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simple_mdff.py
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simple_mdff.py
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from radical.entk import Pipeline, Stage, Task, AppManager
import argparse
import os
import re
import glob
import yaml
from pprint import pprint
def to_file(list_of_cmd, fname):
with open(fname, "w") as f:
for l in list_of_cmd:
f.write(l + "\n")
f.close()
return fname
def set_executable_path(workflow_cfg, resource):
global vmd_path, namd_path
vmd_path = "vmd"
namd_path = "namd2"
if 'path' in workflow_cfg[resource]:
if 'vmd' in workflow_cfg[resource]['path']:
vmd_path = workflow_cfg[resource]['path']['vmd']
if 'namd' in workflow_cfg[resource]['path']:
namd_path = workflow_cfg[resource]['path']['namd']
def set_vmd_run(task, list_of_cmd, name=None):
#fname = to_file(list_of_cmd, name or "input.tcl")
tcl_script_in_string = "\n".join(list_of_cmd) + "\nexit"
task.pre_exec += [ "echo '{}' > {}".format(tcl_script_in_string, name or "input.tcl")]
task.executable = vmd_path + ' -dispdev text -e ' + name or "input.tcl" # to source a tcl script using command line version of vmd
#task.arguments = [ '-eofexit', '<', fname ]
def get_pipeline(workflow_cfg, resource):
## Extract resource-independent global parameters
total_iters = workflow_cfg['global']['total_iters']
ensemble_size = workflow_cfg['global']['ensemble_size']
sim_duration = workflow_cfg['global']['sim_duration']
# Create one Pipeline for the entire workflow. The Pipeline contains 1
# Simulation stage and 1 Analysis stage per iteration.
# Please refer to the API reference for more details about Pipeline, Stage,
# Task. Link: https://radicalentk.readthedocs.io/en/latest/api/app_create.html
p = Pipeline()
p.name = 'simple-mdff'
for _ in range(total_iters):
one_cycle(p, workflow_cfg, resource) # update pipeline, p
return p
def one_cycle(p, workflow_cfgs, resource):
## Simulation related parameters
sim_pre_exec = workflow_cfg[resource]['simulation']['pre_exec'] or []
sim_cpus = workflow_cfg[resource]['simulation']['cpus']
## Analysis related parameters
ana_pre_exec = workflow_cfg[resource]['analysis']['pre_exec'] or []
ana_cpus = workflow_cfg[resource]['analysis']['cpus']
task1_output = ['4ake-target_autopsf.situs']
task2_output = ['4ake-target_autopsf-grid.dx']
task3_output = ['1ake-docked-noh_autopsf-grid.pdb']
task4_output = ['1ake-extrabonds.txt']
task5_output = ['1ake-extrabonds-cispeptide.txt', '1ake-extrabonds-chirality.txt']
if resource[0:11] == "ornl_summit":
summit_hw_thread_cnt = 4
ana_thread_cnt = summit_hw_thread_cnt
ana_process_cnt = ana_cpus // summit_hw_thread_cnt
sim_thread_cnt = summit_hw_thread_cnt
sim_process_cnt = int(sim_cpus) // summit_hw_thread_cnt
else:
ana_thread_cnt = ana_cpus
ana_process_cnt = 1
sim_thread_cnt = int(sim_cpus)
sim_process_cnt = 1
first_stage = Stage()
# We use names of pipelines, stages, tasks to refer to data of a
# particular task
first_stage.name = 'Generating a simulated density map'
# Create tasks and add them to stage
task1 = Task()
task1.name = 'Starting to load the target PDB'
task1.pre_exec = ana_pre_exec.copy()
task1.cpu_reqs = {
'threads_per_process': ana_thread_cnt,
'processes': ana_process_cnt,
'process_type': None,
'thread_type': None}
task1_tcl_cmds = [ 'mol new 4ake-target.pdb' ]
task1_tcl_cmds += [ 'package require autopsf' ]
task1_tcl_cmds += [ 'autopsf 4ake-target.pdb' ]
task1_tcl_cmds += [ 'set sel [atomselect top all]' ]
task1_tcl_cmds += [ 'package require mdff']
task1_tcl_cmds += [ 'mdff sim $sel -res 5 -o {}'.format(task1_output[0]) ]
task1_tcl_cmds += [ 'mol new {}'.format(task1_output[0]) ]
set_vmd_run(task1, task1_tcl_cmds, "first_stage.tcl")
#task.copy_input_data = ["first_stage.tcl"j
task1.link_input_data = [ "$SHARED/%s" % os.path.basename(x) for x in
workflow_cfg[resource]['shared_data'] ]
first_stage.add_tasks(task1)
# Add sim_stage to Pipeline
p.add_stages(first_stage)
second_stage = Stage()
second_stage.name = 'Converting the density map to an MDFF potential'
task2 = Task()
task2.name = 'generate dx file'
task2.pre_exec = ana_pre_exec.copy()
