def __init__(self, easyconfigs):
self.container_base = build_option('container_base')
self.container_build_image = build_option('container_build_image')
self.container_path = container_path()
self.easyconfigs = easyconfigs
self.image_format = build_option('container_image_format')
self.img_name = build_option('container_image_name')
self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
self.mns = ActiveMNS()
self.tmpdir = build_option('container_tmpdir')
def __init__(self, easyconfigs):
self.container_base = build_option('container_base')
self.container_build_image = build_option('container_build_image')
self.container_path = container_path()
self.easyconfigs = easyconfigs
self.image_format = build_option('container_image_format')
self.img_name = build_option('container_image_name')
self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
self.mns = ActiveMNS()
self.tmpdir = build_option('container_tmpdir')
def build_singularity_image(def_path):
"""Build Singularity container image by calling out to 'singularity' (requires admin privileges!)."""
cont_path = container_path()
def_file = os.path.basename(def_path)
# use --imagename if specified, otherwise derive based on filename of recipe
img_name = build_option('container_image_name')
if img_name is None:
# definition file Singularity.<app>-<version, container name <app>-<version>.<img|simg>
img_name = def_file.split('.', 1)[1]
cmd_opts = ''
image_format = build_option('container_image_format')
# squashfs image format (default for Singularity)
if image_format in [None, CONT_IMAGE_FORMAT_SQUASHFS]:
img_path = os.path.join(cont_path, img_name + '.simg')
# ext3 image format, creating as writable container
elif image_format == CONT_IMAGE_FORMAT_EXT3:
img_path = os.path.join(cont_path, img_name + '.img')
cmd_opts = '--writable'
# sandbox image format, creates as a directory but acts like a container
elif image_format == CONT_IMAGE_FORMAT_SANDBOX:
img_path = os.path.join(cont_path, img_name)
cmd_opts = '--sandbox'
else:
raise EasyBuildError("Unknown container image format specified for Singularity: %s" % image_format)
if os.path.exists(img_path):
if build_option('force'):
print_msg("WARNING: overwriting existing container image at %s due to --force" % img_path)
remove_file(img_path)
else:
raise EasyBuildError("Container image already exists at %s, not overwriting it without --force", img_path)
# resolve full path to 'singularity' binary, since it may not be available via $PATH under sudo...
singularity = which('singularity')
cmd_env = ''
singularity_tmpdir = build_option('container_tmpdir')
if singularity_tmpdir:
cmd_env += 'SINGULARITY_TMPDIR=%s' % singularity_tmpdir
cmd = ' '.join(['sudo', cmd_env, singularity, 'build', cmd_opts, img_path, def_path])
print_msg("Running '%s', you may need to enter your 'sudo' password..." % cmd)
run_cmd(cmd, stream_output=True)
print_msg("Singularity image created at %s" % img_path, log=_log)
def generate_singularity_recipe(easyconfigs, container_base):
"""Main function to Singularity definition file and image."""
cont_path = container_path()
# make sure location to write container recipes & images exists
mkdir(cont_path, parents=True)
base_specs = parse_container_base(container_base)
# extracting application name,version, version suffix, toolchain name, toolchain version from
# easyconfig class
bootstrap_agent = base_specs['bootstrap_agent']
base_image, base_image_tag = None, None
# with localimage it only takes 2 arguments. --container-base localimage:/path/to/image
# checking if path to image is valid and verify image extension is '.img' or '.simg'
if base_specs['bootstrap_agent'] == LOCALIMAGE:
base_image = base_specs['arg1']
if os.path.exists(base_image):
# get the extension of container image
image_ext = os.path.splitext(base_image)[1]
if image_ext == '.img' or image_ext == '.simg':
_log.debug("Extension for base container image to use is OK: %s", image_ext)
else:
raise EasyBuildError("Invalid image extension '%s' must be .img or .simg", image_ext)
else:
raise EasyBuildError("Singularity base image at specified path does not exist: %s", base_image)
# otherwise, bootstrap agent is 'docker' or 'shub'
# format --container-base {docker|shub}:<image>:<tag>
else:
base_image = base_specs['arg1']
# image tag is optional
base_image_tag = base_specs.get('arg2', None)
bootstrap_from = base_image
if base_image_tag:
bootstrap_from += ':' + base_image_tag
# if there is osdependencies in easyconfig then add them to Singularity recipe
install_os_deps = ''
for ec in easyconfigs:
for osdep in ec['ec']['osdependencies']:
if isinstance(osdep, basestring):
install_os_deps += "yum install -y %s\n" % osdep
# tuple entry indicates multiple options
elif isinstance(osdep, tuple):
install_os_deps += "yum --skip-broken -y install %s\n" % ' '.join(osdep)
else:
raise EasyBuildError("Unknown format of OS dependency specification encountered: %s", osdep)
# module names to load in container environment
mod_names = [e['ec'].full_mod_name for e in easyconfigs]
# name of Singularity definition file
img_name = build_option('container_image_name')
if img_name:
def_file_label = os.path.splitext(img_name)[0]
else:
def_file_label = mod_names[0].replace('/', '-')
def_file = 'Singularity.%s' % def_file_label
# adding all the regions for writing the Singularity definition file
content = SINGULARITY_TEMPLATE % {
'bootstrap': bootstrap_agent,
'from': bootstrap_from,
'install_os_deps': install_os_deps,
'easyconfigs': ' '.join(os.path.basename(e['spec']) for e in easyconfigs),
'mod_names': ' '.join(mod_names),
}
def_path = os.path.join(cont_path, def_file)
if os.path.exists(def_path):
if build_option('force'):
print_msg("WARNING: overwriting existing container recipe at %s due to --force" % def_path)
else:
raise EasyBuildError("Container recipe at %s already exists, not overwriting it without --force", def_path)
write_file(def_path, content)
print_msg("Singularity definition file created at %s" % def_path, log=_log)
return def_path