def assign_task_output_files(task, replica_list, replica_id,
replica_next_starting_step,
replica_next_ending_step):
#Find pdb file for current replica
replica_pdb = "%s.%d" % (protomol_utils.remove_trailing_dots(
protomol_utils.parse_file_name(pdb_file)), replica_id)
#Assign local and remote xyz output files.
if generate_xyz:
local_xyz_output_file = "%s/simfiles/%s/%s.%d-%d.xyz" % (
protomol_utils.output_path, replica_list[replica_id].temp,
protomol_utils.xyz_file_name, replica_id, replica_next_ending_step)
remote_xyz_output_file = "%d.xyz" % (replica_id)
task.specify_output_file_xyz(remote_xyz_output_file,
local_xyz_output_file)
#Assign local and remote dcd output files.
if generate_dcd:
local_dcd_output_file = "%s/simfiles/%s/%s.%d-%d.dcd" % (
protomol_utils.output_path, replica_list[replica_id].temp,
protomol_utils.dcd_file_name, replica_id, replica_next_ending_step)
remote_dcd_output_file = "%d.dcd" % (replica_id)
task.specify_output_file_dcd(remote_dcd_output_file,
local_dcd_output_file)
#Assign local and remote (output) energies files.
local_energies_file = "%s/simfiles/eng/%d/%d.eng" % (
protomol_utils.output_path, replica_id, replica_id)
remote_energies_file = "%d.eng" % replica_id
task.specify_output_file_energy(local_energies_file,
remote_energies_file,
cache=False)
#Assign local and remote velocity output files.
local_velocity_output_file = "%s/simfiles/%s/%s-%d.vel" % (
protomol_utils.output_path, replica_list[replica_id].temp, replica_pdb,
replica_next_ending_step + 1)
remote_velocity_output_file = "%s-%d.vel" % (replica_pdb,
replica_next_ending_step + 1)
task.specify_output_file_velocity(local_velocity_output_file,
remote_velocity_output_file,
cache=False)
pdb_output_file = "%s/simfiles/%s/%s-%d.pdb" % (
protomol_utils.output_path, replica_list[replica_id].temp, replica_pdb,
replica_next_ending_step + 1)
task.specify_output_file_pdb(
pdb_output_file,
protomol_utils.parse_file_name(pdb_output_file),
cache=False)
def make_directories(output_path, temp_list, num_replicas):
count = 0
for i in temp_list:
target_key = "%s/simfiles/%s/%s.%d-%d.pdb" % (
output_path, i,
protomol_utils.remove_trailing_dots(
protomol_utils.parse_file_name(pdb_file)), count, 0)
file_utils.upload_to_remote_storage(pdb_file, target_key)
count += 1
def make_directories(output_path, temp_list, shared_map):
count = 0
for i in temp_list:
target_key = "%s/simfiles/%s/%s.%d-%d.pdb" % (
output_path, i,
protomol_utils.remove_trailing_dots(
protomol_utils.parse_file_name(pdb_file)), count, 0)
with open(pdb_file, 'rb') as sourceFile:
shared_map[target_key] = sourceFile.readlines()
count += 1
def cf_main(pool_client, replica_list, replicas_to_run):
#Stat collection variables
global replicas_running
global step_time
global total_functions_executed
#Variable that tracks replicas which completed simulations over all MC steps
num_replicas_completed = 0
#-------Perform computation for each replica at current monte carlo step--------
'''Each computation is a pywren_task in work queue.
Each pywren_task will be run on one of the connected workers.'''
