Segfault in the native PairHMM on certain CPU / JVM combinations

[droazen]

We have reports (https://gatk.broadinstitute.org/hc/en-us/community/posts/15590727717659-A-fatal-error-has-been-detected-by-the-Java-Runtime-Environment-when-running-Haplotypecaller-) that the GKL can crash on certain CPU architectures and/or with certain JVMs. Below is an excerpt of a core dump from a user running on an Intel(R) Xeon(R) Gold 6242R CPU with OpenJDK 64-Bit Server VM 17.0.3. Another user added the following:

"This particular error was quite prominent in all of my skylake/cascade lake class hardware especially when I used openjdk provided by the OS repository. Is it possible for you to try openjdk from eclipse temurin (www.adoptium.net). ? There are other options available as well like using the docker instance of gatk could help. Also you may want to try reducing the number of pairHMM threads to 1 instead of the default 4 or any other value being used by your command. AVX512 capable cpus from intel tend to have this issue with certain java builds."

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f799b0bda54, pid=268132, tid=268133
#
# JRE version: OpenJDK Runtime Environment (17.0.3) (build 17.0.3-internal+0-adhoc..src)
# Java VM: OpenJDK 64-Bit Server VM (17.0.3-internal+0-adhoc..src, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64)
# Problematic frame:
# C  [libc.so.6+0x8fa54]  __memset_sse2+0x54
#
# Core dump will be written. Default location: /scale03/nikhil/augustus2/snpcalling1/93Y21/core.268132
#
# If you would like to submit a bug report, please visit:
#   https://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  S U M M A R Y ------------

Command Line: -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 /scale03/nikhil/envs/gatk4/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar HaplotypeCaller -R Gmax_508_v4.0.fa -I 93Y21.bam -O rawvariants.vcf

Host: Intel(R) Xeon(R) Gold 6242R CPU @ 3.10GHz, 40 cores, 2636G, CentOS Linux release 7.9.2009 (Core)
Time: Thu May 18 10:14:49 2023 CDT elapsed time: 28701.945198 seconds (0d 7h 58m 21s)

---------------  T H R E A D  ---------------

Current thread (0x00007f79940146c0):  JavaThread "main" [_thread_in_native, id=268133, stack(0x00007f799b4b7000,0x00007f799b5b8000)]

Stack: [0x00007f799b4b7000,0x00007f799b5b8000],  sp=0x00007f799b462e28,  free space=18014398509481647k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [libc.so.6+0x8fa54]  __memset_sse2+0x54
C  [libgkl_pairhmm_omp8599022423123915931.so+0x1500f]  Java_com_intel_gkl_pairhmm_IntelPairHmm_computeLikelihoodsNative._omp_fn.0+0xcf

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
J 7481  com.intel.gkl.pairhmm.IntelPairHmm.computeLikelihoodsNative([Ljava/lang/Object;[Ljava/lang/Object;[D)V (0 bytes) @ 0x00007f79858c7e9c [0x00007f79858c7e20+0x000000000000007c]
J 8402 c2 com.intel.gkl.pairhmm.IntelPairHmm.computeLikelihoods([Lorg/broadinstitute/gatk/nativebindings/pairhmm/ReadDataHolder;[Lorg/broadinstitute/gatk/nativebindings/pairhmm/HaplotypeDataHolder;[D)V (87 bytes) @ 0x00007f7985bbb200 [0x00007f7985bbb1c0+0x0000000000000040]
J 6576 c2 org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM.computeLog10Likelihoods(Lorg/broadinstitute/hellbender/utils/genotyper/LikelihoodMatrix;Ljava/util/List;Lorg/broadinstitute/hellbender/utils/pairhmm/PairHMMInputScoreImputator;)V (450 bytes) @ 0x00007f798575ef78 [0x00007f798575d840+0x0000000000001738]
J 7873 c2 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(Lorg/broadinstitute/hellbender/utils/genotyper/LikelihoodMatrix;)V (132 bytes) @ 0x00007f79858c0fd4 [0x00007f79858bf100+0x0000000000001ed4]
J 8416 c2 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(Lorg/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyResultSet;Lorg/broadinstitute/hellbender/utils/genotyper/SampleList;Ljava/util/Map;Z)Lorg/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoods; (25 bytes) @ 0x00007f7985bc9850 [0x00007f7985bc70a0+0x00000000000027b0]
J 8280 c2 org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(Lorg/broadinstitute/hellbender/engine/AssemblyRegion;Lorg/broadinstitute/hellbender/engine/FeatureContext;Lorg/broadinstitute/hellbender/engine/ReferenceContext;)Ljava/util/List; (1934 bytes) @ 0x00007f7985b3ca1c [0x00007f7985b3a120+0x00000000000028fc]
J 9114% c2 org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(Lorg/broadinstitute/hellbender/engine/MultiIntervalLocalReadShard;Lorg/broadinstitute/hellbender/engine/ReferenceDataSource;Lorg/broadinstitute/hellbender/engine/FeatureManager;)V (154 bytes) @ 0x00007f7985d843ac [0x00007f7985d83c00+0x00000000000007ac]
j  org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse()V+83
j  org.broadinstitute.hellbender.engine.GATKTool.doWork()Ljava/lang/Object;+19
j  org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool()Ljava/lang/Object;+34
j  org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs()Ljava/lang/Object;+225
j  org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain([Ljava/lang/String;)Ljava/lang/Object;+14
j  org.broadinstitute.hellbender.Main.runCommandLineProgram(Lorg/broadinstitute/hellbender/cmdline/CommandLineProgram;[Ljava/lang/String;)Ljava/lang/Object;+20
j  org.broadinstitute.hellbender.Main.mainEntry([Ljava/lang/String;)V+22
j  org.broadinstitute.hellbender.Main.main([Ljava/lang/String;)V+8
v  ~StubRoutines::call_stub

siginfo: si_signo: 11 (SIGSEGV), si_code: 2 (SEGV_ACCERR), si_addr: 0x00007f799b4a97c0