Adaptive MD

Using radical.pilot

For the NTL9 system



In [1]:

    
import os
import sys



In [2]:

    
# set default verbose level
verbose = os.environ.get('RADICAL_PILOT_VERBOSE', 'REPORT')
os.environ['RADICAL_PILOT_VERBOSE'] = verbose

# set default URL to IMP Mongo DB
# path_to_db = os.environ.get(
#     'RADICAL_PILOT_DBURL', "mongodb://ensembletk.imp.fu-berlin.de:27017/rp")

# assume we run a local
path_to_db = os.environ.get(
    'RADICAL_PILOT_DBURL', "mongodb://localhost:27017/rp")

os.environ['RADICAL_PILOT_DBURL'] = path_to_db



In [3]:

    
import radical.pilot as rp
import radical.utils as ru









    



/Users/jan-hendrikprinz/anaconda/lib/python2.7/site-packages/radical/utils/atfork/stdlib_fixer.py:58: UserWarning: logging module already imported before fixup.
  warnings.warn('logging module already imported before fixup.')



In [5]:

    
# import adaptive components

from adaptivemd import OpenMMEngine, AllegroCluster, Brain, MDCluster, \
    LocalCluster, File, NTrajectories
import adaptivemd.util as amp

1. Select a resource

We pick to run on this machine



In [6]:

    
resource = LocalCluster(runtime=5, cores=1)

We still need to add the necessary path to find the conda installation



In [7]:

    
resource.add_path(amp.path_conda_local_jhp)



In [8]:

    
# we use a reporter class for nicer output
report = ru.LogReporter(name='radical.pilot', level=verbose)
report.title('Getting Started (RP version %s)' % rp.version)









    




================================================================================
 Getting Started (RP version v0.44.RC1)                                         
================================================================================

2. Create the engine

pick a file from the currend working directory



In [9]:

    
pdb_file = File('file://files/input.pdb')



In [10]:

    
engine = OpenMMEngine(
    pdb_file=pdb_file,
    system_file=File('file://files/system.xml'),
    integrator_file=File('file://files/integrator.xml')
)

3. Create the cluster used



In [12]:

    
cluster = MDCluster(
    system='ntl9',
    resource=resource,
    report=report)



In [11]:

    
# add the path to CONDA if now already in the default
cluster.add_path(os.environ.get('~/anaconda/bin'))

select a strategy aka brain



In [12]:

    
brain = Brain(cluster)  # this needs to be smarter

So let's do it...



In [13]:

    
with cluster:
    report.ok('>>ok\n')

    report.header('submit units')

    trajs = [
        cluster.get_new_trajectory_file(pdb_file, 2)
        for x in range(2)
    ]

    # submit the trajectories
    cluster.submit_trajectories(trajs)

    # Run immediately 4 more trajectories
    event = DoMoreTrajectories(
        when=NTrajectories(cluster, 1),
        unless=NTrajectories(cluster, 8),
        number=4,
        length=2
    )
    cluster.add_event(event)
    cluster.wait()

report.header('generated new trajectories')

for f in cluster.files:
    report.info(repr(f) + '\n\t')

report.header()









    



new session: [rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010]        \
database   : [mongodb://localhost:27017/rp]                                   ok
create pilot manager                                                          ok
create unit manager                                                           ok

--------------------------------------------------------------------------------
submit pilots                                                                   

create pilot description [local.localhost:1]                                  ok
submit 1 pilot(s) .                                                           ok
add 1 pilot(s)                                                                ok
stage shared data from engine                                                 ok

--------------------------------------------------------------------------------
submit units                                                                    

