Comments (2)
My guess is some of the cores previously used for PairHMM are now used for preparing active regions.
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Thank you for replying.
https://github.com/cxfustc/Tiny_GKL_test/blob/master/PairHMMTest.java
I write a simple test code, and it comes out you are right. It is the competition for cores that slows down the calculation speed.
Here is the test result. The computer for testing has 4 cores.
If the number of threads for every pairhmm engine is set to 1. The result of the program is:
Cost 4.527874s
Cost 3.670908s
Cost 4.456890s
Cost 4.555578s
Cost 4.757390s
If the number of threads is set to 2. The result of the program is:
Cost 1.798678s
Cost 2.841058s
Cost 3.018658s
Cost 3.194318s
Cost 3.424579s
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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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