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some IMDReader streaming tests time out with imdclient 0.2.4 #5442
Description
Expected behavior
All IMDReader streaming tests continue to pass, regardless of updates to the upstream dependency imdclient.
Actual behavior
Since imdclient 0.2.4, a number of test fail by hitting the 200s timeout on the tests (see below)
Code to reproduce the behavior
See e.g. PR #5423 , https://github.com/MDAnalysis/mdanalysis/actions/runs/29380161861/job/87743056098?pr=5423
FAILED testsuite/MDAnalysisTests/coordinates/test_imd.py::TestIMDReaderBaseAPI::test_transformations_iter - Failed: Timeout (>200.0s) from pytest-timeout.
FAILED testsuite/MDAnalysisTests/coordinates/test_imd.py::TestIMDReaderBaseAPI::test_iter_as_aux_highf - Failed: Timeout (>200.0s) from pytest-timeout.
FAILED testsuite/MDAnalysisTests/coordinates/test_imd.py::TestIMDReaderBaseAPI::test_iter - Failed: Timeout (>200.0s) from pytest-timeout.
FAILED testsuite/MDAnalysisTests/coordinates/test_imd.py::TestStreamIteration::test_iterate_step - Failed: Timeout (>200.0s) from pytest-timeout.
FAILED testsuite/MDAnalysisTests/coordinates/test_imd.py::TestStreamIteration::test_iterate_twice_sliced_raises_error - Failed: Timeout (>200.0s) from pytest-timeout.
FAILED testsuite/MDAnalysisTests/coordinates/test_imd.py::TestStreamIteration::test_iterate_twice_all_raises_error - Failed: Timeout (>200.0s) from pytest-timeout.
FAILED testsuite/MDAnalysisTests/coordinates/test_imd.py::TestStreamIteration::test_iterate_twice_fi_all_raises_error - Failed: Timeout (>200.0s) from pytest-timeout.
FAILED testsuite/MDAnalysisTests/coordinates/test_imd.py::TestStreamIteration::test_subslice_fi_all_after_iteration_raises_error - Failed: Timeout (>200.0s) from pytest-timeout.
FAILED testsuite/MDAnalysisTests/coordinates/test_imd.py::test_imd_stream_empty - Failed: Timeout (>200.0s) from pytest-timeout.
Background
imdclient 0.2.4 increased a timeout value from 5s to 600s, see issue Becksteinlab/imdclient#111 and PR Becksteinlab/imdclient#120
Activity
orbeckst commentedon Jul 19, 2026
@amruthesht @ljwoods2 do you have an idea of what may lead to these failures?
orbeckst commentedon Jul 19, 2026
I can confirm that locally the imd tests pass with imdclient 0.2.3 and also pass with 0.2.4 (
pytest -v test_imd.py) (on Python 3.14, macOS, develop MDA 3d3a53e) BUT they take a LONG timeIt looks as if these 0.2.3 tests take about 5 seconds to pass. This is suspicious because the imdclient default timeout for 0.2.3 is 5s and the same tests now take a long time (after the imdclient timeout was increased to 600s).
I tried adding
timeout=10tomdanalysis/testsuite/MDAnalysisTests/coordinates/test_imd.py
Line 213 in 3d3a53e
orbeckst commentedon Jul 19, 2026
Confirmed that with imdclient 0.2.4 one of the tests in question passes after the 600-s timeout value (=10 min):
orbeckst commentedon Jul 19, 2026
@amruthesht how do I enforce a short timeout for the tests? This is important and urgent to just get the CI working again.
We then need to understand why we need
timeoutfor tests to pass — what kind of behavior in imdclient has IMDReader relying out for properly ending reading??ljwoods2 commentedon Jul 19, 2026
@orbeckst I think the problem is that we never call disconnect or close on the dummy IMDServer's socket until after the test ends, during cleanup- so the only way the reader has of knowing the stream has ended during the test is via the timeout.
mdanalysis/testsuite/MDAnalysisTests/coordinates/test_imd.py
Line 438 in 3d3a53e
So we need two changes: IMDServer needs to call
socket.shutdown(socket.SHUTDOWN_WR)as a part of itsdisconnect()call, and thereaderfixtures in these tests need to callserver.disconnect()after sending frames through the socketljwoods2 commentedon Jul 19, 2026
@orbeckst
imdclient repo side
Becksteinlab/imdclient#149
mda side - can be merged WITHOUT above MR, since
disconnectalready callssocket.close()which will send EOF in the case of only one process holding the file descriptor to the senders socket, as is always currently true in our tests)#5443
orbeckst commentedon Jul 20, 2026
Thanks for quickly digging into this issue. I’m also reviewing the PR on the imdclient side. I might not fully understand how the server is supposed to work so please bear with my questions.
Ensure IMDServer sends EOF to client DURING test (#5443)
amruthesht commentedon Jul 20, 2026
My apologies; I just saw this. Thank you @ljwoods2 for getting to this!