fix: always wait for input files before starting jobs, also upon local execution and within group jobs. This should add further robustness against NFS latency issues.

snakemake/__init__.py

@@ -599,6 +599,7 @@ def snakemake(
             check_envvars=not lint,  # for linting, we do not need to check whether requested envvars exist
             all_temp=all_temp,
             local_groupid=local_groupid,
+            latency_wait=latency_wait,
         )
         success = True
 
@@ -771,7 +772,6 @@ def snakemake(
                     archive=archive,
                     delete_all_output=delete_all_output,
                     delete_temp_output=delete_temp_output,
-                    latency_wait=latency_wait,
                     wait_for_files=wait_for_files,
                     detailed_summary=detailed_summary,
                     nolock=not lock,

snakemake/executors/__init__.py

@@ -65,7 +65,6 @@ def __init__(
         quiet=False,
         printshellcmds=False,
         printthreads=True,
-        latency_wait=3,
         keepincomplete=False,
         keepmetadata=True,
     ):
@@ -75,7 +74,7 @@ def __init__(
         self.printreason = printreason
         self.printshellcmds = printshellcmds
         self.printthreads = printthreads
-        self.latency_wait = latency_wait
+        self.latency_wait = workflow.latency_wait
         self.keepincomplete = keepincomplete
         self.keepmetadata = keepmetadata
 
@@ -221,7 +220,6 @@ def __init__(
         printreason=False,
         quiet=False,
         printshellcmds=False,
-        latency_wait=3,
         assume_shared_fs=True,
         keepincomplete=False,
         keepmetadata=False,
@@ -232,7 +230,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             keepincomplete=keepincomplete,
             keepmetadata=keepmetadata,
         )
@@ -424,7 +421,6 @@ def __init__(
         quiet=False,
         printshellcmds=False,
         use_threads=False,
-        latency_wait=3,
         cores=1,
         keepincomplete=False,
         keepmetadata=True,
@@ -435,7 +431,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             keepincomplete=keepincomplete,
             keepmetadata=keepmetadata,
         )
@@ -659,7 +654,6 @@ def __init__(
         printreason=False,
         quiet=False,
         printshellcmds=False,
-        latency_wait=3,
         cluster_config=None,
         local_input=None,
         restart_times=None,
@@ -680,7 +674,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             assume_shared_fs=assume_shared_fs,
             keepincomplete=keepincomplete,
             keepmetadata=keepmetadata,
@@ -957,7 +950,6 @@ def __init__(
         printreason=False,
         quiet=False,
         printshellcmds=False,
-        latency_wait=3,
         restart_times=0,
         assume_shared_fs=True,
         max_status_checks_per_second=1,
@@ -989,7 +981,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             cluster_config=cluster_config,
             restart_times=restart_times,
             assume_shared_fs=assume_shared_fs,
@@ -1322,7 +1313,6 @@ def __init__(
         printreason=False,
         quiet=False,
         printshellcmds=False,
-        latency_wait=3,
         restart_times=0,
         assume_shared_fs=True,
         keepincomplete=False,
@@ -1336,7 +1326,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             cluster_config=cluster_config,
             restart_times=restart_times,
             assume_shared_fs=assume_shared_fs,
@@ -1432,7 +1421,6 @@ def __init__(
         printshellcmds=False,
         drmaa_args="",
         drmaa_log_dir=None,
-        latency_wait=3,
         cluster_config=None,
         restart_times=0,
         assume_shared_fs=True,
@@ -1448,7 +1436,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             cluster_config=cluster_config,
             restart_times=restart_times,
             assume_shared_fs=assume_shared_fs,
@@ -1635,7 +1622,6 @@ def __init__(
         printreason=False,
         quiet=False,
         printshellcmds=False,
-        latency_wait=3,
         cluster_config=None,
         local_input=None,
         restart_times=None,
@@ -1663,7 +1649,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             cluster_config=cluster_config,
             local_input=local_input,
             restart_times=restart_times,
@@ -2092,7 +2077,6 @@ def __init__(
         printreason=False,
         quiet=False,
         printshellcmds=False,
-        latency_wait=3,
         local_input=None,
         restart_times=None,
         max_status_checks_per_second=1,
@@ -2147,7 +2131,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             local_input=local_input,
             restart_times=restart_times,
             exec_job=exec_job,

