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  1. UGENE
  2. UGENE-7360

SAFE_POINT and crash Smith–Waterman CUDA

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 40
    • Component/s: None
    • Labels:
      None
    • Environment:

      Windows

      Nvidia GPU

    • Sprint:
      DEV-40-4
    • Affect Type:
      Userdefined

      Description

      Open human_T1.fa. Call Smith–Waterman dialog. Fill in the dialog and start search:

      • Pattern: A
        Search in: Translation
        Algorithm version: CUDA

                Expected: no errors.
                Current state: see log with SAFE_POINT below.

      • Pattern: A
        Search in: Translation
        Region: 1-1
        Algorithm version: CUDA

                Expected: no crash
                Current state: crash.

       

      1 case log:

      [Algorithms][DETAILS][12:26] Strand: 0
      [Tasks][DETAILS][12:26] Registering new task: SmithWatermanTask
      [Core Services][TRACE][12:26] AppResource CudaGpu ::tryAcquire 1, available 1
      [Core Services][TRACE][12:26] AppResource Memory ::tryAcquire 2, available 7906
      [Algorithms][DETAILS][12:26] The Smith-Waterman search allocates ~6 bytes (5.72205e-06 Mb) on CUDA device
      [Core Services][DETAILS][12:26] GPU model: GeForce GTX 1050
      [Tasks][TRACE][12:26] Promoting task {SmithWatermanTask} to 'Prepared'
      [Tasks][TRACE][12:26] Promoting task {Smith Waterman2 SequenceWalker} to 'Prepared'
      [Console][TRACE][12:26] AppMemory: 117Mb; Locked memory AppResource: 162/8066; SQLite memory 0Mb, max 1Mb
      [Tasks][TRACE][12:26] Promoting task {Sequence walker subtask} to 'Prepared'
      [Tasks][TRACE][12:26] Promoting task {SmithWatermanTask} to 'Running'
      [Tasks][TRACE][12:26] Promoting task {Smith Waterman2 SequenceWalker} to 'Running'
      [Core Services][TRACE][12:26] AppResource Threads ::tryAcquire 1, available 1000
      [Tasks][TRACE][12:26] Promoting task {Sequence walker subtask} to 'Running'
      [Algorithms][DETAILS][12:26] START SmithWatermanAlgorithmCUDA::launch
      [Smith Waterman CUDA][DETAILS][12:26] partsNumber: 14 queryDevider: 1
      [Smith Waterman CUDA][DETAILS][12:26] seqLen: 66650 partSeqSize: 4764 overlapSize: 3
      [Smith Waterman CUDA][DETAILS][12:26] queryLen 1 partQuerySize: 1
      [Smith Waterman CUDA][DETAILS][12:26] GLOBAL MEMORY USED 1908 KB
      [Smith Waterman CUDA][DETAILS][12:26] SHARED MEM SIZE USED: 24 B
      [Smith Waterman CUDA][TRACE][12:26] CUDA ERROR HAPPEN, errorId: 35
      [Algorithms][DETAILS][12:26] FINISH SmithWatermanAlgorithmCUDA::launch
      [Performance][DETAILS][12:26] SW alg CUDA run time is 0
      [Core Services][TRACE][12:26] AppResource Threads ::release 1, available 999
      [Tasks][TRACE][12:26] Promoting task {Sequence walker subtask} to 'Finished'
      [Tasks][TRACE][12:26] Promoting task {Sequence walker subtask} to 'Prepared'
      [Core Services][TRACE][12:26] AppResource Threads ::tryAcquire 1, available 1000
      [Tasks][TRACE][12:26] Promoting task {Sequence walker subtask} to 'Running'
      [Console][TRACE][12:26] AppMemory: 128Mb; Locked memory AppResource: 162/8066; SQLite memory 0Mb, max 1Mb
      [Algorithms][DETAILS][12:26] START SmithWatermanAlgorithmCUDA::launch
      [Smith Waterman CUDA][DETAILS][12:26] partsNumber: 14 queryDevider: 1