task2.cpu_reqs = {
'threads_per_process': ana_thread_cnt,
'processes': ana_process_cnt,
'process_type': None,
'thread_type': None}
task2_tcl_cmds = [ 'package require mdff' ]
task2_tcl_cmds += [ 'mdff griddx -i {} -o {}'.format(task1_output[0], task2_output[0]) ]
task2.copy_input_data = ['$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, first_stage.name, task1.name, task1_output[0])]
task2.link_input_data = [ ("$SHARED/%s" % os.path.basename(x)) for x in \
workflow_cfg[resource]['shared_data'] ]
set_vmd_run(task2, task2_tcl_cmds, "second_stage.tcl")
second_stage.add_tasks(task2)
p.add_stages(second_stage)
third_stage = Stage()
third_stage.name = 'Preparing the initial structure'
task3 = Task()
task3.name = 'Starting to load the initial structure'
task3.pre_exec = ana_pre_exec.copy()
task3.cpu_reqs = {
'threads_per_process': ana_thread_cnt,
'processes': ana_process_cnt,
'process_type': None,
'thread_type': None}
task3_tcl_cmds = [ 'mol new 1ake-docked-noh.pdb' ]
task3_tcl_cmds += [ 'package require autopsf' ]
task3_tcl_cmds += [ 'autopsf 1ake-docked-noh.pdb' ]
task3_tcl_cmds += [ 'package require mdff' ]
task3_tcl_cmds += [ 'mdff gridpdb -psf 1ake-docked-noh_autopsf.psf -pdb 1ake-docked-noh_autopsf.pdb -o {}'.format(task3_output[0]) ]
task3.link_input_data = [ "$SHARED/%s" % os.path.basename(x) for x in
workflow_cfg[resource]['shared_data']]
set_vmd_run(task3, task3_tcl_cmds, "third_stage.tcl")
third_stage.add_tasks(task3)
p.add_stages(third_stage)
fourth_stage = Stage()
fourth_stage.name = 'Defining secondary structure restraints'
task4 = Task()
task4.pre_exec = ana_pre_exec.copy()
task4.cpu_reqs = {
'threads_per_process': ana_thread_cnt,
'processes': ana_process_cnt,
'process_type': None,
'thread_type': None}
task4_tcl_cmds = [ 'package require ssrestraints',
'mol new 1ake-docked-noh_autopsf.psf',
'mol addfile 1ake-docked-noh_autopsf.pdb',
'ssrestraints -psf 1ake-docked-noh_autopsf.psf -pdb 1ake-docked-noh_autopsf.pdb -o {} -hbonds'.format(task4_output[0]) ]
task4.copy_input_data = ['$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name, task3.name, '1ake-docked-noh_autopsf.pdb'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name, task3.name, '1ake-docked-noh_autopsf.psf')]
set_vmd_run(task4, task4_tcl_cmds, "fourth_stage.tcl")
fourth_stage.add_tasks(task4)
p.add_stages(fourth_stage)
fifth_stage = Stage()
fifth_stage.name = 'cispeptide and chirality restraints'
task5 = Task()
task5.pre_exec = ana_pre_exec.copy()
task5.cpu_reqs = {
'threads_per_process': ana_thread_cnt,
'processes': ana_process_cnt,
'process_type': None,
'thread_type': None}
task5_tcl_cmds = [ 'mol new 1ake-docked-noh_autopsf.psf',
'mol addfile 1ake-docked-noh_autopsf.pdb',
'package require cispeptide',
'package require chirality',
'cispeptide restrain -o {}'.format(task5_output[0]),
'chirality restrain -o {}'.format(task5_output[1])]
task5.copy_input_data = ['$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name, task3.name, '1ake-docked-noh_autopsf.pdb'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name, task3.name, '1ake-docked-noh_autopsf.psf')]
set_vmd_run(task5, task5_tcl_cmds, 'fifth_stage.tcl')
fifth_stage.add_tasks(task5)
p.add_stages(fifth_stage)
sixth_stage = Stage()
sixth_stage.name = 'Running the MDFF simulation with NAMD'
task6 = Task()
task6.pre_exec = ana_pre_exec.copy()
task6.cpu_reqs = {
'threads_per_process': ana_thread_cnt,
'processes': ana_process_cnt,
'process_type': None,
'thread_type': None}
task6_tcl_cmds = [ 'package require mdff' ]
task6_tcl_cmds += [ 'mdff setup -o adk -psf 1ake-docked-noh_autopsf.psf ' \
+ '-pdb 1ake-docked-noh_autopsf.pdb ' \
+ '-griddx 4ake-target_autopsf-grid.dx ' \
+ '-gridpdb 1ake-docked-noh_autopsf-grid.pdb ' \
+ '-extrab {1ake-extrabonds.txt 1ake-extrabonds-cispeptide.txt 1ake-extrabonds-chirality.txt} ' \
+ '-gscale 0.3 -numsteps 50000' ]
