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Failure to serialize on Linux

Details

  • Type: Bug Bug
  • Status: Needs Assessment Needs Assessment
  • Priority: Must Must
  • Resolution: Unresolved
  • Affects Version/s: None
  • Fix Version/s: None
  • Component/s: None
  • Severity:
    3
  • Keywords:
  • Description:
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    When running the linkage process on Linux with a large patient database, some records fail to be serialized.

    Two possible reasons:

    • there is something about each specific record which makes it impossible to serialize
    • due to the large number of records, the garbage collector is failing to close all of the FileOutputStreams used during serialization, causing a garbage collection exception

    Example log:

    [17:52:36|2009-05-28]Failed to serialize record with id 229439...
[17:52:36|2009-05-28]Failed to serialize record with id 229439...
[17:52:36|2009-05-28]Failed to serialize record with id 168504...
[17:52:36|2009-05-28]Failed to serialize record with id 168504...
[17:52:36|2009-05-28]Failed to serialize record with id 137818...
[17:52:36|2009-05-28]Failed to serialize record with id 137818...
[17:52:36|2009-05-28]Failed to serialize record with id 178517...
[17:52:36|2009-05-28]Failed to serialize record with id 178517...
[17:52:36|2009-05-28]Failed to serialize record with id 74872...
[17:52:36|2009-05-28]Failed to serialize record with id 74872...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
    Show
    When running the linkage process on Linux with a large patient database, some records fail to be serialized. Two possible reasons:
    • there is something about each specific record which makes it impossible to serialize
    • due to the large number of records, the garbage collector is failing to close all of the FileOutputStreams used during serialization, causing a garbage collection exception
    Example log: 
    [17:52:36|2009-05-28]Failed to serialize record with id 229439...
[17:52:36|2009-05-28]Failed to serialize record with id 229439...
[17:52:36|2009-05-28]Failed to serialize record with id 168504...
[17:52:36|2009-05-28]Failed to serialize record with id 168504...
[17:52:36|2009-05-28]Failed to serialize record with id 137818...
[17:52:36|2009-05-28]Failed to serialize record with id 137818...
[17:52:36|2009-05-28]Failed to serialize record with id 178517...
[17:52:36|2009-05-28]Failed to serialize record with id 178517...
[17:52:36|2009-05-28]Failed to serialize record with id 74872...
[17:52:36|2009-05-28]Failed to serialize record with id 74872...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...
[17:52:36|2009-05-28]Failed to serialize record with id 15104...

Activity

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Saketh Bhamidipati added a comment - 2009-07-01 15:32:11 EDT

I ran the linkage process on a non-Linux laptop for 50000 entries (original 5000 demo, times ten) without any issues.

Show
Saketh Bhamidipati added a comment - 2009-07-01 15:32:11 EDT I ran the linkage process on a non-Linux laptop for 50000 entries (original 5000 demo, times ten) without any issues.
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Saketh Bhamidipati added a comment - 2009-07-01 21:20:18 EDT

More interestingly, I ran the linkage process on a Ubuntu laptop for the same 50000 entries, and it failed with many hundreds of {{StackOverflowError}}s. This does not reflect the issues from the logs James sent, but it is still interesting.

Show
Saketh Bhamidipati added a comment - 2009-07-01 21:20:18 EDT More interestingly, I ran the linkage process on a Ubuntu laptop for the same 50000 entries, and it failed with many hundreds of {{StackOverflowError}}s. This does not reflect the issues from the logs James sent, but it is still interesting.

People

Dates

  • Created:
    2009-06-26 18:26:15 EDT
    Updated:
    2010-08-02 11:52:43 EDT
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