refresh-bio/agc

Illegal instruction (core dumped)

KamilSJaron opened this issue · 4 comments

KamilSJaron commented

Hi, sounds like a cool tool.

I tried to run the tool installed via conda on Debian GNU/Linux 9 (stretch), but when I tried to compress the toy examples I always get Illegal instruction.

conda install -c bioconda agc
cd toy_ex
agc create ref.fa a.fa b.fa > toy_example.agc
Illegal instruction (core dumped)

I also did try to compile the software on my own, but we have too old gcc and it makes a mess with the <filesystem> library.

Finally, thanks for the effort of making genomes.. small!

sebastiandeorowicz commented

Hi,
Can you tell me what is your CPU? Probably the problem is with AVX extensions, but let's verify this.
Best,

KamilSJaron commented

That is likely the problem! I originally tried just if the program work on our frontend with Intel(R) Xeon(R) CPU L5640 (it is quite old server).

Now I tried again on compute nodes and although I have not checked yet the output and stuff, it is not dropping the core dump error!

sebastiandeorowicz commented

I'll prepare non-AVX binaries for the older CPUs. Let you know soon.

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sebastiandeorowicz commented

It took some time, but precompiled non-AVX version is ready: https://github.com/refresh-bio/agc/releases/tag/v2.0