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Problems building on ARM based servers #475

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olewsaa opened this issue May 24, 2018 · 3 comments · May be fixed by #1147
Closed

Problems building on ARM based servers #475

olewsaa opened this issue May 24, 2018 · 3 comments · May be fixed by #1147
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@olewsaa
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olewsaa commented May 24, 2018

We have an ARM based server for bioinformatics running Ubuntu with a lot of debian-med packages.
A request for dada2 triggered the installation, but very soon run into trouble. The source code should compiler, but there are x86 specific code in the source.
The errors are missing cpuid.h etc.

g++ -march=armv8-a+crc+crypto -mcpu=cortex-a72 -c Rmain.cpp -o Rmain.o
Rmain.cpp:7:10: fatal error: cpuid.h: No such file or directory
#include <cpuid.h>

As ARM based servers are ramping up in this segment I would like to raise the issue here and ask for a fix so that it will build on ARM systems, preferable Ubuntu.

Regards,
Ole W. Saastad
University of Oslo.
[email protected]
@benjjneb
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The issue is probably the explicit SSE2 code we added. We include a cpu check to turn off that branch of the code for cpus w/o SSE2, but it appears that part is failing on ARM due to the lack of the cpuid library: https://github.com/benjjneb/dada2/blob/master/src/Rmain.cpp#L4

Agree this is worth fixing, but this starts to get beyond my dev expertise. Anyone have suggestions on how to keep the SSE2 code branch while playing well w/ non-x86 architectures?

@terjekv
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terjekv commented Sep 28, 2020

I'm running into this problem now. I'll have to dig a bit into the code and see if we can ifdef ourselves out of the problem on __aarch64__ and keep cpuid.h around for x86_64.

@terjekv terjekv mentioned this issue Sep 28, 2020
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@benjjneb
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This was fixed a little after the M1 Macbooks came out. Package builds fine on ARM now.

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Filter out SSE usage for non-x86_64. terjekv/dada2
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@terjekv @benjjneb @olewsaa