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Test out the preview version of the next GKL (DO NOT MERGE) #8712

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Test out the preview version of the next GKL (DO NOT MERGE) #8712

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Commits on Mar 4, 2024

  1. Add in the preview GKL build as a dependency 

    The jar was build using Java 1.8 and contains AVX optimized binaries for Linux hosts and
not optimized binaries for Mac (Intel CPUs)
    @droazen
    droazen committed Mar 4, 2024
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Commits on Mar 6, 2024

  1. Added the java code to wrap the IntelPDPairHMM implementation for DRA… 

    …GEN-GATK testing
    @jamesemery
    jamesemery committed Mar 6, 2024
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Commits on Apr 24, 2024

  1. Switch to gkl-0.8.11-3-g26de538-SNAPSHOT.jar

    @droazen
    droazen committed Apr 24, 2024
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Commits on Jul 19, 2024

  1. Switch to gkl-2024_05_31, incorporate Intel patch to VectorLoglessPai… 

    …rPDHMM
    @droazen
    droazen committed Jul 19, 2024
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  2. Temporarily revert Intel patch to VectorLoglessPairPDHMM.java, for te… 

    …sting purposes
    @droazen
    droazen committed Jul 19, 2024
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Commits on Jul 22, 2024

  1. Restore one-line Intel patch to VectorLoglessPairPDHMM

    @droazen
    droazen committed Jul 22, 2024
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  2. added some debugging for figuring out what is going on with the gkl m… 

    …emory usage
    @jamesemery
    jamesemery committed Jul 22, 2024
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  3. error

    @jamesemery
    jamesemery committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. adding quick remote test

    @jamesemery
    jamesemery committed Jul 23, 2024
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  2. ;

    @jamesemery
    jamesemery committed Jul 23, 2024
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  3. of course i can't run this anywhere

    @jamesemery
    jamesemery committed Jul 23, 2024
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  4. piggybacking off of one that may have worked past?

    @jamesemery
    jamesemery committed Jul 23, 2024
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  5. more permissions

    @jamesemery
    jamesemery committed Jul 23, 2024
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  6. why didn't that last one work?

    @jamesemery
    jamesemery committed Jul 23, 2024
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  7. group

    @jamesemery
    jamesemery committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. restart? hopefully transient

    @jamesemery
    jamesemery committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. Refactored the interface to the new GKL JNI to batch submissions to a… 

    …void overflows or memory issues in oversaturated assembly regions
    @jamesemery
    jamesemery committed Jul 25, 2024
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  2. two tweeks and one bug

    @jamesemery
    jamesemery committed Jul 25, 2024
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  3. yet more guardrails

    @jamesemery
    jamesemery committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. assert failure

    @jamesemery
    jamesemery committed Jul 26, 2024
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Commits on Jul 29, 2024

  1. testing limits for batches

    @jamesemery
    jamesemery committed Jul 29, 2024
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Commits on Aug 8, 2024

  1. Switch to latest GKL build (2024-08-08)

    @droazen
    droazen committed Aug 8, 2024
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Commits on Sep 23, 2024

  1. update to test new jar

    @lbergelson
    lbergelson committed Sep 23, 2024
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