def create_docker_image(filenames, MPI_version=None):
log.info("Creating Docker image...")
if not MPI_version:
MPI_version = "3.2"
# log.warning("You have not specified an MPICH version. "
# "It is strongly encouraged to request the one installed in your cluster,"
# " using '--mpi-version X.Y'. Defaulting to MPICH v%s.", MPI_version)
dc = get_docker_client()
modules = yaml_dump(get_modules(*[load_input(f)
for f in filenames])).strip()
echos_reqs = "RUN " + " && \\ \n ".join([
r'echo "%s" >> %s' % (block, requirements_file_path)
for block in modules.split("\n")
])
echos_help = "RUN " + " && \\ \n ".join([
r'echo "%s" >> %s' % (line, help_file_path)
for line in image_help("docker").split("\n")
])
recipe = r"""
FROM cobaya/base_mpich_%s:latest
%s
RUN cobaya-install %s --%s %s --just-code --force ### NEEDS PYTHON UPDATE! --no-progress-bars
%s
CMD ["cat", "%s"]
""" % (MPI_version, echos_reqs, requirements_file_path, _modules_path_arg,
_modules_path, echos_help, help_file_path)
image_name = "cobaya:" + uuid.uuid4().hex[:6]
with StringIO(recipe) as stream:
dc.images.build(fileobj=stream, tag=image_name)
log.info(
"Docker image '%s' created! "
"Do 'docker save %s | gzip > some_name.tar.gz'"
"to save it to the current folder.", image_name, image_name)
def citation(*infos):
print(make_header("This framework", ""))
print("[Paper in preparation]\n")
for kind, modules in get_modules(*infos).items():
for module in modules:
print(make_header(kind, module))
print(get_citation_info(module, kind))
def citation(*infos):
blocks_text = odict([["Cobaya", "[Paper in preparation]"]])
for kind, modules in get_modules(*infos).items():
for module in modules:
blocks_text["%s:%s" % (kind, module)] = get_citation_info(
module, kind)
return blocks_text
def create_singularity_image(filenames, MPI_version=None):
log.info("Creating Singularity image...")
if not MPI_version:
MPI_version = "2.1.1"
# log.warning("You have not specified an OpenMPI version. "
# "It is strongly encouraged to request the one installed in your cluster,"
# " using '--mpi-version X.Y.Z'. Defaulting to OpenMPI v%s.", MPI_version)
modules = yaml_dump(get_modules(*[load_input(f)
for f in filenames])).strip()
echos_reqs = "\n " + "\n ".join([""] + [
'echo "%s" >> %s' % (block, requirements_file_path)
for block in modules.split("\n")
])
recipe = (dedent("""
Bootstrap: docker
From: cobaya/base_openmpi_%s:latest\n
%%post\n""" % MPI_version) + dedent(echos_reqs) + dedent("""
export CONTAINED=TRUE
cobaya-install %s --%s %s --just-code --force ### --no-progress-bars
mkdir %s
%%help
%s
""" % (requirements_file_path, _modules_path,
os.path.join(_modules_path_arg, _modules_path, _data),
"\n ".join(image_help("singularity").split("\n")[1:]))))
with NamedTemporaryFile(delete=False) as recipe_file:
recipe_file.write(recipe)
recipe_file_name = recipe_file.name
image_name = "cobaya_" + uuid.uuid4().hex[:6] + ".simg"
process_build = Popen(
["singularity", "build", image_name, recipe_file_name],
stdout=PIPE,
stderr=PIPE)
out, err = process_build.communicate()
if process_build.returncode:
log.info(out)
log.info(err)
log.error("Image creation failed! See error message above.")
raise HandledException
log.info("Singularity image '%s' created!", image_name)
def install(*infos, **kwargs):
if not log.root.handlers:
logger_setup()
path = kwargs.get("path", ".")
if not path:
# See if we can get one (and only one) from infos
paths = set(
[p for p in [info.get(_path_install) for info in infos] if p])
if len(paths) == 1:
path = paths[0]
else:
print("logging?")
log.error(
"No 'path' argument given and could not extract one (and only one) "
"from the infos.")