snakemake/executors/ga4gh_tes.py

@@ -28,7 +28,6 @@ def __init__(
         printreason=False,
         quiet=False,
         printshellcmds=False,
-        latency_wait=3,
         cluster_config=None,
         local_input=None,
         restart_times=None,
@@ -83,7 +82,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             cluster_config=cluster_config,
             local_input=local_input,
             restart_times=restart_times,

snakemake/executors/google_lifesciences.py

@@ -51,7 +51,6 @@ def __init__(
         regions=None,
         location=None,
         cache=False,
-        latency_wait=3,
         local_input=None,
         restart_times=None,
         exec_job=None,
@@ -127,7 +126,6 @@ def __init__(
             printreason=printreason,
             quiet=quiet,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             restart_times=restart_times,
             exec_job=exec_job,
             assume_shared_fs=False,

snakemake/jobs.py

@@ -21,6 +21,7 @@
     _IOFile,
     is_flagged,
     get_flag_value,
+    wait_for_files,
 )
 from snakemake.utils import format, listfiles
 from snakemake.exceptions import RuleException, ProtectedOutputException, WorkflowError
@@ -764,6 +765,9 @@ def prepare(self):
         if self.benchmark:
             self.benchmark.prepare()
 
+        # wait for input files
+        wait_for_files(self.input, latency_wait=self.dag.workflow.latency_wait)
+
         if not self.is_shadow:
             return
 

snakemake/scheduler.py

@@ -94,7 +94,6 @@ def __init__(
         keepgoing=False,
         max_jobs_per_second=None,
         max_status_checks_per_second=100,
-        latency_wait=3,
         greediness=1.0,
         force_use_threads=False,
         assume_shared_fs=True,
@@ -169,7 +168,6 @@ def __init__(
                 printreason=printreason,
                 quiet=quiet,
                 printshellcmds=printshellcmds,
-                latency_wait=latency_wait,
             )
         elif touch:
             self._executor = TouchExecutor(
@@ -178,7 +176,6 @@ def __init__(
                 printreason=printreason,
                 quiet=quiet,
                 printshellcmds=printshellcmds,
-                latency_wait=latency_wait,
             )
         elif cluster or cluster_sync or (drmaa is not None):
             if not workflow.immediate_submit:
@@ -191,7 +188,6 @@ def __init__(
                     printreason=printreason,
                     quiet=quiet,
                     printshellcmds=printshellcmds,
-                    latency_wait=latency_wait,
                     cores=local_cores,
                     keepincomplete=keepincomplete,
                     keepmetadata=keepmetadata,
@@ -219,7 +215,6 @@ def __init__(
                     printreason=printreason,
                     quiet=quiet,
                     printshellcmds=printshellcmds,
-                    latency_wait=latency_wait,
                     assume_shared_fs=assume_shared_fs,
                     keepincomplete=keepincomplete,
                     keepmetadata=keepmetadata,
@@ -240,7 +235,6 @@ def __init__(
                     printreason=printreason,
                     quiet=quiet,
                     printshellcmds=printshellcmds,
-                    latency_wait=latency_wait,
                     cluster_config=cluster_config,
                     assume_shared_fs=assume_shared_fs,
                     max_status_checks_per_second=max_status_checks_per_second,
@@ -255,7 +249,6 @@ def __init__(
                 printreason=printreason,
                 quiet=quiet,
                 printshellcmds=printshellcmds,
-                latency_wait=latency_wait,
                 cores=local_cores,
                 keepincomplete=keepincomplete,
                 keepmetadata=keepmetadata,
@@ -269,7 +262,6 @@ def __init__(
                 printreason=printreason,
                 quiet=quiet,
                 printshellcmds=printshellcmds,
-                latency_wait=latency_wait,
                 cluster_config=cluster_config,
                 keepincomplete=keepincomplete,
                 keepmetadata=keepmetadata,
@@ -283,7 +275,6 @@ def __init__(
                 quiet=quiet,
                 printshellcmds=printshellcmds,
                 use_threads=use_threads,
-                latency_wait=latency_wait,
                 cores=local_cores,
                 keepincomplete=keepincomplete,
                 keepmetadata=keepmetadata,
@@ -300,7 +291,6 @@ def __init__(
                 printreason=printreason,
                 quiet=quiet,
                 printshellcmds=printshellcmds,
-                latency_wait=latency_wait,
                 keepincomplete=keepincomplete,
                 keepmetadata=keepmetadata,
             )
@@ -312,7 +302,6 @@ def __init__(
                 printreason=printreason,
                 quiet=quiet,
                 printshellcmds=printshellcmds,
-                latency_wait=latency_wait,
                 cores=local_cores,
             )
 
