[BUG-107] Out of memory error on sequence search - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Fixed
Labels:
None
Environment:

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URL: https://genoviz.svn.sourceforge.net/svnroot/genoviz/branches/igb_6_5
Repository Root: https://genoviz.svn.sourceforge.net/svnroot/genoviz
Repository UUID: 02abc639-694f-0410-96dc-a5594cd59667
Revision: 8134
Node Kind: directory
Schedule: normal
Last Changed Author: hiralv
Last Changed Rev: 8134
Last Changed Date: 2011-05-12 16:40:41 -0400 (Thu, 12 May 2011)

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URL: https://genoviz.svn.sourceforge.net/svnroot/genoviz/branches/igb_6_5 Repository Root: https://genoviz.svn.sourceforge.net/svnroot/genoviz Repository UUID: 02abc639-694f-0410-96dc-a5594cd59667 Revision: 8134 Node Kind: directory Schedule: normal Last Changed Author: hiralv Last Changed Rev: 8134 Last Changed Date: 2011-05-12 16:40:41 -0400 (Thu, 12 May 2011)

Description

Searching for a sequence on reasonably sized region of chromosome produces out of memory error. This may also affect the trunk. Please test trunk, also.

To repeat:

(0) Reset prefs to defaults
(1) Choose genome H_sapiens_Feb_2009
(2) Use coordinates search box to go to region chr1 : 60,920,000 - 69,280,000
(3) Click Load Sequence in View, wait for sequence to load
(4) Click Search Tab, Choose "Search: Residues"
(5) Enter: GTGGCTTTCCCT
(6) Click "search" (binoculars icon)
(7) Observe memory use increase briefly to 500 Mg, out of memory error appears, search stalls and no results appear

[java] Exception in thread "pool-13-thread-1" java.lang.OutOfMemoryError: Java heap space
[java] at java.util.Arrays.copyOf(Arrays.java:2882)
[java] at java.lang.StringValue.from(StringValue.java:24)
[java] at java.lang.String.<init>(String.java:178)
[java] at com.affymetrix.genometryImpl.BioSeq.getResiduesFromComposition(BioSeq.java:544)
[java] at com.affymetrix.genometryImpl.BioSeq.getResiduesNoProvider(BioSeq.java:512)
[java] at com.affymetrix.genometryImpl.BioSeq.getResidues(BioSeq.java:478)
[java] at com.affymetrix.genometryImpl.BioSeq.getResidues(BioSeq.java:469)
[java] at com.affymetrix.genometryImpl.BioSeq.getResidues(BioSeq.java:460)
[java] at com.affymetrix.igb.search.SearchView.regexTF(SearchView.java:616)
[java] at com.affymetrix.igb.search.SearchView.access$2500(SearchView.java:54)
[java] at com.affymetrix.igb.search.SearchView$5.run(SearchView.java:589)
[java] at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
[java] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
[java] at java.lang.Thread.run(Thread.java:680)
[java] Exception in thread "pool-13-thread-2" java.lang.OutOfMemoryError: Java heap space
[java] at java.util.Arrays.copyOf(Arrays.java:2882)
[java] at java.lang.StringValue.from(StringValue.java:24)
[java] at java.lang.String.<init>(String.java:178)
[java] at com.affymetrix.genometryImpl.BioSeq.getResiduesFromComposition(BioSeq.java:544)
[java] at com.affymetrix.genometryImpl.BioSeq.getResiduesNoProvider(BioSeq.java:512)
[java] at com.affymetrix.genometryImpl.BioSeq.getResidues(BioSeq.java:478)
[java] at com.affymetrix.genometryImpl.BioSeq.getResidues(BioSeq.java:469)
[java] at com.affymetrix.genometryImpl.BioSeq.getResidues(BioSeq.java:460)
[java] at com.affymetrix.igb.search.SearchView.regexTF(SearchView.java:616)
[java] at com.affymetrix.igb.search.SearchView.access$2500(SearchView.java:54)
[java] at com.affymetrix.igb.search.SearchView$5.run(SearchView.java:589)
[java] at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
[java] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
[java] at java.lang.Thread.run(Thread.java:680)

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is blocked by

BUG-648 Search bugs

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Ann Loraine created issue - 13/May/11 5:26 AM

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Hiral Vora (Inactive) added a comment - 13/May/11 6:46 AM

Fixed on branch in 8135.

Test that it is not running out of heap while searching. Also make sure it is returning correct results.

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Hiral Vora (Inactive) added a comment - 13/May/11 6:46 AM Fixed on branch in 8135. Test that it is not running out of heap while searching. Also make sure it is returning correct results.

Hiral Vora (Inactive) made changes - 13/May/11 6:46 AM

Field	Original Value	New Value
Assignee	Hiral Vora [ hiralv ]	Alyssa Gulledge [ alyssa ]

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Hiral Vora (Inactive) added a comment - 16/May/11 5:55 AM

Deployed a new version containing this fix. Test it on preview too.