raise HandledException
abspath = os.path.abspath(path)
log.info("Installing modules at '%s'\n", abspath)
kwargs_install = {
"force": kwargs.get("force", False),
"no_progress_bars": kwargs.get("no_progress_bars")
}
for what in (_code, _data):
kwargs_install[what] = kwargs.get(what, True)
spath = os.path.join(abspath, what)
if kwargs_install[what] and not os.path.exists(spath):
try:
os.makedirs(spath)
except OSError:
log.error(
"Could not create the desired installation folder '%s'",
spath)
raise HandledException
failed_modules = []
for kind, modules in get_modules(*infos).items():
for module in modules:
print(make_header(kind, module))
module_folder = get_folder(module, kind, sep=".", absolute=False)
try:
imported_module = import_module(module_folder,
package=_package)
except ImportError:
if kind == _likelihood:
info = (next(info for info in infos if module in info.get(
_likelihood, {}))[_likelihood][module]) or {}
if isinstance(info, string_types) or _external in info:
log.warning(
"Module '%s' is a custom likelihood. "
"Nothing to do.\n", module)
flag = False
else:
log.error("Module '%s' not recognized.\n" % module)
failed_modules += ["%s:%s" % (kind, module)]
continue
is_installed = getattr(imported_module, "is_installed", None)
if is_installed is None:
log.info("Built-in module: nothing to do.\n")
continue
if is_installed(path=abspath, **kwargs_install):
log.info("External module already installed.\n")
if kwargs_install["force"]:
log.info("Forcing re-installation, as requested.")
else:
log.info("Doing nothing.\n")
continue
try:
success = imported_module.install(path=abspath,
**kwargs_install)
except:
traceback.print_exception(*sys.exc_info(), file=sys.stdout)
log.error(
"An unknown error occurred. Delete the modules folder and try "
"again. Notify the developers if this error persists.")
success = False
if success:
log.info("Successfully installed!\n")
else:
log.error(
"Installation failed! Look at the error messages above. "
"Solve them and try again, or, if you are unable to solve, "
"install this module manually.")
failed_modules += ["%s:%s" % (kind, module)]
continue
# test installation
if not is_installed(path=abspath, **kwargs_install):
log.error(
"Installation apparently worked, "
"but the subsequent installation test failed! "
"Look at the error messages above. "
"Solve them and try again, or, if you are unable to solve, "
"install this module manually.")
failed_modules += ["%s:%s" % (kind, module)]
if failed_modules:
bullet = "\n - "
log.error(
"The installation (or installation test) of some module(s) has failed: "
"%s\nCheck output of the installer of each module above "
"for precise error info.\n", bullet + bullet.join(failed_modules))
raise HandledException
def makeGrid(batchPath,
settingName=None,
settings=None,
read_only=False,
interactive=False,
install_reqs_at=None,
install_reqs_force=None):
batchPath = os.path.abspath(batchPath) + os.sep
# # 0: chains, 1: importance sampling, 2: best-fit, 3: best-fit and Hessian
# cosmomcAction = 0
if not settings:
if not settingName:
raise NotImplementedError(
"Re-using previous batch is work in progress...")
# if not pathIsGrid(batchPath):
# raise Exception('Need to give name of setting file if batchPath/config '
# 'does not exist')
# read_only = True
# sys.path.insert(0, batchPath + 'config')
# sys.modules['batchJob'] = batchjob # old name
# settings = __import__(IniFile(batchPath + 'config/config.ini').params['setting_file'].replace('.py', ''))
elif os.path.splitext(settingName)[-1].lower() in (".yml", ".yaml"):
settings = yaml_load_file(settingName)
else:
# ACTUALLY, in the scripted case a DICT or a YAML FILE NAME should be passed
raise NotImplementedError(
"Using a python script is work in progress...")
# settings = __import__(settingName, fromlist=['dummy'])
from cobaya.grid_tools import batchjob
batch = batchjob.batchJob(batchPath, settings.get("yaml_dir", None))
### batch.skip = settings.get("skip", False)
if "skip" in settings:
raise NotImplementedError("Skipping not implemented yet.")
batch.makeItems(settings, messages=not read_only)
if read_only:
for jobItem in [b for b in batch.jobItems]:
if not jobItem.chainExists():
batch.jobItems.remove(jobItem)
batch.save()
print('OK, configured grid with %u existing chains' %
(len(batch.jobItems)))
return batch
else:
# WAS batch.makeDirectories(settings.__file__)
# WHY THE DIR OF settings AND NOT THE GRID DIR GIVEN???
batch.makeDirectories(setting_file=None)
batch.save()
# NOT IMPLEMENTED YET: start at best fit!!!
# start_at_bestfit = getattr(settings, 'start_at_bestfit', False)
defaults = copy.deepcopy(settings)
modules_used = {}
grid_definition = defaults.pop("grid")
models_definitions = grid_definition["models"]
datasets_definitions = grid_definition["datasets"]
for jobItem in batch.items(wantSubItems=False):
jobItem.makeChainPath()
base_info = copy.deepcopy(defaults)
try:
model_info = models_definitions[jobItem.param_set] or {}
except KeyError:
raise ValueError("Model '%s' must be defined." % jobItem.param_set)