      [Smith Waterman CUDA][DETAILS][12:26] seqLen: 66649 partSeqSize: 4764 overlapSize: 3
      [Smith Waterman CUDA][DETAILS][12:26] queryLen 1 partQuerySize: 1
      [Smith Waterman CUDA][DETAILS][12:26] GLOBAL MEMORY USED 1908 KB
      [Smith Waterman CUDA][DETAILS][12:26] SHARED MEM SIZE USED: 24 B
      [Smith Waterman CUDA][TRACE][12:26] CUDA ERROR HAPPEN, errorId: 35
      [Algorithms][DETAILS][12:26] FINISH SmithWatermanAlgorithmCUDA::launch
      [Performance][DETAILS][12:26] SW alg CUDA run time is 0
      [Core Services][TRACE][12:26] AppResource Threads ::release 1, available 999
      [Tasks][TRACE][12:26] Promoting task {Sequence walker subtask} to 'Finished'
      [Tasks][TRACE][12:26] Promoting task {Sequence walker subtask} to 'Prepared'
      [Core Services][TRACE][12:26] AppResource Threads ::tryAcquire 1, available 1000
      [Tasks][TRACE][12:26] Promoting task {Sequence walker subtask} to 'Running'
      [Algorithms][DETAILS][12:26] START SmithWatermanAlgorithmCUDA::launch
      [Smith Waterman CUDA][DETAILS][12:26] partsNumber: 14 queryDevider: 1
      [Smith Waterman CUDA][DETAILS][12:26] seqLen: 66649 partSeqSize: 4764 overlapSize: 3
      [Smith Waterman CUDA][DETAILS][12:26] queryLen 1 partQuerySize: 1
      [Smith Waterman CUDA][DETAILS][12:26] GLOBAL MEMORY USED 1908 KB
      [Console][TRACE][12:26] AppMemory: 129Mb; Locked memory AppResource: 162/8066; SQLite memory 0Mb, max 1Mb
      [Smith Waterman CUDA][DETAILS][12:26] SHARED MEM SIZE USED: 24 B
      [Smith Waterman CUDA][TRACE][12:26] CUDA ERROR HAPPEN, errorId: 35
      [Algorithms][DETAILS][12:26] FINISH SmithWatermanAlgorithmCUDA::launch
      [Performance][DETAILS][12:26] SW alg CUDA run time is 0
      [Core Services][TRACE][12:26] AppResource Threads ::release 1, available 999
      [Tasks][TRACE][12:26] Promoting task {Sequence walker subtask} to 'Finished'
      [Tasks][TRACE][12:26] Promoting task {Smith Waterman2 SequenceWalker} to 'Finished'
      [Tasks][TRACE][12:28] Promoting task {SWResultsPostprocessing} to 'Prepared'
      [Core Services][TRACE][12:28] AppResource Threads ::tryAcquire 1, available 1000
      [Tasks][TRACE][12:28] Promoting task {SWResultsPostprocessing} to 'Running'
      [Core Services][TRACE][12:28] AppResource Threads ::release 1, available 999
      [Tasks][TRACE][12:28] Promoting task {SWResultsPostprocessing} to 'Finished'
      [Algorithms][DETAILS][12:28] 1630 results found
      [Input/Output][TRACE][12:28] SQL: error: Unexpected query result code: 19 (rtree constraint failed: FeatureLocationRTreeIndex.(start
      [Core Services][ERROR][12:28] Trying to recover from error: Invalid DB reference at C:\BuildAgent\work\release\ugene\src\corelibs\U2Core\src\datatype\Annotation.cpp:48
      [Core Services][ERROR][12:28] Trying to recover from error: Unexpected query result code: 19 (rtree constraint failed: FeatureLocationRTreeIndex.(start
      [Input/Output][TRACE][12:28] SQL: error: SQLite: Error finalizing statement: Error querying database: rtree constraint failed: FeatureLocationRTreeIndex.(start

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              Assignee:
              biserova Evelina
              Reporter:
              biserova Evelina
              Assigned Tester:
              Dmitrii Sukhomlinov
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: