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Added singularity in a few places. Runs but permanentfails #487

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31e6eae
updated DockerCommandLineJob.run to invoke Singularity instead of Doc…
johnfonner Jul 20, 2017
b60fe55
Docker now broken, singu fails with permafail
Jul 21, 2017
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59 changes: 32 additions & 27 deletions cwltool/docker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,39 +18,44 @@
def get_image(dockerRequirement, pull_image, dry_run=False):
# type: (Dict[Text, Text], bool, bool) -> bool
found = False

if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]

for ln in subprocess.check_output(
["docker", "images", "--no-trunc", "--all"]).decode('utf-8').splitlines():
try:
m = re.match(r"^([^ ]+)\s+([^ ]+)\s+([^ ]+)", ln)
sp = dockerRequirement["dockerImageId"].split(":")
if len(sp) == 1:
sp.append("latest")
elif len(sp) == 2:
# if sp[1] doesn't match valid tag names, it is a part of repository
if not re.match(r'[\w][\w.-]{0,127}', sp[1]):
sp[0] = sp[0] + ":" + sp[1]
sp[1] = "latest"
elif len(sp) == 3:
if re.match(r'[\w][\w.-]{0,127}', sp[2]):
sp[0] = sp[0] + ":" + sp[1]
sp[1] = sp[2]
del sp[2]

# check for repository:tag match or image id match
if ((sp[0] == m.group(1) and sp[1] == m.group(2)) or dockerRequirement["dockerImageId"] == m.group(3)):
found = True
break
except ValueError:
pass
#DEBUG: CHECKS IMAGE REGISTRY FOR IDS. SINGULARITY EQ WOULD BE TO CHECK THE FOLDER FOR IMG.
#'node:slim'
imageString = dockerRequirement["dockerPull"].split(":")
imageHit = "{}-{}.img".format(imageString[0], imageString[1])
if imageHit:
found = True
# for ln in subprocess.check_output(
# ["docker", "images", "--no-trunc", "--all"]).decode('utf-8').splitlines():
# try:
# m = re.match(r"^([^ ]+)\s+([^ ]+)\s+([^ ]+)", ln)
# sp = dockerRequirement["dockerImageId"].split(":")
# if len(sp) == 1:
# sp.append("latest")
# elif len(sp) == 2:
# # if sp[1] doesn't match valid tag names, it is a part of repository
# if not re.match(r'[\w][\w.-]{0,127}', sp[1]):
# sp[0] = sp[0] + ":" + sp[1]
# sp[1] = "latest"
# elif len(sp) == 3:
# if re.match(r'[\w][\w.-]{0,127}', sp[2]):
# sp[0] = sp[0] + ":" + sp[1]
# sp[1] = sp[2]
# del sp[2]
#
# # check for repository:tag match or image id match
# if ((sp[0] == m.group(1) and sp[1] == m.group(2)) or dockerRequirement["dockerImageId"] == m.group(3)):
# found = True
# break
# except ValueError:
# pass

if not found and pull_image:
cmd = [] # type: List[Text]
if "dockerPull" in dockerRequirement:
cmd = ["docker", "pull", str(dockerRequirement["dockerPull"])]
cmd = ["singularity", "pull", "docker://" + str(dockerRequirement["dockerPull"])]
_logger.info(Text(cmd))
if not dry_run:
subprocess.check_call(cmd, stdout=sys.stderr)
Expand Down Expand Up @@ -103,7 +108,7 @@ def get_from_requirements(r, req, pull_image, dry_run=False):
if r:
errmsg = None
try:
subprocess.check_output(["docker", "version"])
subprocess.check_output(["singularity", "--version"])
except subprocess.CalledProcessError as e:
errmsg = "Cannot communicate with docker daemon: " + Text(e)
except OSError as e:
Expand Down
44 changes: 24 additions & 20 deletions cwltool/job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -316,25 +316,25 @@ def add_volumes(self, pathmapper, runtime, stage_output):
containertgt = vol.target
if vol.type in ("File", "Directory"):
if not vol.resolved.startswith("_:"):
runtime.append(u"--volume=%s:%s:ro" % (docker_windows_path_adjust(vol.resolved), docker_windows_path_adjust(containertgt)))
runtime.append(u"--bind=%s:%s:ro" % (docker_windows_path_adjust(vol.resolved), docker_windows_path_adjust(containertgt)))
elif vol.type == "WritableFile":
if self.inplace_update:
runtime.append(u"--volume=%s:%s:rw" % (docker_windows_path_adjust(vol.resolved), docker_windows_path_adjust(containertgt)))
runtime.append(u"--bind=%s:%s:rw" % (docker_windows_path_adjust(vol.resolved), docker_windows_path_adjust(containertgt)))
else:
shutil.copy(vol.resolved, vol.target)
elif vol.type == "WritableDirectory":
if vol.resolved.startswith("_:"):
os.makedirs(vol.target, 0o0755)
else:
if self.inplace_update:
runtime.append(u"--volume=%s:%s:rw" % (docker_windows_path_adjust(vol.resolved), docker_windows_path_adjust(containertgt)))
runtime.append(u"--bind=%s:%s:rw" % (docker_windows_path_adjust(vol.resolved), docker_windows_path_adjust(containertgt)))
else:
shutil.copytree(vol.resolved, vol.target)
elif vol.type == "CreateFile":
createtmp = os.path.join(host_outdir, os.path.basename(vol.target))
with open(createtmp, "wb") as f:
f.write(vol.resolved.encode("utf-8"))
runtime.append(u"--volume=%s:%s:ro" % (docker_windows_path_adjust(createtmp), docker_windows_path_adjust(vol.target)))
runtime.append(u"--bind=%s:%s:ro" % (docker_windows_path_adjust(createtmp), docker_windows_path_adjust(vol.target)))