# COVMATS NOT IMPLEMENTED YET!!!
# cov_dir_name = getattr(settings, 'cov_dir', 'planck_covmats')
# covdir = os.path.join(batch.basePath, cov_dir_name)
# covmat = os.path.join(covdir, jobItem.name + '.covmat')
# if not os.path.exists(covmat):
# covNameMappings = getattr(settings, 'covNameMappings', None)
# mapped_name_norm = jobItem.makeNormedName(covNameMappings)[0]
# covmat_normed = os.path.join(covdir, mapped_name_norm + '.covmat')
# covmat = covmat_normed
# if not os.path.exists(covmat) and hasattr(jobItem.data_set,
# 'covmat'): covmat = batch.basePath + jobItem.data_set.covmat
# if not os.path.exists(covmat) and hasattr(settings, 'covmat'): covmat = batch.basePath + settings.covmat
# else:
# covNameMappings = None
# if os.path.exists(covmat):
# ini.params['propose_matrix'] = covmat
# if getattr(settings, 'newCovmats', True): ini.params['MPI_Max_R_ProposeUpdate'] = 20
# else:
# hasCov = False
# ini.params['MPI_Max_R_ProposeUpdate'] = 20
# covmat_try = []
# if 'covRenamer' in dir(settings):
# covmat_try += settings.covRenamer(jobItem.name)
# covmat_try += settings.covRenamer(mapped_name_norm)
# if hasattr(settings, 'covrenames'):
# for aname in [jobItem.name, mapped_name_norm]:
# covmat_try += [aname.replace(old, new, 1) for old, new in settings.covrenames if old in aname]
# for new1, old1 in settings.covrenames:
# if old1 in aname:
# name = aname.replace(old1, new1, 1)
# covmat_try += [name.replace(old, new, 1) for old, new in settings.covrenames if old in name]
# if 'covWithoutNameOrder' in dir(settings):
# if covNameMappings:
# removes = copy.deepcopy(covNameMappings)
# else:
# removes = dict()
# for name in settings.covWithoutNameOrder:
# if name in jobItem.data_set.names:
# removes[name] = ''
# covmat_try += [jobItem.makeNormedName(removes)[0]]
# covdir2 = os.path.join(batch.basePath, getattr(settings, 'cov_dir_fallback', cov_dir_name))
# for name in covmat_try:
# covmat = os.path.join(batch.basePath, covdir2, name + '.covmat')
# if os.path.exists(covmat):
# ini.params['propose_matrix'] = covmat
# print('covmat ' + jobItem.name + ' -> ' + name)
# hasCov = True
# break
# if not hasCov: print('WARNING: no matching specific covmat for ' + jobItem.name)
## NOT IMPLEMENTED: start at best fit
## ini.params['start_at_bestfit'] = start_at_bestfit
try:
dataset_info = datasets_definitions[jobItem.data_set.tag]
except KeyError:
raise ValueError("Data set '%s' must be defined." %
jobItem.data_set.tag)
combined_info = merge_info(base_info, model_info, dataset_info)
combined_info[_output_prefix] = jobItem.chainRoot
# ???
# for deffile in settings.defaults:
# ini.defaults.append(batch.commonPath + deffile)
# if hasattr(settings, 'override_defaults'):
# ini.defaults = [batch.commonPath + deffile for deffile in settings.override_defaults] + ini.defaults
# requisites
modules_used = get_modules(modules_used, combined_info)
if install_reqs_at:
combined_info[_path_install] = os.path.abspath(install_reqs_at)
# Write the info for this job
yaml_dump_file(combined_info, jobItem.iniFile())
# if not start_at_bestfit:
# setMinimize(jobItem, ini)
# variant = '_minimize'
# ini.saveFile(jobItem.iniFile(variant))
# # add ini files for importance sampling runs
# for imp in jobItem.importanceJobs():
# if getattr(imp, 'importanceFilter', None): continue
# if batch.hasName(imp.name.replace('_post', '')):
# raise Exception('importance sampling something you already have?')
# for minimize in (False, True):
# if minimize and not getattr(imp, 'want_minimize', True): continue
# ini = IniFile()
# updateIniParams(ini, imp.importanceSettings, batch.commonPath)
# if cosmomcAction == 0 and not minimize:
# for deffile in settings.importanceDefaults:
# ini.defaults.append(batch.commonPath + deffile)
# ini.params['redo_outroot'] = imp.chainRoot
# ini.params['action'] = 1
# else:
# ini.params['file_root'] = imp.chainRoot
# if minimize:
# setMinimize(jobItem, ini)
# variant = '_minimize'
# else:
# variant = ''
# ini.defaults.append(jobItem.iniFile())
# ini.saveFile(imp.iniFile(variant))
# if cosmomcAction != 0: break
# Installing requisites
print("Installing required code and data for the grid.")