submit 2 unit(s)
        ..                                                                    ok
* unit unit.000000 (None) state Failed (134) None - None, out/err:  / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000000/radical_pilot_cu_launch_script.sh: line 16: 28466 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "initial.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000001 (None) state Failed (134) None - None, out/err:  / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000001/radical_pilot_cu_launch_script.sh: line 16: 28474 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "initial.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000002 (None) state Failed (134) None - None, out/err:  / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000002/radical_pilot_cu_launch_script.sh: line 16: 28492 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "initial.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
submit 4 unit(s)
        ....                                                                  ok
* unit unit.000004 (None) state Failed (134) None - None, out/err:  / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000004/radical_pilot_cu_launch_script.sh: line 16: 29079 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "initial.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000007 (None) state Failed (134) None - None, out/err: ['xyz', 'cell_angles', 'cell_lengths', 'topology']
converted 1 frames, 14100 atoms 
 / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000007/radical_pilot_cu_launch_script.sh: line 17: 29100 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "input.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000009 (None) state Failed (134) None - None, out/err:  / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000009/radical_pilot_cu_launch_script.sh: line 16: 29125 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "initial.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000010 (None) state Failed (134) None - None, out/err: ['xyz', 'cell_angles', 'cell_lengths', 'topology']
converted 1 frames, 14100 atoms 
 / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000010/radical_pilot_cu_launch_script.sh: line 17: 29176 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "input.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000011 (None) state Failed (134) None - None, out/err:  / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000011/radical_pilot_cu_launch_script.sh: line 16: 29183 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "initial.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
submit 4 unit(s)
        ....                                                                  ok
* unit unit.000013 (None) state Failed (134) None - None, out/err:  / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000013/radical_pilot_cu_launch_script.sh: line 16: 29275 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "initial.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000014 (None) state Failed (134) None - None, out/err: ['xyz', 'cell_angles', 'cell_lengths', 'topology']
converted 1 frames, 14100 atoms 
 / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000014/radical_pilot_cu_launch_script.sh: line 17: 29290 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "input.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000015 (None) state Failed (134) None - None, out/err: ['xyz', 'cell_angles', 'cell_lengths', 'topology']
converted 1 frames, 14100 atoms 
 / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000015/radical_pilot_cu_launch_script.sh: line 17: 29299 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "input.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000017 (None) state Failed (134) None - None, out/err: ['xyz', 'cell_angles', 'cell_lengths', 'topology']
converted 1 frames, 14100 atoms 
 / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000017/radical_pilot_cu_launch_script.sh: line 17: 29341 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "input.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000018 (None) state Failed (134) None - None, out/err:  / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000018/radical_pilot_cu_launch_script.sh: line 16: 29347 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "initial.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000020 (None) state Failed (134) None - None, out/err: ['xyz', 'cell_angles', 'cell_lengths', 'topology']
converted 1 frames, 14100 atoms 
 / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000020/radical_pilot_cu_launch_script.sh: line 17: 29362 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "input.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok
* unit unit.000021 (None) state Failed (134) None - None, out/err: ['xyz', 'cell_angles', 'cell_lengths', 'topology']
converted 1 frames, 14100 atoms 
 / /Users/jan-hendrikprinz/radical.pilot.sandbox/rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010-pilot.0000/unit.000021/radical_pilot_cu_launch_script.sh: line 17: 29371 Abort trap: 6           python "openmmrun.py" "--report-interval" "1" "-p" "CPU" "--store-interval" "1" "-t" "input.pdb" "--length" "2" "output.dcd"

task did not complete
submit 1 unit(s)
        .                                                                     ok

--------------------------------------------------------------------------------
finalize                                                                        

closing session rp.session.Stevie.fritz.box.jan-hendrikprinz.017177.0010       \
close pilot managerO |-\|/-\|/-\|/-\|/-\|/-\|/-\|                                                           \
wait for 1 pilot(s) O/*|                                                         ok
                                                                              ok
close unit manager                                                            ok
session lifetime: 265.2s                                                      ok

--------------------------------------------------------------------------------
generated new trajectories                                                      

Trajectory('staging:///ntl9/ntl9-4.dcd', Trajectory('staging:///ntl9/ntl9-1.dcd', file:///Users/jan-hendrikprinz/Studium/git/adaptive-sampling/package/examples/ntl9/files/input.pdb -> [2])[1] -> [2])
        Trajectory('staging:///ntl9/ntl9-3.dcd', Trajectory('staging:///ntl9/ntl9-1.dcd', file:///Users/jan-hendrikprinz/Studium/git/adaptive-sampling/package/examples/ntl9/files/input.pdb -> [2])[1] -> [2])
        Trajectory('staging:///ntl9/ntl9-8.dcd', Trajectory('staging:///ntl9/ntl9-3.dcd', Trajectory('staging:///ntl9/ntl9-1.dcd', file:///Users/jan-hendrikprinz/Studium/git/adaptive-sampling/package/examples/ntl9/files/input.pdb -> [2])[1] -> [2])[0] -> [2])
        Trajectory('staging:///ntl9/ntl9-6.dcd', Trajectory('staging:///ntl9/ntl9-3.dcd', Trajectory('staging:///ntl9/ntl9-1.dcd', file:///Users/jan-hendrikprinz/Studium/git/adaptive-sampling/package/examples/ntl9/files/input.pdb -> [2])[1] -> [2])[1] -> [2])
        Trajectory('staging:///ntl9/ntl9-0.dcd', file:///Users/jan-hendrikprinz/Studium/git/adaptive-sampling/package/examples/ntl9/files/input.pdb -> [2])
        Trajectory('staging:///ntl9/ntl9-1.dcd', file:///Users/jan-hendrikprinz/Studium/git/adaptive-sampling/package/examples/ntl9/files/input.pdb -> [2])
        Trajectory('staging:///ntl9/ntl9-5.dcd', Trajectory('staging:///ntl9/ntl9-1.dcd', file:///Users/jan-hendrikprinz/Studium/git/adaptive-sampling/package/examples/ntl9/files/input.pdb -> [2])[0] -> [2])
        Trajectory('staging:///ntl9/ntl9-2.dcd', Trajectory('staging:///ntl9/ntl9-1.dcd', file:///Users/jan-hendrikprinz/Studium/git/adaptive-sampling/package/examples/ntl9/files/input.pdb -> [2])[0] -> [2])
        
--------------------------------------------------------------------------------



In [16]:

    
len(cluster.files)









    Out[16]:





8



In [ ]: