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"
]
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.
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",
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
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)
#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):
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)
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]
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/",
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)
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/",
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)
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",
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,
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) # ------------------------------------------------------------------------------