if install_reqs_at:
install_reqs(modules_used,
path=install_reqs_at,
force=install_reqs_force)
if not interactive:
return batch
print('Done... to run do: cobaya-grid-run %s' % batchPath)
def makeGrid(batchPath,
settingName=None,
settings=None,
read_only=False,
interactive=False,
install_reqs_at=None,
install_reqs_force=None):
print("Generating grid...")
batchPath = os.path.abspath(batchPath) + os.sep
if not settings:
if not settingName:
raise NotImplementedError(
"Re-using previous batch is work in progress...")
# if not pathIsGrid(batchPath):
# raise Exception('Need to give name of setting file if batchPath/config '
# 'does not exist')
# read_only = True
# sys.path.insert(0, batchPath + 'config')
# sys.modules['batchJob'] = batchjob # old name
# settings = __import__(IniFile(batchPath + 'config/config.ini').params['setting_file'].replace('.py', ''))
elif os.path.splitext(settingName)[-1].lower() in _yaml_extensions:
settings = yaml_load_file(settingName)
else:
raise NotImplementedError(
"Using a python script is work in progress...")
# In this case, info-as-dict would be passed
# settings = __import__(settingName, fromlist=['dummy'])
batch = batchjob.batchJob(batchPath, settings.get("yaml_dir", None))
# batch.skip = settings.get("skip", False)
batch.makeItems(settings, messages=not read_only)
if read_only:
for jobItem in [b for b in batch.jobItems]:
if not jobItem.chainExists():
batch.jobItems.remove(jobItem)
batch.save()
print('OK, configured grid with %u existing chains' %
(len(batch.jobItems)))
return batch
else:
batch.makeDirectories(setting_file=None)
batch.save()
infos = {}
modules_used = {}
# Default info
defaults = copy.deepcopy(settings)
grid_definition = defaults.pop("grid")
models_definitions = grid_definition["models"]
datasets_definitions = grid_definition["datasets"]
for jobItem in batch.items(wantSubItems=False):
# Model info
jobItem.makeChainPath()
try:
model_info = copy.deepcopy(models_definitions[jobItem.param_set]
or {})
except KeyError:
raise ValueError("Model '%s' must be defined." % jobItem.param_set)
model_info = merge_info(defaults, model_info)
# Dataset info
try:
dataset_info = copy.deepcopy(
datasets_definitions[jobItem.data_set.tag])
except KeyError:
raise ValueError("Data set '%s' must be defined." %
jobItem.data_set.tag)
# Combined info
combined_info = merge_info(defaults, model_info, dataset_info)
if "preset" in combined_info:
preset = combined_info.pop("preset")
combined_info = merge_info(create_input(**preset), combined_info)
combined_info[_output_prefix] = jobItem.chainRoot
# Requisites
modules_used = get_modules(modules_used, combined_info)
if install_reqs_at:
combined_info[_path_install] = os.path.abspath(install_reqs_at)
# Save the info (we will write it after installation:
# we need to install to add auto covmats
if jobItem.param_set not in infos:
infos[jobItem.param_set] = {}
infos[jobItem.param_set][jobItem.data_set.tag] = combined_info
# Installing requisites
if install_reqs_at:
print("Installing required code and data for the grid.")
from cobaya.log import logger_setup
logger_setup()
install_reqs(modules_used,
path=install_reqs_at,
force=install_reqs_force)
print("Adding covmats (if necessary) and writing input files")
for jobItem in batch.items(wantSubItems=False):
info = infos[jobItem.param_set][jobItem.data_set.tag]
# Covariance matrices
# We try to find them now, instead of at run time, to check if correctly selected
try:
sampler = list(info[_sampler])[0]
except KeyError:
raise ValueError("No sampler has been chosen")
if sampler == "mcmc" and info[_sampler][sampler].get("covmat", "auto"):
modules_path = install_reqs_at or info.get(_path_install, None)
if not modules_path:
raise ValueError(
"Cannot assign automatic covariance matrices because no "
"modules path has been defined.")
