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refresh-bio / agc

Assembled Genomes Compressor
MIT License
152 stars 13 forks source link

Illegal instruction (core dumped) #2

Closed KamilSJaron closed 2 years ago

KamilSJaron commented 2 years ago

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 2 years ago

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

KamilSJaron commented 2 years ago

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 2 years ago

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

sebastiandeorowicz commented 2 years ago

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