def run_remotely(command, task, remote_dir, runtime='01:00:00', submit_helper=uclClusterSubmit):
variables = {}
task_full = '%s_%s'%(task, time.ctime().replace(' ','_' ).replace(':','.' ))
variables['command'] = command
variables['task'] = task_full
variables['remote_dir'] = remote_dir
variables['runtime'] = runtime
t = Template(submit_helper.template)
contents = t.render(variables)
tmp_script_name = 'submit_%s'%(task_full)
tmp_script = open(tmp_script_name,'w')
tmp_script.write(contents)
tmp_script.close()
'''
print("\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print(contents)
print("+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n")'''
scp_cmd = 'scp "%s" "%s@%s:%s"' % (tmp_script_name, submit_helper.username, submit_helper.host, remote_dir)
print execute_command_in_dir(scp_cmd, '.', True)
ssh_cmd = "ssh %s@%s \"cd %s;/bin/bash -ci 'qsub %s'\"" % (submit_helper.username, submit_helper.host, remote_dir, tmp_script_name)
print execute_command_in_dir(ssh_cmd, '.', True)
return tmp_script_name
def run_remotely(command,
task,
remote_dir,
runtime='01:00:00',
submit_helper=uclClusterSubmit):
variables = {}
task_full = '%s_%s' % (task, time.ctime().replace(' ', '_').replace(
':', '.'))
variables['command'] = command
variables['task'] = task_full
variables['remote_dir'] = remote_dir
variables['runtime'] = runtime
t = Template(submit_helper.template)
contents = t.render(variables)
tmp_script_name = 'submit_%s' % (task_full)
tmp_script = open(tmp_script_name, 'w')
tmp_script.write(contents)
tmp_script.close()
'''
print("\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print(contents)
print("+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n")'''
scp_cmd = 'scp "%s" "%s@%s:%s"' % (tmp_script_name, submit_helper.username,
submit_helper.host, remote_dir)
print execute_command_in_dir(scp_cmd, '.', True)
ssh_cmd = "ssh %s@%s \"cd %s;/bin/bash -ci 'qsub %s'\"" % (
submit_helper.username, submit_helper.host, remote_dir,
tmp_script_name)
print execute_command_in_dir(ssh_cmd, '.', True)
return tmp_script_name
def run(a=None, **kwargs):
try:
import neuroml
import pyneuroml
import xlrd
except Exception as e:
print_("Cannot import one of the required packages. Please install!\n"
"Exception: %s\n" % e)
try:
if os.environ.has_key('C302_HOME'):
os.environ['C302_HOME']
sys.path.append(os.environ['C302_HOME'])
print_('Python path now: %s' % sys.path)
import c302
import c302_utils
except Exception as e:
print_(
"Cannot import c302!\n"
"Exception: %s\n" % e +
"Please set environment variable C302_HOME to point to the directory: CElegansNeuroML/CElegans/pythonScripts/c302!\n"
)
exit()
a = build_namespace(a, **kwargs)
gen_start = time.time()
ref = a.reference
if not os.path.isdir('simulations'):
os.mkdir('simulations')
sim_ref = "%s_%s_%s" % (a.c302params, ref, time.ctime().replace(
' ', '_').replace(':', '.'))
sim_dir = "simulations/%s" % (sim_ref)
os.mkdir(sim_dir)
#exec('from %s import ParameterisedModel'%a.c302params)
#params = ParameterisedModel()
id = '%s_%s' % (a.c302params, ref)
exec('from c302_%s import setup' % ref)
setup(a.c302params,
generate=True,
duration=a.duration,
dt=a.dt,
target_directory=sim_dir)
lems_file0 = '%s/LEMS_c302_%s.xml' % (sim_dir, id)
lems_file = '%s/LEMS_c302.xml' % (sim_dir)
print_("Renaming %s -> %s" % (lems_file0, lems_file))
os.rename(lems_file0, lems_file)
announce("Generating NEURON files from: %s..." % lems_file)
pynml.run_lems_with_jneuroml_neuron(lems_file,
only_generate_scripts=True,
nogui=True,
load_saved_data=False,
verbose=True)
main_nrn_py = open('%s/LEMS_c302_nrn.py' % (sim_dir), 'r')
updated = ''
for line in main_nrn_py:
line = line.replace('GenericCell.hoc', '%s/GenericCell.hoc' % sim_dir)
line = line.replace('GenericNeuronCell.hoc',
'%s/GenericNeuronCell.hoc' % sim_dir)
line = line.replace('GenericMuscleCell.hoc',
'%s/GenericMuscleCell.hoc' % sim_dir)
line = line.replace("open('time.dat", "open('%s/time.dat" % sim_dir)
line = line.replace("open('c302_", "open('%s/c302_" % sim_dir)
updated += line
main_nrn_py.close()
main_nrn_py = open('%s/LEMS_c302_nrn.py' % (sim_dir), 'w')
main_nrn_py.write(updated)
main_nrn_py.close()
run_dir = '.'
