Merge pull request #189 from dcmonroe/main

Update happy.py | mem check for singularity containers

CHANGELOG.md

@@ -1,7 +1,8 @@
 # Release history
 
-## Version 3.0alpha2 (12/20/24)
-* (package) Now includes codespell checking thank you to Yaroslav O. Halchenko (yarikoptic)!
+## Version 3.0alpha2 (12/30/24)
+* (happy, rapidtide) Now do more sophisticated container checking to handle both Docker and Singularity. Thank you to Derek Monroe (https://github.com/dcmonroe) for the catch and the fix!
+* (package) Now includes codespell checking thanks to Yaroslav O. Halchenko (https://github.com/yarikoptic)!
 
 ## Version 3.0alpha1 (12/20/24)
 * (rapidtide) The ``--fixdelay`` option has been split into two options.  ``--initialdelay DELAY`` lets you specify either a float that sets the starting delay for every voxel to that value, or a 3D file specifying the initial delay for each voxel.  ``--nodelayfit`` determines whether the delay can be adjusted from its initial value.  Closes https://github.com/bbfrederick/rapidtide/issues/171. KNOWN ISSUE:  If you supply an initial delay map, instead of using the global mean, rapidtide should use the delays to make your first stage regressor.  Currently that is not the case.

pyproject.toml

@@ -48,6 +48,7 @@ authors = [
     {name = "Daniel M. Drucker, Ph.D."},
     {name = "Jeffrey N Stout"},
     {name = "Yaroslav O. Halchenko"},
+    {name = "Derek Monroe"},
 ]
 
 [project.urls]

rapidtide/util.py

@@ -132,6 +132,24 @@ def findavailablemem():
         return free, swap
 
 
+def checkifincontainer():
+    # Determine if the program is running in a container.  If so, we may need to adjust the python memory
+    # limits because they are not set properly.  But check if we're running on CircleCI - it does not seem
+    # to like you twiddling with the container parameters.
+    #
+    # possible return values are: None, "Docker", "Singularity", and "CircleCI"
+    #
+    if os.environ.get("SINGULARITY_CONTAINER") is not None:
+        containertype = "Singularity"
+    elif os.environ.get("RUNNING_IN_CONTAINER") is not None:
+        containertype = "Docker"
+    else:
+        containertype = None
+    if os.environ.get("CIRCLECI") is not None:
+        containertype = "CircleCI"
+    return containertype
+
+
 def setmemlimit(memlimit):
     resource.setrlimit(resource.RLIMIT_AS, (memlimit, memlimit))
 

rapidtide/workflows/happy.py

@@ -78,15 +78,16 @@ def happy_main(argparsingfunc):
     # create the canary file
     Path(f"{outputroot}_ISRUNNING.txt").touch()
 
-    # if we are running in a container, make sure we enforce memory limits properly
-    try:
-        testval = os.environ["RUNNING_IN_CONTAINER"]
-    except KeyError:
-        args.runningincontainer = False
-    else:
-        args.runningincontainer = True
-        args.containermemfree, args.containermemswap = tide_util.findavailablemem()
-        tide_util.setmemlimit(args.containermemfree)
+    # if running in Docker or Apptainer/Singularity, this is necessary to enforce memory limits properly
+    # otherwise likely to  error out in gzip.py or at voxelnormalize step.  But do nothing if running in CircleCI
+    # because it does NOT like you messing with the container.
+    args.containertype = tide_util.checkifincontainer()
+    if args.containertype is not None:
+        if args.containertype != "CircleCI":
+            args.containermemfree, args.containermemswap = tide_util.findavailablemem()
+            tide_util.setmemlimit(args.containermemfree)
+        else:
+            print("running in CircleCI environment - not messing with memory")
 
     # Set up loggers for workflow
     setup_logger(

rapidtide/workflows/rapidtide.py

@@ -269,14 +269,18 @@ def rapidtide_main(argparsingfunc):
         gc.enable()
         print("turning on garbage collection")
 
-    # if we are running in a container, make sure we enforce memory limits properly
-    if "RUNNING_IN_CONTAINER" in os.environ:
-        optiondict["runningincontainer"] = True
-        optiondict["containermemfree"], optiondict["containermemswap"] = tide_util.findavailablemem()
-        if optiondict["containermemfix"]:
+    # if running in Docker or Apptainer/Singularity, this is necessary to enforce memory limits properly
+    # otherwise likely to  error out in gzip.py or at voxelnormalize step.  But do nothing if running in CircleCI
+    # because it does NOT like you messing with the container.
+    optiondict["containertype"] = tide_util.checkifincontainer()
+    if optiondict["containertype"] is not None:
+        if optiondict["containertype"] != "CircleCI":
+            optiondict["containermemfree"], optiondict["containermemswap"] = (
+                tide_util.findavailablemem()
+            )
             tide_util.setmemlimit(optiondict["containermemfree"])
-    else:
-        optiondict["runningincontainer"] = False
+        else:
+            print("running in CircleCI environment - not messing with memory")
 
     # write out the current version of the run options
     optiondict["currentstage"] = "init"