Merge decd2ae into 57fbf69

WDL/CLI.py

@@ -457,6 +457,11 @@ def runner(
     logger = logging.getLogger("miniwdl-run")
     install_coloredlogs(logger)
 
+    if os.geteuid() == 0:
+        logger.warning(
+            "running as root; non-root users should be able to `miniwdl run` as long as they're in the `docker` group"
+        )
+
     # load configuration & apply command-line overrides
     cfg_arg = None
     if cfg:

WDL/_util.py

@@ -10,6 +10,7 @@
 import time
 import copy
 import fcntl
+import subprocess
 from time import sleep
 from datetime import datetime
 from contextlib import contextmanager, AbstractContextManager
@@ -183,7 +184,7 @@ def write_values_json(
 
 
 @export
-def provision_run_dir(name: str, run_dir: Optional[str] = None) -> str:
+def provision_run_dir(name: str, run_dir: Optional[str], last_link: bool = False) -> str:
     here = (
         (run_dir in [".", "./"] or run_dir.endswith("/.") or run_dir.endswith("/./"))
         if run_dir
@@ -192,27 +193,41 @@ def provision_run_dir(name: str, run_dir: Optional[str] = None) -> str:
     run_dir = os.path.abspath(run_dir or os.getcwd())
 
     if here:
+        # user wants to use run_dir exactly
         os.makedirs(run_dir, exist_ok=True)
         return run_dir
 
+    # create timestamp-named directory
     now = datetime.today()
-    run_dir2 = os.path.join(run_dir, now.strftime("%Y%m%d_%H%M%S") + "_" + name)
+    new_dir = os.path.join(run_dir, now.strftime("%Y%m%d_%H%M%S") + "_" + name)
     try:
-        os.makedirs(run_dir2, exist_ok=False)
-        return run_dir2
+        os.makedirs(new_dir, exist_ok=False)
     except FileExistsError:
-        pass
+        new_dir = None
 
-    while True:
-        run_dir2 = os.path.join(
+    while not new_dir:
+        # it already exists; try adding milliseconds
+        new_dir = os.path.join(
             run_dir,
             now.strftime("%Y%m%d_%H%M%S_") + str(int(now.microsecond / 1000)).zfill(3) + "_" + name,
         )
         try:
-            os.makedirs(run_dir2, exist_ok=False)
-            return run_dir2
+            os.makedirs(new_dir, exist_ok=False)
         except FileExistsError:
+            new_dir = None
             sleep(1e-3)
+    assert new_dir
+
+    # update the _LAST link
+    if last_link:
+        last_link_name = os.path.join(run_dir, "_LAST")
+        if not os.path.lexists(last_link_name) or os.path.islink(last_link_name):
+            new_dir_basename = os.path.basename(new_dir)
+            tmp_link_name = last_link_name + "." + new_dir_basename
+            os.symlink(new_dir_basename, tmp_link_name)
+            os.rename(tmp_link_name, last_link_name)
+
+    return new_dir
 
 
 @export
@@ -700,8 +715,9 @@ def flock(  # pyre-fixme
                             openfile.fileno(), ns=(int(time.time() * 1e9), file_st.st_mtime_ns)
                         )
 
-                    # The filename link could have been replaced or removed in the instant between
-                    # our open() and flock() syscalls.
+                    # Even if all concurrent processes obey the advisory flocks, the filename link
+                    # could have been replaced or removed in the duration between our open() and
+                    # fcntl() syscalls.
                     # - if it was removed, the following os.stat will trigger FileNotFoundError,
                     #   which is reasonable to propagate.
                     # - if it was replaced, the subsequent condition won't hold, and we'll loop

WDL/runtime/config_templates/default.cfg

@@ -43,7 +43,6 @@ copy_input_files = false
 # arising from files with multiple hardlinks! See also [task_runtime] delete_work, below.
 output_hardlinks = false
 
-
 [task_runtime]
 # Effective maximum values of runtime.cpu and runtime.memory (bytes), which evaluated values are
 # rounded down to. 0 = detect host resources, -1 = do not apply a limit.

