Python get_engine Examples

Example #1

File: user_script.py Project: xielm12/radical.ensemblemd

import json

from radical.ensemblemd import Kernel
from radical.ensemblemd import Pipeline
from radical.ensemblemd import EnsemblemdError
from radical.ensemblemd import SingleClusterEnvironment

#Used to register user defined kernels
from radical.ensemblemd.engine import get_engine

#Import our new kernel
#from dev_kernel import MyUserDefinedKernel     #Solution
from user_kernel import MyUserDefinedKernel

# Register the user-defined kernel with Ensemble MD Toolkit.
get_engine().add_kernel_plugin(MyUserDefinedKernel)


#Now carry on with your application as usual !
class Sleep(Pipeline):
    def __init__(self, steps, instances):
        Pipeline.__init__(self, steps, instances)

    def step_1(self, instance):
        """Run AMBER MD Simulations"""

        k = Kernel(name="amber")
        k.arguments = [
            "--minfile=min.in", "--topfile=penta.top", "--crdfile=penta.crd",
            "--output=md.crd"
        ]

Example #2

File: hausdorff_example.py Project: mingtaiha/radical.ensemblemd

        arguments  = [self.get_arg("--dist_file="),"--element_set1"]
        arguments.extend(ARG1)
        arguments.extend(["--element_set2"])
        arguments.extend(ARG2)
        arguments.extend(["--output_file",self.get_arg("--outputfile=")])

        self._executable  = executable
        self._arguments   = arguments
        self._environment = cfg["environment"]
        self._uses_mpi    = cfg["uses_mpi"]
        self._pre_exec    = cfg["pre_exec"]
        self._post_exec   = None

# ------------------------------------------------------------------------------
# Register the user-defined kernel with Ensemble MD Toolkit.
get_engine().add_kernel_plugin(MyQPC)
get_engine().add_kernel_plugin(MyHausdorff)

# ------------------------------------------------------------------------------
#
class HausdorffAP(AllPairs):
    """HausdorffAP implements the all pairs pattern described above. It
       inherits from radical.ensemblemd.AllPair, the abstraction
       base class for all All Pairs applications.
    """
    def __init__(self,setelements,windowsize):
        AllPairs.__init__(self, set1elements=setelements,windowsize1=windowsize)

    def set1element_initialization(self,element):
        """The initialization step creates the necessary files that will be
            needed for the comparison over the elements of the set.

Example #3

File: hello_synapse.py Project: xielm12/radical.ensemblemd

from radical.ensemblemd import SimulationAnalysisLoop
from radical.ensemblemd import SingleClusterEnvironment


from radical.ensemblemd.engine import get_engine

### THIS EXAMPLE ASSUMES YOU HAVE SYNAPSE INSTALLED in "$HOME/ves/synapse_local".
### If your synapse is installed in a different directory, please change the value
### of the argument 'path'.


# ------------------------------------------------------------------------------
#Load synapse Kernel

from synapse.kernel import sample_Kernel
get_engine().add_kernel_plugin(sample_Kernel)

# ------------------------------------------------------------------------------
#
class Emulate(Pipeline):
    """The Emulate class implements a 1-step pipeline that uses the synapse sample kernel. 
    	It inherits from radical.ensemblemd.Pipeline, the abstract base class for all pipelines.
    """

    def __init__(self, stages,instances):
        Pipeline.__init__(self, stages,instances)

    def stage_1(self, instance):
        k = Kernel(name="synapse.sample")
        k.arguments = [	"--path=$HOME/ves/synapse_local", 
        				"--mode=sample",

