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Use less memory when loading EDF file #10638

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merged 4 commits into from
May 17, 2022
Merged

Use less memory when loading EDF file #10638

merged 4 commits into from
May 17, 2022

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cbrnr
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@cbrnr cbrnr commented May 17, 2022

Fixes #10634. We need to read through the whole file when annotations are present. However, we accidentally prevented garbage collection in a loop, which led to extremely high memory usage. Because we read annotations when preload=False, this is a problem even when the user does not actually want to load the data. I've fixed this by creating an explicit copy of the subarray in the loop.

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cbrnr commented May 17, 2022

@arnaumanasanch could you please test this PR with your file and report your memory usage?

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Thanks @cbrnr The problem seems to be solved with this PR. The current memory usage is the one in the image below.

image

From a Spike of around 11Gb now it went down to 0.8Gb. This is a size that won't be problematic with the available RAM we have.

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cbrnr commented May 17, 2022

Alright, so this is ready for review then!

@cbrnr cbrnr requested review from agramfort and larsoner May 17, 2022 08:09
agramfort
agramfort approved these changes May 17, 2022
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@cbrnr can I ask you add a what's new entry in bug fixes and send a PR to backport this?

@cbrnr cbrnr added the backport-candidate on-merge: backport to maint/1.7 label May 17, 2022
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cbrnr commented May 17, 2022

Done, I'll do the backport after this is merged.

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Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
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maybe push an empty commit or merge the main branch to see if it fixes the CIs?

@larsoner larsoner merged commit 9d972e4 into mne-tools:main May 17, 2022
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Thanks @cbrnr !

@cbrnr cbrnr deleted the fix-edf-memory branch May 17, 2022 16:07
larsoner added a commit to HanBnrd/mne-python that referenced this pull request May 17, 2022
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Merge remote-tracking branch 'upstream/main' into tddr-hb
bdfb2bb 
* upstream/main: (24 commits)
  Use less memory when loading EDF file (mne-tools#10638)
  BUG: fix ipython console accessibility after MNEQtBrowser in Spyder (mne-tools#10637)
  WIP: Fix mne.time_frequency.multitaper Nyquist adjustment slightly incorrect (mne-tools#10541)
  BUG: Fix bug with fNIRS reordering (mne-tools#10630)
  MNT: PyQt6 for pip pre 3.10 (mne-tools#10636)
  CI: Fix conda (mne-tools#10628)
  MRG: Update installer links to point to 1.0.3_0 (mne-tools#10622)
  [BUG, MRG] fix info write access (mne-tools#10626)
  [MRG] Fixed group_by titles in evoked_plot. (mne-tools#10618)
  [BUG, MRG] Replace image_interp with interpolation in topomap plot arguments (mne-tools#10617)
  MAINT: Fix timeout (mne-tools#10624)
  Simplify mne-tools#10619 (mne-tools#10620)
  Drop EEG rejection thresholds when replacing EEG with CSD channels (mne-tools#10619)
  Add get_montage support for fNIRS (mne-tools#10611)
  ENH: Improve make_head_surface options (mne-tools#10592)
  [ENH, MRG] Add citation for intracranial JOSS paper (mne-tools#10616)
  [ENH] Add sys info for mne-icalabel (mne-tools#10615)
  MRG: Add "highlight" parameter to Evoked.plot() to conveniently highlight time periods (mne-tools#10614)
  MRG: Allow to pass array of "average" values to plot_evoked_topomap() (mne-tools#10610)
  fix: snirf length units (mne-tools#10613)
  ...
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cbrnr commented May 17, 2022

Is this backporting how-to still accurate? I'm not sure where the manually copied changelog line should go in /doc/changes/1.0.inc – do I need to create a new section for the 1.0.4 release?

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Is this backporting how-to still accurate?

Yes in principle, but in practice if you are not familiar/comfortable with the process it's better to open a PR to maint/1.0 than it is to push directly in the last step

do I need to create a new section for the 1.0.4 release?

Yes

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cbrnr commented May 17, 2022

Thanks @larsoner, I'll try to make a PR then.

cbrnr added a commit to cbrnr/mne-python that referenced this pull request May 17, 2022
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Use less memory when loading EDF file (mne-tools#10638)
6b26745 
* Use less memory when loading EDF file

* Add changelog entry

* Formatting

Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>

* Restart CI

Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
This was referenced May 17, 2022
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agramfort added a commit that referenced this pull request May 17, 2022
@cbrnr @agramfort
Backport #10638 (#10643)
6a8dd14 
* Use less memory when loading EDF file (#10638)

* Use less memory when loading EDF file

* Add changelog entry

* Formatting

Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>

* Restart CI

Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>

* Add changelog entry

* Fix version

* Change version to "unreleased"

Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
@cbrnr cbrnr added backported and removed backport-candidate on-merge: backport to maint/1.7 labels May 17, 2022
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@agramfort agramfort agramfort approved these changes

@larsoner larsoner Awaiting requested review from larsoner larsoner is a code owner

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Reading large EDF files with preload = False raises memory error
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