Intel-HLS/GKL

Issues

• Segfault reported by GATK user

  #213 opened a month ago by lbergelson
  0

• Does GKL support arm architecture?

  #173 opened 2 years ago by codeseedling
  3

• cmake install statements for all installed libraries are wrong

  #211 opened 3 months ago by yurivict
  0

• SmithWaterman result inconsistency by optimization level

  #202 opened 8 months ago by wook-choi
  0

• GATK AVX accelerated pairHMM Segfault issue with Long reads - Consistently around the same region

  #200 opened a year ago by gokalpcelik
  0

• the way of docker or apptainer install

  #199 opened a year ago by user-tq
  0

• Deflater.needsInput() Always returns true

  #191 opened a year ago by lechiefe
  4

• Release 0.8.9 is not on maven

  #170 opened a year ago by nh13
  3

• GKL should ideally use commons-logging or similar instead of log4j

  #165 opened a year ago by tfenne
  2

• Segfault in the native PairHMM on certain CPU / JVM combinations

  #187 opened a year ago by droazen
  0

• Confusing warning message in IntelInflater

  #176 opened a year ago by lbergelson
  1

• IntelDeflater intermittently fails to properly compress outputs with GKL 0.8.8

  #177 opened 2 years ago by droazen
  3

• Help, where is the function impl of 'compute_fp_avx512s' ?

  #172 opened 3 years ago by LightSun
  0

• Potential memory leak observed in unusual HaplotypeCaller behavior

  #171 opened 3 years ago by jamesemery
  1

• `smithWatermanBackTrack` is being shared between AVX2 and AVX-512

  #169 opened 3 years ago by philipc
  2

• Smith Waterman Native crashes

  #103 opened 3 years ago by lbergelson
  7

• Systematically test the GKL deflater/inflater with long reads data

  #105 opened 3 years ago by droazen
  7

• Intermittent core dump in native pair hmm

  #133 opened 3 years ago by cmnbroad
  5

• PairHMM stripe initialization of `M_t_1_y` is wrong

  #163 opened 3 years ago by philipc
  1

• GKL uses exploitable Log4J 2 version

  #164 opened 3 years ago by alanhoyle
  1

• Does GKL have plans to support ARM architecture optimization?

  #160 opened 3 years ago by Qiyu8
  2

• Help2man is also needed when building.

  #161 opened 3 years ago by Baohua-Chen
  2

• GATK4 HaplotypeCaller native SmithWaterman: core dumps and JVM errors

  #113 opened 4 years ago by nh13
  2

• Run valgrind on the GKL codebase

  #107 opened 4 years ago by droazen
  2

• SmithWaterman returns incorrect alignments.

  #104 opened 5 years ago by d-cameron
  4

• Zlib performance comparison for genomic data

  #106 opened 5 years ago by lbergelson
  0

• Consistent Segfault in deflater code

  #101 opened 4 years ago by lbergelson
  31

• Uninitialized pointer in IntelDeflater.cc

  #89 opened 4 years ago by mirounga
  4

• How to make the system use these libraries?

  #111 opened 4 years ago by rpomaris
  1

• Can this library be used to accelerate Smith Waterman algorithm powered software, like bwa?

  #93 opened 4 years ago by sfchen
  2

• Add javah support to CMake

  #37 opened 5 years ago by gspowley
  2

• FPGA PairHMM : calculate() stub for double precision

  #97 opened 5 years ago by rick-heig
  2

• GKL hangs on kernel update

  #98 opened 5 years ago by jonn-smith
  3

• Smith Waterman requires GATK classes to use

  #92 opened 5 years ago by d-cameron
  2

• Intel deflater + long reads data = intermittent corrupt bams

  #99 opened 5 years ago by droazen
  9

• Cannot load GKL with java 11 on OSX Mojave

  #102 opened 5 years ago by lbergelson
  1

• Can we get rid of org.apache.logging.log4j?

  #100 opened 6 years ago by nh13
  9

• OpenCL FPGA code not in this repo, right?

  #96 opened 6 years ago by tvandera
  1

• Install Error: "org.eclipse.jgit.jar"

  #95 opened 6 years ago by daizao
  1

• Create new Thread in Mutect2 will slow down the omp and avx accelerated pairHMM calculation?

  #90 opened 7 years ago by cxfustc
  2

• Error: error: ‘__m512’ does not name a type

  #86 opened 7 years ago by haiwufan
  2

• GATK v3.8 GKL memory issues?

  #81 opened 7 years ago by sooheelee
  4

• Error checking for AVX support

  #33 opened 7 years ago by gspowley
  0

• Report OMP threads in PairHMM

  #56 opened 7 years ago by gspowley
  0

• Remove factor of 3 in total cell calculation

  #57 opened 7 years ago by gspowley
  0

• Potential memory leak in IntelDeflater

  #52 opened 8 years ago by gspowley
  3

• Remove fprintf

  #44 opened 8 years ago by gspowley
  1

• Modify IntelInflater API

  #47 opened 8 years ago by gspowley
  1

• Catch UnsatisfiedLinkError in IntelGKLUtils.load

  #38 opened 8 years ago by gspowley
  0

• Restore the AVX check

  #39 opened 8 years ago by gspowley
  0