Example #4

File: 01_static_gromacs_lsdmap_loop.py Project: yuhangwang/radical.ensemblemd

from radical.ensemblemd import SingleClusterEnvironment


from radical.ensemblemd.engine import get_engine

import sys
import imp
import argparse
import os

# ------------------------------------------------------------------------------
# Load all custom Kernels

from custom_kernels.grompp import grompp_Kernel

get_engine().add_kernel_plugin(grompp_Kernel)

from custom_kernels.mdrun import mdrun_Kernel

get_engine().add_kernel_plugin(mdrun_Kernel)

from custom_kernels.pre_grlsd_loop import pre_loop_Kernel

get_engine().add_kernel_plugin(pre_loop_Kernel)

from custom_kernels.pre_lsdmap import pre_lsdmap_Kernel

get_engine().add_kernel_plugin(pre_lsdmap_Kernel)

from custom_kernels.post_lsdmap import post_lsdmap_Kernel

Example #5

File: extasy_gmxcoco.py Project: ashkurti/Hands-on-session-part-2-The-customized-gromacs-coco-workflow-of-ExTASY

from radical.ensemblemd import Kernel
from radical.ensemblemd import EnsemblemdError
from radical.ensemblemd import SimulationAnalysisLoop
from radical.ensemblemd import SingleClusterEnvironment

from radical.ensemblemd.engine import get_engine

import imp
import argparse
import sys
import os
import json

from grompp import grompp_Kernel
get_engine().add_kernel_plugin(grompp_Kernel)

from mdrun import mdrun_Kernel
get_engine().add_kernel_plugin(mdrun_Kernel)

from trjconv import trjconv_Kernel
get_engine().add_kernel_plugin(trjconv_Kernel)

# ------------------------------------------------------------------------------
#

class Extasy_CocoGromacs_Static(SimulationAnalysisLoop):            

    def __init__(self, maxiterations, simulation_instances, analysis_instances):
        SimulationAnalysisLoop.__init__(self, maxiterations, simulation_instances, analysis_instances)

Example #6

File: lf_finder_enMD_comet.py Project: radical-cybertools/midas

#from radical.ensemblemd import BagofTasks
from radical.ensemblemd import SimulationAnalysisLoop
from radical.ensemblemd import EnsemblemdError
from radical.ensemblemd import SingleClusterEnvironment
import math
import numpy as np
import sys

#Used to register user defined kernels
from radical.ensemblemd.engine import get_engine

#Import our new kernel
from conncomp_kernel import MyUserDefinedKernel

# Register the user-defined kernel with Ensemble MD Toolkit.
get_engine().add_kernel_plugin(MyUserDefinedKernel)

from atomdist_kernel import MyUserDefinedKernel
get_engine().add_kernel_plugin(MyUserDefinedKernel)

window_size = None
window_list = []
traj_count = None

#make your globals!!

#Now carry on with your application as usual !

class leaflet(SimulationAnalysisLoop):
    def __init__(self,iterations, simulation_instances, analysis_instances):

Example #7

File: extasy_gromacs_lsdmap_adaptive.py Project: radical-cybertools/ExTASY

from radical.ensemblemd import SimulationAnalysisLoop
from radical.ensemblemd import SingleClusterEnvironment


from radical.ensemblemd.engine import get_engine

import sys
import imp
import argparse
import os

# ------------------------------------------------------------------------------
#Load all custom Kernels

from kernel_defs.grompp import kernel_grompp
get_engine().add_kernel_plugin(kernel_grompp)

from kernel_defs.mdrun import kernel_mdrun
get_engine().add_kernel_plugin(kernel_mdrun)

from kernel_defs.pre_grlsd_loop import kernel_pre_grlsd_loop
get_engine().add_kernel_plugin(kernel_pre_grlsd_loop)

from kernel_defs.pre_lsdmap import kernel_pre_lsdmap
get_engine().add_kernel_plugin(kernel_pre_lsdmap)

from kernel_defs.lsdmap import kernel_lsdmap
get_engine().add_kernel_plugin(kernel_lsdmap)

from kernel_defs.post_lsdmap import kernel_post_lsdmap
get_engine().add_kernel_plugin(kernel_post_lsdmap)

Example #8

File: simple_sim_pool_sal.py Project: yuhangwang/radical.ensemblemd

import sys
import os
import json

from radical.ensemblemd import Kernel
from radical.ensemblemd import SimulationAnalysisLoop
from radical.ensemblemd import EnsemblemdError
from radical.ensemblemd import SingleClusterEnvironment
from radical.ensemblemd.engine import get_engine

from kernel_defs.sleep_mkfile import kernel_sleep_mkfile

get_engine().add_kernel_plugin(kernel_sleep_mkfile)

from kernel_defs.concat import kernel_concat

get_engine().add_kernel_plugin(kernel_concat)