#Assign local and remote psf and par inputs
target_psf_file = "%s/simfiles/input_data/ww_exteq_nowater1.psf" % (
protomol_utils.output_path)
if upload_data:
file_utils.upload_to_remote_storage(psf_file, target_psf_file)
target_par_file = "%s/simfiles/input_data/par_all27_prot_lipid.inp" % (
protomol_utils.output_path)
if upload_data:
file_utils.upload_to_remote_storage(par_file, target_par_file)
while num_replicas_completed < len(replica_list):
print("num_replicas_completed: {}".format(num_replicas_completed))
print("len(replica_list): {}".format(len(replica_list)))
#Iterate through the given set of replicas and start their
# computation for the current monte carlo step.
activation_list = []
task_list_iterdata = []
for j in replicas_to_run:
if not replica_list[j].running:
#Initialize step time.
step_time = time.time()
replica_id = replica_list[j].id
#Each replica does computation at its current temperature
replica_temperature = replica_list[j].temp
'''Get the last seen step of replica. The last_seen_step
is the step at which this replica was brought back and
attempted for an exchange.'''
replica_last_seen_step = replica_list[j].last_seen_step
#record the starting, ending steps for current iteration of
#this replica.
replica_next_starting_step = replica_last_seen_step + 1
if replica_next_starting_step >= protomol_utils.monte_carlo_steps:
break
if use_barrier:
#Barrier version, so run one step at a time.
replica_next_ending_step = replica_next_starting_step
else:
#Run all steps until the step where the replica will be
#chosen to attempt an exchange.
if len(replica_list[j].exch_steps) > 0:
replica_next_ending_step = replica_list[j].exch_steps[
0]
#If there are no more exchange steps for this replica, run the
#remainder of monte carlo steps.
else:
replica_next_ending_step = protomol_utils.monte_carlo_steps - 1
#Set the last_seen_step to the next exchange step at which the
#replica (its output) will be brought back.
replica_list[j].last_seen_step = replica_next_ending_step
task = create_task(replica_id, local_temp_dir)
task.specify_input_psf_file(
target_psf_file, protomol_utils.parse_file_name(psf_file))
task.specify_input_par_file(
target_par_file, protomol_utils.parse_file_name(par_file))
assign_task_input_files(task, replica_list, replica_id,
replica_next_starting_step,
replica_next_ending_step)
assign_task_output_files(task, replica_list, replica_id,
replica_next_starting_step,
replica_next_ending_step)
#Keep count of replicas that iterated through all MC steps.
if (replica_next_ending_step ==
protomol_utils.monte_carlo_steps - 1):
num_replicas_completed += 1
task_dictionary = {}
task_dictionary['task'] = task
task_dictionary['time_per_function'] = 0
task_list_iterdata.append(task_dictionary)
#Submitted for execution. So mark this replica as running.
replica_list[j].running = 1
replicas_running += 1
#Wait for tasks to complete.
total_functions_executed += len(task_list_iterdata)
#serverless_task_process(task_list_iterdata[0]['task'],task_list_iterdata[0]['time_per_function'])
activation_list = pool_client.map(serverless_task_process,
task_list_iterdata)
for j in range(len(activation_list)):
replica_list[j].running = 0
replicas_running -= 1
execution_time_per_function.append(
activation_list[j].function_time)
if use_barrier:
replicas_to_run = wait_barrier(activation_list, replica_list,
replica_next_starting_step, 5)
else:
replicas_to_run = wait_nobarrier(activation_list, replica_list, 5)
def assign_task_input_files(task, replica_list, replica_id,
replica_next_starting_step,
replica_next_ending_step):
#Find pdb file for current replica
replica_pdb = "%s.%d" % (protomol_utils.remove_trailing_dots(
protomol_utils.parse_file_name(pdb_file)), replica_id)
#Find pdb file for replica that exchanged with current replica in last step
if (replica_list[replica_id].exchgd_replica_id > -1):
exchgd_replica_pdb = "%s.%d" % (protomol_utils.remove_trailing_dots(
protomol_utils.parse_file_name(
pdb_file)), replica_list[replica_id].exchgd_replica_id)
else:
exchgd_replica_pdb = "%s.%d" % (protomol_utils.remove_trailing_dots(
protomol_utils.parse_file_name(pdb_file)), replica_id)
'''Local_file: name for file brought back and stored on local site where this is run.