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Hiral Vora (Inactive) added a comment - 16/May/11 5:55 AM Deployed a new version containing this fix. Test it on preview too.

Alyssa Gulledge (Inactive) made changes - 26/May/11 7:25 AM

Assignee

Alyssa Gulledge [ alyssa ]

Nick Ren [ imnick ]

Hiral Vora (Inactive) made changes - 26/May/11 12:30 PM

Project	IGB 6.5.1 [ 10032 ]	IGB6.6 [ 10021 ]
Key	~~SIXFIVEONE-6~~	~~IGBA-90~~

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Nick Ren (Inactive) added a comment - 27/May/11 5:27 AM

I follow repeated step and it works well.

It doesn't produce out of memory error.
Instead, it shows me one result back.

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Nick Ren (Inactive) added a comment - 27/May/11 5:27 AM I follow repeated step and it works well. It doesn't produce out of memory error. Instead, it shows me one result back.

Nick Ren (Inactive) made changes - 27/May/11 5:27 AM

Assignee

Nick Ren [ imnick ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 27/May/11 8:24 AM

Status	Open [ 1 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 27/May/11 8:24 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 27/May/11 8:24 AM

Project	IGB6.6 [ 10021 ]	Bug Repository [ 10030 ]
Key	~~IGBA-90~~	~~BUG-107~~

Alyssa Gulledge (Inactive) made changes - 31/Aug/11 5:54 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]

Nick Ren (Inactive) made changes - 31/Aug/11 7:40 AM

Assignee

Alyssa Gulledge [ alyssa ]

Nick Ren (Inactive) made changes - 31/Aug/11 7:40 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

Nick Ren (Inactive) made changes - 31/Aug/11 7:40 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 10/Jan/12 8:54 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Katharine Kubiak [ kkubiak ]

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Katharine Kubiak (Inactive) added a comment - 12/Jan/12 10:59 AM

Passed v9770 Windows

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Katharine Kubiak (Inactive) added a comment - 12/Jan/12 10:59 AM Passed v9770 Windows

Katharine Kubiak (Inactive) made changes - 12/Jan/12 10:59 AM

Assignee

Katharine Kubiak [ kkubiak ]

Anuj Puram [ anuj ]

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Anuj Puram (Inactive) added a comment - 13/Jan/12 4:32 AM

Passed version 6.7.0 (9791) on Mac

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Anuj Puram (Inactive) added a comment - 13/Jan/12 4:32 AM Passed version 6.7.0 (9791) on Mac

Anuj Puram (Inactive) made changes - 13/Jan/12 4:32 AM

Assignee

Anuj Puram [ anuj ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 17/Jan/12 7:16 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 17/Jan/12 7:17 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

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darius added a comment - 05/Jun/12 7:18 AM

Passed 7.0.0 (11806)

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darius added a comment - 05/Jun/12 7:18 AM Passed 7.0.0 (11806)

darius made changes - 05/Jun/12 7:18 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Darius Bost [ darius ]

darius made changes - 05/Jun/12 7:18 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Darius Bost [ darius ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 13/Nov/12 9:42 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 13/Nov/12 10:04 AM

Priority

Blocker [ 1 ]

Major [ 3 ]

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 11:09 AM

Link

This issue is blocked by ~~BUG-648~~ [ ~~BUG-648~~ ]

Alyssa Gulledge (Inactive) made changes - 17/Dec/12 10:21 AM

Status	Reopened [ 4 ]	Closed [ 6 ]
Resolution		Fixed [ 1 ]

Tarun Santosh (Inactive) made changes - 02/Oct/13 7:06 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Tarun Santosh [ tkanapar ]

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Tarun Santosh (Inactive) added a comment - 04/Oct/13 4:59 AM

Passed (7.0.4) 15389(Mac)

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Tarun Santosh (Inactive) added a comment - 04/Oct/13 4:59 AM Passed (7.0.4) 15389(Mac)

Tarun Santosh (Inactive) made changes - 04/Oct/13 5:00 AM

Status	Reopened [ 4 ]	Closed [ 6 ]
Resolution		Fixed [ 1 ]

Hiral Vora (Inactive) made changes - 16/Oct/13 4:33 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee	Tarun Santosh [ tkanapar ]

Hiral Vora (Inactive) made changes - 16/Oct/13 4:35 AM

Status	Reopened [ 4 ]	Closed [ 6 ]
Resolution		Fixed [ 1 ]

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Assignee:

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Reporter:

Ann Loraine

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Dates

Created:

13/May/11 5:26 AM

Updated:

16/Oct/13 4:35 AM

Resolved:

16/Oct/13 4:35 AM