Some tests fail: Shared object "libm.so.6" not found, required by "libgkl_utils11425681626488905546.so"

[yurivict]

For example, this failures:

Test: Test method testAdjacentIUPACBasesinReads(org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest) produced standard out/err: 22:09:32.975 WARN  NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/tmp/libgkl_utils11425681626488905546.so: Shared object "libm.so.6" not found, required by "libgkl_utils11425681626488905546.so")

Test: Test method testAdjacentIUPACBasesinReads(org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest) produced standard out/err: 22:09:32.975 WARN  NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/tmp/libgkl_utils14578974133264750968.so: Shared object "libm.so.6" not found, required by "libgkl_utils14578974133264750968.so")

Why is gatk expecting to find libm.so.6 ?
The FreeBSD 14.3 has /usr/lib/libm.so.3

Version: 4.6.2.0
OS: FreeBSD 14.3

[gokalpcelik]

Unfortunately FreeBSD or any other BSD derivatives except MacOS (Intel) are not supported through intel GKL library.

[yurivict]

Is glk library bundled?
Unfortunately googling "Intel glk library" doesn't yield any relevant results.

[gokalpcelik]

Yes it is bundled within the jar.

https://github.com/IntelLabs/GKL

[yurivict]

We actually have the package GKL-0.9.1 on FreeBSD.
It is present during gatk build as a dependency.
It only installs these shared libs:

        /usr/local/lib/libgkl_compression.so
        /usr/local/lib/libgkl_pairhmm.so
        /usr/local/lib/libgkl_pairhmm_omp.so
        /usr/local/lib/libgkl_pdhmm.so
        /usr/local/lib/libgkl_smithwaterman.so
        /usr/local/lib/libgkl_utils.so

I am wondering why isn't it used, or whether it is used.
It is also unclear how is GKL related to the problem that "libm.so.6" isn't found.

[gokalpcelik]

You may need to check how intel GKL is wired to the GATK engine through build scripts. GATK does not use the system built in library but uses the one bundled with the jar file. Older GATK versions like 3.0 or early 4.0 betas could use external library path for built in intel GKL for pair hmm acceleration but later versions dropped that support and can only run properly with the bundled version.