Merge pull request #783 from ratt-ru/apptainer

apptainer support init commit

Jenkinsfile.sh

@@ -34,7 +34,11 @@ cp -r $TEST_DATA_DIR/beams $TEST_OUTPUT_DIR/input/beams
 
 # Load newer version of singularity
 source /etc/profile.d/modules.sh
-module load singularity/3.8.4
+
+# TODO(Ben) Singularity seems to be broken; testing with apptainer
+#module load singularity/3.8.4
+
+module load apptainer/1.2.0-rc.1
 
 # Check version
 docker -v

setup.py

@@ -6,7 +6,7 @@
 import glob
 
 PACKAGE_NAME = "stimela"
-__version__ = "1.7.8"
+__version__ = "1.7.9"
 build_root = os.path.dirname(__file__)
 
 

stimela/__init__.py

@@ -7,16 +7,20 @@
 from logging import StreamHandler
 import re
 from pathlib import Path
+import getpass
+import time
 
 try:
     __version__ = pkg_resources.require("stimela")[0].version
 except pkg_resources.DistributionNotFound:
     __version__ = "dev"
 
 # Get to know user
-USER = os.environ["USER"]
-UID = os.getuid()
-GID = os.getgid()
+try:
+    USER = getpass.getuser()
+except:
+    # The point is to avoid containers with the same name when using there multiple users using docker
+    USER = hex(id(time.ctime()))
 CAB_USERNAME = re.sub('[^0-9a-zA-Z]+', '_', USER).lower() 
 
 root = os.path.dirname(__file__)

stimela/cargo/cab/__init__.py

@@ -22,7 +22,6 @@
         "mount": "/stimela_mount",
         }
 
-USER_HOME = os.environ["HOME"]
 
 for item in list(__vol.keys()):
     val = __vol[item]

stimela/cargo/cab/casa_listobs/parameters.json

@@ -133,4 +133,4 @@
       "name": "cachesize"
     }
   ]
-}
+}

stimela/main.py

@@ -11,9 +11,6 @@
 
 BASE = stimela.BASE
 CAB = stimela.CAB
-USER = stimela.USER
-UID = stimela.UID
-GID = stimela.GID
 GLOBALS = stimela.GLOBALS
 CAB_USERNAME = stimela.CAB_USERNAME
 
@@ -230,6 +227,9 @@ def pull(argv):
     add("-cb", "--cab-base", nargs="+",
         help="Pull base image for specified cab")
 
+    add("-at", "--all-tags", action="store_true",
+        help="Pull all tags for this image")
+
     add("-pf", "--pull-folder",
         help="Images will be placed in this folder. Else, if the environmnental variable 'STIMELA_PULLFOLDER' is set, then images will be placed there. "
         "Else, images will be placed in the current directory")
@@ -294,8 +294,12 @@ def pull(argv):
             cabdir = "{:s}/{:s}".format(stimela.CAB_PATH, cab_)
             _cab = info(cabdir, display=False)
             tags = _cab.tag
-            if not isinstance(tags, list):
+            if isinstance(tags, list):
+                if not args.all_tags:
+                    tags = [tags[-1]]
+            else:
                 tags = [tags]
+
             for tag in tags:
                 base.append(f"{_cab.base}:{tag}")
                 repository_.append(param["hub"] if "hub" in param.keys() else args.repository)

stimela/recipe.py

@@ -338,6 +338,7 @@ def setup_job(self, image, config,
             cont.execdir = self.workdir
         else:
             cont.RUNSCRIPT = f"/{self.jtype}_run"
+            cont.add_environ('HOME', cont.IODEST["output"])
 
         runscript = shutil.which("stimela_runscript")
         if runscript:
@@ -349,7 +350,6 @@ def setup_job(self, image, config,
             raise OSError
 
         cont.add_environ('CONFIG', f'{cab.MOUNT}/configfile')
-        cont.add_environ('HOME', cont.IODEST["output"])
         cont.add_environ('STIMELA_MOUNT', cab.MOUNT)
 
         if msdir:

stimela/singularity.py

@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
 import subprocess
 import os
 import sys
@@ -12,16 +11,20 @@
 import hashlib
 from shutil import which
 
-binary = which("singularity")
-if binary:
-    __version_string = subprocess.check_output([binary, "--version"]).decode("utf8")
-    version = __version_string.strip().split()[-1]
-    if version < "3.0.0":
-        suffix = ".img"
-    else:
-        suffix = ".sif"
-else:
-    version = None
+
+version = None
+
+for item in ["apptainer", "singularity"]:
+    BINARY = which(item)
+    BINARY_NAME = item
+    if BINARY:
+        __version_string = subprocess.check_output([BINARY, "--version"]).decode("utf8")
+        version = __version_string.strip().split()[-1]
+        if BINARY_NAME == "singularity" and version < "3.0.0":
+            suffix = ".img"
+        else:
+            suffix = ".sif"
+        break
 
 class SingularityError(Exception):
     pass
@@ -41,7 +44,7 @@ def pull(image, name, docker=True, directory=".", force=False):
     if os.path.exists(image_path) and not force:
         stimela.logger().info(f"Singularity image already exists at '{image_path}'. To replace it, please re-run with the 'force' option")
     else:
-        utils.xrun(f"cd {directory} && singularity", ["pull", 
+        utils.xrun(f"cd {directory} && {BINARY}", ["pull", 
         	"--force" if force else "", "--name", 
          	name, fp])
 
