fo40225

Fix "Broken Gray" didn't change the color of cpu-iowait

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Fix "Broken Gray" didn't change the color of cpu-iowait.

core dumped Intel C++ Compiler 2022.0.0 (2022.0.0.20211123) avx512

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``` [0000] 3. Calling kt_for - worker_sam free(): corrupted unsorted chunks Aborted (core dumped) ``` ``` bwa-mem2.avx512: segfault at 0 ip 00000000004537f8 sp 00007ffeb0d12d60 error 4 in bwa-mem2.avx512bw[400000+7f000] Code: 48...

### build environment Ubuntu 18.04.6 LTS gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04) Intel(R) oneAPI DPC++/C++ Compiler 2022.2.0 (2022.2.0.20220730) boost 1.58 ### run environment #### hardware 2x Intel Xeon Gold 6342 2TB...

Segmentation fault (core dumped) Intel(R) oneAPI DPC++/C++ Compiler 2023.0.0 (2023.0.0.20221201)

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If `-xCORE-AVX512` or `-march=x86-64-v4` is used, it crashes. However, when using `-xCOMMON-AVX512` or `-march=common-avx512`, it runs normally. The minimum reproducible input file has been attached for your reference. [mm2_bug.fastq.gz](https://github.com/bwa-mem2/mm2-fast/files/13402398/mm2_bug.fastq.gz) ```...

fix build break with icpx 2022.1.0

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``` $ icpx --version Intel(R) oneAPI DPC++/C++ Compiler 2022.1.0 (2022.1.0.20220316) Target: x86_64-unknown-linux-gnu Thread model: posix InstalledDir: /opt/intel/oneapi/compiler/2022.1.0/linux/bin-llvm ``` ``` icpx -c -g -Wall -O3 -Wc++-compat -DHAVE_KALLOC -DPARALLEL_CHAINING -DALIGN_AVX -DAPPLY_AVX2 -xCORE-AVX512...

multi gpu support, llama2-70b fix, download revision

update bioconda package

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TRGT released version v1.1.0 on 2024-07-17, but the latest version on bioconda is still 0.9.0-0 Please help to update. Thanks. https://github.com/PacificBiosciences/trgt/releases/ https://bioconda.github.io/recipes/trgt/README.html https://github.com/PacificBiosciences/pbbioconda/issues/702

**Operating system** Which operating system and version are you using? Unrelated to the issue **Package name** Which package / tool is causing the problem? Which version are you using, use...

SortSamSpark Required array length is too large

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## Bug Report ### Affected tool(s) or class(es) _Tool/class name(s), special parameters?_ `SortSamSpark --sort-order coordinate` ### Affected version(s) - [ ] Latest public release version [version?] - [ ] Latest...