def run(self, pull_image=True, rm_container=True,
Expand All @@ -348,6 +348,7 @@ def run(self, pull_image=True, rm_container=True,
try:
env = cast(MutableMapping[Text, Text], os.environ)
if docker_req and kwargs.get("use_container") is not False:
print "Req docker"
img_id = docker.get_from_requirements(docker_req, True, pull_image)
if img_id is None:
find_default_container = self.builder.find_default_container
Expand All @@ -370,25 +371,28 @@ def run(self, pull_image=True, rm_container=True,

self._setup()

runtime = [u"docker", u"run", u"-i"]
runtime = [u"singularity", u"exec"]

runtime.append(u"--volume=%s:%s:rw" % (docker_windows_path_adjust(os.path.realpath(self.outdir)), self.builder.outdir))
runtime.append(u"--volume=%s:%s:rw" % (docker_windows_path_adjust(os.path.realpath(self.tmpdir)), "/tmp"))
runtime.append(u"--bind=%s:%s:rw" % (docker_windows_path_adjust(os.path.realpath(self.outdir)), self.builder.outdir))
runtime.append(u"--bind=%s:%s:rw" % (docker_windows_path_adjust(os.path.realpath(self.tmpdir)), "/tmp"))

self.add_volumes(self.pathmapper, runtime, False)
if self.generatemapper:
self.add_volumes(self.generatemapper, runtime, True)

runtime.append(u"--workdir=%s" % (docker_windows_path_adjust(self.builder.outdir)))
runtime.append(u"--read-only=true")
runtime.append(u"--pwd=%s" % (docker_windows_path_adjust(self.builder.outdir)))
# runtime.append(u"--read-only=true") # true by default for Singularity images

if kwargs.get("custom_net", None) is not None:
runtime.append(u"--net={0}".format(kwargs.get("custom_net")))
elif kwargs.get("disable_net", None):
runtime.append(u"--net=none")
# runtime.append(u"--net={0}".format(kwargs.get("custom_net")))
raise UnsupportedRequirement(
"Singularity implementation does not support networking")
# elif kwargs.get("disable_net", None):
# runtime.append(u"--net=none")

if self.stdout:
runtime.append("--log-driver=none")
# No equivalent flag in Singularity
# if self.stdout:
# runtime.append("--log-driver=none")

if onWindows(): # windows os dont have getuid or geteuid functions
euid = docker_vm_uid()
Expand All @@ -398,18 +402,18 @@ def run(self, pull_image=True, rm_container=True,
if kwargs.get("no_match_user", None) is False and euid is not None:
runtime.append(u"--user=%s" % (euid))

if rm_container:
runtime.append(u"--rm")

runtime.append(u"--env=TMPDIR=/tmp")
# No equivalent
# if rm_container:
# runtime.append(u"--rm")
runtime.insert(0, u"SINGULARITYENV_TMPDIR=/tmp")

# spec currently says "HOME must be set to the designated output
# directory." but spec might change to designated temp directory.
# runtime.append("--env=HOME=/tmp")
runtime.append(u"--env=HOME=%s" % self.builder.outdir)
runtime.insert(0, u"SINGULARITYENV_HOME=%s" % self.builder.outdir)

for t, v in self.environment.items():
runtime.append(u"--env=%s=%s" % (t, v))
runtime.insert(0, u"SINGULARITYENV_%s=%s" % (t, v))

runtime.append(img_id)

Expand Down