WDL/runtime/task.py

@@ -457,8 +457,6 @@ def _run(
                 # poll for container exit
                 while exit_code is None:
                     # spread out work over the GIL
-                    # TODO: adaptive interval before container starts running (poll less frequently
-                    # if it's already been waiting a long time)
                     time.sleep(random.uniform(1.0, 2.0))
                     if terminating():
                         raise Terminated() from None
@@ -678,7 +676,7 @@ def run_local_task(
     # provision run directory and log file
     run_id = run_id or task.name
     _run_id_stack = _run_id_stack or []
-    run_dir = provision_run_dir(task.name, run_dir)
+    run_dir = provision_run_dir(task.name, run_dir, last_link=not _run_id_stack)
 
     logger_prefix = (logger_prefix or ["wdl"]) + ["t:" + run_id]
     logger = logging.getLogger(".".join(logger_prefix))

WDL/runtime/workflow.py

@@ -629,7 +629,7 @@ def run_local_workflow(
     # provision run directory and log file
     run_id = run_id or workflow.name
     _run_id_stack = _run_id_stack or []
-    run_dir = provision_run_dir(workflow.name, run_dir)
+    run_dir = provision_run_dir(workflow.name, run_dir, last_link=not _run_id_stack)
 
     logger_prefix = logger_prefix or ["wdl"]
     logger_id = logger_prefix + ["w:" + run_id]

docs/runner_reference.md

@@ -28,7 +28,9 @@ The top-level run directory also contains:
 * `rerun` can be "sourced" to run the WDL (as found in the original location, possibly updated) using the same inputs
 * The top-level `workflow.log` file is "flocked" while `miniwdl run` is still in progress (`task.log` if running a task directly)
 
-The miniwdl source repository includes several [example scripts](https://github.com/chanzuckerberg/miniwdl/tree/master/examples) illustrating how this structure can inform production automation (e.g. retrieving error messages, uploading output files).
+When miniwdl creates a new timestamp-named subdirectory for a run, it also creates a symbolic link `_LAST` to it in the same parent directory. (For convenience referring to the most recent run; should not be relied upon if multiple runs can start concurrently.)
+
+The miniwdl source repository includes several [example scripts](https://github.com/chanzuckerberg/miniwdl/tree/master/examples) illustrating how the structures described here can inform production automation (e.g. retrieving error messages, uploading output files).
 
 ## Configuration
 

tests/runner.t

@@ -11,7 +11,7 @@ source tests/bash-tap/bash-tap-bootstrap
 export PYTHONPATH="$SOURCE_DIR:$PYTHONPATH"
 miniwdl="python3 -m WDL"
 
-plan tests 52
+plan tests 53
 
 $miniwdl run_self_test
 is "$?" "0" "run_self_test"
@@ -223,9 +223,9 @@ task second {
 }
 EOF
 
-$miniwdl run multitask.wdl --task second | tee stdout
+$miniwdl run multitask.wdl --task second
 is "$?" "0" "multitask"
-is "$(jq -r '.outputs["second.msg"]' stdout)" "two" "multitask stdout"
+is "$(jq -r '.["second.msg"]' _LAST/outputs.json)" "two" "multitask stdout & _LAST"
 
 cat << 'EOF' > mv_input_file.wdl
 version 1.0
@@ -244,6 +244,7 @@ EOF
 
 $miniwdl run --copy-input-files mv_input_file.wdl file=quick
 is "$?" "0" "copy input files"
+is "$(basename `jq -r '.["mv_input_file.xxx"]' _LAST/outputs.json`)" "xxx" "updated _LAST"
 
 cat << 'EOF' > uri_inputs.json
 {"my_workflow.files": ["https://google.com/robots.txt", "https://raw.githubusercontent.com/chanzuckerberg/miniwdl/master/tests/alyssa_ben.txt"]}