Comments (4)
sooheelee
commented on July 20, 2024
Could @erniebrau or @pnvaidya please forward this issue to relevant persons? I've just grabbed your handles because you appear active in this repo. Much appreciated.
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gspowley
commented on July 20, 2024
@sooheelee, We are looking into the issues reported in the GATK discussion list. If GKL is causing the issues, then users should add the -jdk_deflater and -jdk_inflater options to GATK until we resolve the issue.
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sooheelee
commented on July 20, 2024
Thank you. We look forward to hearing back from you and your team.
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lbergelson
commented on July 20, 2024
Another similar report in picard. broadinstitute/picard#975
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Related Issues (20)
- How to make the system use these libraries? HOT 1
- GATK4 HaplotypeCaller native SmithWaterman: core dumps and JVM errors HOT 2
- Intermittent core dump in native pair hmm HOT 5
- Does GKL have plans to support ARM architecture optimization? HOT 2
- Help2man is also needed when building. HOT 2
- PairHMM stripe initialization of `M_t_1_y` is wrong HOT 1
- GKL uses exploitable Log4J 2 version HOT 1
- GKL should ideally use commons-logging or similar instead of log4j HOT 2
- `smithWatermanBackTrack` is being shared between AVX2 and AVX-512 HOT 2
- Release 0.8.9 is not on maven HOT 3
- Potential memory leak observed in unusual HaplotypeCaller behavior HOT 1
- Help, where is the function impl of 'compute_fp_avx512s' ?
- Does GKL support arm architecture? HOT 2
- Confusing warning message in IntelInflater HOT 1
- IntelDeflater intermittently fails to properly compress outputs with GKL 0.8.8 HOT 3
- Segfault in the native PairHMM on certain CPU / JVM combinations
- Deflater.needsInput() Always returns true HOT 4
- the way of docker or apptainer install
- GATK AVX accelerated pairHMM Segfault issue with Long reads - Consistently around the same region
- SmithWaterman result inconsistency by optimization level
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