Merge pull request #599 from ratt-ru/respect-the-environment

Respect the environment

examples/simulation_pipeline.py

@@ -25,7 +25,7 @@
                           log_dir=os.path.join(OUTPUT, "logs"),
                           )
 
-pipeline.JOB_TYPE = "singularity"
+pipeline.JOB_TYPE = "docker"
 
 # 1: Make empty MS
 pipeline.add("cab/simms",                   # Executor image to start container from

stimela/recipe.py

@@ -272,6 +272,10 @@ def setup_job(self, image, config,
 
         if self.jtype == "singularity":
             cont.RUNSCRIPT = f"/{self.jtype}"
+            if _cab.base.startswith("stimela/casa") or _cab.base.startswith("stimela/simms"):
+                cont.add_environ("LANGUAGE", "en_US.UTF-8")
+                cont.add_environ("LANG", "en_US.UTF-8")
+                cont.add_environ("LC_ALL", "en_US.UTF-8")
             cont.execdir = self.workdir
         else:
             cont.RUNSCRIPT = f"/{self.jtype}_run"

stimela/singularity.py

@@ -70,6 +70,8 @@ def __init__(self, image, name,
         self.time_out = time_out
         self.execdir = execdir
 
+        self._env = os.environ.copy()
+
         hashname = hashlib.md5(name.encode('utf-8')).hexdigest()[:3]
         self.name = hashname if version < "3.0.0" else name
 
@@ -94,7 +96,7 @@ def add_environ(self, key, value):
         key_ = f"SINGULARITYENV_{key}"
 
         self.logger.debug(f"Setting singularity environmental variable {key_}={value} on host")
-        os.environ[key_] = value
+        self._env[key_] = value
 
         return 0
 
@@ -119,7 +121,7 @@ def run(self, *args, output_wrangler=None):
         utils.xrun(f"cd {self.execdir} && singularity", ["run", "--workdir", self.execdir] \
                     + list(args) + [volumes, self.image, self.RUNSCRIPT],
                     log=self.logger, timeout=self.time_out, output_wrangler=output_wrangler,
-                    logfile=self.logfile)
+                    env=self._env, logfile=self.logfile)
 
         self.status = "exited"
 

stimela/utils/xrun_poll.py

@@ -98,7 +98,7 @@ def xrun_nolog(command, name=None):
 
     return 0
 
-def xrun(command, options, log=None, logfile=None, timeout=-1, kill_callback=None, output_wrangler=None):
+def xrun(command, options, log=None, logfile=None, env=None, timeout=-1, kill_callback=None, output_wrangler=None):
     command_name = command
 
     # this part could be inside the container
@@ -119,7 +119,7 @@ def xrun(command, options, log=None, logfile=None, timeout=-1, kill_callback=Non
     start_time = time.time()
 
     proc = subprocess.Popen([command], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
-                            bufsize=1, universal_newlines=True, shell=True)
+                            env=env, bufsize=1, universal_newlines=True, shell=True)
 
     poller = Poller(log=log)
     poller.register_process(proc)