Conda executable crashes

[fplazaonate]

Hi @bluenote-1577,

I installed sylph using bioconda but it crashed immediately with the following error "Illegal instruction (core dumped)".
Notably, the executable available on github works.

Best,
Florian

[bluenote-1577]

Hi @fplaza,

Thanks for bringing this to my attention. Since the executable works, I assume you're on linux? I just tried the conda install on my Ubuntu 16 system and it appears to be fine. If you could provide your distribution and any system specifications that would be helpful for me to try and reproduce the crash.

Thanks!

[fplazaonate]

I am using CentOS 8.
The CPU does not have avx2 extensions.

[bluenote-1577]

I'm honestly not sure what's going on here... here's what I've tried

1. Conda install on CentOS 8 - Works fine but has AVX2
2. Building on ARM64 architecture - Works fine, no AVX2, but not from conda (bioconda doesn't support aarch64 yet)

I need to track down a machine with no AVX2 running on x86-64. If the binary works for you, then I'd be surprised if compiling doesn't work.

I'll leave this open until I figure it out, or if someone else has a similar problem

[edwardbirdlab]

I also seem to have the same issue on CentOS 7 without AVX2.

The executable works for me as well, but the bioconda installation crashes immediately with "Illegal instruction (core dumped)".
I am running on older hardware with AVX1.

[bluenote-1577]

@edwardbirdlab thanks for confirming. Does the pre-built binary work for you too?

[edwardbirdlab]

Yes, the pre-built binary works without any issue.

[dawnmy]

Hi, I am testing sylph 0.6.0 installed via conda on my Linux server, but got the same error 1724781 illegal hardware instruction (core dumped) sylph when running it. The machine has avx and avx2. The previous version 0.5.1 worked fine on the same machine.

[bluenote-1577]

@dawnmy thanks for bringing this up. I can reproduce this bug as well even on my computer.

I think this is a bioconda issue, not a sylph issue: I did not change any hardware instruction behaviour between versions. I will update to version v0.6.1 and hope that bioconda fixes this. If not, it looks like I will have to ask the conda folks for help.

[bluenote-1577]

@dawnmy I updated sylph to v0.6.1 on conda. It works okay on my computer now. Let me know on your end

[dawnmy]

Thank you for the quick update. It works!