Remote_file: name for file sent to remote worker and used in execution there.'''
#Assign local and remote execution scripts
local_execn_file = "%s/simfiles/%s/exec-%d.sh" % (
protomol_utils.output_path, "runs", replica_id)
remote_execn_file = "exec-%d.sh" % (replica_id)
task.specify_input_local_execn_file(local_execn_file,
remote_execn_file,
cache=False)
#Assign local and remote pdb inputs
local_pdb_input_file = "%s/simfiles/%s/%s-%d.pdb" % (
protomol_utils.output_path, replica_list[replica_id].temp,
exchgd_replica_pdb, replica_next_starting_step)
remote_pdb_input_file = "%s-%d.pdb" % (replica_pdb,
replica_next_starting_step)
task.specify_input_pdb_file(local_pdb_input_file,
remote_pdb_input_file,
cache=False)
#Velocity input only required after first step since it is output
#of first step.
if (replica_next_starting_step > 0):
#Assign local and remote velocity input files.
local_velocity_input_file = "%s/simfiles/%s/%s-%d.vel" % (
protomol_utils.output_path, replica_list[replica_id].temp,
exchgd_replica_pdb, replica_next_starting_step)
remote_velocity_input_file = "%s-%d.vel" % (replica_pdb,
replica_next_starting_step)
task.specify_input_file_velocity(local_velocity_input_file,
remote_velocity_input_file,
cache=False)
for i in range(replica_next_starting_step, replica_next_ending_step + 1):
#Assign local and remote config files.
local_config_file = "%s/simfiles/config/%d/%d-%d.cfg" % (
protomol_utils.output_path, replica_id, replica_id, i)
remote_config_file = "%d-%d.cfg" % (replica_id, i)
task.specify_input_file(i,
local_config_file,
remote_config_file,
cache=False)
#Call function to generate execution script.
[execn_script_name,
execn_script] = generate_execn_script(replica_list[replica_id],
replica_next_starting_step,
replica_next_ending_step)
print(execn_script)
task.execn_script = execn_script
'''
if upload_data:
target_key = "%s/simfiles/runs/%s" % (pywren_protomol.output_path, pywren_protomol.remove_first_dots(pywren_protomol.parse_file_name(execn_script_name)))
cos.upload_bytes_to_cos(ibm_cos, str.encode(execn_script), input_config['ibm_cos']['bucket'], target_key)
'''
#Assign executable that will be run on remote worker to pywren_task string.
if not protomol_local_install:
local_executable = "%s" % (protomol_utils.EXECUTABLE)
task.specify_executable(local_executable)
print("Number of failures: {}".format(num_task_resubmissions))
print("Replica Exchanges: {}".format(num_replica_exchanges))
print("Acceptance Rate: {}".format(
(num_replica_exchanges * 100) / protomol_utils.monte_carlo_steps))
averageValue = 0
for itr in montecarlo_return_time_list:
averageValue += itr
averageValue = averageValue / protomol_utils.monte_carlo_steps
print("Average Response Time {}".format(averageValue))
#Write stats to a stats file
stat_file_name = "%s/%s.stat" % (
local_temp_dir,
protomol_utils.remove_trailing_dots(
protomol_utils.parse_file_name(pdb_file)))
stat_file_stream = open(stat_file_name, "w")
stat_file_stream.write("%s\n" %
"Printing replica temperature execution matrix:")
#Sort and format the replica exchange matrix.
for itr in range(num_replicas):
replica_temp_execution_list[itr].sort()
unique(replica_temp_execution_list[itr])
stat_file_stream.write("Replica %d: %s\n" %
(itr, replica_temp_execution_list[itr]))
#If barrier version was used, write the MC step times to stats file.
