abPOA conda installer broken?

[Koen-vdl]

I believe there is something wrong with the abPOA conda installer as the installed version breaks even with the test data (seq.fa).

conda create -n abpoa_env -c bioconda abpoa -y
conda activate abpoa_env
abpoa seq.fa > cons.fa
[main] CMD:  abpoa -r3 test_poa.fa
Illegal instruction (core dumped)

As a workaround, I built abPOA from source and experienced no issues there.

[yangao07]

What is the system you were using? Is it Linux 64bit?

[Koen-vdl]

Yes, my OS is Ubuntu 20.04.6 LTS server

[yangao07]

Hi, I pulled the conda update request a few days ago, but still no one reviewed/approved it.
Do you have access to managing bioconda recipes?

[yangao07]

The error is still there after I updated the build.sh in conda recipe.
It may be related to the SIMDE, since the installation is good for versions without SIMDE, v1.2.5 or earlier.

Let me look into this.

[willem-stock]

same issue with the conda install (Linux 64bit; openSUSE Leap 15.4)

[EricKutschera]

I saw a similar Illegal instruction (core dumped) from TideHunter which uses abPOA. It seems that the conda package was built so that it uses instructions that some CPUs might not have. I ran in gdb to get more details about the error

gdb TideHunter
...
(gdb) r some_file.fq -o out_file.fa
Starting program:
...
Thread 4 "TideHunter" received signal SIGILL, Illegal instruction.
[Switching to Thread 0x7fffee9d8640 (LWP 58045)]
0x0000555555580281 in simd_abpoa_align_sequence_to_subgraph ()
...
(gdb) disassemble 0x0000555555580281,+1
Dump of assembler code from 0x555555580281 to 0x555555580282:
=> 0x0000555555580281 <simd_abpoa_align_sequence_to_subgraph+6433>:     vpbroadcastw -0x738(%rbp),%zmm0
End of assembler dump.

Then I searched for "vpbroadcastw instruction" and found: https://www.felixcloutier.com/x86/vpbroadcast
Several variants of vpbroadcastw are listed there but some require: CPUID Feature Flags AVX2, AVX512VL, AVX512BW. I checked /proc/cpuinfo for those flags with commands like grep -i 'AVX2' /proc/cpuinfo
The machine I was using had AVX2, but not AVX512VL or AVX512BW. I tried on a different machine which had all three of those AVX features and didn't get the illegal instruction error

I was also able to run on the machine without AVX512 by building from source

[da-i]

Can confirm that the conda install it is still broken on AMD 5800H