['>','hostname.txt']
        t.cpu_reqs['processes'] = 1
        t.cpu_reqs['threads_per_process'] = 16
        t.cpu_reqs['thread_type'] = ''
        t.cpu_reqs['process_type'] = ''
        t.download_output_data = ['hostname.txt > s2_t%s_hostname.txt'%(x)]
        t.tag = 't%s'%x

        s2.add_tasks(t)


    p1.add_stages(s2)

    res_dict = {
                'resource'      : 'ncsa.bw_aprun',
                'walltime'      : 10,
                'cpus'          : 128,
                'project'       : 'gk4',
                'queue'         : 'high'
            }

    os.environ['RADICAL_PILOT_DBURL'] = MLAB

    appman = AppManager(hostname=hostname, port=port)
    appman.resource_desc = res_dict
    appman.workflow = [p1]
    appman.run()

    for i in range(n):
        assert open('s1_t%s_hostname.txt'%i,'r').readline().strip() == open('s2_t%s_hostname.txt'%i,'r').readline().strip()


    txts = glob('%s/*.txt' % os.getcwd())
    for f in txts:
        os.remove(f)

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
    s1 = Stage()

    # Create a Task object which creates a file named 'output.txt' of size 1 MB
    t1 = Task()
    t1.executable = '/bin/bash'
    t1.arguments = ['-l', '-c', 'base64 /dev/urandom | head -c 1000000 > output.txt']

    # Add the Task to the Stage
    s1.add_tasks(t1)

    # Add Stage to the Pipeline
    p.add_stages(s1)

    # Create another Stage object
    s2 = Stage()
    s2.name = 'Stage 2'

    # Create a Task object
    t2 = Task()
    t2.executable = ['/bin/bash']
    t2.arguments = ['-l', '-c', 'grep -o . output.txt | sort | uniq -c > ccount.txt']
    # Copy data from the task in the first stage to the current task's location
    t2.copy_input_data = ['$Pipline_%s_Stage_%s_Task_%s/output.txt' % (p.uid, s1.uid, t1.uid)]
    # Download the output of the current task to the current location
    t2.download_output_data = ['ccount.txt']

    # Add the Task to the Stage
    s2.add_tasks(t2)

    # Add Stage to the Pipeline
    p.add_stages(s2)

# 需要导入模块: from radical.entk import Stage [as 别名]
# 或者: from radical.entk.Stage import name [as 别名]
    def init_cycle(self, replicas, replica_cores, python_path, md_executable, exchange_method, min_temp, max_temp, timesteps, basename, pre_exec):  # "cycle" = 1 MD stage plus the subsequent exchange computation
        """ 
        Initial cycle consists of:
        1) Create tarball of MD input data 
        2) Transfer the tarball to pilot sandbox
        3) Untar the tarball
        4) Run first cycle
        """

        #Initialize Pipeline
        self._prof.prof('InitTar', uid=self._uid)
        p = Pipeline()
        p.name = 'initpipeline'

        md_dict = dict()  #bookkeeping
        tar_dict = dict()  #bookkeeping

        #Write the input files

        self._prof.prof('InitWriteInputs', uid=self._uid)

        writeInputs.writeInputs(
            max_temp=max_temp,
            min_temp=min_temp,
            replicas=replicas,
            timesteps=timesteps,
            basename=basename)

        self._prof.prof('EndWriteInputs', uid=self._uid)

        self._prof.prof('InitTar', uid=self._uid)
        #Create Tarball of input data

        tar = tarfile.open("input_files.tar", "w")
        for name in [
                basename + ".prmtop", basename + ".inpcrd", basename + ".mdin"
        ]:
            tar.add(name)
        for r in range(replicas):
            tar.add('mdin_{0}'.format(r))
        tar.close()

        #delete all input files outside the tarball

        for r in range(replicas):
            os.remove('mdin_{0}'.format(r))

        self._prof.prof('EndTar', uid=self._uid)

        #Create Untar Stage

        repo = git.Repo('.', search_parent_directories=True)
        aux_function_path = repo.working_tree_dir


        untar_stg = Stage()
        untar_stg.name = 'untarStg'

        #Untar Task
        
        untar_tsk = Task()
        untar_tsk.name = 'untartsk'
        untar_tsk.executable = ['python']

        untar_tsk.upload_input_data = [
            str(aux_function_path)+'/repex/untar_input_files.py', 'input_files.tar'
        ]
        untar_tsk.arguments = ['untar_input_files.py', 'input_files.tar']
        untar_tsk.cpu_reqs = 1
        #untar_tsk.post_exec         = ['']
        untar_stg.add_tasks(untar_tsk)
        p.add_stages(untar_stg)

        tar_dict[0] = '$Pipeline_%s_Stage_%s_Task_%s' % (
            p.name, untar_stg.name, untar_tsk.name)

        # First MD stage: needs to be defined separately since workflow is not built from a predetermined order, also equilibration needs to happen first. 

        md_stg = Stage()
        md_stg.name = 'mdstg0'
        self._prof.prof('InitMD_0', uid=self._uid)

        # MD tasks

        for r in range(replicas):

            md_tsk = AMBERTask(cores=replica_cores, md_executable=md_executable, pre_exec=pre_exec)
            md_tsk.name = 'mdtsk-{replica}-{cycle}'.format(replica=r, cycle=0)
            md_tsk.link_input_data += [
                '%s/inpcrd' % tar_dict[0],
                '%s/prmtop' % tar_dict[0],
                '%s/mdin_{0}'.format(r) %
                tar_dict[0]  #Use for full temperature exchange
            ]
            md_tsk.arguments = [
                '-O',
                '-p',
                'prmtop',
                '-i',
                'mdin_{0}'.format(r),
#.........这里部分代码省略.........