if use_barrier:
#Write run time for each step to stats file
stat_file_stream.write("\n\n%s\n" %
def save_protomol_template(output_path, pdb_file, psf_file, par_file, monte_carlo_step, md_steps, output_freq,
replica_obj, generate_xyz = False, generate_dcd = False):
protomol_config_map = OrderedDict()
# Parse supplied files so only actual file name is passed, not full path of the file name
input_pdb = "%s.%d-%d.pdb" % (protomol_utils.remove_trailing_dots(protomol_utils.parse_file_name(pdb_file)), replica_obj.id, monte_carlo_step)
parsed_psf_file = protomol_utils.parse_file_name(psf_file)
parsed_par_file = protomol_utils.parse_file_name(par_file)
str_output_freq = str(output_freq)
str_md_steps = str(md_steps)
protomol_config_map["randomtype"] = "1"
protomol_config_map["numsteps"] = str_md_steps
protomol_config_map["outputfreq"] = str_output_freq
protomol_config_map["posfile"] = input_pdb
protomol_config_map["psffile"] = parsed_psf_file
protomol_config_map["parfile"] = parsed_par_file
if monte_carlo_step > 0:
protomol_config_map["velfile"] = "%s.%d-%d.vel" % (
protomol_utils.remove_trailing_dots(protomol_utils.parse_file_name(pdb_file)), replica_obj.id, monte_carlo_step)
protomol_config_map["dofinPDBPosFile"] = "true"
protomol_config_map["finPDBPosFile"] = "%s.%d-%d.pdb" % (
protomol_utils.remove_trailing_dots(protomol_utils.parse_file_name(pdb_file)), replica_obj.id, monte_carlo_step + 1)
protomol_config_map["finXYZVelFile"] = "%s.%d-%d.vel" % (
protomol_utils.remove_trailing_dots(protomol_utils.parse_file_name(pdb_file)), replica_obj.id, monte_carlo_step + 1)
protomol_config_map["temperature"] = "%f" % replica_obj.temp
protomol_config_map["boundaryConditions"] = "%s" % DEFAULT_BOUNDARY_CONDITIONS
protomol_config_map["cellManager"] = "Cubic"
protomol_config_map["cellsize"] = "69"
if generate_xyz:
protomol_config_map["XYZPosFile"] = "%d.xyz" % replica_obj.id
protomol_config_map["XYZPosFileOutputFreq"] = "%d" % str_md_steps
if generate_dcd:
protomol_config_map["DCDFile"] = "%d.dcd" % replica_obj.id
protomol_config_map["DCDFileOutputFreq"] = str_output_freq
protomol_config_map["allEnergiesFile"] = "%d.eng" % replica_obj.id
protomol_config_map["allEnergiesFileOutputFreq"] = str_output_freq
protomol_config_map["seed"] = str(random.randint(1, 1000000))
protomol_config_map["shake"] = "on"
langevin_impulse_dictionary = OrderedDict()
langevin_impulse_dictionary["temperature"] = str(replica_obj.temp)
langevin_impulse_dictionary["gamma"] = "5"
langevin_impulse_dictionary["timestep"] = "2"
langevin_impulse_dictionary["force"] = ["bond","angle","dihedral","improper","LennardJones Coulomb"]
langevin_impulse_dictionary["-switchingFunction"] = ["C2","C1","-algorithm NonbondedCutoff"]
langevin_impulse_dictionary["-switchon"] = "10"
langevin_impulse_dictionary["-cutoff"] = ["12","12","12"]
integrator_dictionary = OrderedDict()
integrator_dictionary["level"] = "0"
integrator_dictionary["langevinImpulse"] = langevin_impulse_dictionary
protomol_config_map["integrator"] = integrator_dictionary
cfg_file_name = "%s/%s/%s/%d/%d-%d.cfg" % (
output_path, "simfiles", "config", replica_obj.id, replica_obj.id, monte_carlo_step)
serialized_object = json.dumps(protomol_config_map)
redis_connector.save_file_to_redis(cfg_file_name, serialized_object)
return cfg_file_name