task6.copy_input_data = [ '$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, second_stage.name, task2.name, '4ake-target_autopsf-grid.dx'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name, task3.name, '1ake-docked-noh_autopsf.pdb'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name, task3.name, '1ake-docked-noh_autopsf.psf'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name, task3.name, '1ake-docked-noh_autopsf-grid.pdb'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, fourth_stage.name, task4.name, task4_output[0]),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, fifth_stage.name, task5.name, task5_output[0]),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, fifth_stage.name, task5.name, task5_output[1])]
set_vmd_run(task6, task6_tcl_cmds, "sixth_stage.tcl")
sixth_stage.add_tasks(task6)
p.add_stages(sixth_stage)
seventh_stage = Stage()
seventh_stage.name = "NAMD simulation"
task7 = Task()
task7.cpu_reqs = {
'threads_per_process': sim_thread_cnt,
'processes': sim_process_cnt,
'process_type': 'MPI',
'thread_type': 'OpenMP'}
task7.pre_exec = sim_pre_exec
task7.executable = namd_path
task7.arguments = ['+ppn', sim_thread_cnt, 'adk-step1.namd']
task7.copy_input_data = [ '$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, 'adk-step1.namd'),
#'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, 'adk-step2.namd'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, '1ake-docked-noh_autopsf.psf'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, '1ake-docked-noh_autopsf.pdb'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, '1ake-docked-noh_autopsf-grid.pdb'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, '4ake-target_autopsf-grid.dx'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, '1ake-extrabonds-chirality.txt'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, '1ake-extrabonds-cispeptide.txt'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, '1ake-extrabonds.txt'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name,
task6.name, 'mdff_template.namd'),
#'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name, task6.name, 'par_all27_prot_lipid_na.inp')
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, sixth_stage.name,
task6.name, 'par_all36_prot.prm')
]
task7.download_output_data = ['adk-step1.dcd']
seventh_stage.add_tasks(task7)
#task7_2 = Task()
#task7_2.cpu_reqs['threads_per_process'] = sim_cpus
#task7_2.executable = [ 'namd2' ]
#task7_2.executable = [ 'namd2' ]
#task7_2.arguments = ['+ppn', sim_cpus, 'adk-step2.namd']
#seventh_stage.add_tasks(task7_2)
p.add_stages(seventh_stage)
# Visualizing the MDFF trajectory
#
# mol new 4ake-target_autopsf.psf
# mol addfile 4ake-target_autopsf.pdb
# mol new 1ake-docked-noh_autopsf.psf
# mol addfile 1ake-docked-noh_autopsf-docked.pdb
# mol addfile adk-step1.dcd
# mol addfile adk-step2.dcd
eighth_stage = Stage()
eighth_stage.name = 'Calculating the root mean square deviation'
task8 = Task()
task8.pre_exec = ana_pre_exec.copy()
task8.cpu_reqs = {
'threads_per_process': ana_thread_cnt,
'processes': ana_process_cnt,
'process_type': None,
'thread_type': None}
task8_tcl_cmds = [ 'mol new 1ake-docked-noh_autopsf.psf',
'mol addfile adk-step1.dcd waitfor all',
'mol new 4ake-target_autopsf.pdb',
'package require mdff',
'mdff check -rmsd -refpdb 4ake-target_autopsf.pdb']
task8.copy_input_data = [ '$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name,
first_stage.name, task1.name, '4ake-target_autopsf.pdb'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name,
task3.name, '1ake-docked-noh_autopsf.psf'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, seventh_stage.name,
task7.name, 'adk-step1.dcd')
]
set_vmd_run(task8, task8_tcl_cmds, "eighth_stage.tcl")
eighth_stage.add_tasks(task8)
p.add_stages(eighth_stage)
ninth_stage = Stage()
ninth_stage.name = 'Calculating the root mean square deviation for backbone atoms'
task9 = Task()
task9.pre_exec = ana_pre_exec.copy()
task9.cpu_reqs = {
'threads_per_process': ana_thread_cnt,
'processes': ana_process_cnt,
'process_type': None,
'thread_type': None}
task9_tcl_cmds = [ 'mol new 1ake-docked-noh_autopsf.psf',
'mol addfile adk-step1.dcd waitfor all',
'mol new 4ake-target_autopsf.pdb',
'package require mdff',
'set selbb [atomselect 0 "backbone"]',
'set selbbref [atomselect 1 "backbone"]',
'$selbb frame 0',
'measure rmsd $selbb $selbbref',
'$selbb frame last',
