[Molecuilder-devel] [SCM] MoleCuilder branch ThreadFixes created. v1.4.7-17-g38074bf

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        at  38074bf6c963bbf4bc326b7725ba73b8eccd79f4 (commit)

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commit 38074bf6c963bbf4bc326b7725ba73b8eccd79f4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 29 11:46:02 2014 +0200

    THREADFIX: Fixed ActionQueue with respect to mutex and threads.
    
    - run_thread is now last member variable, hence started after all other
      variables are initialized.
    - separated accesses to queues and to run_thread_isIdle flag. Also renamed
      its mutex for easier association with it.

commit b4d77c0ac2e204573b6a9ae78bdbeddbfca1dd96
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 29 11:43:10 2014 +0200

    DOCU: Update on test policy with respect to now working valgrind tests.

commit f825283d8fd2fad85e199cb3a32f98980f29ceb5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 29 11:44:20 2014 +0200

    MEMFIX: ActionQueue was not stopped() when argument parsing failed.
    
    - this just caused an exception and the ActionQueue thread would be aborted
      uncleanly. This is only affected --enable-action-thread.

commit 052c10a6e270eaffbd69149bcd5c6bbaadab9752
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Aug 28 10:48:24 2014 +0200

    MEMFIX: Tesselation::operator() did not free linkedlist.

commit 7ee21dd85ecc96fef7cf8272cb7e5755f57d1e65
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Aug 28 09:24:18 2014 +0200

    MEMFIX: Many analysis_correlation function allocated return map twice.
    
    - outmap was the culprit, probably when empty (but allocated) was returned when
      no atoms are allocated, two new's appeared.

commit 6b3e5eabbfb866e42ce576818aeadd95719a1ac6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 27 22:10:38 2014 +0200

    MEMFIX: PartialNucleiChargeFitter lost memory.
    
    - operator() and constructMatrix() use heap memory to avoid always allocating
      memory for charge grids but did not always free'd the memory or allocated
      onto pointer with allocated memory.

commit 96c7d2359255253121a4625cd3a9933834b44391
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 27 21:59:01 2014 +0200

    MEMFIX: PotentialRegistry's dstor forgot cleanup().
    
    - also we purge static potential factory and registry instances in cleanup.
    - dstor of SerializablePotential was not virtual.

commit 185e6f9e58b5418b9136e86a172d2cfb6627a2d7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 23:35:29 2014 +0200

    MEMFIX: SaturationDistanceMaximizer::operator() did not delete Advocate.

commit b0b2d2c9d316c1a252e1177412399808f116a2d9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 23:07:40 2014 +0200

    MEMFIX: RealSpaceMatrix's and MatrixContent's serialization leaked memory.
    
    - serialization always works on fully instantiated RealSpaceMatrix, hence
      neither createViews nor re-creating content ptr instance is necessary.
    - MatrixContent newly allocated content but for RealSpaceMatrix it was still
      present as matrix dimensions have been set. Now it is freed when
      free_content_on_exit is true.
    - similar fixes to VectorContent.

commit 7f1a1a7e897d84470656f52ade76a74fef5da063
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 17:28:34 2014 +0200

    MEMFIX: ActionQueue would loose memory when action failed.
    
    - we cleared the queues and forget to delete contained Action instances.

commit 3d70e30645becb764684201ccfc596c838a74c3a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 12:48:28 2014 +0200

    MEMFIX: Mismatched delete in PdbParser::Save().

commit 09f615ff03d6c900818e07a53ee2c183bbf3bf47
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 10:50:02 2014 +0200

    MEMFIX: World's homologies not deleted.
    
    - main() now uses int status for storing saveAll() flag.

commit 62c378a69a5535affe3a0039648a1cea69f07da3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 19:21:49 2014 +0200

    FIX: Made checks in random number engine and distribution regression tests more robust.
    
    - with valgrind we see the command line with "lagged_fibbonacci.." and
      "uniform_smallint", too, resulting in more hits for grep.

commit 5200294b51370a326ff7b6b894366ab63dd343f1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 19:12:05 2014 +0200

    FIX: regression test add atoms outside boundary had given boundary conditions wrong in arguments.
    
    - TESTFIX: test is now marked XFAIL, before it failed because of wrong
      conditions.

commit 25aa5ad00fe2dc8d803d1602be52c8f6e3bc16c7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 20:56:38 2014 +0200

    FIX: Box::setM() did not use const ref as argument.

commit 707a2b0d381b69df9ebf6bc57ce9ffe12636248e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 27 21:58:28 2014 +0200

    FIX: FitPotentialAction's getFirstGraphwithSpecifiedElements() access key_end().

commit 8946a0e70603b6a8930297686e4c9938010b2d9d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 27 20:52:44 2014 +0200

    FIX: Process' dstor would always stop() even if not start()ed.
    
    - this caused assert failure from Observer cause it had not been signed, but
      was suddenly signed off.

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