Duplicate file fails with Unhandled error

Hi,

Really would appreciate any help or suggestions. I have 50GB file that I need to duplicate and move to a different folder. When I try to duplicate the larger file it fails with a “Unhandled error”. Duplicate works just fine with small files.

Jupyterhub: 0.9.2
Amazon Linux: 2 (Karoo)
r5.8xlarge

Here is the debug log.
[I 2022-06-23 16:57:00.293 SingleUserLabApp handlers:134] Copying **path/to/big/file/**bigfile.sas7bdat to path/to/big/file/

[I 2022-06-23 16:58:04.076 JupyterHub log:158] 302 GET / → /hub (@::ffff:10.10.28.26) 0.66ms

[I 2022-06-23 16:58:04.115 JupyterHub log:158] 302 GET /hub → /hub/ (@::ffff:10.10.28.26) 0.55ms

[I 2022-06-23 16:58:04.175 JupyterHub log:158] 302 GET /hub/ → /hub/login (@::ffff:10.10.28.26) 0.56ms

[I 2022-06-23 16:58:04.236 JupyterHub log:158] 200 GET /hub/login (@::ffff:10.10.28.26) 1.14ms

[D 2022-06-23 17:00:59.847 JupyterHub proxy:678] Proxy: Fetching GET http://127.0.0.1:8001/api/routes

17:00:59.848 [ConfigProxy] info: 200 GET /api/routes

[E 2022-06-23 17:09:25.692 SingleUserLabApp web:1793] Uncaught exception POST path/to/big/file/?1656003420351 (::ffff:10.10.28.82)

HTTPServerRequest(protocol=‘http’, host=‘workspace.in.aws:8192’, method=‘POST’, uri=‘path/to/big/file/?1656003420351’, version=‘HTTP/1.1’, remote_ip=‘::ffff:10.10.28.82’)
Traceback (most recent call last):
File “/usr/local/lib64/python3.7/site-packages/tornado/web.py”, line 1704, in _execute
result = await result
File “/usr/local/lib64/python3.7/site-packages/tornado/gen.py”, line 769, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File “/usr/local/lib/python3.7/site-packages/notebook/services/contents/handlers.py”, line 200, in post
yield self._copy(copy_from, path)
File “/usr/local/lib64/python3.7/site-packages/tornado/gen.py”, line 762, in run
value = future.result()
File “/usr/local/lib64/python3.7/site-packages/tornado/gen.py”, line 234, in wrapper
yielded = ctx_run(next, result)
File “/usr/local/lib/python3.7/site-packages/notebook/services/contents/handlers.py”, line 136, in _copy
model = yield maybe_future(self.contents_manager.copy(copy_from, copy_to))
File “/usr/local/lib/python3.7/site-packages/notebook/services/contents/manager.py”, line 446, in copy
model = self.get(path)
File “/usr/local/lib/python3.7/site-packages/notebook/services/contents/filemanager.py”, line 434, in get
model = self._file_model(path, content=content, format=format)
File “/usr/local/lib/python3.7/site-packages/notebook/services/contents/filemanager.py”, line 361, in _file_model
content, format = self._read_file(os_path, format)
File “/usr/local/lib/python3.7/site-packages/notebook/services/contents/fileio.py”, line 320, in _read_file
return encodebytes(bcontent).decode(‘ascii’), ‘base64’
File “/usr/lib64/python3.7/base64.py”, line 532, in encodebytes
return b"".join(pieces)
MemoryError
[W 2022-06-23 17:09:25.700 SingleUserLabApp handlers:608] Unhandled error

Has anybody seen this type of error?

Is there a limit to the size of a file that can be duplicated?

Thanks in advance.
Abe

This is a problem with your singleuser server (e.g. Jupyter notebook or lab), not JupyterHub- from the error it sounds you might be running out of memory?

If you give us more information about your setup e.g. versions of Jupyter notebook/server/lab, and your compute setup, someone here might know whether this is to be expected.

Under Help > About JupyterLab > Version 3.0.15
Via linux CLI I can copy the file without issue.

It’s running on Amazon Linux: 2 (Karoo), r5.8xlarge (256 GIB Memory)

What’s odd is the move function works on the larger file without issue.

Thanks for response.

It appears to be running out of memory.

Why is Jupyterlab consuming so many resources to copy a 50GB file?

Would implementing memory limits make the problem worse?

Thanks