Comments (2)
Kmannth
commented on July 20, 2024
@droazen Do happen to have BKMs for Valgrind and GATK? We have spent some time trying to get symbol resoltion for GATK and GKL with valgrind but so far not much sucess.
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Kmannth
commented on July 20, 2024
Summary: The Valgrind and Java do not work well. #91 was updated to run with Master was was last tested Jan 2021. We will work to run this test as part of our regular release process.
With the latest code base and the limtied unit test cases no errors were found.
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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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