bugfix run tasks spawned by Cluster.run() now log to separate log fil…

…es, whereas before their logs were sent to the ether

removed check function from singularity because the checks were not working from inside the container
workstation now always checks mpiexec, even if nproc == 1

seisflows/system/cluster.py

@@ -159,7 +159,7 @@ def run(self, funcs, single=False, **kwargs):
                                                      path=self.path.scratch,
                                                      **kwargs)
         logger.info(f"running functions {[_.__name__ for _ in funcs]} on "
-                    f"system {self.ntask} times")
+                    f"system {ntasks} times")
 
         # Create the run call which will simply call an external Python script
         # e.g., run --funcs func.p --kwargs kwargs.p --environment ...
@@ -194,7 +194,7 @@ def _run_task(self, run_call, task_id):
         :param task_id: given task id, used for log messages and to format
             the run call
         """
-        logger.debug(f"running task id {task_id} ({task_id + 1}/{self.ntask})")
+        logger.debug(f"running task id {task_id}")
         try:
             f = open(self._get_log_file(task_id), "w")
             subprocess.run(run_call.format(task_id=task_id), shell=True,

seisflows/system/runscripts/run_funcs.py

@@ -16,6 +16,9 @@
 import dill
 import os
 
+from seisflows import logger
+from seisflows.tools.config import config_logger
+
 
 def parse_args():
     """
@@ -94,8 +97,19 @@ def export(myenv):
     else:
         kwargs = {}
 
+    # Hold onto the main handler for after the task is finished
+    handlers = logger.handlers
+
+    # Redirect the logger to point at stdout, which the Cluster system (or sub
+    # class of it) will redirect to a task specific log file. Currently no
+    # way of accessing user defiend 'verbose' or 'log_level' parameters
+    config_logger(filename=None, stream_handler=True)
+
     # Evaluate the function with given keyword arguments
     for func in funcs:
         func(**kwargs)
 
+    # Replace original log handler now that the tasks have finished
+    logger.handlers = handlers
+
 

seisflows/system/singularity.py

@@ -81,27 +81,27 @@ def __init__(self, title=None, mpiexec="", ntask_max=None,
         self.path["container"] = path_container
         self.path["run"] = os.path.join(self.path.scratch, "run")
 
-    def check(self):
-        """
-        Checks path and parameter validity
-        """
-        super().check()
-
-        assert(self.path.container and os.path.exists(self.path.container)), (
-            f"`Singularity` System class requires a Docker Image specified in "
-            f" path `path_container`"
-        )
-
-        # # Check that 'singularity' exists on system
-        try:
-            subprocess.run(f"which {self.singularity_exec}", check=True,
-                           shell=True, stdout=subprocess.DEVNULL)
-        except subprocess.CalledProcessError:
-            logger.critical(f"Singularity exectuable {self.singularity_exec} "
-                            f"not found on sytem (using `which`), but is "
-                            f"required to run a `Singularity` System. Please "
-                            f"check your parameter: `singularity_exec`.")
-            sys.exit(-1)
+    # def check(self):
+    #     """
+    #     Checks path and parameter validity
+    #     """
+    #     super().check()
+    #
+    #     assert(self.path.container and os.path.exists(self.path.container)), (
+    #         f"`Singularity` System class requires a Docker Image specified in "
+    #         f" path `path_container`"
+    #     )
+    #
+    #     # # Check that 'singularity' exists on system
+    #     try:
+    #         subprocess.run(f"which {self.singularity_exec}", check=True,
+    #                        shell=True, stdout=subprocess.DEVNULL)
+    #     except subprocess.CalledProcessError:
+    #         logger.critical(f"Singularity exectuable {self.singularity_exec} "
+    #                         f"not found on sytem (using `which`), but is "
+    #                         f"required to run a `Singularity` System. Please "
+    #                         f"check your parameter: `singularity_exec`.")
+    #         sys.exit(-1)
 
     def setup(self):
         """

seisflows/system/workstation.py

@@ -107,6 +107,7 @@ def check(self):
                 f"Multi-core workflows (`nproc`>1) require an MPI executable " 
                 f"`mpiexec`"
             )
+        if self.mpiexec is not None:
             # Make user that `mpiexec` exists on system
             try:
                 stdout = subprocess.run(f"which {self.mpiexec}", shell=True,