runner.singularity: Support for build's --cpus and --memory options

Only available since Singularity 3.10.0 and on systems with cgroups v2.¹
With older Singularity versions, these options will continue to be
ignored (as before this change).  If the Singularity version is new
enough but the system doesn't support cgroups v2 (or it is
administratively disabled in the Singularity config), then Singularity
will error when these options are used.

¹ <https://docs.sylabs.io/guides/latest/user-guide/cgroups.html#requirements-linux-cgroups>

doc/installation.rst

@@ -193,7 +193,8 @@ dependencies as validated versions are already bundled into a container image
 by the Nextstrain team.
 
 Run ``nextstrain setup singularity`` to get started.
-Singularity version 3.0.0 or newer is required.
+Singularity version 3.0.0 or newer is required, but we recommend at least
+version 3.10.0 or newer when possible.
 
 Note that the Singularity project forked into two separate projects in late
 2021: `SingularityCE`_ under `Sylabs`_ and `Apptainer`_ under the `Linux

nextstrain/cli/command/build.py

@@ -51,7 +51,7 @@ def register_parser(subparser):
     parser.add_argument(
         "--cpus",
         help    = "Number of CPUs/cores/threads/jobs to utilize at once.  "
-                  "Limits containerized (Docker, AWS Batch) builds to this amount.  "
+                  "Limits containerized (Docker, Singularity, AWS Batch) builds to this amount.  "
                   "Informs Snakemake's resource scheduler when applicable.  "
                   "Informs the AWS Batch instance size selection.  "
                   "By default, no constraints are placed on how many CPUs are used by a build; "
@@ -63,7 +63,7 @@ def register_parser(subparser):
         "--memory",
         help    = "Amount of memory to make available to the build.  "
                   "Units of b, kb, mb, gb, kib, mib, gib are supported.  "
-                  "Limits containerized (Docker, AWS Batch) builds to this amount.  "
+                  "Limits containerized (Docker, Singularity, AWS Batch) builds to this amount.  "
                   "Informs Snakemake's resource scheduler when applicable.  "
                   "Informs the AWS Batch instance size selection.  ",
         metavar = "<quantity>",

nextstrain/cli/runner/singularity.py

@@ -193,6 +193,17 @@ def run(opts, argv, working_volume = None, extra_env = {}, cpus: int = None, mem
         # Change the default working directory if requested
         *(("--pwd", "/nextstrain/%s" % working_volume.name) if working_volume else ()),
 
+        # Set resource limits if any.  These options are equivalent to Docker's
+        # and are first available in Singularity 3.10.0.  The lower-level
+        # --apply-cgroups option first available in 3.9.0 can do the same
+        # things, but the version difference seems marginally useful and
+        # there's more implementation overhead required to use --apply-cgroups.
+        *(["--cpus", str(cpus)]
+            if cpus is not None and singularity_version_at_least("3.10.0") else []),
+
+        *(["--memory", str(memory)]
+            if memory is not None and singularity_version_at_least("3.10.0") else []),
+
         str(image_path(image)),
         *argv,
     ], extra_env)