Task #10348 (closed)
Opened 7 years ago
Closed 5 years ago
Investigate PyCHRM/WND-CHRM/OMERO.script memory usage
| Reported by: | spli | Owned by: | spli |
|---|---|---|---|
| Priority: | minor | Milestone: | Partner-1 |
| Component: | General | Version: | 4.4.9 |
| Keywords: | n.a. | Cc: | analysis@… |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | n.a. |
Description
Processing three 8 bit 1388x1040 tifs (Original RGB split into three grayscale tifs) uses up to 250MB. When processing a list of images this grows to 1+GB and eventually the OS kills the process (Fedora 18 VM, with limited memory).
Attachments (1)
Change History (13)
comment:1 Changed 7 years ago by spli
- Status changed from new to accepted
comment:2 Changed 6 years ago by spli
Changed 6 years ago by spli
comment:3 Changed 6 years ago by spli
Plot updated with the Python garbage collector called after every set of 3 images gc.collect(), no difference. Looks like excessive memory consumption by Python.
comment:4 Changed 6 years ago by jburel
- Sprint changed from 2013-02-12 (5) to 2013-03-12 (6))
Moved from sprint 2013-02-12 (5)
comment:5 Changed 6 years ago by jburel
- Sprint changed from 2013-03-12 (6)) to 2013-04-09 (7))
Moved from sprint 2013-03-12 (6))
comment:6 Changed 6 years ago by jburel
- Sprint changed from 2013-04-09 (7)) to 2013-05-07 (8)
Moved from sprint 2013-04-09 (7))
comment:7 Changed 6 years ago by jburel
- Milestone changed from OMERO-4.4.x to OMERO-4.4.9
- Sprint changed from 2013-05-07 (8) to Blocker 4.4.9 (1)
Moved from sprint 2013-05-07 (8)
comment:8 Changed 6 years ago by spli
- Milestone changed from OMERO-4.4.x to OMERO-4.4.10
- Version set to 4.4.9
comment:9 Changed 6 years ago by spli
Referencing ticket #9946 has changed sprint.
comment:10 Changed 6 years ago by jburel
Referencing ticket #9946 has changed sprint.
comment:11 Changed 6 years ago by spli
- Milestone changed from OMERO-4.4.10 to Partner-1
comment:12 Changed 5 years ago by spli
- Remaining Time changed from 1 to 0
- Resolution set to fixed
- Status changed from accepted to closed
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24 RGB images, 1388x1040
PyChrm? SmallFeatureSet?
https://github.com/manics/omero-pychrm/tree/8485a8b62d48667ac0f69a5ef541d2b5510c5aa8
OS X 10.8: hdf5 stable 1.8.9, python tables 2.4.0
Fedora 18 (Virtualbox): hdf5-1.8.9-5.fc18.x86_64 python-tables-2.4.0-1.fc18.x86_64