'measure rmsd $selbb $selbbref' ]
task9.copy_input_data = [
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, first_stage.name,
task1.name, '4ake-target_autopsf.pdb'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name,
task3.name, '1ake-docked-noh_autopsf.psf'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, seventh_stage.name,
task7.name, 'adk-step1.dcd')
]
set_vmd_run(task9, task9_tcl_cmds, "ninth_stage.tcl")
ninth_stage.add_tasks(task9)
p.add_stages(ninth_stage)
tenth_stage = Stage()
tenth_stage.name = 'Calculating the cross-correlation coefficient'
task10 = Task()
task10.pre_exec = ana_pre_exec.copy()
task10.cpu_reqs = {
'threads_per_process': ana_thread_cnt,
'processes': ana_process_cnt,
'process_type': None,
'thread_type': None}
task10_tcl_cmds = [ 'mol new 1ake-docked-noh_autopsf.psf' ]
task10_tcl_cmds += [ 'mol addfile adk-step1.dcd waitfor all' ] # load the full mdff trajectory
#task10_tcl_cmds += [ 'mol new 4ake-target_autopsf.stius' ] # load target EM density
task10_tcl_cmds += [ 'package require mdff',
'set selall [atomselect 0 "all"]',
'$selall frame 0',
'mdff ccc $selall -i target-density-5A.dx -res 5',
'$selall frame last',
'mdff ccc $selall -i target-density-5A.dx -res 5' ]
task10.copy_input_data = [
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, second_stage.name,
task2.name, '4ake-target_autopsf-grid.dx'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, third_stage.name,
task3.name, '1ake-docked-noh_autopsf.psf'),
'$Pipeline_{}_Stage_{}_Task_{}/{}'.format(p.name, seventh_stage.name,
task7.name, 'adk-step1.dcd')
]
task10.link_input_data = [ "$SHARED/%s" % os.path.basename(x) for x in
workflow_cfg[resource]['shared_data'] ]
set_vmd_run(task10, task10_tcl_cmds, "tenth_stage.tcl")
tenth_stage.add_tasks(task10)
p.add_stages(tenth_stage)
if os.environ.get('RADICAL_ENTK_VERBOSE') == None:
os.environ['RADICAL_ENTK_REPORT'] = 'True'
if __name__ == '__main__':
# Parse arguments from the command line
parser = argparse.ArgumentParser(description='Process some arguments to get resource and workflow cfgs')
parser.add_argument('--resource', help='path to workflow cfg file',
required=False, default='ornl_summit')
parser.add_argument('--nodes', help='the number of nodes to use',
required=False)
args = parser.parse_args()
resource = args.resource
# Load resource cfg
with open('cfg/resource_cfg.yml','r') as fp:
resource_cfg = yaml.load(fp, Loader=yaml.Loader)
# Load workflow cfg
with open('cfg/workflow_cfg.yml','r') as fp:
workflow_cfg = yaml.load(fp, Loader=yaml.Loader)
set_executable_path(workflow_cfg, resource)
# Create Pipeline
p = get_pipeline(workflow_cfg, resource)
# configure mongodb
if 'mongodb' in resource_cfg:
os.environ['RADICAL_PILOT_DBURL'] = resource_cfg['mongodb']['url']
# Create Application Manager
appman = AppManager(hostname=os.environ.get('RMQ_HOSTNAME',
resource_cfg['rabbitmq']['hostname']),
port=os.environ.get('RMQ_PORT', resource_cfg['rabbitmq']['port']),
username=os.environ.get('RMQ_USERNAME',None),
password=os.environ.get('RMQ_PASSWORD',None))
# override the number of nodes to start from user input parameter
if args.nodes and int(args.nodes) > 0:
resource_cfg[resource]['cpus'] = \
int(resource_cfg[resource]['cpus_per_node']) * int(args.nodes)
# Create a dictionary describe five mandatory keys:
# resource, walltime, cores, queue and access_schema
res_dict = {
'resource': resource_cfg[resource]['label'],
'walltime': resource_cfg[resource]['walltime'],
'cpus': resource_cfg[resource]['cpus'],
'access_schema': resource_cfg[resource]['access_schema']
}
if 'queue' in resource_cfg[resource]:
res_dict['queue'] = resource_cfg[resource]['queue']
if 'project' in resource_cfg[resource]:
res_dict['project'] = resource_cfg[resource]['project']
# Assign resource manager to the Application Manager
appman.resource_desc = res_dict
# Data shared between multiple tasks can be transferred while the
# job is waiting on queue
appman.shared_data = workflow_cfg[resource]['shared_data']
# Assign the workflow as a set or list of Pipelines to the Application Manager
appman.workflow = [p]
# Run the Application Manager
appman.run()