# ------------------------------------------------------------------------------
#
class SAL_1(SimulationAnalysisLoop):
    def __init__(self, iterations, simulation_instances, analysis_instances):
        SimulationAnalysisLoop.__init__(self, iterations, simulation_instances, analysis_instances)

    def simulation_step(self, iteration, instance):
        """In the simulation step we
        """
        k = Kernel(name="custom.sleep_mkfile")
        k.arguments = ["--maxsleep=10", "--upperlimit=1000", "--filename=asciifile.dat".format(instance)]
        return [k]

Example #9

File: submission_script.py Project: polar-computing/SeaIce

from radical.ensemblemd import Kernel
from radical.ensemblemd import PoE
from radical.ensemblemd import EnsemblemdError
from radical.ensemblemd import ResourceHandle

from radical.ensemblemd.engine import get_engine
from qbird import kernel_qbird
get_engine().add_kernel_plugin(kernel_qbird)

import os
import json
import sys

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

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


class MyApp(PoE):

	def __init__(self, stages,instances):
		 PoE.__init__(self, stages,instances)

	def stage_1(self, instance):
		k = Kernel(name="qbird")
		k.upload_input_data = ['SeaIceUnSuperGMM.py']
		k.arguments = ["--script=SeaIceUnSuperGMM.py",
				"--imagepath=/home/vivek91/xsede-hack/IMG/XinImages/TEST/072610_00332.jpg",
				"--trainingpath=/home/vivek91/xsede-hack/IMG/XinImages/TRAINING/",

Example #10

File: extasy_amber_coco.py Project: radical-experiments/enmd-pattern-testing

import argparse
import sys
import os
import json

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

if os.environ.get('RADICAL_ENMD_VERBOSE') == None:
    os.environ['RADICAL_ENMD_VERBOSE'] = 'REPORT'

# ------------------------------------------------------------------------------
#Load all custom Kernels

from kernel_defs.amber import kernel_amber
get_engine().add_kernel_plugin(kernel_amber)

from kernel_defs.coco import kernel_coco
get_engine().add_kernel_plugin(kernel_coco)


# ------------------------------------------------------------------------------


# ------------------------------------------------------------------------------
#

class Extasy_CocoAmber_Static(SimulationAnalysisLoop):

    def __init__(self, maxiterations, simulation_instances, analysis_instances):
        SimulationAnalysisLoop.__init__(self, maxiterations, simulation_instances, analysis_instances)

Example #11

File: submission_script.py Project: lijunde/SeaIce

from radical.ensemblemd import Kernel
from radical.ensemblemd import PoE
from radical.ensemblemd import EnsemblemdError
from radical.ensemblemd import ResourceHandle

from radical.ensemblemd.engine import get_engine
from qbird import kernel_qbird
get_engine().add_kernel_plugin(kernel_qbird)

import os
import json
import sys

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

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


class MyApp(PoE):
    def __init__(self, stages, instances):
        PoE.__init__(self, stages, instances)

    def stage_1(self, instance):
        k = Kernel(name="qbird")
        k.upload_input_data = ['SeaIceUnSuperGMM.py']
        k.arguments = [
            "--script=SeaIceUnSuperGMM.py",
            "--imagepath=/home/vivek91/xsede-hack/IMG/XinImages/TEST/072610_00332.jpg",
            "--trainingpath=/home/vivek91/xsede-hack/IMG/XinImages/TRAINING/",

Example #12

File: hausdorff_example.py Project: xielm12/radical.ensemblemd

        arguments.extend(ARG1)
        arguments.extend(["--element_set2"])
        arguments.extend(ARG2)
        arguments.extend(["--output_file", self.get_arg("--outputfile=")])

        self._executable = executable
        self._arguments = arguments
        self._environment = cfg["environment"]
        self._uses_mpi = cfg["uses_mpi"]
        self._pre_exec = cfg["pre_exec"]
        self._post_exec = None


