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Reduce bind mounting (and thus --bind args) in containers. #1387

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Reduce bind mounting (and thus --bind args) in containers. #1387

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31e409f
Add bones of idea without actually running the script.
DailyDreaming Dec 10, 2020
b44af89
Simple stage files.
DailyDreaming Feb 17, 2021
22e3d48
Only bindmount basedirs.
DailyDreaming Feb 23, 2021
c86a522
cleanups
mr-c Mar 11, 2021
abf2fc9
type fix
mr-c Mar 11, 2021
14814ae
Update uuids.
DailyDreaming Mar 16, 2021
c361501
New approach.
DailyDreaming Aug 25, 2021
8e6e789
Rebase.
DailyDreaming Aug 25, 2021
44116dd
Cruft.
DailyDreaming Aug 25, 2021
af0c1da
Cruft.
DailyDreaming Aug 25, 2021
abf614c
Cruft.
DailyDreaming Aug 25, 2021
f171a22
Update with new staging.
DailyDreaming Oct 19, 2021
664df85
Merge branch 'main' into mount-only-dirs
DailyDreaming Oct 19, 2021
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7 changes: 6 additions & 1 deletion cwltool/command_line_tool.py
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Original file line number Diff line number Diff line change
Expand Up @@ -877,8 +877,13 @@ def update_status_output_callback(
)
_logger.debug("[job %s] %s", j.name, json_dumps(builder.job, indent=4))

separateDirs = True
# sufficient conditional for docker/singularity?
if runtimeContext.use_container:
separateDirs = False

builder.pathmapper = self.make_path_mapper(
reffiles, builder.stagedir, runtimeContext, True
reffiles, builder.stagedir, runtimeContext, separateDirs
)
builder.requirements = j.requirements

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8 changes: 6 additions & 2 deletions cwltool/docker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -251,6 +251,9 @@ def append_volume(
runtime: List[str], source: str, target: str, writable: bool = False
) -> None:
"""Add binding arguments to the runtime list."""
if os.path.isfile(source) and target.endswith(os.path.basename(source)) and not writable:
source = os.path.dirname(source)
target = os.path.dirname(target)
options = [
"type=bind",
"source=" + source,
Expand All @@ -260,8 +263,9 @@ def append_volume(
options.append("readonly")
output = StringIO()
csv.writer(output).writerow(options)
mount_arg = output.getvalue().strip()
runtime.append("--mount={}".format(mount_arg))
mount_arg = f"--mount={output.getvalue().strip()}"
if mount_arg not in runtime:
runtime.append(mount_arg)
# Unlike "--volume", "--mount" will fail if the volume doesn't already exist.
if not os.path.exists(source):
os.makedirs(source)
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26 changes: 12 additions & 14 deletions cwltool/singularity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -280,16 +280,17 @@ def get_from_requirements(

@staticmethod
def append_volume(
runtime: List[str], source: str, target: str, writable: bool = False
runtime: List[str], source: str, target: str, writable: bool = False
) -> None:
runtime.append("--bind")
runtime.append(
"{}:{}:{}".format(
docker_windows_path_adjust(source),
docker_windows_path_adjust(target),
"rw" if writable else "ro",
)
)
src = docker_windows_path_adjust(source)
dst = docker_windows_path_adjust(target)
writable = "rw" if writable else "ro"
if os.path.isfile(src) and dst.endswith(os.path.basename(src)) and writable == 'ro':
src = os.path.dirname(src)
dst = os.path.dirname(dst)
bind_arg = f"--bind={src}:{dst}:{writable}"
if bind_arg not in runtime:
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@ionox0 ionox0 Jun 28, 2021 •
edited
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I have tried running this PR after getting the argument list too long error when using large number of input directories, and it seems that the source directory here is actually different for each file, and therefore it did not reduce the number of --bind arguments:

...
--bind=/juno/work/access/testing/users/johnsoni/access_qc/5500_HF/jobStore/files/for-job/kind-CWLJob/instance-aop8iz_w/file-34cfcc9ed208473bb67710a5108f1a32:/var/lib/cwl/s5g5ff703f1-41b2-56d3-93b3-7e36c1a37224/all_qc_files/duplex_bam_sequence_qc_dir/C-R0CLHU-N001-d:ro \
--bind=/juno/work/access/testing/users/johnsoni/access_qc/5500_HF/jobStore/files/for-job/kind-CWLJob/instance-aop8iz_w/file-fee328e946c9448c92ee501c6daa4b5a:/var/lib/cwl/s5g5ff703f1-41b2-56d3-93b3-7e36c1a37224/all_qc_files/duplex_bam_sequence_qc_dir/C-R0CLHU-N001-d:ro \
...

It seems toil actually produces different parent directories for files that might have originally came from the same Directory object. So if files that came from the same directory can be stored as such in the jobstore, I would expect this change to fix the issue

runtime.append(bind_arg)

def add_file_or_directory_volume(
self, runtime: List[str], volume: MapperEnt, host_outdir_tgt: Optional[str]
Expand Down Expand Up @@ -403,17 +404,14 @@ def create_runtime(
)
)
else:
runtime.append("--bind")
runtime.append(
"{}:{}:rw".format(
runtime.append("--bind={}:{}:rw".format(
docker_windows_path_adjust(os.path.realpath(self.outdir)),
self.builder.outdir,
)
)
runtime.append("--bind")
tmpdir = "/tmp" # nosec
runtime.append(
"{}:{}:rw".format(
"--bind={}:{}:rw".format(
docker_windows_path_adjust(os.path.realpath(self.tmpdir)), tmpdir
)
)
Expand Down