# Need full info for covmats: includes renames
full_info = get_full_info(info)
# Ideally, we use slow+sampled parameters to look for the covariance matrix
# but since for that we'd need to initialise a model, we approximate that set
# as theory+sampled
from itertools import chain
like_params = set(
chain(*[
list(like[_params])
for like in full_info[_likelihood].values()
]))
params_info = {
p: v
for p, v in full_info[_params].items()
if is_sampled_param(v) and p not in like_params
}
best_covmat = get_best_covmat(os.path.abspath(modules_path),
params_info, full_info[_likelihood])
info[_sampler][sampler]["covmat"] = os.path.join(
best_covmat["folder"], best_covmat["name"])
# Write the info for this job
try:
yaml_dump_file(jobItem.iniFile(), info, error_if_exists=True)
except IOError:
raise IOError(
"Can't write chain input file. Maybe the chain configuration "
"files already exists?")
# Non-translated old code
# if not start_at_bestfit:
# setMinimize(jobItem, ini)
# variant = '_minimize'
# ini.saveFile(jobItem.iniFile(variant))
## NOT IMPLEMENTED: start at best fit
## ini.params['start_at_bestfit'] = start_at_bestfit
# ---
# for deffile in settings.defaults:
# ini.defaults.append(batch.commonPath + deffile)
# if hasattr(settings, 'override_defaults'):
# ini.defaults = [batch.commonPath + deffile for deffile in settings.override_defaults] + ini.defaults
# ---
# # add ini files for importance sampling runs
# for imp in jobItem.importanceJobs():
# if getattr(imp, 'importanceFilter', None): continue
# if batch.hasName(imp.name.replace('_post', '')):
# raise Exception('importance sampling something you already have?')
# for minimize in (False, True):
# if minimize and not getattr(imp, 'want_minimize', True): continue
# ini = IniFile()
# updateIniParams(ini, imp.importanceSettings, batch.commonPath)
# if cosmomcAction == 0 and not minimize:
# for deffile in settings.importanceDefaults:
# ini.defaults.append(batch.commonPath + deffile)
# ini.params['redo_outroot'] = imp.chainRoot
# ini.params['action'] = 1
# else:
# ini.params['file_root'] = imp.chainRoot
# if minimize:
# setMinimize(jobItem, ini)
# variant = '_minimize'
# else:
# variant = ''
# ini.defaults.append(jobItem.iniFile())
# ini.saveFile(imp.iniFile(variant))
# if cosmomcAction != 0: break
if not interactive:
return batch
print('Done... to run do: cobaya-grid-run %s' % batchPath)
def install(*infos, **kwargs):
path = kwargs.get("path", ".")
abspath = os.path.abspath(path)
kwargs_install = {
"force": kwargs.get("force", False),
"no_progress_bars": kwargs.get("no_progress_bars")
}
for what in (_code, _data):
kwargs_install[what] = kwargs.get(what, True)
spath = os.path.join(abspath, what)
if kwargs_install[what] and not os.path.exists(spath):
try:
os.makedirs(spath)
except OSError:
log.error(
"Could not create the desired installation folder '%s'",
spath)
raise HandledException
failed_modules = []
for kind, modules in get_modules(*infos).items():
for module in modules:
print(make_header(kind, module))
module_folder = get_folder(module, kind, sep=".", absolute=False)
try:
imported_module = import_module(module_folder, package=package)
except ImportError:
if kind == _likelihood:
log.warn(
"Module '%s' not recognised. Assuming it's a custom "
"likelihood. Nothing to do.\n", module)
else:
log.error("Module '%s' not recognised.\n" % module)
failed_modules += ["%s:%s" % (kind, module)]
continue
is_installed = getattr(imported_module, "is_installed", None)
if is_installed is None:
log.info("Built-in module: nothing to do.\n")
continue
if is_installed(path=abspath, **kwargs_install):
log.info("External module already installed.\n")
if kwargs_install["force"]:
log.info("Forcing re-installation, as requested.")
else:
log.info("Doing nothing.\n")
continue
try:
success = imported_module.install(path=abspath,
**kwargs_install)
except:
traceback.print_exception(*sys.exc_info(), file=sys.stdout)
log.error(
"An unknown error occurred. Delete the modules folder and try "
"again. Notify the developers if this error persists.")
success = False
if success:
log.info("Successfully installed!\n")
else:
log.error(
"Installation failed! Look at the error messages above. "
"Solve them and try again, or, if you are unable to solve, "
"install this module manually.")
failed_modules += ["%s:%s" % (kind, module)]
continue
# test installation
if not is_installed(path=abspath, **kwargs_install):
log.error(
"Installation apparently worked, "
"but the subsequent installation test failed! "
"Look at the error messages above. "
"Solve them and try again, or, if you are unable to solve, "
"install this module manually.")
failed_modules += ["%s:%s" % (kind, module)]
if failed_modules:
log.error(
"The instalation (or installation test) of some module(s) has failed: "
"%r. Check output above.\n", failed_modules)
raise HandledException