# ------------------------------------------------------------------------------
# Register the user-defined kernel with Ensemble MD Toolkit.
get_engine().add_kernel_plugin(MyQPC)
get_engine().add_kernel_plugin(MyHausdorff)


# ------------------------------------------------------------------------------
#
class HausdorffAP(AllPairs):
    """HausdorffAP implements the all pairs pattern described above. It
       inherits from radical.ensemblemd.AllPair, the abstraction
       base class for all All Pairs applications.
    """
    def __init__(self, setelements, windowsize):
        AllPairs.__init__(self,
                          set1elements=setelements,
                          windowsize1=windowsize)

Example #13

File: hello_synapse.py Project: xielm12/radical.ensemblemd

from radical.ensemblemd import Pipeline
from radical.ensemblemd import EnsemblemdError
from radical.ensemblemd import SimulationAnalysisLoop
from radical.ensemblemd import SingleClusterEnvironment

from radical.ensemblemd.engine import get_engine

### THIS EXAMPLE ASSUMES YOU HAVE SYNAPSE INSTALLED in "$HOME/ves/synapse_local".
### If your synapse is installed in a different directory, please change the value
### of the argument 'path'.

# ------------------------------------------------------------------------------
#Load synapse Kernel

from synapse.kernel import sample_Kernel
get_engine().add_kernel_plugin(sample_Kernel)


# ------------------------------------------------------------------------------
#
class Emulate(Pipeline):
    """The Emulate class implements a 1-step pipeline that uses the synapse sample kernel. 
    	It inherits from radical.ensemblemd.Pipeline, the abstract base class for all pipelines.
    """
    def __init__(self, stages, instances):
        Pipeline.__init__(self, stages, instances)

    def stage_1(self, instance):
        k = Kernel(name="synapse.sample")
        k.arguments = [
            "--path=$HOME/ves/synapse_local", "--mode=sample", "--flops=1000",

Example #14

File: extasy_gmxcoco.py Project: techeye220/Hands-on-session-part-2-The-customized-gromacs-coco-workflow-of-ExTASY

from radical.ensemblemd import Kernel
from radical.ensemblemd import EnsemblemdError
from radical.ensemblemd import SimulationAnalysisLoop
from radical.ensemblemd import SingleClusterEnvironment

from radical.ensemblemd.engine import get_engine

import imp
import argparse
import sys
import os
import json

from grompp import grompp_Kernel
get_engine().add_kernel_plugin(grompp_Kernel)

from mdrun import mdrun_Kernel
get_engine().add_kernel_plugin(mdrun_Kernel)

from trjconv import trjconv_Kernel
get_engine().add_kernel_plugin(trjconv_Kernel)

# ------------------------------------------------------------------------------
#


class Extasy_CocoGromacs_Static(SimulationAnalysisLoop):
    def __init__(self, maxiterations, simulation_instances,
                 analysis_instances):
        SimulationAnalysisLoop.__init__(self, maxiterations,

Example #15

File: 01_static_gromacs_lsdmap_loop.py Project: xielm12/radical.ensemblemd

from radical.ensemblemd import EnsemblemdError
from radical.ensemblemd import SimulationAnalysisLoop
from radical.ensemblemd import SingleClusterEnvironment

from radical.ensemblemd.engine import get_engine

import sys
import imp
import argparse
import os

# ------------------------------------------------------------------------------
#Load all custom Kernels

from custom_kernels.grompp import grompp_Kernel
get_engine().add_kernel_plugin(grompp_Kernel)

from custom_kernels.mdrun import mdrun_Kernel
get_engine().add_kernel_plugin(mdrun_Kernel)

from custom_kernels.pre_grlsd_loop import pre_loop_Kernel
get_engine().add_kernel_plugin(pre_loop_Kernel)

from custom_kernels.pre_lsdmap import pre_lsdmap_Kernel
get_engine().add_kernel_plugin(pre_lsdmap_Kernel)

from custom_kernels.post_lsdmap import post_lsdmap_Kernel
get_engine().add_kernel_plugin(post_lsdmap_Kernel)


# ------------------------------------------------------------------------------