command = 'nrnivmodl %s' % sim_dir
announce("Compiling NMODL files for NEURON...")
pynml.execute_command_in_dir(command, run_dir, prefix="nrnivmodl: ")
command = './Release/Sibernetic -c302 -f worm -no_g -l_to lpath=%s timelimit=%s timestep=%s' % (
sim_dir, a.duration / 1000.0, a.dt / 1000)
env = {"PYTHONPATH": "./src:./%s" % sim_dir}
sim_start = time.time()
announce(
"Executing main Sibernetic simulation of %sms using: \n\n %s \n\n in %s with %s"
% (a.duration, command, run_dir, env))
#pynml.execute_command_in_dir('env', run_dir, prefix="Sibernetic: ",env=env,verbose=True)
pynml.execute_command_in_dir(command,
run_dir,
prefix="Sibernetic: ",
env=env,
verbose=True)
sim_end = time.time()
reportj = {}
reportj['duration'] = '%s ms' % a.duration
reportj['dt'] = '%s ms' % a.dt
reportj['sim_ref'] = sim_ref
reportj['reference'] = a.reference
reportj['c302params'] = a.c302params
reportj['generation_time'] = '%s s' % (sim_start - gen_start)
reportj['run_time'] = '%s s' % (sim_end - sim_start)
reportj['command'] = '%s' % (command)
report_file = open("%s/report.json" % sim_dir, 'w')
report_file.write(pp.pformat(reportj))
report_file.close()
announce("Generating images for neuronal activity...")
results = pynml.reload_saved_data(lems_file,
plot=False,
show_plot_already=False,
simulator=None,
verbose=True)
c302_utils.plot_c302_results(results,
config=a.reference,
parameter_set=a.c302params,
directory=sim_dir,
save=True,
show_plot_already=False)
pos_file_name = os.path.abspath('%s/position_buffer.txt' % sim_dir)
announce("Plotting positions of worm body particles in %s..." %
pos_file_name)
from plot_positions import plot_positions
if not os.path.isfile(pos_file_name):
time.sleep(2)
plot_positions(pos_file_name, rate_to_plot=int(a.duration / 5))
announce("Finished in %s sec!\n\nSimulation saved in: %s\n\n"%((sim_end-sim_start),sim_dir) + \
"Report of simulation at: %s/report.json\n\n"%(sim_dir)+ \
"Rerun simulation with: ./Release/Sibernetic -l_from lpath=%s\n"%(sim_dir))
def run(a=None,**kwargs):
try:
import neuroml
import pyneuroml
import xlrd
except Exception as e:
print_("Cannot import one of the required packages. Please install!\n"
"Exception: %s\n"%e)
try:
if os.environ.has_key('C302_HOME'):
os.environ['C302_HOME']
sys.path.append(os.environ['C302_HOME'])
print_('Python path now: %s'%sys.path)
import c302
import c302_utils
except Exception as e:
print_("Cannot import c302!\n"
"Exception: %s\n"%e
+"Please set environment variable C302_HOME to point to the directory: CElegansNeuroML/CElegans/pythonScripts/c302!\n")
exit()
a = build_namespace(a,**kwargs)
gen_start = time.time()
ref = a.reference
if not os.path.isdir('simulations'):
os.mkdir('simulations')
sim_ref = "%s_%s_%s"%(a.c302params,ref, time.ctime().replace(' ','_' ).replace(':','.' ))
sim_dir = "simulations/%s"%(sim_ref)
os.mkdir(sim_dir)
#exec('from %s import ParameterisedModel'%a.c302params)
#params = ParameterisedModel()
id = '%s_%s'%(a.c302params,ref)
exec('from c302_%s import setup'%ref)
