def _run_spawn(self):
LogMgr.info("_run_spawn() [Pickling Sim]")
(bundle, resfilename) = MetaDataBundleBuilder.build_std_pickler(self)
(_bundlefname, sim_cmd) = bundle.write_to_file_and_get_exec_string()
# if Exists(resfilename):
# os.unlink(resfilename)
if not os.path.exists(resfilename):
# Setup the LD_LIBRARY PATH:
# It may be nessesary to add the following to .mfrc
# ld_library_path_suffix = /home/michael/hw/morphforge/src/morphforgecontrib/neuron_gsl/cpp
ld_path_additions = RCMgr.get("Neuron", "ld_library_path_suffix").split(":")
old_ld_path = os.environ.get("LD_LIBRARY_PATH", "")
os.environ["LD_LIBRARY_PATH"] = ":".join([old_ld_path] + ld_path_additions)
LogMgr.info("_run_spawn() [Spawning subprocess]")
ret_code = subprocess.call(sim_cmd, shell=True)
if ret_code != 1:
raise ValueError("Unable to simulate %s" % self.name)
LogMgr.info("_run_spawn() [Finished spawning subprocess]")
# Load back the results:
LogMgr.info("_run_spawn() [Loading results]")
print "_run_spawn() [Loading results from %s ]" % resfilename
self.result = SimulationResult.load_from_file(resfilename)
LogMgr.info("_run_spawn() [Finished loading results]")
# We have to do this so that the simulation object
# within the result is correct!!
self.result.simulation = self
# Save the simulation summary:
do_summary = False
if do_summary:
fname = "~/Desktop/pdfs/%s.pdf" % (self._sim_desc_str().replace(" ", ""))
summary = SimulationMRedoc.build(self)
summary.to_pdf(fname)
# And unlink the old files (so we don't go mad on disk space)
os.unlink(resfilename)
os.unlink(_bundlefname)
return self.result
def _run_spawn(self):
LogMgr.info('_run_spawn() [Pickling Sim]')
(bundle, resfilename) = MetaDataBundleBuilder.build_std_pickler(self)
(_bundlefname, sim_cmd) = bundle.write_to_file_and_get_exec_string()
# if Exists(resfilename):
# os.unlink(resfilename)
if not os.path.exists(resfilename):
# Setup the LD_LIBRARY PATH:
# It may be nessesary to add the following to .mfrc
# ld_library_path_suffix = /home/michael/hw/morphforge/src/morphforgecontrib/neuron_gsl/cpp
ld_path_additions = RCMgr.get('Neuron',
'ld_library_path_suffix').split(':')
old_ld_path = os.environ.get('LD_LIBRARY_PATH', '')
os.environ['LD_LIBRARY_PATH'] = ':'.join([old_ld_path] +
ld_path_additions)
LogMgr.info('_run_spawn() [Spawning subprocess]')
ret_code = subprocess.call(sim_cmd, shell=True)
if ret_code != 1:
raise ValueError('Unable to simulate %s' % self.name)
LogMgr.info('_run_spawn() [Finished spawning subprocess]')
# Load back the results:
LogMgr.info('_run_spawn() [Loading results]')
self.result = SimulationResult.load_from_file(resfilename)
LogMgr.info('_run_spawn() [Finished loading results]')
# We have to do this so that the simulation object
# within the result is correct!!
self.result.simulation = self
# Save the simulation summary:
do_summary = False
if do_summary:
fname = '~/Desktop/pdfs/%s.pdf' % (self._sim_desc_str().replace(
' ', ''))
summary = SimulationMRedoc.build(self)
summary.to_pdf(fname)
return self.result
def _RunSpawn(self):
LogMgr.info("_RunSpawn() [Pickling Sim]")
b, resfilename = MetaDataBundleBuilder.buildStdPickler(self)
bundlefilename, simCmd = b.writeToFileAndGetExecString()
#if Exists(resfilename):
# os.unlink(resfilename)
if not Exists(resfilename):
# Setup the LD_LIBRARY PATH:
# It may be nessesary to add the following to .mfrc
# ld_library_path_suffix = /home/michael/hw/morphforge/src/morphforgecontrib/neuron_gsl/cpp
ld_path_additions = RCMgr.get("Neuron","ld_library_path_suffix").split(":")
old_ld_path = os.environ.get('LD_LIBRARY_PATH','')
os.environ['LD_LIBRARY_PATH'] = ":".join( [old_ld_path] + ld_path_additions )
LogMgr.info("_RunSpawn() [Spawning subprocess]")
retCode = ExecCommandGetRetCode(simCmd)
if retCode != 1: raise ValueError("Unable to simulate %s" % self.name)
LogMgr.info("_RunSpawn() [Finished spawning subprocess]")
# Load back the results:
LogMgr.info("_RunSpawn() [Loading results]")
self.result = SimulationResult.loadFromFile(resfilename)
LogMgr.info("_RunSpawn() [Finished loading results]")
# We have to do this so that the simulation object
# within the result is correct!!
self.result.simulation = self
return self.result
class ModBuilderParams(object):
nocmodlpath = RCReader.get('Neuron', 'nocmodlpath')
libtoolpath = RCReader.get('Neuron', 'libtoolpath')
compile_includes = ['.', '..'] + \
RCReader.get('Neuron', 'compileincludes').split(':')
compile_defs = ['HAVE_CONFIG_H']
std_link_libs = [
'nrnoc',
'oc',
'memacs',
'nrnmpi',
'scopmath',
'sparse13',
'readline',
'ncurses',
'ivoc',
'neuron_gnu',
'meschach',
'sundials',
'm',
'dl',
]
nrn_link_dirs = RCReader.get('Neuron', 'nrnlinkdirs').split(':')
rpath = RCReader.get('Neuron', 'rpath')
rnd_alone_link_statement = RCReader.get('Neuron', 'rndalonelinkstatement')
modlunitpath = RCReader.get('Neuron', 'modlunitpath')
@classmethod
def get_compile_str(cls,
c_filename,
lo_filename,
additional_compile_flags=''):
incl_str = ' '.join(
["""-I"%s" """ % _incl for _incl in cls.compile_includes])
def_str = ' '.join(["""-D%s """ % _def for _def in cls.compile_defs])
variables = {
'lo': lo_filename,
'c': c_filename,
'incs': incl_str,
'defs': def_str,
'additional_flags': additional_compile_flags
}
return """--mode=compile gcc %(defs)s %(incs)s %(additional_flags)s -g -O2 -c -o %(lo)s %(c)s """ % variables
@classmethod
def get_link_str(cls, lo_filename, la_filename, additional_link_flags=''):
std_lib_str = ' '.join(['-l%s' % lib for lib in cls.std_link_libs])
std_lib_dir_str = ' '.join(
['-L%s' % _dir for _dir in cls.nrn_link_dirs])
link_dict = {
'la': la_filename,
'lo': lo_filename,
'std_lib_str': std_lib_str,
'std_lib_dir_str': std_lib_dir_str,
'rpath': cls.rpath,
'randSt': cls.rnd_alone_link_statement,
'additional_flags': additional_link_flags
}
return """--mode=link gcc -module -g -O2 -shared -o %(la)s -rpath %(rpath)s %(lo)s %(std_lib_dir_str)s %(randSt)s %(std_lib_str)s %(additional_flags)s """ % link_dict