@@ -55,7 +58,8 @@ def __init__(self, image, name,
                  runscript="/singularity",
                  environs=None,
                  workdir=None,
-                 execdir="."):
+                 execdir=".",
+                ):
         """
         Python wrapper to singularity tools for managing containers.
         """
@@ -95,7 +99,7 @@ def add_environ(self, key, value):
         self.logger.debug("Adding environ varaible [{0}={1}] "\
                     "in container {2}".format(key, value, self.name))
         self.environs.append("=".join([key, value]))
-        key_ = f"SINGULARITYENV_{key}"
+        key_ = f"{BINARY_NAME.upper()}ENV_{key}"
 
         self.logger.debug(f"Setting singularity environmental variable {key_}={value} on host")
         self._env[key_] = value
@@ -118,9 +122,10 @@ def run(self, *args, output_wrangler=None):
             raise SystemExit from None
 
         self.status = "running"
+        extras = "--userns" if BINARY_NAME == "singularity" else "--writable-tmpfs"
         self._print("Starting container [{0:s}]. Timeout set to {1:d}. The container ID is printed below.".format(
             self.name, self.time_out))
-        utils.xrun(f"cd {self.execdir} && singularity run --userns --workdir {self.execdir} --containall",
+        utils.xrun(f"{BINARY} run --workdir {self.execdir} --containall {extras}",
 		    list(args) + [volumes, self.image, self.RUNSCRIPT],
                     log=self.logger, timeout=self.time_out, output_wrangler=output_wrangler,
                     env=self._env, logfile=self.logfile)

stimela/tests/unit_tests/test-containertech.py

@@ -29,7 +29,12 @@ def setUpClass(cls):
         global SINGULARITY, PODMAN
         SINGULARITY = False
         PODMAN = False
-        SINGULARITY = singularity.version and singularity.version >= "2.6.0"
+        if singularity.version:
+            if singularity.BINARY_NAME == "singularity":
+                SINGULARITY = singularity.version >= "2.6.0"
+            else:
+                SINGULARITY = True
+
 
     @classmethod
     def tearDownClass(cls):
@@ -55,40 +60,40 @@ def setUp(self):
         if not os.path.isdir(INPUT):
             os.mkdir(INPUT)
 
-#    def test_singularity(self):
-#        global MSDIR
-#        global INPUT
-#        global OUTPUT
-#        global SINGULARITY
-#        
-#        if SINGULARITY is False:
-#            return
-#
-#        stimela.register_globals()
-#        rrr = stimela.Recipe("singularitypaths",
-#                             ms_dir=MSDIR,
-#                             JOB_TYPE="singularity",
-#                             cabpath="cab/",
-#                             singularity_image_dir=os.environ["STIMELA_PULLFOLDER"],
-#                             log_dir="logs")
-#        rrr.add("cab/custom", "test1", {
-#            "bla1": "a", # only accepts a, b or c
-#            "bla5": ["testinput2.txt:input",
-#                     "testinput3.txt:msfile",
-#                     spf("{}hello\{reim\}.fits,{}to.fits,{}world.fits", "input", "msfile", "output")],
-#        }, input=INPUT, output=OUTPUT)
-#        rrr.run() #validate and run
-#
-#        assert rrr.jobs[0].job._cab.parameters[4].value[0] == os.path.join(rrr.jobs[0].job.IODEST["input"], 
-#                    "testinput2.txt")
-#        assert rrr.jobs[0].job._cab.parameters[4].value[1] == os.path.join(rrr.jobs[0].job.IODEST["msfile"],
-#                    "testinput3.txt")
-#        assert rrr.jobs[0].job._cab.parameters[4].value[2] == \
-#                "{}/hello{{reim}}.fits,{}/to.fits,{}/world.fits".format(
-#                    rrr.jobs[0].job.IODEST["input"],
-#                    rrr.jobs[0].job.IODEST["msfile"],
-#                    rrr.jobs[0].job.IODEST["output"]
-#                )
+    def test_singularity(self):
+        global MSDIR
+        global INPUT
+        global OUTPUT
+        global SINGULARITY
+
+        if SINGULARITY is False:
+            return
+
+        stimela.register_globals()
+        rrr = stimela.Recipe("singularitypaths",
+                             ms_dir=MSDIR,
+                             JOB_TYPE="singularity",
+                             cabpath="cab/",
+                             singularity_image_dir=os.environ["STIMELA_PULLFOLDER"],
+                             log_dir="logs")
+        rrr.add("cab/custom", "test1", {
+            "bla1": "a", # only accepts a, b or c
+            "bla5": ["testinput2.txt:input",
+                     "testinput3.txt:msfile",
+                     spf("{}hello\{reim\}.fits,{}to.fits,{}world.fits", "input", "msfile", "output")],
+        }, input=INPUT, output=OUTPUT)
+        rrr.run() #validate and run
+
+        assert rrr.jobs[0].job._cab.parameters[4].value[0] == os.path.join(rrr.jobs[0].job.IODEST["input"], 
+                    "testinput2.txt")
+        assert rrr.jobs[0].job._cab.parameters[4].value[1] == os.path.join(rrr.jobs[0].job.IODEST["msfile"],
+                    "testinput3.txt")
+        assert rrr.jobs[0].job._cab.parameters[4].value[2] == \
+                "{}/hello{{reim}}.fits,{}/to.fits,{}/world.fits".format(
+                    rrr.jobs[0].job.IODEST["input"],
+                    rrr.jobs[0].job.IODEST["msfile"],
+                    rrr.jobs[0].job.IODEST["output"]
+                )
 
     def test_podman(self):
         global MSDIR