setup(a.c302params,
generate=True,
duration = a.duration,
dt = a.dt,
target_directory=sim_dir)
lems_file0 = '%s/LEMS_c302_%s.xml'%(sim_dir,id)
lems_file = '%s/LEMS_c302.xml'%(sim_dir)
print_("Renaming %s -> %s"%(lems_file0,lems_file))
os.rename(lems_file0,lems_file)
announce("Generating NEURON files from: %s..."%lems_file)
pynml.run_lems_with_jneuroml_neuron(lems_file,
only_generate_scripts=True,
nogui=True,
load_saved_data=False,
verbose=True)
main_nrn_py = open('%s/LEMS_c302_nrn.py'%(sim_dir),'r')
updated =''
for line in main_nrn_py:
line = line.replace('GenericCell.hoc','%s/GenericCell.hoc'%sim_dir)
line = line.replace('GenericNeuronCell.hoc','%s/GenericNeuronCell.hoc'%sim_dir)
line = line.replace('GenericMuscleCell.hoc','%s/GenericMuscleCell.hoc'%sim_dir)
line = line.replace("open('time.dat","open('%s/time.dat"%sim_dir)
line = line.replace("open('c302_","open('%s/c302_"%sim_dir)
updated += line
main_nrn_py.close()
main_nrn_py = open('%s/LEMS_c302_nrn.py'%(sim_dir),'w')
main_nrn_py.write(updated)
main_nrn_py.close()
run_dir = '.'
command = 'nrnivmodl %s'%sim_dir
announce("Compiling NMODL files for NEURON...")
pynml.execute_command_in_dir(command, run_dir, prefix="nrnivmodl: ")
command = './Release/Sibernetic -c302 -f worm -no_g -l_to lpath=%s timelimit=%s timestep=%s'%(sim_dir,a.duration/1000.0,a.dt/1000)
env={"PYTHONPATH":"./src:./%s"%sim_dir}
sim_start = time.time()
announce("Executing main Sibernetic simulation of %sms using: \n\n %s \n\n in %s with %s"%(a.duration, command, run_dir, env))
#pynml.execute_command_in_dir('env', run_dir, prefix="Sibernetic: ",env=env,verbose=True)
pynml.execute_command_in_dir(command, run_dir, prefix="Sibernetic: ",env=env,verbose=True)
sim_end = time.time()
reportj = {}
reportj['duration'] = '%s ms'%a.duration
reportj['dt'] = '%s ms'%a.dt
reportj['sim_ref'] = sim_ref
reportj['reference'] = a.reference
reportj['c302params'] = a.c302params
reportj['generation_time'] = '%s s'%(sim_start-gen_start)
reportj['run_time'] = '%s s'%(sim_end-sim_start)
reportj['command'] = '%s'%(command)
report_file = open("%s/report.json"%sim_dir,'w')
report_file.write(pp.pformat(reportj))
report_file.close()
announce("Generating images for neuronal activity...")
results = pynml.reload_saved_data(lems_file,
plot=False,
show_plot_already=False,
simulator=None,
verbose=True)
c302_utils.plot_c302_results(results,
config=a.reference,
parameter_set=a.c302params,
directory=sim_dir,
save=True,
show_plot_already=False)
pos_file_name = os.path.abspath('%s/position_buffer.txt'%sim_dir)
announce("Plotting positions of worm body particles in %s..."%pos_file_name)
from plot_positions import plot_positions
if not os.path.isfile(pos_file_name):
time.sleep(2)
plot_positions(pos_file_name,rate_to_plot = int(a.duration/5))
announce("Finished in %s sec!\n\nSimulation saved in: %s\n\n"%((sim_end-sim_start),sim_dir) + \
"Report of simulation at: %s/report.json\n\n"%(sim_dir)+ \
"Rerun simulation with: ./Release/Sibernetic -l_from lpath=%s\n"%(sim_dir))