@@ -327,7 +316,6 @@ def __init__(
                 printreason=printreason,
                 quiet=quiet,
                 printshellcmds=printshellcmds,
-                latency_wait=latency_wait,
                 preemption_default=preemption_default,
                 preemptible_rules=preemptible_rules,
             )
@@ -339,7 +327,6 @@ def __init__(
                 printreason=printreason,
                 quiet=quiet,
                 printshellcmds=printshellcmds,
-                latency_wait=latency_wait,
                 cores=local_cores,
                 keepincomplete=keepincomplete,
             )
@@ -351,7 +338,6 @@ def __init__(
                 printreason=printreason,
                 quiet=quiet,
                 printshellcmds=printshellcmds,
-                latency_wait=latency_wait,
                 tes_url=tes,
                 container_image=container_image,
             )
@@ -365,7 +351,6 @@ def __init__(
                 quiet=quiet,
                 printshellcmds=printshellcmds,
                 use_threads=use_threads,
-                latency_wait=latency_wait,
                 cores=cores,
                 keepincomplete=keepincomplete,
                 keepmetadata=keepmetadata,

snakemake/workflow.py

@@ -149,6 +149,7 @@ def __init__(
         max_threads=None,
         all_temp=False,
         local_groupid="local",
+        latency_wait=3,
     ):
         """
         Create the controller.
@@ -234,6 +235,7 @@ def __init__(
         self.all_temp = all_temp
         self.scheduler = None
         self.local_groupid = local_groupid
+        self.latency_wait = latency_wait
 
         _globals = globals()
         _globals["workflow"] = self
@@ -599,7 +601,6 @@ def execute(
         delete_all_output=False,
         delete_temp_output=False,
         detailed_summary=False,
-        latency_wait=3,
         wait_for_files=None,
         nolock=False,
         unlock=False,
@@ -701,7 +702,9 @@ def files(items):
 
         if wait_for_files is not None:
             try:
-                snakemake.io.wait_for_files(wait_for_files, latency_wait=latency_wait)
+                snakemake.io.wait_for_files(
+                    wait_for_files, latency_wait=self.latency_wait
+                )
             except IOError as e:
                 logger.error(str(e))
                 return False
@@ -1024,7 +1027,6 @@ def files(items):
             container_image=container_image,
             printreason=printreason,
             printshellcmds=printshellcmds,
-            latency_wait=latency_wait,
             greediness=greediness,
             force_use_threads=force_use_threads,
             assume_shared_fs=self.assume_shared_fs,

test-environment.yml

@@ -38,7 +38,7 @@ dependencies:
   - ratelimiter
   - configargparse
   - appdirs
-  - python-irodsclient
+  - python-irodsclient <1.1.2 # bug in 1.1.2 leads to KeyError
   - cwltool
   - jsonschema
   - pandas